• Chemical shift changes upon the addition of single-stranded RNAs (ssRNAs) identified a group of residues that form a positively charged patch on the protein surface as the binding site responsible for the previously reported affinity for nucleic acids. (pdfroom.com)
  • Experimental methods of multi-dimensional NMR spectroscopy, dynamics and theoretical description of spin system evolution, multiple resonance NMR technique for structural studies of proteins and nucleic acids by NMR spectroscopy, contemporary methods of structural biology, studies of complex biomolecular systems. (muni.cz)
  • Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within cells. (transectscience.org)
  • Nature provides biomolecules such as nucleic acids, proteins, and viruses which can be used to integrate the nanoparticles. (ukdiss.com)
  • Protein-protein interactions involving intrinsically disordered proteins are important for cellular function and common in all organisms. (elifesciences.org)
  • Experiments together with molecular modeling using NMR chemical shifts suggest that new interactions involving intrinsically disordered proteins may evolve via a low-affinity complex which is optimized by modulating direct interactions as well as dynamics, while tolerating several potentially disruptive mutations. (elifesciences.org)
  • However, a group of proteins called 'intrinsically disordered proteins' are flexible in their shape and lack a stable three-dimensional structure. (elifesciences.org)
  • analyzed the amino acid sequences of two specific intrinsically disordered proteins from different organisms to reconstruct the versions of the proteins that were likely found in their common ancestors 450-600 million years ago. (elifesciences.org)
  • Intrinsically disordered proteins and their contraction and folding can be monitored using this technique. (utmb.edu)
  • Sequence-based method of predicting the solubility of peptides and proteins containing post-translationally modified and/or non natural amino acids. (cam.ac.uk)
  • To support our discovery programs we can use CD spectroscopy for different applications for the study of secondary structure content of peptides and proteins, monitoring conformational transitions , and the study of the thermodynamics of unfolding and protein-ligand interactions . (irbm.com)
  • The findings shed light on fundamental principles of how new protein-protein interactions emerge and evolve on a molecular level. (elifesciences.org)
  • A deeper knowledge of how this molecular evolution happened will broaden our understanding of present day protein-protein interactions and might aid the design of drugs that can mimick proteins. (elifesciences.org)
  • Here we describe a method of using methyl chemical shifts as restraints in replica-averaged molecular dynamics (MD) simulations, which enables us to determine the conformational ensemble of the HU dimer and characterize the range of motions accessible to its flexible β-arms. (ox.ac.uk)
  • We have a set of biophysical tools available that allow, for example, the determination of binding kinetics , affinity and specificity , secondary structure and thermodynamic profiles, or structural insights on the molecular interactions of a small molecule or a peptide to its target. (irbm.com)
  • Solution molecular biophysics and thermodynamic techniques are used both as a primary research tool as well as means to structural studies (for example in the exploration of conditions for crystallization of proteins). (utmb.edu)
  • Chemical shift as a probe of molecular interfaces: NMR studies of DNA binding by the three amino-terminal zinc finger domains from transcription factor IIIA. (colorado.edu)
  • His research sped a shift in many biologists' attention from organismic biology, the study of creatures great and small, to molecular biology, which focuses on the individual biochemical reactions that underpin all living processes and on the molecules - usually proteins - responsible for catalyzing those reactions. (stanford.edu)
  • His discoveries laid the groundwork for our understanding of how a newborn protein accurately folds up into its adult shape within milliseconds - an insight that's informed molecular biology ever since. (stanford.edu)
  • However, most low-molecular-weight chemical sensitizers induce asthma through mechanisms that are poorly understood, despite a phenotype suggesting sensitization. (cdc.gov)
  • Given that the structural and dynamic information contained within chemical shifts is often quite subtle, it is critical that protein chemical shifts be properly referenced so that these subtle differences can be detected. (wikipedia.org)
  • This means that the structural changes of (bio-)polymers, such as proteins and DNA, can be monitored in situ to understand their sensitivity to changes in chemical environments. (rsc.org)
  • Collagen, the most abundant protein in the animal kingdom, represents a promising biomaterial for regenerative medicine applications due to its structural diversity and self-assembling complexity. (biomedcentral.com)
  • Collagen is one of the most important structural proteins, accounting for up to one quarter of protein biomass in mammals [ 1 ]. (biomedcentral.com)
  • Nuclear Magnetic Resonance ( NMR ) spectroscopy is a powerful tool for the study of structural biology, structure/activity relationships and macromolecule and small-molecule analysis. (irbm.com)
  • To obtain structural information of the glycans, the pseudocontact shift (PCS) values were determined for each proton and carbon as the difference of 1H and 13C chemical shift values between the carbohydrate complex with paramagnetic metal ion and diamagnetic reference in all the three fragments. (fu-berlin.de)
  • Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. (transectscience.org)
  • They are sorted according to the structure of there capsids withholding the genomes, chemical and structural composition of their genomes, and the mechanism of mRNA production. (ukdiss.com)
  • Those structural motifs are well known to play a key role in stabilizing protein structure and likely to be important in the protein folding process. (nih.gov)
  • The MICS program is developed based on a systematic study of the NMR chemical shift (and amino acid sequence) patterns observed for each type of structural motif by using a database of proteins of known structure and known NMR chemical shifts. (nih.gov)
  • Performs the secondary structure and structural motif classifications, then summarizes the predictions. (nih.gov)
  • The current view of protein folding and stability is largely based on SAXS and DLS data13-16 and the extensive exposure of hydropho- a generic structural classification into native (N), compact dena- bic residues suggested by the finding that the heat capacity of the tured or molten globule (MG), and unfolded or denatured (D) MG state is midway between that of the N and D states7 have been conformational states1-10. (lu.se)
  • Inferences about hydration have usually been indirect (where the ous structural and dynamic information about the internal peptide chain is not, there is solvent) or have relied on uncertain (buried) and external (surface) hydration of globular proteins in premises. (lu.se)
  • The most important parameter archived in the BMRB is assigned chemical shifts, which can be used directly to determine protein secondary structure and to assist in the determination of their solution structures, to identify interactions of small molecules with target proteins for drug discovery, and to characterize protein-protein interactions. (biomedcentral.com)
  • The fast and real time analysis of the kinetic and thermodynamic binding parameters of small molecules , peptides , antibodies , or other protein-protein interactions, are crucial information for target characterization, hit identification, lead optimization or characterization of the binding properties of a molecule to its target. (irbm.com)
  • Compounds of interest include not only classical "drug-like" organic small molecules, but also peptides, proteins, and other bioactive chemical classes. (cancer.gov)
  • Therefore, it became apparent that each of these fungi possesses considerable potential as expression hosts for producing numerous small molecules and heterologous proteins 14 . (nature.com)
  • Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. (transectscience.org)
  • Short polypeptides, containing less than 20-30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. (transectscience.org)
  • The sequence of amino acid residues in a protein is defined by the sequence of a gene which is encoded in the genetic code. (transectscience.org)
  • Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. (transectscience.org)
  • The tables of random coil shifts, adjustments values from neighboring residues used in the prediction process (the same tables as used in TALOS). (nih.gov)
  • Several methods have been developed that make use of the estimated (via 1H or 13C shifts) or predicted (via sequence) secondary structure content of the protein being analyzed. (wikipedia.org)
  • Sequence-specific 1H, 13C and 15N chemical shift assignment and secondary structure of the HTLV-I capsid protein. (expasy.org)
  • 2009 ). The designated dysbindin paralogs show very limited sequence homology which raised the question whether DBNDD1 and DBNDD2 are dysbindin-like proteins or proteins that share a less conserved domain with DTNBP1 in the context of otherwise unrelated sequences (Ghiani and Dell'Angelica 2011 ). (springer.com)
  • As an outcome human DBNDD1 revealed a high sequence identity to dysbindin domain-containing proteins from other Hominidae (e.g. (springer.com)
  • Proteins with high sequence identity to human DBNDD1 can also be found in evolutionarily more distant species (e.g. (springer.com)
  • Sequence-based method of predicting protein solubility and generic aggregation propensity. (cam.ac.uk)
  • A method of predicting secondary structure populations of proteins from the amino acid sequence. (cam.ac.uk)
  • PINE is a probailistic method for automated protein backbone and sidechain assignments, detection and correction of referencing and secondary structure determination from input protein sequence and NMR data set peak lists. (wisc.edu)
  • it provides as output a probabilistic assignment of NMR signals (chemical shifts) to sequence-specific backbone and aliphatic side chain atoms plus a probabilistic determination of the protein secondary structure. (wisc.edu)
  • Protein sequence input file The protein sequence input text file should contain the amino acid sequence in a single column, using either 1- or 3-letter amino acid codes. (wisc.edu)
  • Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific three-dimensional structure that determines its activity. (transectscience.org)
  • 12] These errors, mutations, can affect an organism's phenotype, especially if they occur within the protein coding sequence of a gene. (mercinewyork.com)
  • The genetic code is so well-structured for hydropathicity that a mathematical analysis (Singular Value Decomposition) of 12 variables (4 nucleotides x 3 positions) yields a remarkable correlation (C = 0.95) for predicting the hydropathicity of the encoded amino acid directly from the triplet nucleotide sequence, without translation. (mercinewyork.com)
  • We provide thorough characterization of the effect of pH, effect of salts and protein conformation on self-assembled collagen samples via several complementary biophysical techniques, including circular dichroism (CD), Fourier Transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), atomic force microscopy (AFM), scanning electron microscopy (SEM), dynamic mechanical thermal analysis (DMTA) and thermogravimetric analysis (TGA). (biomedcentral.com)
  • CD is a powerful tool for studying peptide and protein conformation requiring a minimal amount of sample compared to other techniques. (irbm.com)
  • After obtaining his degree in 1997, he worked as a Wellcome Trust and BBSRC Research Fellow, designing joint theoretical and experimental approaches to study the dynamic conformation of hyaluronan, both free and in the presence of protein, and expanding his research into other polysaccharides and oligosaccharides. (gr.jp)
  • Abietane-Type Diterpenoids Inhibit Protein Tyrosine Phosphatases by Stabilizing an Inactive Enzyme Conformation. (colorado.edu)
  • To obtain a better understanding of the GPI structures and biological functions of these glycolipids, in the second part of this work a paramagnetic NMR technique was employed along with the MD simulations to study the conformation and dynamics of the glycan part of the core of GPI anchors. (fu-berlin.de)
  • Protein conformation is critically linked to function and often controlled by interactions with regulatory factors. (cipsm.de)
  • Here we report the selection of camelid-derived single-domain antibodies (nanobodies) that modulate the conformation and spectral properties of the green fluorescent protein (GFP). (cipsm.de)
  • Simplified representation illustrating the backbone conformation, colored by secondary structure. (transectscience.org)
  • A method for the automated structure-based optimisation of solubility and conformational stability of antibodies and proteins. (cam.ac.uk)
  • A conformational ensemble derived using NMR methyl chemical shifts reveals a mechanical clamping transition that gates the binding of the HU protein to DNA. (ox.ac.uk)
  • Such advances also suggest the possibility of using chemical shifts to characterize the conformational fluctuations of these molecules. (ox.ac.uk)
  • This information can be used to analyze protein-protein interactions, the presence of oligomeric states, and conformational rearrangement of molecules. (utmb.edu)
  • The reference frequency for the ppm scale is the signal of the methyl groups of tetramethylsilan (TMS, the chemical shift of which is defined as 0 ppm). (bbk.ac.uk)
  • Semi-synthetic approaches offer an alternative means to manipulate proteins post-translationally, but these modifications have typically been performed in vitro 3 - 8 . (biorxiv.org)
  • Structure Determination of. (bionmr.com)
  • Hence, Ectoine is shown to provide a non-disturbing way to improve structure-determination of proteins via bio-SAXS in future studies. (rsc.org)
  • PINE-NMR achieves robust and consistent results that have been shown to be effective in subsequent steps of NMR structure determination. (wisc.edu)
  • The Jasco J-815 Circular Dichroism Spectrometer housed in the SBL allows for the quick and easy determination of secondary and tertiary structures of protein samples. (utmb.edu)
  • Data collection and structure determination. (auckland.ac.nz)
  • Powder X-ray diffraction for phase identification of materials including minerals and Rietveld refinement for crystal structure determination. (auckland.ac.nz)
  • At multiple time points during evolution, new or modified proteins - and consequently new potential interactions between proteins - have emerged. (elifesciences.org)
  • A next step for the future will be to investigate how other protein-protein interactions have evolved and to identify general underlying patterns. (elifesciences.org)
  • Through these interactions, PH domains play a role in recruiting proteins to different membranes, thus targeting them to appropriate cellular compartments or enabling them to interact with other components of the signal transduction pathways. (embl.de)
  • Monitor the hydrodynamic properties of biomacromolecules and protein-protein interactions. (utmb.edu)
  • Considering the widely acknowledged Accordingly, theoretical models of the MG state invariably invoke importance of protein-solvent interactions for stability and fold- a substantial internal hydration20-22. (lu.se)
  • Recent improvements in the accuracy of structure-based methods for the prediction of nuclear magnetic resonance chemical shifts have inspired numerous approaches for determining the secondary and tertiary structures of proteins. (ox.ac.uk)
  • Proteins perform a vast array of functions within organisms, including catalyzing metabolic reactions, DNA replication, responding to stimuli providing structure to cells and organisms, and molecules from one location to another. (transectscience.org)
  • This doesn't matter in RNA, since new RNA copies can be produced from DNA at any time, and most RNA molecules are intentionally destroyed by the cell a short time after they're produced so that the cell does not waste resources producing unneeded proteins from old RNA molecules. (mercinewyork.com)
  • Gold nanoparticles have been under study as model drug delivery platforms because of their surface properties and low toxicity which allows convenient functionalization with chemical and biological molecules. (ukdiss.com)
  • Whereas the N state has been character- taken to imply that hundreds of water molecules penetrate the MG ized at high resolution, many aspects of the D and MG states are protein (except for a relatively small hydrophobic core)5,7,8,17-19. (lu.se)
  • Fig. 1 Crystal structures of human -lactal- bumin (PDB file 1HML), lysozyme (2LZT) and ribonuclease A (7RSA) showing potentially long-lived internal water molecules, disul- fide bonds (yellow), and the Ca2+ ion (green) in -lactalbumin. (lu.se)
  • For -lactalbu- min, only water molecules conserved in the human and baboon structures are shown (the structure of the bovine protein has not been reported). (lu.se)
  • The described case study demonstrates that a simple query of the SPARQL endpoints of the BMRB, UniProt, and Online Mendelian Inheritance in Man (OMIM), can be used in NMR and structure-based analysis of proteins combined with information of single nucleotide polymorphisms (SNPs) and their phenotypes. (biomedcentral.com)
  • This demonstration and Baldwin's follow-on findings simplified the analysis of proteins, accelerating the pace of discovery in medicinal chemistry and drug development. (stanford.edu)
  • The aim of the present study was to determine the secondary structures of the cementoin domain and to characterize the antibacterial properties of these peptides against P. aeruginosa . (biomedcentral.com)
  • We determined subnanometer-resolution cryo-electron microscopy structures of eukaryotic ribosome-Sec61 complexes. (cipsm.de)
  • Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes. (transectscience.org)
  • In contrast to LACS and PANAV/PSSI, CheckShift uses secondary structure predicted from high-performance secondary structure prediction programs such as PSIPRED to iteratively adjust 13C and 15N chemical shifts so that their secondary shifts match the predicted secondary structure. (wikipedia.org)
  • The prediction performance of Dicer cleavage site improved significantly from 66% to 86% when we integrated secondary structure information. (biomedcentral.com)
  • MICS prediction from NMR chemical shifts has been trained and validated using a recently constructed database. (nih.gov)
  • During the prediction, MICS will generate a single output file ' predMICS.tab ' to store the the normalized probability of finding each motif at any given position in the protein, respectively. (nih.gov)
  • Because the approach can introduce virtually any chemical modification into both intracellular and extracellular regions of target proteins, we anticipate that it will overcome some of the drawbacks of other semi-synthetic or ribosome-dependent methods to engineer proteins. (biorxiv.org)
  • These GPI-anchored proteins are known to play an important role in various biological processes and have gained the interest of synthetic chemists and biologists. (fu-berlin.de)
  • Biological monitoring was done for creatinine-adjusted levoglucosan in urine pre- and post-shift. (cdc.gov)
  • Additionally, it is a proline-rich (10% prolines) cytoplasmatic protein with expression in nearly all organs and e.g., neuronal cells. (springer.com)
  • A method of calculating random coil chemical shifts from protein sequences. (cam.ac.uk)
  • Here we present a new approach to incorporate single or multiple post-translational modifications or non-canonical amino acids into soluble and membrane proteins expressed in eukaryotic cells. (biorxiv.org)
  • We thus sought to complement these approaches with a method that could incorporate synthetic peptides carrying multiple post-translational modifications (PTMs) or ncAAs into both cytosolic and membrane proteins in live eukaryotic cells. (biorxiv.org)
  • The trimeric Sec61/SecY complex is a protein-conducting channel (PCC) for secretory and membrane proteins. (cipsm.de)
  • SHIFTCOR identifies potential chemical shift referencing problems by comparing the difference between the average value of each set of observed backbone (1Hα, 13Cα, 13Cβ, 13CO, 15N and 1HN) shifts and their corresponding predicted chemical shifts. (wikipedia.org)
  • Here, we present the backbone and side chain nuclear magnetic resonance assignments for the human DBNDD1 protein. (springer.com)
  • CD spectra in the far UV range report for secondary structures while in the near UV they are characteristics of the tertiary structure of proteins. (irbm.com)
  • It has been estimated that up to 20% of 13C and up to 35% of 15N shift assignments are improperly referenced. (wikipedia.org)
  • In order to ensure that certain extreme outliers do not unduly bias these average offset values, the average of the observed shifts is only calculated after excluding potential mis-assignments or typographical errors. (wikipedia.org)
  • The results contain the chemical shift analyses (including lists of potential mis-assignments, the estimated referencing errors, the estimated error in the calculated reference offset (95% confidence interval), the applied or suggested reference offset, correlation coefficients, RMSD values) and the corrected BMRB formatted chemical shift file (see Figure 1 for details). (wikipedia.org)
  • By comparing the predicted shifts to the observed shifts, SHIFTCOR is able to accurately identify chemical shift reference offsets as well as potential mis-assignments. (wikipedia.org)
  • Given that chemical shift assignments are typically made before the structure is determined, it was soon realized that structure-independent approaches were required to develop. (wikipedia.org)
  • We demonstrate the successful application of PINE to a key task in protein NMR spectroscopy: that of converting peak lists extracted from various NMR experiments into assignments associated with probabilities for their correctness. (wisc.edu)
  • PINE returns several types of output, detailing the probabilistic chemical shift assignments and secondary structure determined, in several different formats. (wisc.edu)
  • Prepare the input table of shift assignments (for example ' myshifts.tab '), according to the format given below . (nih.gov)
  • Because of the historic problems with chemical shift referencing, chemical shifts are perhaps the most precisely measurable but the least accurately measured parameters in all of NMR spectroscopy. (wikipedia.org)
  • Nuclear magnetic resonance chemical shift re-referencing is a chemical analysis method for chemical shift referencing in biomolecular nuclear magnetic resonance (NMR). (wikipedia.org)
  • Their amino acid sequences suggest that they are mainly cytosolic or nuclear proteins partly associating with membranes (Talbot et al. (springer.com)
  • Cytoskeletal proteins such as dynamin (see IPR001401 ), Caenorhabditis elegans kinesin-like protein unc-104 (see IPR001752 ), spectrin beta-chain, syntrophin (2 PH domains) and S. cerevisiae nuclear migration protein NUM1. (embl.de)
  • 2009 Nuclear Magnetic Resonance Structure of the. (pdfroom.com)
  • The structure elucidation was facilitated by utilizing long-range heteronuclear single quantum multiple bond correlation (LR-HSQMBC) and heteronuclear multiple bond correlation (HMBC) nuclear magnetic resonance (NMR) pulse sequences optimized to detect four- and five-bond 1 H- 13 C heteronuclear correlations. (cancer.gov)
  • Methods commonly used to study protein structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance and mass spectrometry. (transectscience.org)
  • Despite recent progress in ribosome-dependent and semi-synthetic chemical modifications, these techniques sometimes have limitations in the number and type of modifications that can be simultaneously introduced or their application in live eukaryotic cells. (biorxiv.org)
  • Additionally, insertion of multiple chemical modifications by genetic code expansion remains a challenge, particularly in eukaryotic cells. (biorxiv.org)
  • Furthermore, the dominant type of damage shifted from aggregation in pure solutions towards a fragmentation for solutions containing Ectoine as a cosolute. (rsc.org)
  • The co-chaperone Hep1 is required to prevent the aggregation of mitochondrial Hsp70 proteins. (cipsm.de)
  • Confocal microscopy of fluorescein-labeled pre-elafin/trappin-2 suggests that this protein possesses the ability to translocate across membranes. (biomedcentral.com)
  • This new version of LACS exploits the well-known relationship between 15N shifts and the 13Cα (or 13Cβ shifts of the preceding residue. (wikipedia.org)
  • GPIs can be found as free glycolipids or attached to the C-terminus of the proteins using a phosphoethanolamine unit on the Man-III residue of the glycan core forming the so-called GPI-anchored proteins (GPI-APs). (fu-berlin.de)
  • The MICS output assigns a normalized probability for each residue to participate in any of the specific motifs, or to be part of a regular element of secondary structure. (nih.gov)
  • Emphasis was made on the use of isothermal titration calorimetry (ITC) for the thermodynamic monitoring of fibrillogenesis stages of the protein. (biomedcentral.com)
  • Thermodynamic data such as protein stability parameters and binding constants can also be obtained. (utmb.edu)
  • i) The virulence of the biocontrol agent must be enhanced to overcome evolutionary barriers either by mixing with synergistic chemicals or with one or more organisms, and/or by mutagenic or transgenic enhancing of virulence of the biocontrol fungus. (weizmann.ac.il)
  • Our group offers performed extensive chemical investigations of bioactive secondary metabolites derived from insect-associated microbes and recognized cytotoxic beauvetetraones A?C (phomaligadione-derived polyketide dimers) from your entomopathogenic fungus [11], neuroprotective isoflavonoids from a termite-associated sp. (baxkyardgardener.com)
  • Preexisting antivector immunity can severely compromise the ability of Salmonella enterica serovar Typhimurium live vaccines to induce protective CD8 T-cell frequencies after type III secretion system-mediated heterologous protein translocation in orally immunized mice. (cipsm.de)
  • Here we demonstrate that PSRP1 is not a bona fide ribosomal protein, but rather a functional homologue of the Escherichia coli cold-shock protein pY. (cipsm.de)
  • To enhance the interoperability of the BMRB database, we present a full conversion of BMRB entries to two standard structured data formats, XML and RDF, as common open representations of the NMR-STAR data. (biomedcentral.com)
  • The best approach for enhancing interoperability of the BMRB would be to convert the archive into standard web formats, XML and RDF, using a data structure that corresponds closely to the NMR-STAR ontology described by an XML schema and OWL. (biomedcentral.com)
  • The experimental results supported by quantum chemical calculations indicate that this functional symmetry occurs in PSI despite similarly sized chemical shift differences between the cofactors of PSI and the functionally asymmetric special pair donor of the bacterial RC of Rhodobacter sphaeroides . (copernicus.org)
  • Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. (transectscience.org)
  • A search of the protein structure database indicates that the globular domain of the NAB represents a new fold, with a parallel four-strand �-sheet holding two �-helices of three and four turns that are oriented antiparallel to the �-strands. (pdfroom.com)
  • This binding site is similar to the ssRNA-binding site of the sterile alpha motif domain of the Saccharomyces cerevisiae Vts1p protein, although the two proteins do not share a common globular fold. (pdfroom.com)
  • Structure-based method of calculating a solubility profile, which accounts for the proximity of the amino acids in the structure and for their solvent exposure. (cam.ac.uk)
  • The structurally corrected profile can be color-coded on the structure of the protein to spot patches of low solubility that may elicit self-assembly. (cam.ac.uk)
  • Cells possess cilia, which are hair-like structures that modulate and sense the extracellular environment. (biomedcentral.com)
  • Baldwin developed tools and designed rigorous experiments to show that instead of simply switching in binary fashion from their initial linear conformations into correctly folded final shapes, as had been postulated, proteins transition into their final shapes through short-lived intermediate structures. (stanford.edu)
  • Pleckstrin, the protein where this domain was first detected, is the major substrate of protein kinase C in platelets. (embl.de)
  • Fusion of a kinase gene, ALK , to a nucleolar protein gene, NPM , in non-Hodgkin's lymphoma. (nature.com)
  • fridamycin A induced glucose uptake in 3T3-L1 cells by activating the AMP-activated protein kinase (AMPK) signaling pathway but did not impact adipocyte differentiation, suggesting that the glucose uptake took place through activation of the AMPK signaling pathway without inducing adipogenesis. (baxkyardgardener.com)
  • Recently, natural products have been reported to improve insulin level of sensitivity via RU 24969 hemisuccinate the activation of AMP-activated protein kinase (AMPK), which is definitely believed to be a restorative target for the treatment of type 2 diabetes [4,7,8]. (baxkyardgardener.com)
  • UTMB also pioneered the use of osmolytes in the stabilization of intrinsically unstructured regions of proteins ( 2 ) and the SBL has a long tradition of the use of protecting osmolytes in biophysical studies ( 3 ). (utmb.edu)
  • These findings shed new light on hydrophobic stabilization of proteins. (lu.se)
  • An extensive bioinformatics analysis of the coronavirus replicase proteins by Snijder et al. (pdfroom.com)
  • Regulators of small G-proteins like guanine nucleotide releasing factor GNRP (Ras-GRF) (which contains 2 PH domains), guanine nucleotide exchange proteins like vav, dbl, SoS and Saccharomyces cerevisiae CDC24, GTPase activating proteins like rasGAP and BEM2/IPL2, and the human break point cluster protein bcr. (embl.de)
  • Additionally, there are a number of conditions in which a genetic defect causes secondary mitochondrial dysfunction. (msdmanuals.com)
  • A directory with example chemical shift input data and scripts for a demo of MICS. (nih.gov)
  • SHIFTCOR uses the chemical shift calculation program SHIFTX to predict 1Hα, 13Cα,15N shifts based on the 3D structure coordinates of the protein being analyzed. (wikipedia.org)
  • Atomic coordinates have been deposited in the Protein Data Bank (PDB) with accession codes 7N00 (cryoEM structure of ALK-ECR ABR -ALKAL2), 7MZY (X-ray structure of ALK-ECR ABR (ΔEGF)), 7MZW (NMR structure of ALK-ECR ABR ), 7MZX (NMR structure of ALKAL2) and 7MZZ (NMR structure of ALKAL1). (nature.com)
  • The chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and beta-turn motifs, are then used as input data for training an artificial neural network algorithm, which outputs the statistical probability of finding each motif at any given position in the protein. (nih.gov)
  • The N-terminal cementoin domain adopts α-helical secondary structures in a membrane mimetic environment, which is common in antimicrobial peptides. (biomedcentral.com)
  • These results are interpreted in terms of indirect radiation damage by reactive secondary species, as well as post-irradiation effects, related to preferential-exclusion of the cosolute from the protein surface. (rsc.org)
  • The latter facilitates the simultaneous use of two orthogonal split inteins within the same peptide or protein, an approach termed tandem protein trans-splicing (tPTS). (biorxiv.org)
  • All recognized mutations for AD are associated with increased deposition of amyloid-beta (Abeta), a peptide fragment comprising 39-43 amino acids that derive from the catabolism of the amyloid precursor protein (APP) molecule. (medscape.com)
  • 10 kD, usually a protein or glycopeptide) that can cause production of specific IgE antibodies and typical allergic responses. (cdc.gov)
  • In this study we investigate the feasibility of applying the compatible solute, osmolyte and radiation protector Ectoine (THP(B)), as a scavenger molecule during SAXS measurements of the single-stranded DNA-binding protein Gene-V Protein (G5P/GVP). (rsc.org)
  • The ancestral proteins were then 'resurrected' by recreating them in test tubes and their characteristics and properties analyzed with experimental and computational biophysical methods. (elifesciences.org)
  • From its initial isolation, the properties of HA provided a challenge to classical biophysical methods of analysis, which were primarily developed for proteins and required that the properties approached those of perfect Newtonian solutes. (gr.jp)
  • How does a protein know how to fold up, without mistakes and almost instantaneously, into a functional three-dimensional structure? (stanford.edu)
  • These methods dramatically increase the likelihood of producing proteins that cannot fold or assemble appropriately. (cipsm.de)
  • · http://structbio.nature.com ness, secondary structure, tertiary fold, and side-chain packing. (lu.se)
  • The results show that nonnative proteins are more structured and less solvent exposed than commonly believed. (lu.se)
  • Proteins denatured by guanidinium chloride are not fully solvent exposed but contain strongly perturbed occluded water. (lu.se)
  • The PSSI and PANAV programs use the secondary structure determined by 1H shifts (which are almost never mis-referenced) to adjust the target protein's 13C and 15N shifts to match the 1H-derived secondary structure. (wikipedia.org)
  • Baldwin propelled leaps in scientists' understanding of how proteins assemble themselves into the three-dimensional shapes that are essential to their function. (stanford.edu)
  • The whole-genome sequencing has revealed that fungi could produce a far greater number of secondary metabolites that have been isolated. (nature.com)
  • The genome mining of secondary metabolites produced by A. fumigatus , A. nidulans , A. niger , and A. terreus revealed unique biosynthetic gene clusters and biosynthetic pathways 9 . (nature.com)
  • These results illustrate that using side-chain chemical shift data in conjunction with MD simulations can provide quantitative information about the free energy landscapes of proteins and yield detailed insights into their functional mechanisms. (ox.ac.uk)
  • Baldwin devoted his career to studying how proteins, which begin life as linear chains of chemical building blocks, quickly assume their characteristic highly complex, functional structures. (stanford.edu)
  • The hydration of nonnative states is central to protein folding and stability but has been probed mainly by indirect methods. (lu.se)
  • It is typically discussed using the "codons" found in mRNA, as mRNA is the messenger that carries information from the DNA to the site of protein synthesis. (mercinewyork.com)
  • The seeded growth strategy for the synthesis of large citrate gold nanoparticles based on controlling the size and shape is described by the inhibition of secondary nucleation throughout the homogenous growth process which allows the magnification of Au Nps via the reduction of AU3+ by sodium citrate. (ukdiss.com)
  • This assembly results in a spontaneous, essentially traceless splicing reaction that covalently links the two flanking protein segments through native chemical ligation 9 . (biorxiv.org)
  • Our chemical-shift based secondary structure analysis reveals the human DBNDD1 as an intrinsically disordered protein. (springer.com)
  • Ser/Thr protein kinases such as the Akt/Rac family, the beta-adrenergic receptor kinases, the mu isoform of PKC and the trypanosomal NrkA family. (embl.de)
  • Tyrosine protein kinases belonging to the Btk/Itk/Tec subfamily. (embl.de)
  • Chemical or genetic engineering of proteins provides great potential to study protein function and pharmacology or to generate proteins with novel properties. (biorxiv.org)
  • Our Surface Plasmon Resonance (SPR) Biacore T100 biosensor instrument is a high-throughput equipment that allows the study of protein-protein and protein-ligand kinetics and thermodynamics. (utmb.edu)