A method for determining points of contact between interacting proteins or binding sites of proteins to nucleic acids. Protein footprinting utilizes a protein cutting reagent or protease. Protein cleavage is inhibited where the proteins, or nucleic acids and protein, contact each other. After completion of the cutting reaction, the remaining peptide fragments are analyzed by electrophoresis.
The univalent radical OH. Hydroxyl radical is a potent oxidizing agent.
A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Chemical reactions effected by light.
Devices for accelerating protons or electrons in closed orbits where the accelerating voltage and magnetic field strength varies (the accelerating voltage is held constant for electrons) in order to keep the orbit radius constant.
An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. The enzyme has a preference for double-stranded DNA.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.

Identification of two transmembrane regions and a cytosolic domain of rat mitochondrial glycerophosphate acyltransferase. (1/92)

The topography of rat glycerophosphate acyltransferase (GAT) in the transverse plane of the mitochondrial outer membrane (MOM) was investigated. Computer analysis of the amino acid (aa) sequence derived from rat mitochondrial GAT cDNA (GenBanktrade mark accession nos. and ) predicts the presence of two possible transmembrane domains (aa 473-493 and 574-594) separated by an 80-aa stretch (aa 494-573). To determine the actual orientation of the native protein, we prepared anti-peptide antibodies to three regions: one in between (aa 543-559) and the other two (aa 420-435 and 726-740) flanking the two putative transmembrane regions. Both immunoreaction and immunoprecipitation experiments employing intact and solubilized mitochondria indicate that regions on the N- and C-terminal sides of the transmembrane regions are sequestered on the inner surface of the MOM, while the region between the transmembrane domains is present on the cytosolic face of the MOM. Additionally, two green fluorescent protein (GFP) fusion proteins consisting of full-length GAT fused to GFP at either the C terminus or inserted 115 amino acids from the N terminus were also constructed to determine the orientation of the N and C termini. COS-1 cells expressing these fusion proteins were fractionated to obtain mitochondria. Protease digestion of intact and solubilized COS-1 cell mitochondria revealed that the GFP domains of these fusion proteins are sequestered on the inner side of the MOM. The present findings indicate that GAT is a dual-spanning, transmembrane protein adopting an inverted "U" conformation in the transverse plane of the MOM, where the N and C termini are sequestered on the inner surface of the MOM, while aa 494-573 are exposed on the cytosolic surface of the MOM.  (+info)

Interaction of the eIF4G initiation factor with the aphthovirus IRES is essential for internal translation initiation in vivo. (2/92)

The strategies developed by internal ribosome entry site (IRES) elements to recruit the translational machinery are poorly understood. In this study we show that protein-RNA interaction of the eIF4G translation initiation factor with sequences of the foot-and-mouth disease virus (FMDV) IRES is a key determinant of internal translation initiation in living cells. Moreover, we have identified the nucleotides required for eIF4G-RNA functional interaction, using native proteins from FMDV-susceptible cell extracts. Substitutions in the conserved internal AA loop of the base of domain 4 led to strong impairment of both eIF4G-RNA interaction in vitro and IRES-dependent translation initiation in vivo. Conversely, substitutions in the vicinity of the internal AA loop that did not impair IRES activity retained their ability to interact with eIF4G. Direct UV-crosslinking as well as competition assays indicated that domains 1-2, 3, and 5 of the IRES did not contribute to this interaction. In agreement with this, binding to domain 4 alone was as efficient as to the full-length IRES. The C-terminal fragment of eIF4G, proteolytically processed by the FMDV Lb protease, was sufficient to interact with the IRES or to its domain 4 alone. Additionally, we show here that binding of the eIF4B initiation factor to the IRES required domain 5 sequences. Moreover, eIF4G-IRES interaction was detected in the absence of eIF4B-IRES binding, suggesting that both initiation factors interact with the 3' region of the IRES but use different residues. The strong correlation found between eIF4G-RNA interaction and IRES activity in transfected cells suggests that eIF4G acts as a linker to recruit the translational machinery in IRES-dependent initiation.  (+info)

Search for the autoantibody immunodominant region on thyroid peroxidase: epitopic footprinting with a human monoclonal autoantibody locates a facet on the native antigen containing a highly conformational epitope. (3/92)

Autoantibodies to thyroid peroxidase (TPO) are the hallmark of the humoral autoimmune response in human autoimmune thyroiditis (Hashimoto's thyroiditis). The majority of TPO autoantibodies in individual patients' sera interact with a restricted immunodominant region on TPO. Although this region can be mapped, previous studies have failed to localize its position on the TPO molecule. We, therefore, used a footprinting approach that can localize a highly conformational, discontinuous epitope on a very large molecule. Extensive biotinylation ( approximately 15 biotins/molecule protein) of lysine residues on the surface of purified, native TPO resulted in loss of multiple tryptic cleavage sites, as determined by analysis of tryptic polypeptide fragments on reverse-phase HPLC. TPO was then complexed with a monoclonal human autoantibody Fab (TR1.9) before biotinylation. After dissociation from TR1.9, TPO was recovered by gel filtration. A trypsin site, previously observed to be lost after TPO biotinylation, was restored when biotinylation was performed on the TPO-TR1.9 complex. The epitope-protected lysine (K) was present in a 30-aa TPO fragment that, by N-terminal sequencing, was found to be K713. Altered recognition by TR1.9 of a TPO-myeloperoxidase chimeric molecule involving this region supported the epitope protection data. In conclusion, we provide the first identification of an amino acid residue (K713) comprising part of an epitope within the TPO immunodominant region. This focal residue localizes the facet on the large, highly complex TPO molecule that contains the immunodominant region and provides the basis for rational guided mutagenesis studies to more fully characterize this region.  (+info)

Mapping DNA-binding sites of HIV-1 integrase by protein footprinting. (4/92)

The HIV-1 integrase protein catalyzes integration of the viral genome into host cell DNA. Whereas the structures of the three domains of integrase have been solved separately, both the structural organization of the full-length protein and its interaction with DNA remain unresolved. A protein footprinting approach was employed to investigate the accessibility of residues in the full-length soluble integrase mutant, INF(185K,C280S), to proteolytic attack in the absence and presence of DNA. The N-terminal and C-terminal domains were relatively more accessible to proteolytic attack than the core domain. The susceptibility to proteolytic attack was specifically affected by DNA at residues Lys34, in the N-terminal domain, Lys111, Lys136, Glu138, Lys156-Lys160, Lys185-Lys188, in the core domain, and Asp207, Lys 215, Glu246, Lys258 and Lys273 in the linker and C-terminal domain, suggesting that these regions are involved in, or shielded by, DNA binding. Lys34 is positioned in a putative dimerization domain, consistent with the notion that DNA stabilizes the dimeric state of integrase.  (+info)

Characterization of the mouse islet-specific glucose-6-phosphatase catalytic subunit-related protein gene promoter by in situ footprinting: correlation with fusion gene expression in the islet-derived betaTC-3 and hamster insulinoma tumor cell lines. (5/92)

Glucose-6-phosphatase (G6Pase) is a multicomponent system located in the endoplasmic reticulum comprising a catalytic subunit and transporters for glucose-6-phosphate, inorganic phosphate, and glucose. We have recently cloned a novel gene that encodes an islet-specific G6Pase catalytic subunit-related protein (IGRP) (Ebert et al., Diabetes 48:543-551, 1999). To begin to investigate the molecular basis for the islet-specific expression of the IGRP gene, a series of truncated IGRP-chloramphenicol acetyltransferase (CAT) fusion genes were transiently transfected into the islet-derived mouse betaTC-3 and hamster insulinoma tumor cell lines. In both cell lines, basal fusion gene expression decreased upon progressive deletion of the IGRP promoter sequence between -306 and -66, indicating that multiple promoter regions are required for maximal IGRP-CAT expression. The ligation-mediated polymerase chain reaction footprinting technique was then used to compare trans-acting factor binding to the IGRP promoter in situ in betaTC-3 cells, which express the endogenous IGRP gene, and adrenocortical Y1 cells, which do not. Multiple trans-acting factor binding sites were selectively identified in betaTC-3 cells that correlate with regions of the IGRP promoter identified as being required for basal IGRP-CAT fusion gene expression. The data suggest that hepatocyte nuclear factor 3 may be important for basal IGRP gene expression, as it is for glucagon, GLUT2, and Pdx-1 gene expression. In addition, binding sites for several trans-acting factors not previously associated with islet gene expression, as well as binding sites for potentially novel proteins, were identified.  (+info)

HMG-D complexed to a bulge DNA: an NMR model. (6/92)

An NMR model is presented for the structure of HMG-D, one of the Drosophila counterparts of mammalian HMG1/2 proteins, bound to a particular distorted DNA structure, a dA(2) DNA bulge. The complex is in fast to intermediate exchange on the NMR chemical shift time scale and suffers substantial linebroadening for the majority of interfacial resonances. This essentially precludes determination of a high-resolution structure for the interface based on NMR data alone. However, by introducing a small number of additional constraints based on chemical shift and linewidth footprinting combined with analogies to known structures, an ensemble of model structures was generated using a computational strategy equivalent to that for a conventional NMR structure determination. We find that the base pair adjacent to the dA(2) bulge is not formed and that the protein recognizes this feature in forming the complex; intermolecular NOE enhancements are observed from the sidechain of Thr 33 to all four nucleotides of the DNA sequence step adjacent to the bulge. Our results form the first experimental demonstration that when binding to deformed DNA, non-sequence-specific HMG proteins recognize the junction between duplex and nonduplex DNA. Similarities and differences of the present structural model relative to other HMG-DNA complex structures are discussed.  (+info)

Peptide bis-intercalator binds DNA via threading mode with sequence specific contacts in the major groove. (7/92)

BACKGROUND: We previously described a general class of DNA polyintercalators in which 1,4,5,8-naphthalenetetracarboxylic diimide (NDI) intercalating units are connected via peptide linkers, resulting in the first known tetrakis- and octakis-intercalators. We showed further that changes in the composition of the peptide tether result in novel DNA binding site specificities. We now examine in detail the DNA binding mode and sequence specific recognition of Compound 1, an NDI bis-intercalator containing the peptide linker gly-gly-gly-lys. RESULTS: 1H-NMR structural studies of Compound 1 bound to d(CGGTACCG)(2) confirmed a threading mode of intercalation, with four base pairs between the diimide units. The NMR data, combined with DNAse I footprinting of several analogs, suggest that specificity depends on a combination of steric and electrostatic contacts by the peptide linker in the floor of the major groove. CONCLUSIONS: In view of the modular nature and facile synthesis of our NDI-based polyintercalators, such structural knowledge can be used to improve or alter the specificity of the compounds and design longer polyintercalators that recognize correspondingly longer DNA sequences with alternating access to both DNA grooves.  (+info)

Quantitative effects on gene silencing by allelic variation at a tetranucleotide microsatellite. (8/92)

Microsatellites are common repeated sequences, which are useful as genetic markers and lack any clearly established function. In a previous study we suggested that an intronic polymorphic TCAT repeat in the tyrosine hydroxylase (TH) gene, the microsatellite HUMTH01, may regulate transcription. The TH gene encodes the rate-limiting enzyme in the synthesis of catecholamines, and the microsatellite HUMTH01 has been used in genetic studies of neuropsychiatric and cardiovascular diseases, in which disturbances of catecholaminergic neurotransmission have been implicated. HUMTH01 alleles associated with these diseases act as transcriptional enhancers when linked to a minimal promoter and are recognized by specific nuclear factors. Here we show that allelic variations of HUMTH01 commonly found in humans have a quantitative silencing effect on TH gene expression. Two specific proteins, ZNF191, a zinc finger protein, and HBP1, an HMG box transcription factor, which bind the TCAT motif, were then cloned. Finally, allelic variations of HUMTH01 correlate with quantitative and qualitative changes in the binding by ZNF191. Thus, this repeated sequence may contribute to the control of expression of quantitative genetic traits. As the HUMTH01 core motif is ubiquitous in the genome, this phenomenon may be relevant to the quantitative expression of many genes in addition to TH.  (+info)

Protein footprinting is a group of techniques used in structural biology to investigate the interactions between proteins and other molecules, such as DNA, RNA, or other proteins. These methods provide information about the spatial arrangement of atoms within a protein or protein complex, as well as details about the binding site and the nature of the interaction with another molecule.

In protein footprinting, the protein of interest is treated with a reagent that modifies specific amino acid residues in a way that can be detected and quantified. The reagents used for protein footprinting can be chemical or enzymatic, and they often target specific side chains or backbone atoms. Examples of such reagents include hydroxyl radicals, which modify the side chains of exposed amino acids; or proteases, which cleave the protein backbone at specific sequences.

The key to protein footprinting is that the presence of another molecule (e.g., DNA, RNA, or protein) can shield certain residues from modification by the reagent. By comparing the pattern of modifications in the presence and absence of the binding partner, researchers can infer which residues are in close proximity to the binding site and thus obtain information about the protein-protein or protein-nucleic acid interface.

Protein footprinting techniques include hydroxyl radical footprinting, chemical modification footprinting, enzymatic footprinting, and crosslinking mass spectrometry. These methods can be used to study various aspects of protein structure and function, such as protein folding, protein-protein interactions, protein-nucleic acid interactions, and post-translational modifications.

A hydroxyl radical is defined in biochemistry and medicine as an extremely reactive species, characterized by the presence of an oxygen atom bonded to a hydrogen atom (OH-). It is formed when a water molecule (H2O) is split into a hydroxide ion (OH-) and a hydrogen ion (H+) in the process of oxidation.

In medical terms, hydroxyl radicals are important in understanding free radical damage and oxidative stress, which can contribute to the development of various diseases, including cancer, cardiovascular disease, and neurodegenerative disorders. They are also involved in the body's natural defense mechanisms against pathogens. However, an overproduction of hydroxyl radicals can cause damage to cellular components such as DNA, proteins, and lipids, leading to cell dysfunction and death.

DNA footprinting is a laboratory technique used to identify specific DNA-protein interactions and map the binding sites of proteins on a DNA molecule. This technique involves the use of enzymes or chemicals that can cleave the DNA strand, but are prevented from doing so when a protein is bound to the DNA. By comparing the pattern of cuts in the presence and absence of the protein, researchers can identify the regions of the DNA where the protein binds.

The process typically involves treating the DNA-protein complex with a chemical or enzymatic agent that cleaves the DNA at specific sequences or sites. After the reaction is stopped, the DNA is separated into single strands and analyzed using techniques such as gel electrophoresis to visualize the pattern of cuts. The regions of the DNA where protein binding has occurred are protected from cleavage and appear as gaps or "footprints" in the pattern of cuts.

DNA footprinting is a valuable tool for studying gene regulation, as it can provide insights into how proteins interact with specific DNA sequences to control gene expression. It can also be used to study protein-DNA interactions involved in processes such as DNA replication, repair, and recombination.

Photochemical processes refer to chemical reactions that are initiated or driven by the absorption of light. In these reactions, photons (light particles) interact with molecules, causing electrons in the molecules to become excited and leading to the formation of new chemical bonds or the breaking of existing ones. This results in the creation of different molecular structures or products.

In the context of human health and medicine, photochemical processes can occur both naturally and artificially. For instance, the body uses light-dependent reactions in the process of vision, where light is absorbed by rhodopsin in the retina, triggering a series of chemical events that ultimately lead to visual perception.

Additionally, photochemotherapy is a medical treatment that utilizes photochemical processes to achieve therapeutic effects. In this approach, a photosensitizing agent is administered to a patient, and then exposed to specific wavelengths of light. The light causes the photosensitizer to react with oxygen, generating reactive oxygen species that can destroy targeted cells or tissues, such as cancer cells or bacteria.

Overall, photochemical processes play an essential role in various biological and medical contexts, enabling critical functions like vision and offering promising therapeutic avenues for a range of conditions.

A synchrotron is not a medical term, but rather a type of particle accelerator used in physics and related fields. Therefore, it doesn't have a specific medical definition. However, synchrotrons do have important applications in medicine, particularly in the field of medical imaging and radiation therapy.

In brief, a synchrotron is a large circular accelerator that uses magnetic fields to bend and focus a beam of charged particles (such as electrons) into a narrow, intense beam. The particles are then accelerated to very high speeds using electric fields. As the particles pass through special devices called insertion devices, they emit light in the form of X-rays or other forms of electromagnetic radiation. These X-rays can be used for a variety of scientific and medical applications, including:

1. Medical imaging: Synchrotron X-rays can produce high-resolution images of the body's internal structures, such as bones, tissues, and organs. This is particularly useful in the study of complex anatomical structures or diseases that affect them.
2. Radiation therapy: Synchrotron radiation can be used to deliver highly targeted doses of radiation to cancer cells while minimizing damage to surrounding healthy tissue. This technique, known as synchrotron-based radiotherapy, is still in the experimental stage but shows promise for improving the effectiveness and safety of radiation therapy.
3. Biomedical research: Synchrotron X-rays can be used to study the structure and function of biological molecules, such as proteins and DNA, at a molecular level. This information can help researchers better understand the mechanisms of diseases and develop new drugs and therapies.

In summary, while synchrotrons are not medical terms themselves, they have important applications in medicine, particularly in medical imaging, radiation therapy, and biomedical research.

Mass spectrometry (MS) is an analytical technique used to identify and quantify the chemical components of a mixture or compound. It works by ionizing the sample, generating charged molecules or fragments, and then measuring their mass-to-charge ratio in a vacuum. The resulting mass spectrum provides information about the molecular weight and structure of the analytes, allowing for identification and characterization.

In simpler terms, mass spectrometry is a method used to determine what chemicals are present in a sample and in what quantities, by converting the chemicals into ions, measuring their masses, and generating a spectrum that shows the relative abundances of each ion type.

Molecular models are three-dimensional representations of molecular structures that are used in the field of molecular biology and chemistry to visualize and understand the spatial arrangement of atoms and bonds within a molecule. These models can be physical or computer-generated and allow researchers to study the shape, size, and behavior of molecules, which is crucial for understanding their function and interactions with other molecules.

Physical molecular models are often made up of balls (representing atoms) connected by rods or sticks (representing bonds). These models can be constructed manually using materials such as plastic or wooden balls and rods, or they can be created using 3D printing technology.

Computer-generated molecular models, on the other hand, are created using specialized software that allows researchers to visualize and manipulate molecular structures in three dimensions. These models can be used to simulate molecular interactions, predict molecular behavior, and design new drugs or chemicals with specific properties. Overall, molecular models play a critical role in advancing our understanding of molecular structures and their functions.

Molecular sequence data refers to the specific arrangement of molecules, most commonly nucleotides in DNA or RNA, or amino acids in proteins, that make up a biological macromolecule. This data is generated through laboratory techniques such as sequencing, and provides information about the exact order of the constituent molecules. This data is crucial in various fields of biology, including genetics, evolution, and molecular biology, allowing for comparisons between different organisms, identification of genetic variations, and studies of gene function and regulation.

In the context of medical and biological sciences, a "binding site" refers to a specific location on a protein, molecule, or cell where another molecule can attach or bind. This binding interaction can lead to various functional changes in the original protein or molecule. The other molecule that binds to the binding site is often referred to as a ligand, which can be a small molecule, ion, or even another protein.

The binding between a ligand and its target binding site can be specific and selective, meaning that only certain ligands can bind to particular binding sites with high affinity. This specificity plays a crucial role in various biological processes, such as signal transduction, enzyme catalysis, or drug action.

In the case of drug development, understanding the location and properties of binding sites on target proteins is essential for designing drugs that can selectively bind to these sites and modulate protein function. This knowledge can help create more effective and safer therapeutic options for various diseases.

Protein conformation refers to the specific three-dimensional shape that a protein molecule assumes due to the spatial arrangement of its constituent amino acid residues and their associated chemical groups. This complex structure is determined by several factors, including covalent bonds (disulfide bridges), hydrogen bonds, van der Waals forces, and ionic bonds, which help stabilize the protein's unique conformation.

Protein conformations can be broadly classified into two categories: primary, secondary, tertiary, and quaternary structures. The primary structure represents the linear sequence of amino acids in a polypeptide chain. The secondary structure arises from local interactions between adjacent amino acid residues, leading to the formation of recurring motifs such as α-helices and β-sheets. Tertiary structure refers to the overall three-dimensional folding pattern of a single polypeptide chain, while quaternary structure describes the spatial arrangement of multiple folded polypeptide chains (subunits) that interact to form a functional protein complex.

Understanding protein conformation is crucial for elucidating protein function, as the specific three-dimensional shape of a protein directly influences its ability to interact with other molecules, such as ligands, nucleic acids, or other proteins. Any alterations in protein conformation due to genetic mutations, environmental factors, or chemical modifications can lead to loss of function, misfolding, aggregation, and disease states like neurodegenerative disorders and cancer.

An amino acid sequence is the specific order of amino acids in a protein or peptide molecule, formed by the linking of the amino group (-NH2) of one amino acid to the carboxyl group (-COOH) of another amino acid through a peptide bond. The sequence is determined by the genetic code and is unique to each type of protein or peptide. It plays a crucial role in determining the three-dimensional structure and function of proteins.

Deoxyribonuclease I (DNase I) is an enzyme that cleaves the phosphodiester bonds in the DNA molecule, breaking it down into smaller pieces. It is also known as DNase A or bovine pancreatic deoxyribonuclease. This enzyme specifically hydrolyzes the internucleotide linkages of DNA by cleaving the phosphodiester bond between the 3'-hydroxyl group of one deoxyribose sugar and the phosphate group of another, leaving 3'-phosphomononucleotides as products.

DNase I plays a crucial role in various biological processes, including DNA degradation during apoptosis (programmed cell death), DNA repair, and host defense against pathogens by breaking down extracellular DNA from invading microorganisms or damaged cells. It is widely used in molecular biology research for applications such as DNA isolation, removing contaminating DNA from RNA samples, and generating defined DNA fragments for cloning purposes. DNase I can be found in various sources, including bovine pancreas, human tears, and bacterial cultures.

A base sequence in the context of molecular biology refers to the specific order of nucleotides in a DNA or RNA molecule. In DNA, these nucleotides are adenine (A), guanine (G), cytosine (C), and thymine (T). In RNA, uracil (U) takes the place of thymine. The base sequence contains genetic information that is transcribed into RNA and ultimately translated into proteins. It is the exact order of these bases that determines the genetic code and thus the function of the DNA or RNA molecule.

These approaches have since been used to determine protein structures, protein folding, protein dynamics, and protein-protein ... This method was the first employed to apply protein footprinting to the study of a protein complex. The exposure of proteins to ... has also been written to help model protein complexes using data from the RP-MS/Protein footprinting approach. RP-MS/Protein ... Protein footprinting is a term used to refer to a method of biochemical analysis that investigates protein structure, assembly ...
A DNase footprinting assay is a DNA footprinting technique from molecular biology/biochemistry that detects DNA-protein ... Galas DJ, Schmitz A (Sep 1978). "DNAse footprinting: a simple method for the detection of protein-DNA binding specificity". ... is compared to the cleavage pattern of DNA in the presence of a DNA binding protein. If the protein binds DNA, the binding site ... By varying the concentration of the DNA-binding protein, the binding affinity of the protein can be estimated according to the ...
Tijerina P, Mohr S, Russell R (2007). "DMS footprinting of structured RNAs and RNA-protein complexes". Nat Protoc. 2 (10): 2608 ... DMS modification can also be used for DNA, for example in footprinting DNA-protein interactions. Selective 2′-hydroxyl ... Tullius, T. D.; Dombroski, B. A. (1986). "Hydroxyl radical "footprinting": high-resolution information about DNA-protein ... NMR is also useful for probing the binding of nucleic acid molecules to other molecules, such as proteins or drugs, by seeing ...
... is unrelated to Senescence Related Gene 1 (SRG1), a protein-coding gene found in Arabidopsis thaliana, and is also ... "Finding functional features in Saccharomyces genomes by phylogenetic footprinting". Science. 301 (5629): 71-76. Bibcode:2003Sci ... "Uniprot Knowledgebase - Protein SRG1". Retrieved 2010-08-02. Truesdell GM, Dickman MB (March 1997). "Isolation of pathogen/ ... TATA-binding protein and RNA Polymerase II were still bound to the SER3 DNA in such a way that should have caused active ...
DNA footprinting is a method aimed at identifying protein-bound DNA. It uses labeling and fragmentation coupled to gel ... using any DNA-binding proteins that condenses the molecule. These proteins are usually referred to nucleoid-associated proteins ... Galas, D. J.; Schmitz, A. (1978-09-01). "DNAse footprinting: a simple method for the detection of protein-DNA binding ... In terms of initiating 5' end DNA repair, the p53 binding protein 1 (53BP1) and BRCA1 are important protein components that ...
Before phylogenetic footprinting, DNase footprinting was used, where protein would be bound to DNA transcription factor binding ... Unlike DNase footprinting, phylogenetic footprinting relies on evolutionary constraints within the genome, with the "important ... One such technique is Phylogenetic Footprinting. Phylogenetic footprinting relies upon two major concepts: The function and DNA ... Phylogenetic footprinting is a technique used to identify transcription factor binding sites (TFBS) within a non-coding region ...
He also co-developed protein footprinting experiments, in the same year, employing radicals to study protein structures and was ... Maleknia, Simin D.; Downard, Kevin M. (March 2014). "Advances in Radical Probe Mass Spectrometry for Protein Footprinting in ... During this time, he has developed new proteotyping approaches to study viruses, viral proteins, and protein structures and ... Downard, Kevin M. (2006). "Ions of the interactome: The role of MS in the study of protein interactions in proteomics and ...
Galas DJ, Schmitz A (1978). "DNAse footprinting: a simple method for the detection of protein-DNA binding specificity". Nucleic ... Deoxyribonucleoprotein Protein-DNA interaction site prediction software RNA-binding protein Single-strand binding protein Zinc ... is a widespread qualitative technique to study protein-DNA interactions of known DNA binding proteins. DNA-Protein-Interaction ... Also proteins that repair DNA such as uracil-DNA glycosylase interact closely with it. In general, proteins bind to DNA in the ...
"Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3 (1): 89. doi:10.1038/ ... Bachman NJ, Yang TL, Dasen JS, Ernst RE, Lomax MI (1996). "Phylogenetic footprinting of the human cytochrome c oxidase subunit ... The protein is a subunit of Complex IV, which consists of 13 mitochondrial- and nuclear-encoded subunits. The sequence of ... "Cytochrome c oxidase subunit 5B, mitochondrial". Cardiac Organellar Protein Atlas Knowledgebase (COPaKB). Archived from the ...
Computational footprinting methods can be performed on ATAC-seq to find cell specific binding sites and transcription factors ... October 2015). "CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins". Genome Research. 25 (10): 1581-9. doi: ... This can be achieved by looking at the number of reads around TF motifs or footprinting analysis. Buenrostro JD, Giresi PG, ... DNA-binding proteins and nucleosome position". Nature Methods. 10 (12): 1213-8. doi:10.1038/nmeth.2688. PMC 3959825. PMID ...
Nucleosomes are bound by 147 base pairs of DNA whereas transcription factors or other proteins will only bind a region of ... M.CviPl was not the only methyltransferase used for nucleosome foot-printing; Methylase-sensitive Single Promoter Analysis (M- ... In addition to nucleosome foot-printing, NOMe-seq can determine locations bound by transcription factors. ... "Footprinting of mammalian promoters: use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule ...
PAGE gels are widely used in techniques such as DNA foot printing, EMSA and other DNA-protein interaction techniques. The ... A globular protein or a random coil DNA moves through the connected pores large enough to accommodate its passage, and the ...
... candidate proteins must instead be identified by protein/protein interaction assays instead of an EMSA. This is an example ... Site-directed mutagenesis Restriction digest DNA footprinting Kamvysselis, M. (2003). Computational molecular genomics: genes, ... Proteins which affect the promoter must also be added to those cells - often those proteins are placed on the same or different ... As the promoter commonly contains binding sequences for proteins affecting transcription, those proteins are also necessary ...
These protein factors may be involved in controlling gene expression. Unlike electrophoretic mobility shift and DNA foot ... This could end up affecting how well the protein factor binds to DNA in later steps of the technique. Not all proteins renature ... As a result, large proteins do not travel very far on the gel in comparison to smaller proteins that travel further. After ... a procedure for detecting DNA-binding proteins but also procedures for RNA-binding proteins as well as histone-binding proteins ...
Louis working with Michael Gross on MassSpec-based protein foot-printing. After her postdoctoral research, she joined Indiana ... FPOP can provide information on the sites of ligand binding, protein interaction and protein conformational changes in vivo. ... Hydroxyl radicals go on to oxidise the side chains of amino acids and provide solvent accessibility of proteins within a cell. ... Jones, Lisa Michelle (4 August 2008). Using Protein Design to Understand the Role of Electrostatic Interactions on Calcium ...
It is different from the more commonly used DNA footprinting assay. The toeprinting assay has been utilized to examine the ... in molecular biology that allows one to examine the interactions between messenger RNA and ribosomes or RNA-binding proteins. ...
Most of these have been classified into three groups: leader peptides, ribosomal proteins, and toxic proteins. Leader proteins ... "Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation". The EMBO Journal. 33 (9 ... Ribosomal proteins include L36 (rpmJ) and L34 (rpmH), two components of the 50S ribosomal subunit. Toxic proteins, such as ldrD ... The 24 amino acid micropeptide, Humanin (HN), interacts with the apoptosis-inducing protein Bcl2-associated X protein (Bax). In ...
The second is the helix-loop-helix (HLH) region, which facilitates protein-protein interactions. Also contained with the AhR ... identification by phylogenetic footprinting". Biochemical and Biophysical Research Communications. 321 (3): 707-715. doi: ... TGF-β cytokines are members of a signaling protein family that includes activin, Nodal subfamily, bone morphogenetic proteins, ... also known as hepatitis B virus X-associated protein 2 (XAP2), AhR interacting protein (AIP), and AhR-activated 9 (ARA9). The ...
In vitro foot-printing with the chromosomal protein MeCP2 showed that the MBD could protect a 12 nucleotide region surrounding ... MBD-containing proteins appear to act as structural proteins, which recruit a variety of histone deacetylase (HDAC) complexes ... In human MBD3 and SETDB1, the MBD has been shown to mediate protein-protein interactions. MBDs are also found in DNA ... Effects of DNA methylation are mediated through proteins that bind to symmetrically methylated CpGs. Such proteins contain a ...
DNase footprinting Protein footprinting Toeprinting assay Galas, D; Schmitz, A (1978). "DNAse footprinting: a simple method for ... In vivo footprinting is a technique used to analyze the protein-DNA interactions that are occurring in a cell at a given time ... The DNA footprinting technique can be modified to assess the binding strength of a protein to a region of DNA. Using varying ... DNA footprinting is a method of investigating the sequence specificity of DNA-binding proteins in vitro. This technique can be ...
... though there is some ribosome footprinting signal. When experimentally overexpressed, the ORF10 protein has been reported to ... Articles with short description, Short description matches Wikidata, Protein pages needing a picture, Coronavirus proteins). ... ORF10 is located downstream of the N gene, which encodes coronavirus nucleocapsid protein. It is the annotated open reading ... It encodes a 38-amino acid hypothetical protein. It is unlikely that ORF10 is translated under natural conditions, since ...
"Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. Bibcode:2005Natur. ... Strauss EC, Andrews NC, Higgs DR, Orkin SH (1992). "In vivo footprinting of the human alpha-globin locus upstream regulatory ... NFE2+protein,+human at the U.S. National Library of Medicine Medical Subject Headings (MeSH) FactorBook NF-E2 This article ... Chan JY, Han XL, Kan YW (1994). "Isolation of cDNA encoding the human NF-E2 protein". Proc. Natl. Acad. Sci. U.S.A. 90 (23): ...
... that are specifically bound by one or more DNA-binding proteins or protein complexes. It has been reported that some binding ... the experimental techniques of choice to discover and analyze DNA binding sites have been the DNAse footprinting assay and the ... they are bound by DNA-binding proteins. DNA binding sites are often associated with specialized proteins known as transcription ... An example of such tool is the ULPB DNA binding protein Binding site Transcriptional regulation Halford E.S.; Marko J.F. (2004 ...
Footprinting at the U.S. National Library of Medicine Medical Subject Headings (MeSH) DNA-Binding+Proteins at the U.S. National ... Many proteins involved in the regulation of gene expression contain DNA-binding domains. For example, proteins that regulate ... One or more DNA-binding domains are often part of a larger protein consisting of further protein domains with differing ... OB-folds bind single-stranded DNA, and hence are single-stranded binding proteins. OB-fold proteins have been identified as ...
Assays are created that combine reporter fusions, electrophoretic mobility shift assays, DNase footprinting, and fluorescence ... Following elution, the protein readily binds DNA, indicating the protein's high affinity for DNA. Histone-like proteins were ... Histone-like proteins are present in many Eubacteria, Cyanobacteria, and Archaebacteria. These proteins participate in all DNA- ... Wang SL, Liu XQ (December 1991). "The plastid genome of Cryptomonas phi encodes an hsp70-like protein, a histone-like protein, ...
... on structural proteomics where he uses mass spectrometry in developing and implementing new approaches to protein footprinting ... Part A: Peptides and Proteins," Encyclopedia of Mass Spectrometry, Vol 2, Elsevier, 2005, 435 pp. Joint Ed., Ionization Methods ...
... protein MeSH E05.393.760.705.685 - peptide mapping MeSH E05.393.760.705.685.690 - protein footprinting MeSH E05.393.760.710 - ... protein footprinting MeSH E05.196.712.224 - densitometry MeSH E05.196.712.224.187 - absorptiometry, photon MeSH E05.196.712.224 ... protein array analysis MeSH E05.196.630.570.850 - tissue array analysis MeSH E05.196.680.100 - blotting, northern MeSH E05.196. ... protein array analysis MeSH E05.393.525.700 - random amplified polymorphic dna technique MeSH E05.393.525.870 - two-hybrid ...
No high energy cofactors such as ATP or accessory proteins are required for the recombinase activity of the purified protein. ... to non specific DNA sequences whilst having a 20 fold higher affinity for loxP sequences and results of early DNA footprinting ... The Cre protein was purified in 1983 and was found to be a 35,000 Da protein. ... The protein will stay in this location in its inactivated state until tamoxifen is given. Once tamoxifen is introduced, it is ...
DNase footprinting assay Filter binding assay Gel shift assay Bicinchoninic acid assay (BCA assay) Bradford protein assay Lowry ... Lowry OH, Rosebrough NJ, Farr AL, Randall RJ (November 1951). "Protein measurement with the Folin phenol reagent". J. Biol. ... usually a large protein). Immunoassay when the response is an antigen antibody binding type reaction. Depending on the nature ... protein assay Secretion assay Nuclear run-on Ribosome profiling A cell-counting assay may determine the number of living cells ...
Most E2F have a pocket protein binding domain. Pocket proteins such as pRB and related proteins p107 and p130, can bind to E2F ... In vivo footprinting experiments obtained on Cdc2 and B-myb promoters demonstrated E2F DNA binding site occupation during G0 ... pRb is one of the targets of the oncogenic human papilloma virus protein E7, and human adenovirus protein E1A. By binding to ... Homo sapiens E2F1 mRNA or E2F1 protein sequences from NCBI protein and nucleotide database. X-ray crystallographic analysis has ...
These approaches have since been used to determine protein structures, protein folding, protein dynamics, and protein-protein ... This method was the first employed to apply protein footprinting to the study of a protein complex. The exposure of proteins to ... has also been written to help model protein complexes using data from the RP-MS/Protein footprinting approach. RP-MS/Protein ... Protein footprinting is a term used to refer to a method of biochemical analysis that investigates protein structure, assembly ...
Extension of Hydroxyl Radical-Based Footprinting Coupled with Mass Spectrometry for In Cell and In Vivo Protein Analysis ... In recent years, protein footprinting coupled with mass spectrometry has been used to identify protein-protein interaction ... Extension of Hydroxyl Radical-Based Footprinting Coupled with Mass Spectrometry for In Cell and In Vivo Protein Analysis. ... Extension of Hydroxyl Radical-Based Footprinting Coupled with Mass Spectrometry for In Cell and In Vivo Protein Analysis. ...
To tap the full quantitative potential of HRF, we describe a protocol, hydroxyl-radical footprinting interpretation for DNA ( ... is a powerful method for probing structures of nucleic acid-protein complexes with single-nucleotide resolution in solution. ... Mapping protein-ligand interactions by hydroxyl-radical protein footprinting. Loizos N. Loizos N. Methods Mol Biol. 2004;261: ... Footprinting protein-DNA complexes using the hydroxyl radical. Jain SS, Tullius TD. Jain SS, et al. Nat Protoc. 2008;3(6):1092- ...
Carbocation Footprinting of Soluble and Transmembrane Proteins. / Sun, Jie; Li, Shuang; Li, Weikai et al. In: Analytical ... Sun, J., Li, S., Li, W., & Gross, M. L. (2021). Carbocation Footprinting of Soluble and Transmembrane Proteins. Analytical ... Sun, J, Li, S, Li, W & Gross, ML 2021, Carbocation Footprinting of Soluble and Transmembrane Proteins, Analytical Chemistry, ... Carbocation Footprinting of Soluble and Transmembrane Proteins. In: Analytical Chemistry. 2021 ; Vol. 93, No. 39. pp. 13101- ...
Cell Cycle Proteins / ultrastructure * DNA / genetics * DNA / metabolism* * DNA Footprinting * DNA Primers ... The ORC-Cdc6 structure is predicted to contain six AAA+ subunits, analogous to other ATP-dependent protein machines. We suggest ...
PROTEIN FOOTPRINTING. HUELLA DE PROTEINA. PEPTÍDIOS CATIÔNICOS ANTIMICROBIANOS. ANTIMICROBIAL CATIONIC PEPTIDES. PEPTIDOS ... ANTIFREEZE PROTEINS, TYPE I. PROTEINAS ANTICONGELANTES TIPO I. PROTEÍNAS ANTICONGELANTES TIPO II. ANTIFREEZE PROTEINS, TYPE II ... ANTIFREEZE PROTEINS, TYPE IV. PROTEINAS ANTICONGELANTES TIPO IV. PROTEÍNAS DE LIGAÇÃO A TACROLIMUS. TACROLIMUS BINDING PROTEINS ... TACROLIMUS BINDING PROTEIN 1A. PROTEINA 1A DE ENLACE A TACROLIMUS. PROTEÍNA ALFA INTENSIFICADORA DE LIGAÇÃO A CCAAT. CCAAT- ...
Tijerina, P., Mohr, S. & Russell, R. DMS footprinting of structured RNAs and RNA-protein complexes. Nat. Protoc. 2, 2608-2623 ( ... Hentze, M. W., Castello, A., Schwarzl, T. & Preiss, T. A brave new world of RNA-binding proteins. Nat. Rev. Mol. Cell Biol. 19 ... Lunde, B. M., Moore, C. & Varani, G. RNA-binding proteins: modular design for efficient function. Nat. Rev. Mol. Cell Biol. 8, ... N-terminal protein modification using simple aminoacyl transferase substrates. J. Am. Chem. Soc. 133, 15139-15147 (2011). ...
Powers T, Noller H (1995) Hydroxyl radical footprinting of ribosomal proteins on 16S rRNA. RNA 1:194 ... Shcherbakova I, Mitra S (2009) Hydroxyl-radical footprinting to probe equilibrium changes in RNA tertiary structure. Methods ... selectively changing protein-binding affinities and regulating mRNA repression and activation. Proc Natl Acad Sci USA 109:8417- ... including mediation of RNA folding and catalysis by ribozymes and proteins. Understanding the influence of Fe2+ on nucleic acid ...
DNase I footprinting, revealed that four regions of the HPD promoter were protected by rat liver nuclear proteins. Computer- ... allowed mapping of the HPD protein in the human keratinocyte 2D database. ...
Electrophoretic Mobility Shift Assays for RNA-Protein Complexes. Donald C. Rio. RNase Footprinting to Map Sites of RNA-Protein ... LIGHT MODULATION OF PROTEINS. Constructing and Expressing Fluorescent Protein Fusions. David L. Spector and Robert D. Goldman. ... Imaging Synaptic Protein Dynamics Using Photoactivatable Green Fluorescent Protein. Robby M. Weimer, Travis C. Hill, Andrew M. ... PROTEIN-DNA INTERACTIONS. Electrophoretic Mobility-Shift Assays. Michael F. Carey, Craig L. Peterson, and Stephen T. Smale. ...
... high throughput automated DNA sequencing and DNA-protein footprinting; peptide synthesis and purification; protein sequencing; ... Last year, this core expanded its proteomics capabilities with the acquisition of two mass spectrometers and a 2D protein gel ... protein, other biomarkers) as well as genomics analysis including DNA arrays, RNase protection assays and differential display ... analyzer and a Beckman ProteomeLab 2D liquid protein separation and analysis system which greatly increased the cores ...
Chemical footprinting and x-ray crystallography demonstrated direct binding of MLSK to specific nucleotides in domains II and V ... The antibiotics constituting the MLSK group inhibit protein synthesis at the ribosome level and are bacteriostatic except the ... Tetracyclines and the related glycylcyclines inhibit bacterial protein synthesis. They exert bacteriostatic activity by binding ... to the ribosomal 30S subunit, composed of 16S rRNA and several ribosomal proteins. The major tetracycline binding site is ...
Liver nuclear protein-binding sites within the mouseUGT1A1 promoter. DNase I footprinting experiment carried out with a −253/+ ... DNase I footprinting was carried out using a −253/+81 UGT1A1 promoter fragment (noncoding strand) and protein extracts from ... HNF1 proteins bind to the C site of the mouseUGT1A1 promoter. A, EMSA experiments using a MLNE were performed with a ... The footprinting experiment using MLNEs revealed a binding site for Sp1 in the mouse UGT1A1 promoter, which is conserved in the ...
a. Binding locations of HapR and CRP upstream of murQP. The gel shows the result of DNase I footprinting experiment. The gel is ... The pattern of DNase I cleavage in the absence of any proteins is in lane 1. Protection of DNA from DNase I cleavage in the ... For clarity, not all protein factors involved in the cascade have been included. ...
Fast photochemical oxidation of proteins is an emerging technique for the structural characterization of proteins. Different ... In Vivo Hydroxyl Radical Protein Footprinting for the Study of Protein Interactions in Caenorhabditis elegans… ... In Vivo Hydroxyl Radical Protein Footprinting for the Study of Protein Interactions in Caenorhabditis elegans… ... Laser-free Hydroxyl Radical Protein Footprinting to Perform Higher Order Structural Analysis of Proteins… ...
CONCLUSIONS: These findings demonstrate that ribosomal footprinting can be used to detect novel protein coding genes, ... In addition, protein structure and function were predicted computationally and compared between EHEC-encoded proteins and 100- ... times randomly shuffled proteins. Based on this comparison, 61 of the 72 novel proteins exhibit predicted structural and ... RESULTS: Using the above methods, 72 short, non-annotated protein-coding genes were detected. All of these showed signals in ...
Protein interactions at Sp1-like sites in the TGF alpha promoter as visualized by in vivo genomic footprinting.. Chen X; Wright ... Analysis of proteins binding to the proximal promoter region of the human cytomegalovirus IE-1/2 enhancer/promoter reveals both ... the promoter of human transcription factor Sp3 and evidence of the role of factors Sp1 and Sp3 in the expression of Sp3 protein ... domain of the androgen receptor gene promoter interacting with Sp1 and a pyrimidine single strand DNA-binding protein.. Chen S ...
We looked at traditional plant-based and alternative proteins trends and potential transition risks to food companies ... The Protein Transformation: A Critical Driver of the Net-Zero Economy. Jan 18, 2022 ... In this paper, we looked at current trends toward traditional plant-based and alternative proteins and potential transition ...
... possible protein-coding circRNAs and their polypeptides. In summary, this is a comprehensive online resource for exploring ... possible protein-coding circRNAs and their polypeptides. In summary, this is a comprehensive online resource for exploring ... 2.4 Potential protein-coding circRNAs. Here, we used the CPAT v3.0.4 to analyze the protein-coding potential of pancreatic ... ribosome footprinting assays also identified circRNAs associated with ribosomes, suggesting possible translation of circRNAs ...
The advantage of this protein footprinting method is that it utilizes the reactivity of hydroxyl radicals to stably modify ... invariance during labeling can be applied generally to any footprinting methodology where perturbation to protein structure by ... has shown great promise in the elucidation of the regions of a proteins structure that are changed upon interaction with other ... by FPOP-labeling three oxidation-sensitive proteins and examining their global FPOP product outcomes. The novel test developed ...
... and the binding site at the narX promoter for the NtrX protein was determined by DNA footprinting. In silico analyses revealed ... Gao F, Danson AE, Ye F, Jovanovic M, Buck M, Zhang Xet al., 2020, Bacterial enhancer binding proteins - AAA+ proteins in ... Total Nif protein accumulation was reduced 10-fold when the NifK protein was truncated and nitrogenase catalysis lost (nifK1- ... and accessory proteins. We estimate that the nitrogenase may account for more than 40% of cell protein during diazotrophic ...
The first focuses on the mechanisms that coordinate contractile protein expression in striated muscle. A variety of approaches ... and phylogenetic footprinting provides evidence for hierarchical control of the extraocular muscle specific myosin. ... The third centers on the novel proteins and physiological systems responsible for the superfast contractile properties of ... Strong evidence that posttranscriptional controls are critical to the coordinate expression of myofibrillar proteins has been ...
Protein footprinting reveals specific binding modes of a high mobility group protein I to DNAs of different conformation. J. ... Inhibition of protein kinase C, p34-kinase or histone deacetylases increases HMGA1a mobility in heterochromatin. HMGA1 proteins ... HMGA1a-GFP proteins are enriched in heterochromatin in vivo. During interphase, HMGA1-GFP proteins were distributed throughout ... Insect proteins homologous to mammalian high mobility group proteins I/Y (HMG I/Y). Characterization and binding to linear and ...
... and RNA/DNA protein footprinting. The separate transitions reported by individual probes yield unique insight into folding ...
DNasel footprinting indicated that approximately 66-85 bp of DNA was protected by poly ADP-ribose polymerase from DNasel attack ... and that a segment of DNA probably lies outside on the surface of the polymerase protein in the polymerase-DNA complex. ... to DNA was greatly augmented when both enzyme protein and histones were present simultaneously. Part III. Analysis of the ... Binding of the polymerase protein, or histones, to DNA was greatly augmented when both enzyme protein and histones were present ...
The environmental impact of beef and dairy is halved by a new assessment method that calculates a foods protein quality, say ... Therefore, we argue that, if nutritional science is going to be integrated into environmental footprinting, it should be done ... "We are advising environmental footprint experts on the fallacy of using protein (i.e., total protein) as an impact scaling ... Protein quality evaluation halves environment impact of meat and dairy By Oliver Morrison 06-Jan-2023. - Last updated on 06- ...
DNase I Footprinting. * DNase I footprinting was performed as previously described[49-51]. The results were analyzed using an ... Protein Expr Purif, 2000; 19, 419−24. doi: 10.1006/prep.2000.1265. [47] Gao H, Zhou DS, Li YL, et al. The iron-responsive Fur ... Thus, the VCA0560 protein might play some roles in the early stage of V. cholerae infection by promoting c-di-GMP synthesis and ... More than 50 genes encode GGDEF- and/or EAL-type proteins in V. cholerae[20], and about 50% of these genes contribute to c-di- ...
  • This method, fast photochemical oxidation of proteins (FPOP), claimed to footprint proteins faster than they change their fold though this timeframe has been challenged given hydrogen peroxide, not present in the original studies, and secondary radicals, react alone in situ over tens of milliseconds. (wikipedia.org)
  • One HRBF method, fast photochemical oxidation of proteins (FPOP), utilizes an excimer laser for photolysis of hydrogen peroxide to generate hydroxyl radicals. (nih.gov)
  • We screened seven candidates and selected trifluomethoxy benzyl bromide (TFBB) as an effective precursor for the electrophilic trifluomethoxy benzyl carbocation (TFB + ) under laser (248 nm) irradiation on the fast photochemical oxidation of proteins (FPOP) platform. (wustl.edu)
  • Fast photochemical oxidation of proteins is an emerging technique for the structural characterization of proteins. (jove.com)
  • Fast photochemical oxidation of proteins: FPOP) has shown great promise in the elucidation of the regions of a protein's structure that are changed upon interaction with other macromolecules, ligands, or by folding. (wustl.edu)
  • This latter method was adapted through the direct treatment of proteins and their complexes with hydroxyl radicals and can be generally denoted RP-MS (for Radical Probe - Mass Spectrometry) akin to the designation used for Hydrogen-deuterium exchange Mass Spectrometry (denoted HD-MS or HX-MS). Time-resolved hydroxyl radical protein footprinting (HRPF) employing mass spectrometry analysis was originated and developed in the late 1990s in synchrotron radiolysis studies. (wikipedia.org)
  • 4. Kiselar J, Chance MR High-Resolution Hydroxyl Radical Protein Footprinting: Biophysics Tool for Drug Discovery Annu Rev Biophys. (neoproteomics.net)
  • The regulation of the VCA0560 gene by Fur and HapR was analyzed by luminescence assay, electrophoretic mobility shift assay, and DNase I footprinting. (besjournal.com)
  • In recent years, protein footprinting coupled with mass spectrometry has been used to identify protein-protein interaction sites and regions of conformational change through modification of solvent accessible sites in proteins. (nih.gov)
  • Comparison of apo- and holo-myoglobin footprints shows that the TFB + footprinting is sensitive to protein conformational change and solvent accessibility. (wustl.edu)
  • The novel test developed to validate conformational invariance during labeling can be applied generally to any footprinting methodology where perturbation to protein structure by the footprint labeling is suspected. (wustl.edu)
  • The MS-based footprinting technique can investigate protein conformational change upon its binding to other molecules or under the stimulus of pH change or other factors. (wustl.edu)
  • Research interests include protein-nucleic acid interactions, including kinetics and mechanism of transcription initiation, characterization of DNA wrapping in protein DNA complexes, development of small molecule solutes as thermodynamic and mechanistic probes of protein and DNA conformational changes. (winstepforward.org)
  • The biological activity of certain proteins is regulated by ligands which do not directly bind at the active site to make products rather induce conformational alterations. (edu.pk)
  • Such allosteric binding of a ligand or any post translational modification results in reshaping of protein conformational landscape. (edu.pk)
  • Current techniques provide very little information regarding energy distribution and conformational dynamics of protein allostery. (edu.pk)
  • This high throughput integrated analysis will furnish a comprehensive understanding of the complex landscape of protein folding and conformational dynamics which can further be implemented in various fields like drug discovery, disease development etc. (edu.pk)
  • reported on the use of an electrical discharge source to effect the oxidation of proteins on millisecond timescales as proteins pass from the electrosprayed solution into the mass spectrometer. (wikipedia.org)
  • Years later in 2005, researchers Hambly and Gross introduced a method for protein oxidation on the microsecond timescale using laser flash photolysis of hydrogen peroxide to generate hydroxyl radicals. (wikipedia.org)
  • A critical feature of these experiments is the need to expose proteins to hydroxyl radicals for limited timescales on the order of 1-50 ms inducing 10-30% oxidation of total protein. (wikipedia.org)
  • We have corroborated the predicted profoundly short timescale of labeling empirically, by FPOP-labeling three oxidation-sensitive proteins and examining their global FPOP product outcomes. (wustl.edu)
  • Protein footprinting is a term used to refer to a method of biochemical analysis that investigates protein structure, assembly, and interactions within a larger macromolecular assembly. (wikipedia.org)
  • These approaches have since been used to determine protein structures, protein folding, protein dynamics, and protein-protein interactions. (wikipedia.org)
  • This review focuses on experimental work investigating the interactions and functions of RNA and nucleic acid processing proteins with Fe 2+ under anoxic, early Earth conditions. (springer.com)
  • The method facilitates measurement of protein confirmation and protein interactions. (jove.com)
  • 15. Protein interactions at Sp1-like sites in the TGF alpha promoter as visualized by in vivo genomic footprinting. (nih.gov)
  • Taken together, our data provide evidence for an expanded range for CARF domain signaling, including the first evidence of its control via in trans protein-protein interactions, and a feed-forward mechanism to regulate RNA repair required for a functioning translation apparatus. (imperial.ac.uk)
  • Interactions of high mobility group box proteins with DNA and chromatin. (ucdenver.edu)
  • Although numerous approaches have been developed to map RNA-binding sites of individual RNA-binding proteins (RBPs), few methods exist that allow assessment of global RBP-RNA interactions. (github.io)
  • Native MS can investigate the conformation and topology of protein complexes in a near-native environment where the non-covalent interactions are preserved. (wustl.edu)
  • We have further extended the FPOP method for in cell analysis of proteins. (nih.gov)
  • Results demonstrate that in cell FPOP (IC-FPOP) can oxidatively modify over 1300 proteins in various cellular compartments. (nih.gov)
  • Preliminary results indicate a number of proteins can be oxidatively modified in C. elegans byin vivo FPOP (IV-FPOP) leading to the possibility of studying protein structure in human diseases directly in animal model systems. (nih.gov)
  • Unlike nucleic acids, proteins oxidize rather than cleave on these timescales. (wikipedia.org)
  • A method for determining points of contact between interacting proteins or binding sites of proteins to nucleic acids. (nih.gov)
  • Protein cleavage is inhibited where the proteins, or nucleic acids and protein, contact each other. (nih.gov)
  • A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids. (galaxyproject.org)
  • In DNA footprinting the protein is envisioned to make an imprint (or footprint) at a particular point of interaction. (wikipedia.org)
  • Interestingly, because the TFB + is amphiphilic, the reagent can potentially footprint membrane proteins as demonstrated for vitamin K epoxide reductase (VKOR) stabilized in a micelle. (wustl.edu)
  • In a study, the authors took a measure of protein quality called the Digestible Indispensable Amino Acid Score (DIAAS) and used it to create 'adjusted' environmental footprint metrics for a variety of foods. (foodnavigator.com)
  • Here, we describe PIP-seq, a universal, high-throughput, ribonuclease-mediated protein footprint sequencing approach that reveals RNA-protein interaction sites throughout a transcriptome of interest. (github.io)
  • Genomes of E. coli, including that of the human pathogen Escherichia coli O157:H7 (EHEC) EDL933, still harbor undetected protein-coding genes which, apparently, have escaped annotation due to their small size and non-essential function. (rostlab.org)
  • BACKGROUND: The Escherichia coli RuvA and RuvB proteins promote the branch migration of 4-way (Holliday) junctions during genetic recombination. (dundee.ac.uk)
  • To validate this methodology, I have chosen the model protein Escherichia coli (E.coli) CheY - a small protein with a single surface for binding that belongs to a large bacterial superfamily and is part of two-component regulatory system. (edu.pk)
  • This will allow for study of proteins in their native cellular environment and be especially useful for the study of membrane proteins which can be difficult to purify for in vitro studies. (nih.gov)
  • Carbocation precursors are stable and amenable for tailoring their properties and those of the incipient carbocation, enabling targeting their soluble or membrane-associated or embedded regions and distinguishing between the extra- and trans-membrane domains of membrane proteins. (wustl.edu)
  • Binding and allostery in drug binding to membrane proteins. (neoproteomics.net)
  • Membrane proteins are notoriously difficult to study. (wustl.edu)
  • The development of MS-based membrane protein detection platforms largely benefits the study of photosynthesis, as reaction center and light-harvesting complexes are usually membrane proteins.In this dissertation, a variety of MS-based techniques were utilized to study reaction center proteins, light harvesting proteins and the proteins involved in the photoprotection process. (wustl.edu)
  • Applying orthogonal single-molecule footprinting methods, we quantify the absolute levels of physical protection of H. volcanii and find that Haloferax chromatin is similarly or only slightly more accessible, in aggregate, than that of eukaryotes. (biomedcentral.com)
  • The buffer composition, sample purity and protein concentration requirements are flexible allowing the method to address challenging structural problems. (jove.com)
  • Based on this comparison, 61 of the 72 novel proteins exhibit predicted structural and functional features similar to those of annotated proteins. (rostlab.org)
  • 1. Xu, G., Chance, M.R., Hydroxyl radical-mediated modification of proteins as probes for structural proteomics, Chem Rev. (2007) Aug;107(8):3514-43. (neoproteomics.net)
  • We have used cells expressing proteins fused to green fluorescent protein (GFP) and fluorescence recovery after photobleaching (FRAP) to analyze the distribution and dynamics of HMGA1a in vivo. (biologists.com)
  • Serganov, A. & Patel, D. J. Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. (nature.com)
  • To find such genes, global gene expression of EHEC EDL933 was examined, using strand-specific RNAseq (transcriptome), ribosomal footprinting (translatome) and mass spectrometry (proteome). (rostlab.org)
  • 8. Functional role of a conformationally flexible homopurine/homopyrimidine domain of the androgen receptor gene promoter interacting with Sp1 and a pyrimidine single strand DNA-binding protein. (nih.gov)
  • 14-17 Hypermethylation of the fragile X chromosome region is associated with histone deacetylation and chromatin remodelling, 18 that is, processes that by themselves could cause transcriptional silencing of the FMR1 gene, 19-21 followed by lack of FMR1 protein (FMRP), which is required to allow normal brain development. (bmj.com)
  • Mode of interaction of the zinc finger protein TFIIIA with a 5S RNA gene of Xenopus. (ucdenver.edu)
  • Using the well-characterized signaling pathway of the phytohormone ethylene and plant-optimized genome-wide ribosome footprinting, we have uncovered a molecular mechanism linking this hormone's perception to the activation of a gene-specific translational control mechanism. (ncsu.edu)
  • Using proBAMr, peptide-spectrum-matches can be easily reannotated using user-specified gene annotation schemes and assembled into both protein and gene identifications. (galaxyproject.org)
  • Due to their overlapping nature, each of these transcripts encodes the major 372-bp gene, yielding the 14.5-kDa SarA protein (2). (cgp60474.com)
  • The application of ion mobility mass spectrometry has conclusively demonstrated that the conditions employed in RP-MS/Protein footprinting experiments do not alter the structure of proteins. (wikipedia.org)
  • Using the electromobility shift and DNase I footprinting experiments, we have identified a hepatocyte nuclear factor 1-binding site in the mouse UGT1A1 promoter that confers responsiveness to both factors HNF1α and HNF1β in HEK293 cells. (aspetjournals.org)
  • DNase I footprinting, revealed that four regions of the HPD promoter were protected by rat liver nuclear proteins. (nih.gov)
  • Analysis of the RuvAB-junction complex by DNase footprinting showed that RuvA bound asymmetrically to the junction and targeted a single hexameric RuvB ring to one arm of DNA. (dundee.ac.uk)
  • Analysis of the RuvAB-junction complex by DNase footprinting showed that RuvA bound asymmetrically to the junction and targeted a single hexameric RuvB ring to one arm of DNA.CONCLUSION: Branch migration of a three-armed junction occurs in a unidirectional manner that is determined by the assembly of a single RuvB ring onto one arm of the DNA. (dundee.ac.uk)
  • Using the above methods, 72 short, non-annotated protein-coding genes were detected. (rostlab.org)
  • These findings demonstrate that ribosomal footprinting can be used to detect novel protein coding genes, contributing to the growing body of evidence that hypothetical genes are not annotation artifacts and opening an additional way to study their functionality. (rostlab.org)
  • The noncoding RNA family contains several types of RNAs and is mainly involved in regulating protein-coding genes. (frontiersin.org)
  • previously named HMGI/Y) function as architectural chromatin-binding proteins and are involved in the transcriptional regulation of several genes. (biologists.com)
  • These results are consistent with a mode of action for natural selection that is based on similar rates of elimination of del- eterious protein coding sequence variants for functionally related genes. (nih.gov)
  • For instance, genes that encode physically interacting proteins tend to evolve at similar rates (Fraser et al. (nih.gov)
  • Both genes encode proteins with DNA binding motifs and a conserved protein-protein interaction domain, known as the Broad complex, Tramtrack, Bric-a-brac (BTB) domain. (sdbonline.org)
  • Longitudinals lacking (lola) is one of the most complex genes in Drosophila melanogaster, encoding up to 20 protein isoforms that include key transcription factors involved in axonal pathfinding and neural reprogramming. (sdbonline.org)
  • The researchers show that, when ethylene is perceived, transcription of certain genes that function as circuit breakers of ethylene signaling occurs, but protein production becomes restricted until ethylene is removed. (ncsu.edu)
  • Our findings indicate that mitotic chromosomes in general and ribosomal genes in particular, although highly condensed, are accessible to transcription factors and chromatin proteins. (rupress.org)
  • To date, HRBF methods have been used in vitro on relatively pure protein systems. (nih.gov)
  • They exert bacteriostatic activity by binding to the ribosomal 30S subunit, composed of 16S rRNA and several ribosomal proteins. (medscape.com)
  • All of these showed signals in the ribosomal footprinting assay indicating mRNA translation. (rostlab.org)
  • For a more-detailed investigation on the interaction of HMGA1a with chromatin, the contribution of the AT-hook DNA-binding motifs was analyzed using point-mutated HMGA1a-GFP proteins. (biologists.com)
  • Furthermore, by inhibiting kinase or histone deacetylase activities, and with the help of fusion proteins lacking specific phosphorylation sites, we analyzed the effect of reversible modifications of HMGA1a on chromatin binding. (biologists.com)
  • The regulated dynamic properties of HMGA1a fusion proteins indicate that HMGA1 proteins are mechanistically involved in local and global changes in chromatin structure. (biologists.com)
  • Protein Containing the GGDEF Domain Affects Motility and Biofilm Formation in Vibrio cholerae and is Negatively Regulated by Fur and HapR[J]. Biomedical and Environmental Sciences, 2023, 36(10): 949-958. (besjournal.com)
  • The antibiotics constituting the MLSK group inhibit protein synthesis at the ribosome level and are bacteriostatic except the streptogramin combinations and ketolides. (medscape.com)
  • Tetracyclines and the related glycylcyclines inhibit bacterial protein synthesis. (medscape.com)
  • As models, we study the troponin-tropomyosin thin filament calcium regulatory complex of mammalian skeletal muscle and uncoordinated mutants of the nematode C. elegans whose phenotypes are consistent with disproportionate synthesis of thick and thin filament proteins. (duke.edu)
  • Essentially, that means the messenger RNA is being made and stored, but the flow of information does not continue into protein synthesis," Stepanova said. (ncsu.edu)
  • EIN2 protein binds to the messenger RNA of the ethylene circuit breaker EBF2, incapacitating its protein synthesis, and thus allowing for a full activation of plant ethylene responses. (ncsu.edu)
  • RNAIII is the regulatory molecule of the response and hence responsible for the up-regulation of extracellular protein production and down-regulation of cell wall-associated protein synthesis during the postexponential phase (20, 34). (cgp60474.com)
  • In contrast to locus activates the synthesis of both extracellular (e.g., alpha- and beta-hemolysins) and cell wall proteins (e.g., fibronectin binding protein) in (11). (cgp60474.com)
  • It was originally coined in reference to the use of limited proteolysis to investigate contact sites within a monoclonal antibody - protein antigen complex and a year later to examine the protection from hydroxyl radical cleavage conferred by a protein bound to DNA within a DNA-protein complex. (wikipedia.org)
  • Not only does footprinting of the extra-membrane domain occur, but also some footprinting of the hydrophobic transmembrane domain is achieved owing to the interaction of TFB + with the micelle. (wustl.edu)
  • rib and lola are expressed in the SGPs of the developing gonad, and genetic interaction analysis suggests these proteins cooperate to regulate gonad development. (sdbonline.org)
  • The advantage of this protein footprinting method is that it utilizes the reactivity of hydroxyl radicals to stably modify solvent accessible residues non-specifically in a microsecond. (wustl.edu)
  • Protein footprinting utilizes a protein cutting reagent or protease. (nih.gov)
  • Analysis of the products by mass spectrometry reveals that proteins are oxidized in a limited manner (some 10-30% of total protein) at a number of amino acid side chains across the proteins. (wikipedia.org)
  • The exposure of proteins to a "white" X-ray beam of synchrotron light or an electrical discharge for tens of milliseconds provides sufficient oxidative modification to the surface amino acid side chains without damage to the protein structure. (wikipedia.org)
  • Hydroxyl radical-based footprinting (HRBF) approaches utilize hydroxyl radicals to oxidatively modify the side chains of solvent accessible amino acids. (nih.gov)
  • Initial results demonstrate that this electrophilic cation reagent affords residue coverage of nucleophilic amino acids including H, W, M, and S. Further, the addition of TFB + increases the hydrophobicity of the peptides so that separation of isomeric peptide products by reversed-phase LC is improved, suggesting opportunities for subresidue footprinting. (wustl.edu)
  • Protein is a highly complex nutrient comprising amino acids, nine of which, known as essential or indispensable amino acids (IAA), cannot be produced directly by humans and must come from dietary sources. (foodnavigator.com)
  • At issue are the plant cell's transcription and translation processes, in which genetic instructions encoded in DNA are transcribed into messenger RNAs, which are then translated into amino acids to create proteins that carry out specific functions. (ncsu.edu)
  • Hydrogen-deuterium exchange Peptide mass fingerprinting Protein sequencing DNA profiling Sheshberadaran H, Payne LG (January 1988). (wikipedia.org)
  • 11. Identification of the promoter of human transcription factor Sp3 and evidence of the role of factors Sp1 and Sp3 in the expression of Sp3 protein. (nih.gov)
  • 19. Analysis of proteins binding to the proximal promoter region of the human cytomegalovirus IE-1/2 enhancer/promoter reveals both consensus and aberrant recognition sequences for transcription factors Sp1 and CREB. (nih.gov)
  • The knowledge of the structure and function as well as the molecular mechanism of those protein complexes are desired.Today, mass spectrometry is being widely used in proteomics studies. (wustl.edu)
  • A subcomponent of this core, the Biomarkers Core, also supports the development, validation and analysis of specific molecular biomarkers (DNA, RNA, protein, other biomarkers) as well as genomics analysis including DNA arrays, RNase protection assays and differential display of mRNA expression. (nih.gov)
  • Chemical footprinting and x-ray crystallography demonstrated direct binding of MLSK to specific nucleotides in domains II and V of 23S rRNA. (medscape.com)
  • Binding of the polymerase protein, or histones, to DNA was greatly augmented when both enzyme protein and histones were present simultaneously. (dtic.mil)
  • Following analysis by mass spectrometry, information could be inferred regarding the binding site of an Ub-IsoT ZnF protein complex. (nottingham.ac.uk)
  • DNA binding of a non-sequence-specific HMG-D protein is entropy driven with a substantial non-electrostatic contribution. (ucdenver.edu)
  • The role of intercalating residues in chromosomal high-mobility-group protein DNA binding, bending and specificity. (ucdenver.edu)
  • The environmental footprints of certain foodstuffs, calculated per unit of protein produced, risk misinforming food stakeholders and consumers, the researchers claimed. (foodnavigator.com)
  • HMGA1-GFP proteins localize preferentially to heterochromatin and remain bound to chromosomes during mitosis. (biologists.com)
  • The active complex is a tripartite structure in which RuvA protein is bound to the crossover and is sandwiched between two hexameric rings of RuvB. (dundee.ac.uk)
  • A GOE-induced Fe 2+ to Mg 2+ substitution predicts that under 'early Earth' (anoxic) conditions, Fe 2+ can participate in a variety of functions, including mediation of RNA folding and catalysis by ribozymes and proteins. (springer.com)
  • Lastly, we study the orange carotenoid protein (OCP) and the fluorescence recovery protein, two major players in the non-photochemical quenching process in cyanobacteria. (wustl.edu)
  • Over the past year, through funding of a Dartmouth COBRE grant, this core added a Biacore Surface Plasmon Resonance (SPR) analyzer and a Beckman ProteomeLab 2D liquid protein separation and analysis system which greatly increased the core's proteomics capabilities. (nih.gov)
  • A variety of approaches, including comparative genomics, cDNA analysis, PCR, and genetic/biochemical analyses of expression in transgenic mice and C. elegans mutants are being used to define the how the expression of different thin filament proteins is coordinated and how the accumulation of thick and thin filament proteins is regulated. (duke.edu)
  • These include, but are not limited to, NMR deuterium exchange and shift perturbation analysis, Fluorescence Resonance Energy Transfer (FRET), and RNA/DNA protein footprinting. (simtk.org)
  • 10. Kaur P, Kiselar J, Yang S, Chance MR. Quantitative protein topography analysis and high- resolution structure prediction using hydroxyl radical labeling and tandem-ion mass spectrometry (MS). Molecular & cellular proteomics : MCP. (neoproteomics.net)
  • Footprinting analysis confirmed these results. (cnrs.fr)
  • In addition to the XFMS analysis, MD simulation and protein- water hydrogen bond network analysis will be performed to capture the collective motion of proteins constituent atoms and to identify important water nodes. (edu.pk)
  • RP-MS/Protein footprinting studies of protein complexes can also employ computational approaches to assist with this modeling. (wikipedia.org)
  • Finally, vaccinia virus-based expression provided evidence that HPD is subject to phosphorylation, and furthermore, allowed mapping of the HPD protein in the human keratinocyte 2D database. (nih.gov)
  • Collectively our data show that the kinetic properties of HMGA1a proteins are governed by the number of functional AT-hooks and are regulated by specific phosphorylation patterns. (biologists.com)
  • 2. Takamoto, K., Chance, M.R., Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes, Annu Rev Biophys Biomol Struct. (neoproteomics.net)
  • Chapter 2 focusses on the use of diazirines, high energy but remarkably stable functionality as tools to probe protein structure. (nottingham.ac.uk)
  • A computer program (PROXIMO) has also been written to help model protein complexes using data from the RP-MS/Protein footprinting approach. (wikipedia.org)
  • The two most crucial protein machineries involved in this process are reaction center and light harvesting complexes. (wustl.edu)
  • They are usually giant protein complexes with different numbers of co-factors. (wustl.edu)
  • The ORC-Cdc6 structure is predicted to contain six AAA+ subunits, analogous to other ATP-dependent protein machines. (nih.gov)
  • To compare the protein structure in different conditions, real-time compensation of hydroxyl radicals generated in the reaction is required to normalize reaction conditions. (jove.com)
  • One application of this technology is in drug development because it allows researchers to test widely different drug formulations and how they affect protein structure. (jove.com)
  • In addition, protein structure and function were predicted computationally and compared between EHEC-encoded proteins and 100-times randomly shuffled proteins. (rostlab.org)
  • 3. Wang L, Chance MR Protein Footprinting Comes of Age: Mass Spectrometry for Biophysical Structure Assessment Mol Cell Proteomics. (neoproteomics.net)
  • The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequence-specific DNA recognition. (ucdenver.edu)
  • Structure prediction of a complex between the chromosomal protein HMG-D and DNA. (ucdenver.edu)
  • Its capabilities include but are not limited to the protein primary structure investigation. (wustl.edu)
  • Last year, this core expanded its proteomics capabilities with the acquisition of two mass spectrometers and a 2D protein gel system. (nih.gov)
  • This dissertation focuses on using mass spectrometry-based techniques to study photosynthetic protein assemblies. (wustl.edu)
  • To elucidate these concepts, an integrated X-ray hydroxy-radical footprinting with mass spectroscopy (XFMS) and MD simulation approach that can provide residue level resolution has been proposed. (edu.pk)
  • Characterization of one of the targets of this translation regulatory machinery, the ethylene signaling component EBF2, indicates that the signaling molecule EIN2 and the nonsensemediated decay proteins UPFs play a central role in this ethylene-induced translational response. (ncsu.edu)
  • Using a DNA-specific column containing a 49-bp sequence upstream of the P2 promoter that shares homology with the region between the P1 and MG-262 P3 promoters, we previously described the purification of a 12-kDa protein (27). (cgp60474.com)
  • Based on the data presented here, we propose that SarR is a regulatory protein that binds to the promoter region to down-regulate transcripts. (cgp60474.com)
  • This thesis primarily concerns the development of new tools and reactions through the activation of chemical moieties to generate either function, as protein labels or the synthetically valuable sulfonyl azides, or unusual chemical reactivity. (nottingham.ac.uk)
  • Additionally, protein misfolding was selectively restored by 4-phenylbutyrate, a chemical chaperone. (ubc.ca)
  • This method was the first employed to apply protein footprinting to the study of a protein complex. (wikipedia.org)
  • Other studies have extended the method to study early onset protein damage given the radical basis of the method and the significance of oxygen based radicals in the pathogenesis of many diseases including neurological disorders and even blindness. (wikipedia.org)
  • However, further optimization of the method is required to increase the number of oxidatively modified proteins. (nih.gov)
  • The environmental impact of beef and dairy is halved by a new assessment method that calculates a food's protein quality, say scientists at Rothamsted Research. (foodnavigator.com)
  • Hydroxyl radical footprinting: a high-resolution method for mapping protein-DNA contacts. (ucdenver.edu)
  • DNasel footprinting indicated that approximately 66-85 bp of DNA was protected by poly ADP-ribose polymerase from DNasel attack, and that a segment of DNA probably lies outside on the surface of the polymerase protein in the polymerase-DNA complex. (dtic.mil)
  • Lastly, the complex information will be reduced to certain diagnostic measures that can differentiate among the various states of CheY protein. (edu.pk)
  • That includes the ammonia emissions and runoff that can cause algal blooms in rivers and lakes, said David Styles, who studies product life cycles and carbon footprinting at Bangor University in Wales and was one of the researchers who collaborated with Black. (insidescience.org)