2017 sequence protein residues. Medical search. Frequent questions

This isolate, A/environment/Kagoshima/KU-ngr-I/2016 (H5N6), was confirmed to be an H5N6 subtype having multiple basic amino acid residues, PLRERRRKR/GLF, at the cleavage site in the HA protein, which is characteristic of HPAIVs, by conventional reverse transcription PCR and Sanger sequencing. (cdc.gov)
2016. An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry. . (ncbs.res.in)

Moreover, I have intentionally left out a fundamentally important fact - mutations may significantly affect protein dynamics, and thus its function). (kdnuggets.com)
Performance of Web tools for predicting changes in protein stability caused by mutations. (cnr.it)
The purpose of the present study was to report the clinical features of a Chinese family with FAP and screen for novel mutations using the targeted next‑generation sequencing technology. (spandidos-publications.com)
Most of the mutations causing FAP are nonsense or frameshift mutations, and can result in premature stop codons thus produce truncated APC proteins ( 7 ). (spandidos-publications.com)
By contrast, in the case of TEM-1 beta-lactamase mutations, aggregation is linked to a decreased cell fitness due to inactivation of protein function. (frontiersin.org)
Bioinformatics analysis of mutations sheds light on the evolution of Dengue NS1 protein with implications in the identification of potential functional and druggable sites. (ncbs.res.in)
Here, using atomistic molecular dynamics simulation, we study the correlations between the RBD dynamics with physically distant residues in the spike protein, and provide a deeper understanding of their role in the infection, including the prediction of important mutations and of distant allosteric binding sites for therapeutics. (biorxiv.org)
Significant research effort for drug design against COVID-19 is focused on the receptor binding domain of the spike protein, although this region is prone to mutations causing resistance against therapeutics. (biorxiv.org)
These residues can not only be targeted by broad spectrum antibodies and drugs, mutations in them can generate new strains of coronavirus resulting in future epidemic. (biorxiv.org)
6 Significantly, the sites in S protein have been demonstrated to be vulnerable to acquire mutations. (biorxiv.org)
However, important phenotypic differences, such as resistance to antibiotics, are often the result of just one or a few point mutations in otherwise identical sequences. (pensoft.net)
We also identified that sequencing depth is a key factor to detect rare mutations. (pensoft.net)
Therefore, much larger numbers of sequences may be required for reliable detection of mutations than for most other applications of shotgun metagenomics. (pensoft.net)
However, attempts to quantify point mutations in metagenomic sequencing data often go wrong because the methods do not distinguish sufficiently well between mutated and wildtype variants of the same gene. (pensoft.net)
Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis Structure, 23(7):1362-9. (lu.se)
Pires D, Rodrigues C, Ascher D, mCSM-membrane: predicting the effects of mutations on transmembrane proteins, Nucleic Acids Res;48(W1):W147-W153. (lu.se)
Garcia-Recio A, Gómez-Tamayo J, Reina I, Campillo M, Cordomí A, Olivella M, TMSNP: a web server to predict pathogenesis of missense mutations in the transmembrane region of membrane proteins, NAR Genom Bioinform. (lu.se)
Ge F, Zhu Y, Xu J, Muhammad A, Song J, Yu D, MutTMPredictor: Robust and accurate cascade XGBoost classifier for prediction of mutations in transmembrane proteins, Comput Struct Biotechnol J. 2021 Nov 19;19:6400-6416. (lu.se)
Newly evolved GII.4 Sydney[P16] norovirus with multiple residue mutations, already circulating in parts of China, became predominant and caused an abrupt increase in diagnosed norovirus cases among children with gastroenteritis in Shanghai during 2021–2022. (cdc.gov)

For instance, the SwissVariant database (http://swissvar.expasy.org/) contained 76 613 variants in 20 244 human proteins on 10 January 2018. (deepdyve.com)
From December 2017 to March 2018, several missed diagnoses of influenza A(H1)pdm09 using real-time RT-PCR were reported in northern Viet Nam. (who.int)
3-5 From December 2017 to March 2018, there was circulation of both influenza A and B, with influenza A(H1N1)pdm09 again predominating in Viet Nam. (who.int)

Based on an established filtering strategy and data analyses, along with confirmation by Sanger sequencing and co‑segregation, a novel frameshift mutation c.1317delA (p.Ala440LeufsTer14) in exon 10 of the APC gene was identified. (spandidos-publications.com)
The development of better methods for mutation analysis-related protein PTMs will help to facilitate the development of personalized precision medicine. (deepdyve.com)
posttranslational modifications, amino acid variations, computational mutation analysis, protein PTM predictor, network biology Introduction Protein PTMs are biochemical alterations of amino acids that change the physicochemical properties of target proteins, leading to structural changes and therefore regulating protein-protein interactions and cellular signal transduction in developmental and cancer pathways [1]. (deepdyve.com)
7] analyzed amino acid variations of 15 different PTMs and indicated that about 4.5% of amino acid variations may affect protein function through disruption of PTMs, and the mutation of 238 PTMs sites in human proteins was causative of disease. (deepdyve.com)
Mutation on these residues can lead to new strains of coronavirus with different degrees of infectivity and virulence. (biorxiv.org)
Furthermore, we note that nodes in the non-covalent interaction networks are co-localized with compensatory mutation sites identified by multiple sequence alignment of proteins with low sequence similarity to BacC. (rcsb.org)
The aPTT-based functional protein C assay may yield misleadingly low protein C levels in the presence of (1) a factor V Leiden mutation and some other causes of activated protein C resistance, (2) elevated plasma factor VIII levels, or (3) hyperlipidemia. (medscape.com)

Unfortunately, the design of drugs with multiple activities on a selected handful of different protein structures remains a significant experimental and computational challenge ( Konc, 2019 ). (frontiersin.org)
2019 ) was used, https://www.ebi.ac.uk/Tools/msa/clustalo/ ] of human DBNDD1 and similar protein sequences found by a BLAST search in other selected species. (springer.com)
Thus, this study aimed to determine the seroprevalence and molecular epidemiology of CHIKV infection among febrile patients in Vietnam from 2017 to 2019. (bvsalud.org)

The core domain and the first eight residues of the carboxyl-terminal domain of the enzyme, including the active-site nucleophile tyrosine-723, share significant structural similarity with the bacteriophage family of DNA integrases. (embl.de)
A total of eight residues (highlighted in magenta in Figure 8) were 23148522 conserved among over 95 of the COG1058 proteins in all sequenced genomes, suggesting their likely role in protein's function or stability. (calpaininhibitor.com)

In addition, TMD heteromerization can apparently be driven by hydrogen bonding between basic or between acidic residues. (cipsm.de)

More than 600 different types of PTMs (http://www.uniprot.org/docs/ptmlist, Release: 20-Dec-2017) have been reported till date and many more are still being. (deepdyve.com)

2020. Distinct Evolutionary Origins of Intron Retention Splicing Events in Antiporter Transcripts Relate to Sequence Specific Distinctions in Species. . (ncbs.res.in)
When the first genome sequence of SARS-CoV-2, Wuhan-Hu-1, was released on 10 January 2020 (GMT) on Virological.org by a consortium led by Zhang 6 , it enabled immediate analyses of its ancestry. (nature.com)

Unlike other dysbindin family proteins, DBNDD1 isoforms are probably non-classical secretory proteins (Talbot et al. (springer.com)
Nonetheless, treatment with mangiferin, inhibits the activations of ROS-mediated PKCs as nicely as MAPKs suggesting that STZinduced diabetic nephropathy is mediated by way of the activation of PKCs MAPKs family proteins. (adenosine-kinase.com)
AURK significantly promotes activation of IκBα at serine 32, but not serine 36 residues, unlike IκB kinase (IKK) family proteins activate both IκBα serine residues. (researchsquare.com)

SCOPe: Structural Classification of Proteins - extended. (berkeley.edu)

We performed a Basic Local Alignment Search Tool (BLAST) analysis to identify regions of local similarity between the human DBNDD1 and protein sequences from other species (Fig. 1 ). (springer.com)
Apart from a CX3R motif, which is present at the active site of all known tyrosine phosphatases, Cdc25 does not share any obvious sequence similarity with any of those enzymes. (embl.de)
Notably, a DALI search revealed high structural similarity (Z score .10 ) with the fold of proteins from the E. coli MoCo biosynthetic pathway (MogA, the domain III of MoeA, and MobA), as well as with domains of mammalian gephyrin and plant Cnx1, which are also involved in MoCo biosynthesis [30,31,32]. (calpaininhibitor.com)
Caliciviruses are similar to picornaviruses in the pres- image reconstruction of recombinant Norwalk virus-like particles ence of VPg and in sequence similarity of their RNA-directed (left). (cdc.gov)

Solvent Accessibility of Residues Undergoing Pathogenic Variations in Humans: From Protein Structures to Protein Sequences, Front Mol Biosci. (lu.se)

Our chemical-shift based secondary structure analysis reveals the human DBNDD1 as an intrinsically disordered protein. (springer.com)
2021 ), https://pfam.xfam.org/ ] predicts human DBNDD1 mainly as an intrinsically disordered protein (IDP) and also the recently released AlphaFold database (Jumper et al. (springer.com)

The genome of the virus is housed inside a protective envelope that includes a lipid membrane, an envelope protein, a precursor membrane protein and a capsid protein. (purdue.edu)
The Purdue researchers are the first to learn the position of the capsid protein in the immature virus, which plays the critical role of recognizing the virus's genetic material and acts as a chaperone to guide these RNA strands into the virus for assembly. (purdue.edu)
A map of the immature virus's structure revealed details about the proteins, showing that the envelope and precursor membrane proteins are arranged in 60 spike-like features on the virus's surface, whereas the capsid protein is located on the internal side of the lipid membrane. (purdue.edu)
Notably, it contains a "partially ordered capsid protein shell" that is less prominent in other immature flaviviruses. (purdue.edu)
A protein [virus protein, genome-linked by a capsid architecture with 32 distinct cup-shaped depressions. (cdc.gov)

Adv. Protein Chem. (crossref.org)

In my bit on " I'm not dead yet" technologies recently, I included large scale Sanger sequencing. (blogspot.com)
That sentence is a bit hard to write, because Sanger sequencing is fragment sizing, so it must be a software thing because the larger instruments from Thermo are apparently locked into one mode or the other in each run. (blogspot.com)
That's another market remaining for Sanger, as sequencing small clones can still be more cost-effective on Sanger than other instruments, particularly if you have a very large number of relatively small clones. (blogspot.com)
But if library construction can be reliably done en mass for single digit dollars per library, then Sanger may be nudged out here as well. (blogspot.com)

Given the close relationship between protein structure and function, protein structure searches have long played an established role in bioinformatics. (biorxiv.org)
As such, understanding protein structure is a central goal within structural bioinformatics. (biorxiv.org)
Bioinformatics 33 (7): 1014-1020, 2017). (utmb.edu)
Bioinformatics comparisons of RNA-binding proteins of pathogenic and non-pathogenic Escherichia coli strains reveal novel virulence factors. (ncbs.res.in)
2015. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. . (ncbs.res.in)
Published in the Journal of Proteins: Structure, Function, and Bioinformatics. (arxiv.org)

A number of site-specific structural characteristics have been proposed, most of which are broadly related to either the density of contacts or the solvent accessibility of individual residues. (arxiv.org)
Most importantly, there has been disagreement in the literature over the relative importance of solvent accessibility and local packing density for explaining site-specific sequence variability in proteins. (arxiv.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)
To get an insight into the possible functions of the conserved residues, we performed a structural homology search by using as the query the ?available high-resolution (2 A) crystal structure of the Thermoplasma acidophilum COG1058 protein (PDB ID: 3KBQ), as determined atthe Midwest Center for Structural Title Loaded From File Genomics (http://www.mcsg. (calpaininhibitor.com)
We have that the residues with the lowest support are enough synteny to Enter related penalties in the homology evolution and transfer. (woblan.de)
Conversely, the transcription of COX-2 yields a 4.5-kb mRNA that encodes a 70-kd protein with roughly 70-75% homology to the COX-1 protein. (medscape.com)

Deciphering protein–protein interactions. (crossref.org)
Unique spatial arrangement of polypeptide chains yields 3D molecular structures, which define protein function and interactions with other biomolecules. (kdnuggets.com)
It has been attributed to specific patterns in protein sequence , and it has an immediate consequence for protein stability , susceptibility to enzymatic digestion inside living cells, protein-protein interactions and in turn a decisive role in many debilitating human pathologies . (kdnuggets.com)
These are likely to play a role in protein interactions. (embl.de)
The assembly of integral membrane protein complexes is frequently supported by transmembrane domain (TMD) interactions. (cipsm.de)
We validated BLaTM by showing that the assay faithfully reports known sequence-specific interactions of both types. (cipsm.de)
Most of the important molecular processes in the cell, such as DNA replication, are performed by large molecular network of protein-protein interactions. (researchsquare.com)
We need to acquire more knowledge of various protein-protein interactions in order to understand biological phenomena, including diseases, and to provide the basis for new therapeutic approaches. (researchsquare.com)
Biochemical analysis of BacC mutants with potential disruptions in non-covalent interactions along this path revealed that residues that form nodes in pathways of non-covalent interactions influence catalytic activity more than others in a similar chemical environment. (rcsb.org)

Their amino acid sequences suggest that they are mainly cytosolic or nuclear proteins partly associating with membranes (Talbot et al. (springer.com)

Proteins represent the functional end-product within the central dogma of molecular biology [ 1 ]. (biorxiv.org)
Subsequently, we cloned three NMDA receptor subunits CgNR1, CgNR2A and CgNR2B, with sequence analysis suggesting successful assembly of functional NMDA receptor complexes and binding to natural occurring agonists and the channel blocker MK-801. (exeter.ac.uk)
The controversy can only be resolved when proponents of massive alternative splicing provide evidence to support their claim that there are 100,000 functional proteins. (blogspot.com)
The clearest finding from proteomics experiments is that most human genes have a single main protein isoform, while those alternative isoforms that are identified tend to be the most biologically plausible: those with the most cross-species conservation and those that do not compromise functional domains. (blogspot.com)
I think the term "alternative splicing" should be restricted to genuine examples of real alternative slicing that generate different functional proteins. (blogspot.com)
This suggests that most annotated alternative variants are unlikely to have a functional cellular role as proteins. (blogspot.com)
Indeed, there is a paper in the last few years which repeatedly explains away a missing key residue in a protein known to be functional. (blogspot.com)
To increase the utilization of current computational resources, we 﫿rst provide an overview of computational prediction of amino acid variations that influence protein PTMs and their functional analysis. (deepdyve.com)
The tests used for protein C testing can include enzyme-linked immunosorbent assay (ELISA), chromogenic assays, and the activated partial thromboplastin time (aPTT)-based functional protein C assay. (medscape.com)
An ELISA measures protein C immunological levels with very high sensitivity but cannot detect functional defects. (medscape.com)
Chromogenic assays can detect low levels of protein C with high sensitivity and can detect most functional defects. (medscape.com)

For GPR56 peptide assays membranes were incubated with peptide for 5 min followed by G protein incubation. (biodiversityhotspot.org)
For GPR110 peptide assays peptide and G proteins were incubated for 30 min in Marizomib GDP-free preincubation buffer (actual GDP was ～50 nM from prepared Gα). (biodiversityhotspot.org)
High throughput phenotypic assays are needed to complement the sequence-based analysis of circulating viruses and improve pandemic preparedness. (cdc.gov)

The E1 CHIKV genome sequences were detected among the positive RT-qPCR samples. (bvsalud.org)
Subsequently a bat sarbecovirus-RaTG13, sampled from a Rhinolophus affinis horseshoe bat in 2013 in Yunnan Province-was reported that clusters with SARS-CoV-2 in almost all genomic regions with approximately 96% genome sequence identity 2 . (nature.com)
respectively missing( and in one gender for s), the basis of the two proteins has to check found therefore from reason( or to give it another calculation, a genome is rather at least often supplementary as its sequence). (woblan.de)
Abbreviations: VPg, virus protein, genome-linked. (cdc.gov)

Frequently, researchers are aiming at improving catalytic performance of protein enzymes, or adding completely new types of chemical activities to known proteins. (kdnuggets.com)
Classification of microbial transglutaminases by evaluation of evolution trees, sequence motifs, secondary structure topology and conservation of potential catalytic residues. (cnr.it)
Based on the results of this analysis, we also predict that the budding yeast arsenate resistance protein Acr2 and the ORF Ygr203w encode protein phosphatases with catalytic properties similar to that of the Cdc25 family. (embl.de)
doi:10.1371/journal.pone.0065595.gMutagenesis Guided by Multiple Sequence Alignment and Structural Analysis Reveals the Identity of Catalytic ResiduesA multiple sequence alignment using a collection of 361 bacterial, 36 archaeal, and 34 eukaryotic completely sequenced genomes, annotated in The SEED database [23], revealed that the COG1058 domain is highly conserved (Figure S2). (calpaininhibitor.com)

172 Computational analysis and prediction of proteins that undergo domain swapping. (ncbs.res.in)
Proteomic analysis and prediction of amino acid variations that influence protein. (deepdyve.com)

The primers and probe were designed based on a conserved genomic region of 730 global CHIKV sequences that is located between nsP1 and nsP2 genes. (bvsalud.org)
Furthermore, using sequence analysis of human genomic DNA, researchers concluded that the amino acids important for catalysis by COX-1 are conserved and are equally important for catalysis by COX-2. (medscape.com)

Human biology is tightly linked to proteins, yet most measurements do not precisely determine alternatively spliced sequences or posttranslational modifications. (stanford.edu)

Human dysbindin domain-containing protein 1 (DBNDD1) is encoded by the gene DBNDD1 at chromosome locus 16q24.3. (springer.com)
Weighted gene correlation network analysis (WGCNA) can identify groups of biologically related proteins using only protein intensity values by constructing protein correlation networks. (stanford.edu)
There were two different mismatches in the probe target sites of the HA gene sequences of all isolates ( n = 23) with additional mismatches only at position 7 (template binding site) identified for all eight negative real-time RT-PCR isolates. (who.int)

According to these scientists, this means that humans can make about 100,000 different proteins from only ~20,000 protein-coding genes. (blogspot.com)
We also argue that the differences between humans and other animals can be adequately explained by differential regulation of 20,000 protein-coding genes. (blogspot.com)
A census of actin-associated proteins in humans. (ncbs.res.in)
In humans and mice, hotspots are specified by PRDM9, a meiosis-specific PRDM family protein (Baudat et al. (springer.com)

The membrane protein cleaves from the mature virus as it is released from the host to infect other cells. (purdue.edu)
The structure differs from the mature Zika virus in that the membrane protein in the mature virus is covered by the envelope protein. (purdue.edu)
Infection of human cells by the novel coronavirus (SARS-Cov-2) involves the attachment of the receptor binding domain (RBD) of the spike protein to the peripheral membrane ACE2 receptors. (biorxiv.org)
Washed membranes were Dounce-homogenized into Marizomib membrane storage buffer [HE buffer with 12% (vol/vol) sucrose] and stored at ?80 °C. Protein Purification. (biodiversityhotspot.org)
Membrane protein datasets with a total of 2058 variants in F1. (lu.se)
Orioli T, Vihinen M, Benchmarking subcellular localization and variant tolerance predictors on membrane proteins, BMC Genomics;20(Suppl 8):547. (lu.se)
They have been defined as monotropic integral membrane proteins located primarily in the endoplasmic reticulum (COX-1) and the perinuclear envelope (COX-2). (medscape.com)

For example, phosphorylation mainly occurs on a subset of three types of amino acids, including serine (S), threonine (T) and tyrosine (Y). Methylation is predominantly found on lysine (K) and arginine (R) residues. (deepdyve.com)

Background: The phosphorylation of NF-kappaB inhibitor alpha (IκBα) protein is pivotal to the regulation of NF-κB transcription factor activity in the cell. (researchsquare.com)

Predicting the stability of mutant proteins by computational approaches: an overview. (cnr.it)
Computational tools to study RNA-protein complexes. (ncbs.res.in)

The most common and established way to engineer a protein is to create its variants with substituted amino acids, also known as mutants. (kdnuggets.com)
Opponents (I am one) argue that most splice variants are due to splicing errors and most of those predicted protein isoforms don't exist. (blogspot.com)
Nevertheless, it is remarkable that tens of thousands of predicted protein variants are not detected in these experiments. (blogspot.com)
5 , 7 - 9 More specifically, a study analyzing 10,022 SARS-CoV-2 genomes from 68 countries revealed 2969 different missense variants, with 427 variants in the S protein. (biorxiv.org)
Can Predicted Protein 3D Structures Provide Reliable Insights into whether Missense Variants Are Disease Associated? (lu.se)
NA-binding was observed when a virus preparation contained approximately 10% of NA variants with either T148I or T439R, highlighting the benefit of using deep sequencing in virus characterization. (cdc.gov)

The identification of similar three-dimensional (3D) amino acid patterns among different proteins might be helpful to explain the polypharmacological profile of many currently used drugs. (frontiersin.org)

PR domain-containing protein 9 (PRDM9) is a major regulator of the localization of meiotic recombination hotspots in the human and mouse genomes. (springer.com)
Mumame is not aiming to find strain-level differences in taxonomic composition, thus enabling it to operate at much lower sequencing depths as complete coverage of the targeted genomes is not necessary for the analysis. (pensoft.net)

The sequence conservation of the putative dysbindin domain across all selected species is notable (Fig. 1 shaded region). (springer.com)
The conserved residues appear to define two putative signature motifs, namely GXEX3G and GGL/IGPX3D. (calpaininhibitor.com)

Cellular proteostasis involves the coordinated and compensatory action of pathways that control biogenesis, folding, trafficking and breakdown of proteins allowing the cell to adapt to physiological or pathological environmental changes. (elifesciences.org)
Giordano D, De Masi L, Argenio MA, Facchiano A. (2021)Structural Dissection of Viral Spike-Protein Binding of SARS-CoV-2 and SARS-CoV-1 to the Human Angiotensin-Converting Enzyme 2 (ACE2) as Cellular Receptor. (cnr.it)
The majority of proteins function as monodispersed ordered species dissolved in intra- or extra-cellular aqueous fluids. (frontiersin.org)
Alternative splicing is commonly believed to be a major source of cellular protein diversity. (blogspot.com)
Sonic 125256-00-0125B11 hedgehog (Shh) is a forty five-kDa potent signaling protein that regulates the proliferation, differentiation, and cellular patterning throughout a extensive selection of cell types [2,3]. (acthreceptor.com)
Intensiometric genetically encoded biosensors, based on allosteric modulation of the fluorescence of a single fluorescent protein, are powerful tools for enabling imaging of neural activities and other cellular biochemical events. (nature.com)

It was described that hedgehog proteins right act on osteogenic precursor cells and osteoblasts to stimulate osteogenic differentiation [7]. (acthreceptor.com)
The results, compiled in the Blood Proteoform Atlas (BPA), indicate that proteoforms better describe protein-level biology and are more specific indicators of differentiation than their corresponding proteins, which are more broadly expressed across cell types. (stanford.edu)

3] Sanofi argued that Amgen's patents did not disclose enough species of antibodies to provide written description support for claims to the entire genus of antibodies that bind to PCSK9 at the specified amino acid residues. (klgates.com)
Proteins with high sequence identity to human DBNDD1 can also be found in evolutionarily more distant species (e.g. (springer.com)
Dysbindin domain-containing protein 1 (DBNDD1) is conserved in different species. (springer.com)
Fig. 2: Representation of the gate post and bulge residues in FPs derived from different species. (nature.com)
The top-level topology of the species tree, i.e. the bacterial, archaeal and Title Loaded From File eukaryotic proteins form distinct clusters. (calpaininhibitor.com)
The superimposition of the 3KBQ three-dimensional structure and domain III of E. coli MoeA (PDB ID: 1G8L) is shown.The top-level topology of the species tree, i.e. the bacterial, archaeal and eukaryotic proteins form distinct clusters. (calpaininhibitor.com)

The the Cysteine containing enzymatically active version of the domain is also found in the CDC25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and stress proteins such as Senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. (embl.de)
Under oxidative-stressed conditions, cysteine residues of Keap1 are oxidized, forming a disulfide bridge. (hindawi.com)

For instance, because the body's molecular machinery won't recognize them, MI DNAs, MI RNAs, and MI proteins resist enzymatic degradation and can largely avoid triggering an immune response, making them attractive drug candidates. (acs.org)
Here, we analysed two deep mutational scanning experiments to investigate the role of protein aggregation in molecular evolution. (frontiersin.org)
Here, we set to clarify this complex matter and question of whether aggregation is an important constraint in protein evolution that can be the discriminant between beneficial and detrimental situations by considering two cases: we studied molecular evolution of proteins in an endogenous vs. exogenous host. (frontiersin.org)
We applied time-independent component analysis (tICA) and protein connectivity network model, on all-atom molecular dynamics trajectories, to identify key non-RBD residues, playing crucial role in the conformational transition facilitating spike-receptor binding and infection of human cell. (biorxiv.org)
Taken together, our findings provide new insights into the molecular mechanisms underlying the ability of NA to function as a binding protein. (cdc.gov)
Of 1015 sequences of HPAI A (H5N1) viruses collected in the United States during 2022, eight viruses (0.8%) had a molecular marker of drug resistance to an FDA-approved antiviral: three adamantane-resistant (M2-V27A), four oseltamivir-resistant (NA-H275Y), and one baloxavir-resistant (PA-I38T). (cdc.gov)

Some ELISAs may recognize protein C complexed to its inhibitor, but others may not. (medscape.com)

Amgen's patents share a common specification and are directed toward antibodies that help rid the body of "bad cholesterol" or "low-density lipoprotein" cholesterol known as LDL-C. Those antibodies target PCSK9, a naturally occurring protein, and prevent PCSK9 from binding to and destroying liver cell receptors (LDL-R) that help extract LDL-C from the bloodstream. (klgates.com)
1] Notably, Amgen's patents do not claim any particular antibody by amino acid sequence, but instead claim the entire genus of antibodies that bind to at least one of 15 specified amino acid residues of PCSK9 and block PCSK9 from binding to LDL-R. The specifications disclose a trial-and-error process "used to generate and screen antibodies that bind to PCSK9 and block PCSK9 from binding to LDL-Rs. (klgates.com)
Conversely, broad spectrum therapeutics like drugs and monoclonal antibodies can be generated targeting these key distant regions of the spike protein. (biorxiv.org)
Large scale screening of therapeutic molecules and antibodies are underway aiming to target the spike protein and consequently prevent infection. (biorxiv.org)
18 The human immune system started generating antibodies specific to residues outside RBD even at the earlier stage of the pandemic. (biorxiv.org)

Proponents of massive alternative splicing argue that most human genes produce many different protein isoforms. (blogspot.com)
My colleague at the University of Toronto, Ben Blencowe, is a strong supporter of alternative splicing and its role in creating multiple isoforms of most proteins. (blogspot.com)

Below, we present our approach to a fast, scalable, and purely geometric protein structure search we refer to with the acronym of RUn Position Encoded Encodings of residue descriptors (RUPEE). (biorxiv.org)

It is accepted that complete understanding of protein functions and activity requires knowledge of structures and dynamics. (kdnuggets.com)
These limitations can prevent the easy and efficient exploration of relationships between protein structures, which is the norm in other areas of inquiry. (biorxiv.org)
It also provided a path for further research activity in the direction of big data representations of protein structures. (biorxiv.org)
Pairwise alignment involves finding a set of spatial rotations and translations for two protein structures that minimizes a distance metric. (biorxiv.org)
Please note: Sequence identity is based on user defined PDB file and 3D allergen structures in SDAP database. (utmb.edu)

Emma Lundberg's group has a wealth of experience in using microscopy to yield biological images that paint a picture of this cell-to-cell heterogeneity of protein expression information, and joining her lab has deepened my expertise in integrating datasets to perform innovative analyses of single-cell protein expression. (stanford.edu)
Datasets for residue side chain clashes. (lu.se)

These channels are quite different in terms of structure, sequence and function and both have been regarded as important targets for drugs aimed at treating atrial fibrillation. (frontiersin.org)
Protein structure, function and dynamics predictions through Machine Learning methodology are not an exception. (kdnuggets.com)
The dysbindin domain-containing protein 1 (DBNDD1) is a conserved protein among higher eukaryotes whose structure and function are poorly investigated so far. (springer.com)
Loss of solubility and aggregation can lead to the partial or complete abrogation of protein function. (frontiersin.org)
Consequently, amino acid variations through changing the type of residues of the target sites or key flanking residues could directly or indirectly influence PTM of protein and bring about a detrimental effect on protein function. (deepdyve.com)
Impact of genetic variation on three dimensional structure and function of proteins. (lu.se)
If the protein is not functioning properly (ie, normal protein levels but improper function), insufficient regulation of the coagulation process ensues, which can result in an increased risk of clot development and vein blockage. (medscape.com)

In this regard, comprehensive studies of the impact of amino acid variation on protein PTMs will be helpful for further understanding of how genetic polymorphisms are involved in regulating biological and pathological processes and providing instructive information for drug development of various related diseases. (deepdyve.com)

We further identified changes in module eigenproteins indicative of dysregulation in protein translation and trafficking pathways. (stanford.edu)

However, even with the relatively sparse (compared to a number of possible combinations of all protein amino acids in lengthy polypeptide chains) protein databases, Machine Learning can help to unravel complex, non-linear relationships between protein sequences and their structural variability and dynamics. (kdnuggets.com)

2022 ) predicts human DBNDD1 - with a short stretch of helical propensity between residues L77 and S95 - entirely as an IDP. (springer.com)

Planning of homogenates from liver aliquots, perseverance of the protein concentration in the homogenates and protein separation by ten% SDS-Website page proteins from 250 mg liver have been fractionated according to hydrophobicity, into proteins soluble at reduced ionic energy, mainly water-soluble proteins, and proteins soluble at high ionic energy, mainly hydrophobic proteins. (adenosine-kinase.com)

Proteins are complex biomolecules made of 20 building blocks , amino acids, which are connected sequentially into long non-branching chains, commonly known as polypeptide chains. (kdnuggets.com)
Although the very basic forces that govern protein 3D structure formation are known and understood, the exact nature of polypeptide folding remains elusive and has been studied extensively for the past 50 years. (kdnuggets.com)
However, since there are 20 standard protein amino acids, a complete mutagenesis of 100-residue long polypeptide would yield 20 100 mutant combinations, should you decide to explore all possible combinations of typical protein amino acids. (kdnuggets.com)

As an outcome human DBNDD1 revealed a high sequence identity to dysbindin domain-containing proteins from other Hominidae (e.g. (springer.com)
The etiological agent, SARS-CoV-2, is a member of the Coronaviridae family including SARS-CoV-1 (2002-2004) and MERS-CoV (since 2012), with the sequence identity of 79.6% and 50%, respectively. (biorxiv.org)

Additionally, it can be argued that the kinds of matches that RUPEE does return have more added value than the current state of the art in that with equal scores it is able to return results not biased toward a structure classification hierarchy such as SCOPe or sequence clusters such as the PDB-90. (biorxiv.org)
Additionally, it is a proline-rich (10% prolines) cytoplasmatic protein with expression in nearly all organs and e.g., neuronal cells. (springer.com)
This online The Animal Activist's Handbook: Maximizing is the structure essentially constructed in GPCRs and had Additionally, where sequences may instead calculate subscribed but the first sustainable chains are formed based during effect. (woblan.de)

Oxidative stress can denature lipids and proteins [ 10 , 12 - 14 ], as well as induce DNA and RNA fragmentation [ 15 - 17 ], leading to cell dysfunction, injury, and death. (hindawi.com)

Anatomy10

Organisms11

Chemicals and Drugs109

Analytical, Diagnostic and Therapeutic Techniques and Equipment46

Phenomena and Processes78

Disciplines and Occupations3

Technology, Industry, Agriculture1

Information Science10

Health Care4

20162

Mutations19

20183

Mutation7

20193

Eight residues2

Acidic residues1

Uniprot1

20202

Family proteins3

Structural Classifi1

Similarity4

Front Mol Biosci1

Intrinsically disordered protein2

Capsid5

Chem1

Sanger4

Bioinformatics6

Solvent accessibility2

Homology4

Interactions9

Amino acid sequences1

Functional11

Assays3

Genome4

Catalytic4

Analysis and prediction2

GENOMIC2

Alternatively spliced1

Gene3

Humans4

Membrane7

Serine1

Phosphorylation1

Computational2

Variants6

Different proteins1

Genomes2

Putative2

Cellular6

Differentiation2

Species6

Cysteine2

Molecular6

Inhibitor1

Antibodies5

Isoforms2

Descriptors1

Structures5

Datasets2

FUNCTION7

Genetic1

Pathways1

Variability1

20221

Hydrophobic1

Polypeptide3

Identity2

Additionally3

Lipids1