Sequence or structural protein conformation. Medical search. Frequent questions

Click molecule labels to explore molecular sequence information. (nih.gov)
This review aims to link recent molecular data, often translated into amino acid sequences and predicted three dimensional structural motifs, to known mechanical properties. (bioone.org)
Identifying the molecular states relevant to protein functioning is necessary for our understanding of biological processes. (biorxiv.org)
In order to understand the functions of proteins at a molecular level, it is often necessary to determine the three dimensional structure of proteins. (phys.org)
The mission of the Pittsburgh Center for HIV Protein Interactions (PCHPI) is to understand HIV maturation and the early cellular events of HIV infection by characterizing HIV-host cell protein interactions/complexes at a high-resolution, molecular level. (pitt.edu)
B ) Table showing observed molecular weight and calculated molecular weight for monomeric protein of H-NS 1-57. (elifesciences.org)
Successful interspecies prion transmission at the molecular level depends on the compatibility of the invading prion conformers and structural determinants imposed by host PrP C . One structural motif is the loop region between β sheet 2 and α helix 2 of PRP C at aa 170-174 ( Technical Appendix ). (cdc.gov)
Hijacking pathogenic membrane proteins to engineer cellular entry: A molecular biophysics approach Invasive pathogenic bacteria feature many cellular niches and life cycles, for which they have developed functions that are potentially attractive in biotechnology and therapeutic delivery applications. (umich.edu)
Our hybrid NMR and molecular dynamics structure of an Opa reveals that the variable regions are dynamic and disordered, and sample conformations that may be competent for receptor binding. (umich.edu)
The course covers both the principles that determine the properties of proteins and the experimental methods that are used to study these properties in modern molecular protein science. (lu.se)

Structure of the EGL-1/CED-9 complex revealed that EGL-1 adopts an extended alpha-helical conformation and induces substantial structural rearrangements in CED-9 upon binding. (nih.gov)
The average hydropathy plot for SSSF proteins predicts 11 to 15 putative transmembrane domains (TMs) in alpha-helical conformation. (embl.de)

This is thought to make globular proteins stable and soluble in the watery environment of the cell. (anl.gov)
Resonance Group, Chemical of the globular proteins bovine pancreatic trypsin inhibitor (BPTI) and Center, Lund University ubiquitin in aqueous solution. (lu.se)
This difference was ascribed to the abscence, in ubiquitin, of highly ordered internal water molecules, which are known to be present in BPTI and in most other globular proteins. (lu.se)

Although the sequence homology of PrP among mammals is high, the ability of particular prion strains to cause disease in different species is determined by the conformational compatibility between a given strain and the host PrP C ( 2 ). (cdc.gov)

beta-Turns related by the characteristic threefold structural symmetry of this superfold exhibit different primary structures, and in some cases, different secondary structures. (rcsb.org)
Proteins from thermophilic organisms must retain their native structures under extreme conditions, where their homologues from mesophilic organisms denature. (berkeley.edu)
Tetrapetide sequences and structures were expressed by letter codes. (medscimonit.com)
RESULTS: High values of the rho-coefficient extracted sequences of strong structural determinability and structures of high sequence selectivity. (medscimonit.com)
The primary question addressed in this work is how to determine structural and therefore functional similarity from 3D protein structures. (biomedcentral.com)
Most current structural alignment tools are based on geometric properties of protein structures, and do not incorporate the effect of physical properties responsible for protein shape and similarity. (biomedcentral.com)
The resolution attained by cryo-EM is very often lower than that of X-ray structures, mainly due to the structural heterogeneity of the measured samples. (biorxiv.org)
Actual algorithms work on both protein sequences and structures, some of them accounting also for conformational fluctuations around the native state and the protein microenvironment. (uab.cat)
Current hypotheses on protein folding suggest that folding is initiated by formation of secondary structures followed by association of the hydrophobic regions of the emerging structure to orient them toward the interior of the protein in a process termed hydrophobic collapse. (anl.gov)
Here, we present a methodology that relies upon graph and centrality analyses, augmented by bioinformatics, to identify and characterize large H-bond clusters in protein structures. (ugr.es)
Here, we show that we can expand the application of well-characterized antibodies by "transplanting" the epitopes that they recognize to proteins with completely different structures and sequences. (postech.ac.kr)
Using X-ray crystallography, we determined the structures of the engineered protein-antibody complexes. (postech.ac.kr)
All of the antibodies bound to the epitope-transplanted proteins, forming accurately predictable structures. (postech.ac.kr)
PDBsum is a pictorial database of protein 3D structures deposited in the Data Bank. (projectguru.in)
The general aim of the course is to enable students to acquire an advanced understanding of proteins with an emphasis on their three-dimensional structures, the connection of structures to biological function and how these structures are produced. (lu.se)
Distinguishing three-dimensional structures characteristically formed by homologous protein sequences. (bvsalud.org)

This additional task objective acts as a regularizer and also allows to incorporate domain knowledge to inform the virus-human protein-protein interaction prediction model. (biomedcentral.com)
Experimental results show that our proposed model works effectively for both virus-human and bacteria-human protein-protein interaction prediction tasks. (biomedcentral.com)
Matching of structural motifs using hashing on residue labels and geometric filtering for protein function prediction. (uni-marburg.de)
The development of computational tools opened a new avenue to rationalize this phenomenon, enabling prediction of the aggregation propensity of individual proteins as well as proteome-wide analysis. (uab.cat)
In this study, computational models for 11 influenza proteins have been constructed using the machine learning algorithm random forest for prediction of host tropism. (springer.com)
The prediction models were trained on influenza protein sequences isolated from both avian and human samples, which were transformed into amino acid physicochemical properties feature vectors. (springer.com)
From the prediction models constructed, all achieved high prediction performance, indicating clear distinctions in both avian and human proteins. (springer.com)
When used together as a host tropism prediction system, zoonotic strains could potentially be identified based on different protein prediction results. (springer.com)
Prediction of local conformation of a query protein chain around examined site is done with the specially prepared library of short local structural segments (LSSs). (psnc.pl)
MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. (rostlab.org)
However, the uniqueness of MuD is that user-reported protein-specific structural and functional information can be added at run-time, thereby enhancing the prediction accuracy further. (rostlab.org)
The MuD server, available at http://mud.tau.ac.il , assigns a reliability score to every prediction, thus offering a useful tool for the prioritization of substitutions in proteins with an available 3D structure. (rostlab.org)

Short coding motifs, which appear to lack secondary structure, include those that label proteins for delivery to particular parts of a cell, or mark them for phosphorylation. (wikipedia.org)
BTK, a TEC-family tyrosine kinase activated by the B-cell antigen receptor, contains a variety of regulatory domains and it is subject to complex regulation by membrane phospholipids, protein ligands, phosphorylation, and dimerization. (elifesciences.org)
We estimate in this paper the level of improvement over purely sequence based methods gained by incorporating predicted structural information into the local description of phosphorylation sites. (psnc.pl)

Exactly how the interaction between antibiotic and leader peptides occurs at the structural level, so as to cause the ribosome to stall, has remained unclear," Wilson says. (uni-muenchen.de)
Previously, several antibodies have been shown to recognize the alphahelical conformation of antigenic peptides. (postech.ac.kr)

As such, they represent a useful system with which to study the role that turn sequences play in determining structure, stability, and folding of the protein. (rcsb.org)
Two turns related by the threefold structural symmetry, the beta4/beta5 and beta8/beta9 turns, were subjected to both sequence-swapping and poly-glycine substitution mutations, and the effects upon stability, folding, and structure were investigated. (rcsb.org)
Understanding the sequence determinants of the energy landscape is therefore fundamental to the biological process that proteins carry out as well as protein folding itself. (berkeley.edu)
Our use of different hydrogen exchange methods to study three different types of intermediates of E. coli ribonuclease H (the acid molten globule, the higher energy conformations of the native state and a kinetic folding intermediate) has been particularly powerful. (berkeley.edu)
This hypothesis unites a lot of work in the field of and has also provided insight and experimental tests for current theoretical work on protein folding. (berkeley.edu)
Other projects in the lab focus on the mechanism of protein misfolding, the structural and energetic mechanism of signaling, computational identification of folding modules, and the role of ligand binding. (berkeley.edu)
Our studies on the mechanism of folding include investigating the role of topological complexity using permuted proteins, the nature and function of folding intermediates, and studies on the role of mechanical unfolding using single molecule measurements. (berkeley.edu)
BACKGROUND: Experimental observations classify the protein-folding process as a multi-step event. (medscimonit.com)
Their correlation seems to be essential in protein-folding simulation. (medscimonit.com)
CONCLUSIONS: The results revealed sequence-to-structure (and vice versa) correlation in early-stage folding. (medscimonit.com)
Protein folding is one of the fascinating unanswered questions in biology. (anl.gov)
Autotransporter proteins then remain in an unfolded state in the periplasm until they pass through the outer bacterial membrane, folding properly along the way. (anl.gov)
This highly specialized protein folding process has attracted the attention of a team of researchers who have used this bacterial system as a model to determine what allows these unique proteins to maintain their disordered state in the periplasm. (anl.gov)
The authors believe their work will provide important information toward understanding basic questions of protein folding and tests long-held theories about how this remarkable biological process works. (anl.gov)
The first step was to analyze the impact of the sequence of the amino acids in the passenger domain on the folding process. (anl.gov)
Going forward, the team will test the extent of collapse in an even wider range of sequences, to more fully understand the importance of maintaining a highly expanded conformation prior to folding. (anl.gov)

Using complementary approaches, i.e. controlled enzymatic hydrolysis and production of recombinant fusion proteins, we demonstrated that, for these patients, the allergenicity of the caprine β-casein could be abolished by substituting five amino acids residues. (cea.fr)

This is the topic of the scientific field of structural biology, that employs techniques such as X-ray crystallography or NMR spectroscopy, to determine the structure of proteins. (phys.org)
Our method is simple and efficient, and it will have applications in protein X-ray crystallography, electron microscopy, and nanotechnology. (postech.ac.kr)

In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. (wikipedia.org)
To carry out their activities, Research Teams of the Frédéric Joliot Institute for Life Sciences have developed high-profile technological platforms in many areas : biomedical imaging, structural biology, metabolomics, High-Throughput screening, level 3 microbiological safety laboratory. (cea.fr)
Antibodies are indispensable tools in protein engineering and structural biology. (postech.ac.kr)
Section F, Structural biology communications. (lu.se)

In many aspects, rhodopsin might provide a structural and functional template for other members of the GPCR family. (nih.gov)
We still, however, don't have enough biophysical knowledge to translate this sequence information into functional insights. (berkeley.edu)
The functional properties of a protein are strongly dependent on its structural conformation. (biomedcentral.com)
The approach we take relies on protein structure alignment, which elucidates functional protein relationships that are not depicted by the sequence. (biomedcentral.com)
Moreover, targeting protein functional motions bears a great potential to control and modulate proteins' activities and interactions in physio-pathological contexts. (biorxiv.org)
Protein sizes range from this lower limit to several thousand residues in multi-functional or structural proteins. (phys.org)
Moreover, binding site comparisons are used as an idea generator for bioisosteric replacements of individual functional groups of the newly developed drug and to unravel the function of hitherto orphan proteins. (uni-marburg.de)
Structural as well as oxidative modifications can result from coordination of α S with redox active iron, which could have functional and/or pathological implications. (hindawi.com)
Furthermore, we showed that binding of these antihelix antibodies to the engineered target proteins can modulate their catalytic activities by trapping them in selected functional states. (postech.ac.kr)

In regards to DNA inter-ligation, fragments that are tethered by common protein complexes have greater kinetic advantages under dilute conditions, than those freely diffusing in solution or anchored in different complexes. (wikipedia.org)
ChIA-PET takes advantage of this concept by incorporating linker sequences onto the free ends of the DNA fragments tethered to the protein complexes. (wikipedia.org)
In order to build connectivity of the fragments tethered by regulatory complexes, the linker sequences are ligated during nuclear proximity ligation. (wikipedia.org)
Wet-lab portion of the workflow: Formaldehyde is used to cross-link the DNA-protein complexes. (wikipedia.org)
MMDB and VAST+: tracking structural similarities between macromolecular complexes. (nih.gov)
Large macromolecules, including proteins and their complexes, very often adopt multiple conformations. (biorxiv.org)
Large macromolecules, including proteins and their complexes, are intrinsically flexible, and this flexibility is often linked with their function. (biorxiv.org)

Exocytosis of secretory or synaptic vesicles is executed by a mechanism including the SNARE (soluble N -ethylmaleimide-sensitive factor attachment protein receptor) proteins. (jneurosci.org)
Progesterone receptor membrane component 1 (PGRMC1) is a multifunctional protein implicated in multiple pathologies, including cancer and Alzheimer's disease. (oncotarget.com)
Progesterone receptor membrane component 1 (PGRMC1) is 195 residue membrane-bound protein which contains a short luminal peptide, a single N -terminal transmembrane domain, and a C -terminal cytochrome b 5 -related heme-binding domain ( Figure 1A ). (oncotarget.com)
Protein binding site comparisons are frequently used receptor-based techniques in early stages of the drug development process. (uni-marburg.de)
Characterization of the solubilized receptors will emphasize the structural features of the opiate binding sites, receptor size, protein conformation, amino acid sequence, and mechanism of action. (elsevierpure.com)
To complement our structural studies, Opa - human receptor interactions are being examined in vitro and in vivo, using liposomes and nanodiscs. (umich.edu)
We apply this methodology to protein S ectodomain and find that, in the closed conformation, the three protomers of protein S bring the same contribution to an extensive central network of H-bonds, and contribute symmetrically to a relatively large H-bond cluster at the receptor binding domain, and to a cluster near a protease cleavage site. (ugr.es)
Markedly different H-bonding at these three clusters in open and pre-fusion conformations suggest dynamic H-bond clusters could facilitate structural plasticity and selection of a protein S protomer for binding to the host receptor, and proteolytic cleavage. (ugr.es)

Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET or ChIA-PETS) is a technique that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and High-throughput sequencing to determine de novo long-range chromatin interactions genome-wide. (wikipedia.org)
While ChIP-Seq is able to identify TFBS genome-wide, it provides only linear information of protein binding sites along the chromosomes (but not interactions between them), and can suffer from high genomic background noise (false positives). (wikipedia.org)
Despite whole genome profiling methods for both TFBS and long range interactions, combining approaches with the ChIA-PET method allows for identification of genomic areas in which the protein of interest is bound as well as the genomic region which it interacts with. (wikipedia.org)
Therefore, the products of linker-connected ligation can be analyzed by ultra-high-throughput PET sequencing and mapped to the reference genome. (wikipedia.org)
Non (protein)-coding RNAs are the most abundant transcriptional products of the coding genome, and comprise several different classes of molecules with unique lengths, conformations and targets. (frontiersin.org)
Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review. (cdc.gov)
Clade distribution of Candida auris in South Africa using whole genome sequencing of clinical and environmental isolates. (cdc.gov)

These proteins are synthesized in the bacterial cytoplasm and cross one membrane into the bacterial periplasm. (anl.gov)
A secondary structure model of PutP from Escherichia coli suggests the protein contains 13 TMs with the N terminus located on the periplasmic side of the membrane and the C terminus facing the cytoplasm. (embl.de)
The formation of the ternary complex induces another structural change that exposes sodium and substrate to the other site of the membrane. (embl.de)
Opacity-associated (Opa) proteins of Neisseria gonorrhoeae and N. meningitides are eight-stranded outer membrane proteins that bind to different host receptors, triggering engulfment of the bacterium. (umich.edu)
Corona virus spike protein S is a large homo-trimeric protein anchored in the membrane of the virion particle. (ugr.es)

Proteins are an important class of biological macromolecules present in all biological organisms, made up of such elements as carbon, hydrogen, nitrogen, oxygen, and sulphur. (phys.org)

ChIP-Sequencing (ChIP-Seq) is a popular method used to identify TFBS while 3C has been used to identify long-range chromatin interactions. (wikipedia.org)
Compared to Hi-C, the use of an antibody pulldown limits the number of sequenced fragments to chromatin interactions bound by the protein of interest which also can ease the data analysis. (wikipedia.org)
Pathogenic Signal Sequence Mutations in Progranulin Disrupt SRP Interactions Required for mRNA Stability. (academictree.org)
However, the task of predicting protein-protein interactions between a new virus and human cells is extremely challenging due to scarce data on virus-human interactions and fast mutation rates of most viruses. (biomedcentral.com)
Additionally, we employ an additional objective which aims to maximize the probability of observing human protein-protein interactions. (biomedcentral.com)
Virus infection involves several types of protein-protein interactions (PPIs) between the virus and its host. (biomedcentral.com)
In this work, we cast the problem of predicting virus-human protein interactions as a binary classification problem and focus specifically on emerging viruses that has limited experimentally verified interaction data. (biomedcentral.com)
These techniques provide valuable insights on proteins' functioning and interactions with their environment. (biorxiv.org)
To be able to perform their biological function, proteins fold into one, or more, specific spatial conformations, driven by a number of noncovalent interactions such as hydrogen bonding, ionic interactions, Van Der Waals forces and hydrophobic packing. (phys.org)
Current projects are focused on CA and capsid interactions, proteins involved in trafficking and nuclear import, retroviral intasome structure, and analyses of the HIV-1 pre-integration complex. (pitt.edu)
Moreover, iron interactions with N-terminally acetylated α S, the physiologically relevant form of the human protein, will be addressed to shed light on the current understanding of protein dynamics and the physiological environment in the disease state. (hindawi.com)
To date, most of our understanding of epigenetic regulation and its participation in leukemogenesis is based on the enzymatic activities and protein-protein interactions of histone and DNA modifiers. (frontiersin.org)

This study represents a breakthrough in our understanding of the pathological conformation of tau," commented Markus Zweckstetter of the Max Planck Institute for Biophysical Chemistry in Göttingen, Germany. (alzforum.org)

As a result of agonist-induced conformation changes, GPCRs become activated and catalyze nucleotide exchange within the G proteins, thus detecting and amplifying the signal. (nih.gov)
Two different linkers are designed (A and B) with specific nucleotide barcodes (CG or AT) for each of the two linker sequences (this will allow the identification of the chimeric ligation product as described in Figure 5. (wikipedia.org)
conserved structural features are consistent with nucleotide binding within the cleft. (ox.ac.uk)
The drug-induced stalling allows for a change in the structural conformation of the mRNA, which in turn, unmasks a ribosome-binding site downstream, enabling the nucleotide sequence that encodes the resistance factor itself to be translated. (uni-muenchen.de)

The systematic description of the variety of shapes a protein adopts under particular environmental conditions, upon post-translational modifications and/or partner binding still remains out of reach. (biorxiv.org)
Instead, the signal peptide adopts a specific conformation in the presence of the antibiotic, which blocks and inhibits the active center of the ribosome, thus accounting for the premature stop. (uni-muenchen.de)

Silks are composed principally of proteins with a predominance of alanine, serine and glycine and silk proteins are able to undergo irreversible transformations from soluble protein to insoluble fibres. (bioone.org)
However it has proved challenging to identify a heterologous expression platform that can produce a soluble protein-based vaccine in a manner compliant with current Good Manufacturing Practice (cGMP). (nature.com)
This work identifies Drosophila S2 cells as a clinically-relevant platform suited for the production of 'difficult-to-make' proteins from Plasmodium parasites, and identifies a PfRH5 sequence variant that can be used for clinical production of a non-glycosylated, soluble full-length protein vaccine immunogen. (nature.com)
This toolbox allows to delineate conformation-specific routines to assist in the identification of aggregation-prone regions and to guide the optimization of more soluble and stable biotherapeutics. (uab.cat)

The backbone conformation has been experimentally recognized as responsible for the early-stage structural forms of a polypeptide. (medscimonit.com)
The top-down approach in protein sequencing requires simple methods in which the analyte can be readily dissociated at every position along the backbone. (fu-berlin.de)
beta - also called the beta sheet, it shows the position and length extended backbone conformation. (projectguru.in)

In addition to the native conformation, a protein sequence populates small fluctuations around the native state, partially unfolded forms and even the globally unfolded conformation. (berkeley.edu)

In the present work, accelerated methods for the comparison of protein binding sites as well as an extended procedure for the assessment of ligand poses in protein binding sites are presented. (uni-marburg.de)
Methods for the assessment of ligand poses in protein binding sites are also used in the early phase of drug development within docking programs. (uni-marburg.de)
These programs are utilized to screen entire libraries of molecules for a possible ligand of a binding site and to furthermore estimate in which conformation the ligand will most likely bind. (uni-marburg.de)
How to Measure the Similarity Between Protein Ligand-binding Sites. (uni-marburg.de)
The Automatic Search for Ligand Binding Sites in Proteins of Known Three-dimensional Structure Using only Geometric Criteria. (uni-marburg.de)

This antibody binds the amino acids 318-510 in the S1 domain of the SARS-CoV Spike protein as well as SARS-CoV-2 (COVID-19) Spike protein. (abcam.com)
The antibody also binds to P462L-substituted S318-510 fragments of the SARS spike protein. (abcam.com)
The binding epitope is only accessible in the "open" conformation of the spike protein (Joyce et al. (abcam.com)
Precisely, this antibody binds to the 'open' conformation of the spike protein to the amino acids 318-510 in the S1 domain of the SARS-CoV as well as SARS-CoV-2 strains (32245784, Joyce et al. (abcam.com)
Protein S binds to angiotensin-converting-enzyme 2, ACE2, of the host cell, followed by proteolysis of the spike protein, drastic protein conformational change with exposure of the fusion peptide of the virus, and entry of the virion into the host cell. (ugr.es)
The structural elements that govern conformational plasticity of the spike protein are largely unknown. (ugr.es)
From analyses of spike protein sequences we identify patches of histidine and carboxylate groups that could be involved in transient proton binding. (ugr.es)
Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy. (cdc.gov)
Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda. (cdc.gov)

Kinesin motor proteins use adenosine triphosphate hydrolysis to do work on microtubules (MTs). (silverchair.com)

Understanding the interaction patterns between a particular virus and human proteins plays a crucial role in unveiling the underlying mechanism of viral infection and pathogenesis. (biomedcentral.com)

A specific antibody of choice is used to enrich protein-of-interest-bound chromatin fragments. (wikipedia.org)
ISWI slides nucleosomes along DNA, enabling the structural changes of chromatin required for the regulated use of eukaryotic genomes. (cipsm.de)
Epigenetic regulation refers to the multiple chemical modifications of DNA or DNA-associated proteins that alter chromatin structure and DNA accessibility in a heritable manner, without changing DNA sequence. (frontiersin.org)

For example, many DNA binding proteins that have affinity for specific DNA binding sites bind DNA in only its double-helical form. (wikipedia.org)
Unlike sequence-specific transcription factors, epigenetic regulators do not necessarily bind DNA at consensus sequences, but still achieve reproducible target binding in a manner that is cell and maturation-type specific. (frontiersin.org)
100 K bp in length, that recognize, and bind unique and largely uncharacterized DNA conformations. (frontiersin.org)
Despite sequence identities ranging from 87% to 91% between caprine and bovine caseins, these patients possess IgE antibodies that bind specifically to the caprine caseins without recognizing the bovine ones. (cea.fr)
We demonstrate that these antibodies can be made to bind to a variety of unrelated "off-target" proteins by modifying amino acids in the preexisting alpha helices of such proteins. (postech.ac.kr)

Usually, however, the first letter is I, and both [RK] choices resolve to R. Since the last choice is so wide, the pattern IQxxxRGxxxR is sometimes equated with the IQ motif itself, but a more accurate description would be a consensus sequence for the IQ motif. (wikipedia.org)
Human and mouse prion proteins share a structural motif that regulates resistance to common chronic wasting disease (CWD) prion strains. (cdc.gov)

However, experimental approaches to unravel PPIs are limited by several factors, including the cost and time required, the generation, cultivation and purification of appropriate virus strains, the availability of recombinantly expressed proteins, generation of knock in or overexpression cell lines, availability of antibodies and cellular model systems. (biomedcentral.com)
In addition, features from all 11 proteins were used to construct a combined model to predict host tropism of influenza virus strains. (springer.com)
Within their conformation, prion strains encipher the information that directs the templated misfolding and aggregation of PrP C molecules into additional prions ( 1 ). (cdc.gov)

however, a detailed understanding of effects of specific residues upon beta-turn stability and conformation is lacking. (rcsb.org)
We have found that although protein stability can be altered by single amino acid substitution, evolution for optimal function requires more subtle and delocalized mechanisms.Recent results implicate structure in the unfolded state as playing an important and novel role for the thermostability of these proteins. (berkeley.edu)
However, a growing body of evidence suggests that recruitment, stability, and function of epigenetic factors can be mediated by non-protein-coding RNAs. (frontiersin.org)

Proteins undergo an incredible transformation from one-dimensional sequence information into complex three-dimensional shapes that carry out intricate cellular functions. (berkeley.edu)

This structural heterogeneity is not occasional and is frequently linked with specific biological function. (biorxiv.org)
Significance Statement Proteins perform their biological functions by changing their shapes and interacting with each other. (biorxiv.org)
The abnormal expression of follistatin-like protein 1 (FSTL1) in various tumors is a crucial regulator of the biological process of tumorigenesis. (bvsalud.org)

CWD results from the conformational transformation of the host-encoded cellular prion protein (PrP C ) into protease-resistant, detergent-insoluble, β-sheet rich, amyloidogenic conformers, termed prions (PrP CWD ). (cdc.gov)
The infectious agent in the prion disease is composed mainly or entirely of an abnormal conformation of a host-encoded glycoprotein called the prion protein. (medscape.com)

MATERIAL/METHODS: The polypeptide chains of all the proteins in the Protein Data Bank were transformed into their early-stage structural forms. (medscimonit.com)
Despite its deleterious impact on fitness, protein aggregation is a generic property of polypeptide chains, indissociable from protein structure and function. (uab.cat)

Within a sequence or database of sequences, researchers search and find motifs using computer-based techniques of sequence analysis, such as BLAST. (wikipedia.org)
Structural analysis suggests that residues flanking the turn are a primary structural determinant of the conformation within the turn. (rcsb.org)
We have extended our analysis to investigate the energy landscape of thermophilic proteins. (berkeley.edu)
Full-length BTK has been refractory to structural analysis. (elifesciences.org)
Our method guaranties preservation of the protein structure during the transition and allows to access conformations that are unreachable with classical normal mode analysis. (biorxiv.org)
An algorithm for constraint-based structural tem- plate matching: application to 3D templates with statistical analysis. (uni-marburg.de)
This hypothesis was borne out by analysis of other autotransporter sequences that also appear to have patterning based on spacing of hydrophobic clusters. (anl.gov)
SIGNIFICANCE: The comparative analysis identified new structural features in the MST ATP binding pocket and has also defined the mechanism for autophosphorylation. (ox.ac.uk)

Erythromycin targets bacterial ribosomes - the nanomachine responsible for the translation of messenger RNA (mRNA) sequences into protein - thus preventing synthesis of the proteins required for continued growth and survival. (uni-muenchen.de)

The discrimination between functionally neutral amino acid substitutions and non-neutral mutations, affecting protein function, is very important for our understanding of diseases. (rostlab.org)
Identification of Bruton tyrosine kinase mutations in 12 Chinese patients with X-linked agammaglobulinaemia by long PCR-direct sequencing. (lu.se)

However, previous work by this team of researchers from the University of Notre Dame and The University of Chicago has shown that, contrary to popular belief, intrinsically disordered proteins, which sample a variety of conformational forms the way the autotransporter proteins do, can remain quite extended in water even if they have high ratios of hydrophobic to charged amino acids. (anl.gov)

These amyloid plaques are immunoreactive with antibodies to the prion protein and do not immunoreact with antibodies to other amyloidogenic proteins, such as the amyloid-beta (which is deposited in Alzheimer disease). (medscape.com)

The antibodies induced by one protein variant were shown to be qualitatively similar to responses induced by other vaccine platforms. (nature.com)
Application of antihelix antibodies in protein structure determination. (postech.ac.kr)
Antibodies suitable for structural studies should recognize the 3-dimensional (3D) conformations of target proteins. (postech.ac.kr)

Binding sites of other proteins which are similar to the binding site of the target protein can offer hints for possible side effects of a new drug prior to clinical studies. (uni-marburg.de)
The structural comparison of binding sites is especially useful when applied on distantly related proteins as a comparison solely based on the amino acid sequence is not sufficient in such cases. (uni-marburg.de)
Efficient Similarity Retrieval for Protein Binding Sites based on Histogram Comparison. (uni-marburg.de)
Further it defines functions which refer to co-factor binding sites or non-protein binding sites. (projectguru.in)

The replication of prions involves the recruitment of the normally expressed prion protein, which has mainly an alpha-helical structure, into a disease-specific conformation that is rich in beta-sheet. (medscape.com)

Several influenza proteins have been shown to be major determinants in host tropism. (springer.com)

The polymers, also known as polypeptides, consist of a sequence of 20 different L-α-amino acids, also referred to as residues. (phys.org)
For chains under 40 residues the term peptide is frequently used instead of protein. (phys.org)
However, the current estimate for the average protein length is around 300 residues. (phys.org)
The site2 sequence alignment indicates in red the residue sites that potentially form salt bridges in H-NS ST , and in green the residues that form nonpolar contacts in H-NS ST . For additional details, see Figure S1. (elifesciences.org)
For both proteins, the oxygen-17 relaxation depended only very weakly on pD, showing that ionic residues do not perturb hydration water dynamics more than other surface residues. (lu.se)

Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical shape (e.g. the "B-form" DNA double helix). (wikipedia.org)
Highly divergent hypotheses have been put forward regarding the makeup of the prions, including that they consist of nucleic acid only or protein only, are lacking both protein and nucleic acid, or are a polysaccharide. (medscape.com)

that is a stereotypical element of the overall structure of the protein. (wikipedia.org)
This allows us to produce a wide range of motions, some of them previously inaccessible, and to preserve the structure of the protein during the motion. (biorxiv.org)
The methods to study and visualize the 3D structure of the protein are discussed in the Methodology part (NMR and X-ray). (projectguru.in)

We developed a multitask transfer learning approach that exploits the information of around 24 million protein sequences and the interaction patterns from the human interactome to counter the problem of small training datasets. (biomedcentral.com)
Predicted regulatory interaction sites for SH2- and SH3-domain proteins are in non-structured regions that could be available to cytoplasmic enzymes. (oncotarget.com)
protein interaction has still not emerged. (lu.se)

A tabular approach to the sequence-to-structure relation in proteins (tetrapeptide representation) for de novo protein design. (medscimonit.com)

Here, we describe a Random Forests-based classifier, named Mutation Detector (MuD) that utilizes structural and sequence-derived features to assess the impact of a given substitution on the protein function. (rostlab.org)
Bacteria can become resistant to the antibiotic either as the result of a spontaneous mutation or by picking up an appropriate "resistance gene" (which codes for a protein that confers resistance) from another bacterium via genetic exchange. (uni-muenchen.de)

A tetrameric form of α S has also been identified in human tissues that has been postulated as the inactive storage form of this structurally dynamic protein due to its aggregation resistance [ 6 , 7 ]. (hindawi.com)
The main results of the team are the lack of cross-reactivity between allergens with strong sequence homologies, the relationship between the structure, resistance to proteolysis and allergenicity and the effect of technological processes and composition of the matrix on digestibility and allergenicity. (cea.fr)
Allergenicity of food proteins has been correlated to their structural conformation and their resistance to proteolysis. (cea.fr)
High-resolution cryo-electron microscopy has now revealed in unprecedented detail the structural changes in the bacterial ribosome which results in resistance to the antibiotic erythromycin. (uni-muenchen.de)

Our work suggests that a high degree of structural plasticity is required to tolerate the diverse sequences, and the dynamic ensemble allows sampling of conformers competent to engage receptors. (umich.edu)

Our laboratory uses a combination of biophysical, structural and computational techniques to understand these features. (berkeley.edu)

These conformations were observed to be retained during sequence-swapping and glycine substitution mutagenesis. (rcsb.org)

Outside of gene exons, there exist regulatory sequence motifs and motifs within the "junk", such as satellite DNA. (wikipedia.org)

Although the function of YegS is not definitively known, it has been annotated as a potential diacylglycerol or sphingosine kinase based on sequence similarity with eukaryotic enzymes of known function. (ox.ac.uk)

In particular, we incorporate dominant physical features in one of the exact protein structure alignment tools, CMOS [ 1 ], which is based on the contact map overlap maximization (MAX-CMO) formulation of protein structure alignment. (biomedcentral.com)

The ChIA-PET method combines ChIP-based methods, and Chromosome conformation capture (3C) based methods, to extend the capabilities of both approaches. (wikipedia.org)

Protein aggregation is behind the onset of neurodegenerative disorders and one of the serious obstacles in the production of protein-based therapeutics. (uab.cat)
These studies spotted aggregation as a major force driving protein evolution. (uab.cat)
Here we review how the advent of predictive tools has change the way we think and address protein aggregation. (uab.cat)
D ) Table showing the aggregation temperature of H-NS 1-57 proteins. (elifesciences.org)

The physical features responsible for protein structural similarities are not well understood. (biomedcentral.com)

We believe that the present results resolve the long-standing controversy regarding the mechanism behind the spin relaxation dispersion of water nuclei in protein solutions, thus establishing oxygen-17 relaxation as a powerful tool for studies of structurally and functionally important water molecules in proteins and other biomolecules. (lu.se)

This finding suggests that spacing of hydrophobic amino acids must be under selective pressure in bacterial proteins to facilitate their virulence functions. (anl.gov)

Anatomy12

Organisms40

Diseases1

Chemicals and Drugs83

Analytical, Diagnostic and Therapeutic Techniques and Equipment47

Phenomena and Processes75

Disciplines and Occupations5

Information Science10

Health Care2

Molecular10

Alpha-helical conformation2

Globular proteins3

Homology1

Structures16

Prediction12

Phosphorylation3

Peptides2

Folding16

Recombinant Fusion P1

Crystallography2

Biology4

Functional9

Complexes7

Receptor8

Genome7

Membrane5

Macromolecules1

Interactions12

Chemistry1

Nucleotide4

Adopts2

Soluble4

Backbone3

Fluctuations around the native state1

Ligand5

Spike protein9

Adenosine Triphosphate1

Human proteins1

Chromatin3

Bind5

Motif2

Strains3

Stability3

Undergo1

Biological3

Host-encoded2

Polypeptide chains2

Analysis8

MRNA1

Mutations2

Conformational1

Amyloidogenic1

Antibodies3

Binding Sites4

Prion protein1

Determinants1

Residues5

Nucleic2

Structure of the protein3

Interaction3

Novo1

Mutation2

Resistance4

Plasticity1

Computational1

Glycine1

Motifs1

Similarity1

Formulation1

Methods1

Aggregation4

Similarities1

Mechanism1

Bacterial1