Protein footprinting. Medical search. Frequent questions

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)

small molecule - protein docking. (galaxyproject.org)

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)

Chemicals and Drugs2

Analytical, Diagnostic and Therapeutic Techniques and Equipment5

Phenomena and Processes5

Information Science3

Photochemical oxidation of proteins5

Hydroxyl radical protein2

Electrophoretic Mobil1

Conformational9

Oxidation4

Interactions9

FPOP3

Nucleic4

Footprint4

Escherichia3

Membrane proteins5

Single-molecule1

Structural3

Vivo1

Gene8

Experiments2

DNase3

Genes10

Methods1

Ribosomal2

Chromatin3

20231

Synthesis7

Monoclonal antibody1

Interaction2

Utilizes2

Amino6

Peptide1

Transcription2

Mechanism1

MRNA1

Binding5

Footprints1

Small molecule1

Bound2

Ribozymes1

Fluorescence recovery1

Analysis6

Approaches1

Phosphorylation2

Probe2

Complexes3

Structure8

Mass3

Characterization1

Purification1

Promoter region1

Chemical2

Method5

Complex2

Studies1