Alignments tertiary protein residues. Medical search. Frequent questions

Structural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. (wikipedia.org)
This process is usually applied to protein tertiary structures but can also be used for large RNA molecules. (wikipedia.org)
In contrast to simple structural superposition, where at least some equivalent residues of the two structures are known, structural alignment requires no a priori knowledge of equivalent positions. (wikipedia.org)
Because these alignments rely on information about all the query sequences' three-dimensional conformations, the method can only be used on sequences where these structures are known. (wikipedia.org)
It is possible to perform a structural alignment on structures produced by structure prediction methods. (wikipedia.org)
The outputs of a structural alignment are a superposition of the atomic coordinate sets and a minimal root mean square deviation (RMSD) between the structures. (wikipedia.org)
Structural alignment can be complicated by the existence of multiple protein domains within one or more of the input structures, because changes in relative orientation of the domains between two structures to be aligned can artificially inflate the RMSD. (wikipedia.org)
The minimum information produced from a successful structural alignment is a set of residues that are considered equivalent between the structures. (wikipedia.org)
The structural alignment also implies a corresponding one-dimensional sequence alignment from which a sequence identity, or the percentage of residues that are identical between the input structures, can be calculated as a measure of how closely the two sequences are related. (wikipedia.org)
Because protein structures are composed of amino acids whose side chains are linked by a common protein backbone, a number of different possible subsets of the atoms that make up a protein macromolecule can be used in producing a structural alignment and calculating the corresponding RMSD values. (wikipedia.org)
When aligning structures with very different sequences, the side chain atoms generally are not taken into account because their identities differ between many aligned residues. (wikipedia.org)
Only when the structures to be aligned are highly similar or even identical is it meaningful to align side-chain atom positions, in which case the RMSD reflects not only the conformation of the protein backbone but also the rotameric states of the side chains. (wikipedia.org)
The most basic possible comparison between protein structures makes no attempt to align the input structures and requires a precalculated alignment as input to determine which of the residues in the sequence are intended to be considered in the RMSD calculation. (wikipedia.org)
Structural superposition is commonly used to compare multiple conformations of the same protein (in which case no alignment is necessary, since the sequences are the same) and to evaluate the quality of alignments produced using only sequence information between two or more sequences whose structures are known. (wikipedia.org)
Although protein structures have been solved by experiments at an increasing rate, a flood of new sequences have been determined even more rapidly due to the advance of sequencing technologies[ 6 , 7 ]. (biomedcentral.com)
Since protein structures have a much higher degree of conservation than the sequences2, comparison of protein structures may reveal distant evolutionary relationships that would not be detected from sequence information alone3,4. (researchsquare.com)
Multiply aligned set of sequences serve as convenient models to depict evolutionary drifts and provide convenient frameworks for mapping allied information such as secondary structures and functionally important residues. (researchsquare.com)
Rapid structure-based sequence alignments employ a comparison of the orientations of the secondary structures (Murthy20, SSAP7,21, and SEA22 programs) or hexapeptide fragments (DALI5,6) to recognize accurate alignments of protein domains that belong to the same superfamilies. (researchsquare.com)
Sequence alignments, key amino acid residues, and conserved predicted secondary and tertiary structures were examined, including active site residues (absent in ENO4 and ENOF1) and sites for Mg2+ and plasminogen binding and for acetylation and phosphorylation. (edu.au)
Experimental results show that ThreaderAI outperforms currently popular template-based modelling methods HHpred, CNFpred, and the latest contact-assisted method CEthreader, especially on the proteins that do not have close homologs with known structures. (biomedcentral.com)
The crystal structures of the protein-tyrosine phosphatase SHP-1 catalytic domain and the complex it forms with the substrate analogue tungstate have been determined and refined to crystallographic R values of 0.209 at 2.5 A resolution and 0.207 at 2.8 A resolution, respectively. (umassmed.edu)
Despite low sequence similarity, the catalytic domain of SHP-1 shows high similarity in secondary and tertiary structures with other protein-tyrosine phosphatases (PTPs). (umassmed.edu)
Based on primary sequence comparisons, β subunits are predicted to be modular structures composed of five domains (A-E) that are related to the large family of membrane-associated guanylate kinase proteins. (jneurosci.org)
During the first section of the course, we will focus on DNA and protein sequence databases and analysis, secondary structures and 3D structural analysis. (nptel.ac.in)
If the observation-to-parameter ratio is small, for example when diffraction data only extend to low resolution, the Bayesian framework implemented in REFMAC 5 uses external restraints to inject additional information extracted from structures of homologous proteins, prior knowledge about secondary-structure formation and even data obtained using different experimental methods, for example NMR. (iucr.org)
Analysis of non-redundant SCOP structures from Y. Zhang's group shows that the average number of short, medium, and long-range contacts of a well folded protein domain is 0.3*L, 0.4*L, and 1.2*L, respectively. (predictioncenter.org)
Tertiary structures of AgrA proteins of some pathogenic bacteria like Listeria monocytogenes, Chlamydia trachomatis, Enterococcus faecalis, Streptococcus pyogenes and Macrococcus canis showing antimicrobial resistance are not yet available in structural databases like PDB. (ijpsr.com)
3D structures of these proteins are essential to determine most of their functions, and for the development of agents that can be explored as therapeutic agents. (ijpsr.com)
In order to derive structures of these AgrA proteins, homology modeling approach was employed. (ijpsr.com)
The modeled proteins were validated by several methods, and the physico-chemical properties of these refined protein structures were predicted using in-silico methods. (ijpsr.com)
Although the number of AgrA protein sequences has increased exponentially, the number of experimentally determined protein structures lags far behind. (ijpsr.com)
It's critical to note, even so, that numerous standard small cysteine-rich pathogen effectors adopt AMP-like confirmations and that tertiary structures of several AMP families strongly resemble each other (27, 28). (hivinhibitor.com)
As a result, the database is not only a database of aligned sequence families, but also a database of implied secondary and tertiary structures covering 29% of all SwissProt-stored sequences. (tu-muenchen.de)
Here, more than a million sequence alignments were analysed between protein pairs of known structures to re-define a line distinguishing between true and false positives for low levels of similarity. (tu-muenchen.de)
This entailed mining available transcriptomic and/or genomic sequence datasets for the presence of homologues of known TIMPs, predicting secondary structures of defined protein sequences, systematic phylogenetic analyses and assessment of differential expression of genes encoding putative TIMPs in the developmental stages of A. suum , N. americanus and Schistosoma haematobium which infect the mammalian hosts. (biomedcentral.com)
Differences in the observed inhibitor conformation between the yeast and human structures are caused by differing residues in the binding pocket. (duke.edu)
Using a homology search, we obtained a set of candidate sequences, modelled the tertiary structure of the selected enzymes, and compared them with experimental and model structures of known DAAOs. (actanaturae.ru)
This review critically focuses on opportunities to employ protein-graphene oxide structures either as nanocomposites or as biocomplexes and highlights the effects of carbonaceous nanostructures on protein conformation and structural stability for applications in tissue engineering and regenerative medicine. (mdpi.com)

However, caution should be used in using the results as evidence for shared evolutionary ancestry because of the possible confounding effects of convergent evolution by which multiple unrelated amino acid sequences converge on a common tertiary structure. (wikipedia.org)
Structural alignments can compare two sequences or multiple sequences. (wikipedia.org)
Profiles generated using structure-based sequence alignments of distantly related proteins at the family or superfamily level could be utilized to predict the fold of hypothetical sequences through profile-sequence search method is another success in the structure prediction area. (researchsquare.com)
The alignments of protein sequences are required for the organization and assimilation of vast amounts of data. (researchsquare.com)
Fig. 1: Photochemistry of light-oxygen-voltage receptors and sequences of proteins under study. (nature.com)
To test this, we aligned 97 protein sequences consisting of homologs of UMAMIT clade I from 27 plant species and created sequence logos containing the 51 residues identified in the structural analysis ( Supplementary Figure 1 ). (frontiersin.org)
By now you get the idea that cells generate proteins, which are sequences of amino acids. (ainews.one)
For HMPV, the existence of different genetic lineages has been described on the basis of variation in a limited set with F being one of the most conserved proteins and G the of available sequences. (cdc.gov)
In addition, we analyzed the genetic diversity of sequences of the G protein and neutralization tests by HMPV by phylogenetic analysis of sequences obtained for using monoclonal antibodies that also recognize the G pro- part of the fusion protein (n = 84) and the complete attach- tein, but these subgroups belonged to one serotype (21). (cdc.gov)
On the basis of APV type C, a possible second serotype, was identified sequence diversity between attachment protein genes and based on the lack of cross-reactivity with antisera specific the differences in virus neutralization titers, two HMPV for groups A and B, and the nucleotide sequences also serotypes were defined. (cdc.gov)
iv) Using intermediate sequences for finding links between more distant families was almost as successful: pairs were predicted to be homologous when the respective sequence families had proteins in common. (tu-muenchen.de)
The program accepts either a set of sequences in FASTA format or a list of identifiers from either of the following protein databases: SWISS-PROT (13), PDB (14) or TrEMBL (13). (tu-muenchen.de)
A total of 15 protein sequences with high homology to known eukaryotic TIMPs were predicted from the complement of sequence data available for parasitic helminths and subjected to in-depth bioinformatic analyses. (biomedcentral.com)

Three dimensional structure is highly conserved in protein evolution1. (researchsquare.com)
Likely via a radical-pair mechanism 12 , T 1 reacts within microseconds to the signaling state, characterized by a covalent thioadduct between a highly conserved cysteine residue in the LOV photosensor and the C4a atom of the flavin isoalloxazine ring system. (nature.com)
A highly conserved glutamine residue in strand Iβ is situated immediately adjacent to the flavin and has been identified as instrumental in reading out the flavin N5 position and eliciting the downstream transitions. (nature.com)
Based on a predicted model of UMAMIT29, we propose that the substrate transporting cavity consists of 51 residues, of which four are highly conserved residues across all the analyzed homologs of UMAMIT29. (frontiersin.org)
We hypothesised that the transport cavity contains highly conserved residues that are key for the transport activity. (frontiersin.org)
PURA encodes Pur-α, a highly conserved multifunctional protein that has an important role in normal postnatal brain development in animal models. (bmj.com)

A proper encoding of residue contact information is crucial for structure prediction because in principle, a full distance map or a residue contact map has sufficient information for reconstructing the tertiary structure of a protein[ 25 ]. (biomedcentral.com)

Template-based modeling, including protein threading and homology modeling, is a popular method for protein tertiary structure prediction. (biomedcentral.com)
These results demonstrate that with the help of deep learning, ThreaderAI can significantly improve the accuracy of template-based structure prediction, especially for distant-homology proteins. (biomedcentral.com)
ii) Whether or not sequence homology implied structural identity depended crucially on the alignment length. (tu-muenchen.de)
Profundice en los temas de investigación de 'Sequence determination and homology modeling of lipase from Marinobacter sp. (edu.pe)

The second section will be devoted to applications such as prediction of protein structure, folding rates, stability upon mutation, and intermolecular interactions. (nptel.ac.in)
Mutation on these residues can lead to new strains of coronavirus with different degrees of infectivity and virulence. (biorxiv.org)

Structural alignments are especially useful in analyzing data from structural genomics and proteomics efforts, and they can be used as comparison points to evaluate alignments produced by purely sequence-based bioinformatics methods. (wikipedia.org)
Computational protein structure prediction remains one of the most challenging problems in structural bioinformatics. (biomedcentral.com)
He is teaching courses on bioinformatics, protein structure and function, protein interactions: computational techniques, big data analysis and handling computational biology lab. (nptel.ac.in)
His main research interests are structural analysis, prediction, folding and stability of globular and membrane proteins, protein interactions and development of bioinformatics databases and tools. (nptel.ac.in)
He has published over 200 research articles, 40 reviews, 5 editorials and a book on Protein Bioinformatics: From Sequence to Function by Elsevier/Academic Press. (nptel.ac.in)
Bioinformatics approaches were used to predict the tertiary structure and cellular localization along with phylogenetic analysis of TPD52. (biomedcentral.com)

A cysteine peptidase is a proteolytic enzyme that hydrolyses a peptide bond using the thiol group of a cysteine residue as a nucleophile. (embl.de)

The tertiary structure of proteins provides crucial information for understanding molecular mechanisms of biological functions. (biomedcentral.com)
Its molecular interactions were determined through KEGG analysis, and real-time PCR-based expression analysis was performed to assess its co-expression with another oncogenic cellular pathway (miR-223, KLF9, and PKCε) proteins in ovarian cancer. (biomedcentral.com)
The aim of this study is to predict the tertiary structure of TPD52 for the first time to provide a deep insight towards a better understanding regarding the functional structure as well as the molecular basis of TPD52 as well as other members of the TPD family. (biomedcentral.com)
This interdisciplinary connection between protein chemists, molecular biologists and stereo-chemists is essential for the protein-design cycle (Fig. 1) consisting of design, cloning, expression andtesting new proteins starting from known ones. (helmholtz-hzi.de)
A molecular model of the FMDV 3A protein, derived from the nuclear magnetic resonance (NMR) structure of the poliovirus 3A protein, predicted a hydrophobic interface spanning residues 25 to 44 as the main determinant for 3A dimerization. (asm.org)
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)
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)
The tertiary structure was elucidated using the 1EX9 lipase from Pseudomonas aeruginosa PAO1 as a template and molecular docking was executed with three substrates. (edu.pe)

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)
Most, although not all, of the mutations causing skeletal abnormalities involve conserved residues that are predicted to play an important structural role in the correct folding of FGFRs, and substitutions with other residues result in constitutive activation of FGFRs with ligand-independent dimerization (11) . (aacrjournals.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)
Results Protein-altering de novo mutations in PURA were identified in four subjects. (bmj.com)

To validate the prediction of VdAMP3 as a member of this ancient antimicrobial protein family, we aligned its amino acid sequence CCR9 Purity & Documentation together with the antibacterial CS defensins plectasin and eurocin, from the saprophytic Ascomycete species Pseudoplectania nigrella and Eurotium amstelodami (formerly Aspergillus amstelodami), respectively (291). (hivinhibitor.com)
The primary amino acid sequence of a protein is a translated version from its gene sequence which carries important messages and information concealed therein. (springeropen.com)

Recently, with the combination of deep learning and direct coupling techniques, the performance of residue contact prediction has achieved significant progress. (sciopen.com)
We have accordingly proposed a feature extraction method to obtain various categories of statistical information from only the multi-sequence alignment, followed by training a DL model for residue-residue contact prediction based on the massive statistical information. (sciopen.com)

Tissue inhibitors of metalloproteases (TIMPs) are a multifunctional family of proteins that orchestrate extracellular matrix turnover, tissue remodelling and other cellular processes. (biomedcentral.com)

Orthologues identified by transcriptome sequencing were characterized using phylogenetic, ab initio protein modelling and comparative and population-based methods. (biomedcentral.com)

At the neuromuscular junction, the acetylcholine receptor (AChR) is specifically clustered in the postsynaptic membrane via interactions with rapsyn and other scaffolding proteins. (jneurosci.org)
The mechanism by which MuSK signaling regulates the interaction of the AChR with scaffolding proteins that localize it in the postsynaptic membrane, however, remain unknown. (jneurosci.org)
Endocytic trafficking dynamically regulates neuronal plasma membrane protein presentation and activity, and plays a central role in excitability and plasticity. (umassmed.edu)
Over the course of my dissertation research I investigated endocytic mechanisms regulating two neuronal membrane proteins: the anesthetic-activated potassium leak channel, KCNK3, as well as the psychostimulant-sensitive dopamine transporter (DAT). (umassmed.edu)
Taken together, these results demonstrate that novel, non-classical endocytic mechanisms dynamically control the plasma membrane presentation of these two important neuronal proteins. (umassmed.edu)
A total of five major Open Reading Frames (ORF) were found in COVID-19: the ORF 1a/b region coding replicase and other enzymes, the spike or S protein ORF, M or membrane glycoprotein ORF, E or small membrane protein ORF and the N or nucleocapsid ORF ( fig. 1 )[ 5 ]. (ijpsonline.com)
Serine protease present on cell membrane, is used by SARS-CoV-2 for associating spike protein to enable its fusion with host cells[ 12 - 14 ]. (ijpsonline.com)
Analysis of the transcriptome identified several orthologues required for intra-erythrocytic survival and erythrocyte invasion, including the rhoptry neck protein 2 (RON2) and the apical membrane antigen-1 (AMA-1). (biomedcentral.com)
in poliovirus (PV), the interaction between the RNA replication complex and intracellular membranes appears to be accomplished by proteins 3A and 2C, which have membrane-binding properties ( 11 , 60 ). (asm.org)
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)

Effective encoding of residue contact information is crucial for protein structure prediction since it has a unique role to capture long-range residue interactions compared to other commonly used scoring terms. (biomedcentral.com)
Among various structure-based terms, residue-residue contact potentials[ 21 - 23 ] are unique in that they capture long-range interactions in a protein structure[ 24 ]. (biomedcentral.com)
However, it remains unclear where these proteins bind on the AChR and how the interactions are regulated. (jneurosci.org)
Each subunit has a large intracellular loop between the third and fourth transmembrane domains that is the likely site for regulated interactions with postsynaptic scaffolding proteins. (jneurosci.org)
Replacements that favored (Q44R) or impaired (Q44D) the polar interactions predicted between residues Q44 and D32 did not abolish dimer formation of transiently expressed 3A, indicating that these interactions are not critical for 3A dimerization. (asm.org)
Biological processes are commonly controlled by precise protein-protein interactions. (ox.ac.uk)

However, accurate template-query alignment and template selection are still very challenging, especially for the proteins with only distant homologs available. (biomedcentral.com)
Protein sequence alignment of VdAMP3 with a subset of its homologs identified in greater (Ascomycota and Autotaxin supplier Basidiomycota) and reduce fungi (Mucoromycotina and Zoopagomycota ). (hivinhibitor.com)
An ancient antimicrobial protein co-opted by a fungal plant pathogen for in planta mycobiome manipulationqueried the predicted proteomes on the fungi in the Joint Genome Institute (JGI) 1000 Fungal Genomes Project (32) for homologs of VdAMP3 with larger sequence identity and integrated a subset of those within the protein alignment (Fig. 1C). (hivinhibitor.com)

Hydrolysis involves usually a catalytic triad consisting of the thiol group of the cysteine, the imidazolium ring of a histidine, and a third residue, usually asparagine or aspartic acid, to orientate and activate the imidazolium ring. (embl.de)
Also typicall catalytic triad residues of family I lipases (Ser78, Asp229 and His251) were identified. (edu.pe)
Cas9 nuclease can be converted into an RNA-guided DNA binding protein (dCas9) via inactivation of its two catalytic domains 12 , 13 and then fused to transcription activation domains. (cdc.gov)

3. Definition of contacts (residue centers and distance thresholds) (i) The definition historically used in CASP: a pair of residues is defined to be in contact when the distance between their Cβ atoms (Cα in case of glycine) is smaller than 8.0 Å. (predictioncenter.org)
The very conserved cysteine and glycine residues that contribute for the CS defensin structure are highlighted by yellow and red backgrounds, respectively. (hivinhibitor.com)

As recently proposed 25 , glutamine reorientation, and signal propagation may be aided by transient rearrangements of two conserved asparagine residues that coordinate the pteridin portion of the flavin. (nature.com)

Other comparison criteria that reduce noise and bolster positive matches include secondary structure assignment, native contact maps or residue interaction patterns, measures of side chain packing, and measures of hydrogen bond retention. (wikipedia.org)
Comparison of the binding activity of the JNK isoforms demonstrated that the JNK proteins differ in their interaction with ATF2, Elk-1 and Jun transcription factors. (umassmed.edu)

Replacements L38E and L41E, involving charge acquisition at residues predicted to contribute to the hydrophobic interface, reduced the dimerization signal in the protein ligation assay and prevented the detection of dimer/multimer species in both transiently expressed 3A proteins and in synthetic peptides reproducing the N terminus of 3A. (asm.org)
Defensins are small cationic peptides of 45-54 amino acid residues with a conserved signature of cysteines, which can form three to four disulfide bridges. (frontiersin.org)
Due to their large surface area and ability to interact with proteins and peptides, graphene oxides offer valuable physiochemical and biological features for biomedical applications and have been successfully employed for optimizing scaffold architectures for a wide range of organs, from the skin to cardiac tissue. (mdpi.com)

For this reason it is common for structural alignment methods to use by default only the backbone atoms included in the peptide bond. (wikipedia.org)
We found that overall the residue contact pattern can distinguish protein folds best when contacts are defined for residue pairs whose Cβ atoms are at 7.0 Å or closer to each other. (biomedcentral.com)
For capturing contacts between neighboring β strands, considering the distance between Cα atoms is better than the Cβ−based distance because the side-chain of interacting residues on β strands sometimes point to opposite directions. (biomedcentral.com)

TBM method predicts the structure of query protein by modifying the structural framework of its homologous protein with known structure in accordance with template-query alignment. (biomedcentral.com)

Variations in the amino acids are reflected by small conformational changes in the tertiary structure that contribute to the broad range of biological activities in these proteins. (frontiersin.org)

It also comprised 133 genes, including 37 tRNAs, eight rRNAs, and 88 protein-coding genes. (bvsalud.org)
Vertebrate ENO1, ENO2, and ENO3 genes usually contained 11 coding exons, while ENO4 (encoding an ENO-like protein, ENOLL) usually contained 14 coding exons. (edu.au)
Overexpression of constitutive active DREB2A which had a transcriptional activation domain between residues 254 and 335 resulted in significant drought stress tolerance through regulates expression of many water stress-inducible genes [ 9 ]. (biomedcentral.com)
These protein kinases correspond to alternatively spliced isoforms derived from the JNK1, JNK2 and JNK3 genes. (umassmed.edu)
The accessory gene regulator ( agr ), a well-studied QS system, controls the expression of a series of virulence-associated protein genes in some Gram-positive bacteria 19, 20 . (ijpsr.com)
In general, most genes that encode antigens of Plasmodium parasites are highly polymorphic and encode proteins that are important targets for host protective antibody responses [ 5 ]. (biomedcentral.com)
In protein expression, we are particularly interested in mRNA, which acts as a portable transcript, of the instructions written in genes, to ribosomes, the cell's machinery responsible for producing a protein. (ainews.one)
The expression of foreign genes using recombinant DNA technology in various host systems has permitted the production of human proteins of therapeutic interest in high amounts. (helmholtz-hzi.de)

However, such alignments of distantly related proteins are often hard to obtain by automatic multiple sequence alignment programs. (researchsquare.com)
For each protein of known 3-D structure from the Protein Data Bank (PDB), the database has a multiple sequence alignment of all available homologues and a sequence profile characteristic of the family. (tu-muenchen.de)
However, we assume that for each protein, we have a reference structure and a multiple sequence alignment of homologues. (ox.ac.uk)

Lower fold recognition accuracy was observed when inaccurate threading alignments were used to identify common residue contacts between protein pairs. (biomedcentral.com)
In particular, in terms of alignment accuracy measured with TM-score, ThreaderAI outperforms HHpred, CNFpred, and CEthreader by 56, 13, and 11%, respectively, on template-query pairs at the similarity of fold level from SCOPe data. (biomedcentral.com)
in the second, these lists are "padded" with zero-probabilities for pairs of residues that are not predicted as being in contact. (predictioncenter.org)
It gives 59% precision with 20% recall on a blind test set of 31 protein pairs. (ox.ac.uk)

The mature form of the protein is predicted to contain three transmembrane domains and 204 residues. (nih.gov)
There are 106401 EGF_Lam domains in 19990 proteins in SMART's nrdb database. (embl.de)
Results are presented that have been obtained by our group during the last four years concerning the expression of the glycoproteins human Interleukin 2 (Il-2) and Interferon-8 (IFN-8) in different mammalian cell lines, the determination of their carbohydrate residues, the effect of site-directed mutagenesis on their carbohydrate attachment sites and the insertion of peptide domains which function as acceptors for carbohydrates. (helmholtz-hzi.de)
Among the established custom DNA binding domains, Cas9 is most easily scaled to facilitate genome-scale perturbations 3 , 4 due to its simplicity of programming relative to zinc finger proteins and transcription activator-like effectors (TALEs). (cdc.gov)

Accurate sequence alignments of distantly related proteins are crucial for the better understanding of proteins at their family/superfamily level. (researchsquare.com)
The availability of accurate structure-based sequence alignments of protein families and superfamilies is crucial to inferring their evolutionary relationships, functional properties4 and to understand the structural variances between the different classes of proteins. (researchsquare.com)
High quality of sequence alignments are crucial for comparative modeling and docking in computing and for the design of rational experiments. (researchsquare.com)
NS proteins are involved in crucial aspects of the viral cycle and pathogenesis, such as rearrangements of intracellular membranes required for endomembrane recruitment and the lysis of host cells ( 1 , 12 , 14 , 18 , 73 ). (asm.org)
1 , 2 Largely expressed on the surface of SARS-CoV-2, the spike (S) protein plays a crucial role in binding to the host angiotensin-converting enzyme 2 (ACE2) through the receptor-binding domain (RBD) and facilitating viral entry, 3 , 4 which is therefore considered as one of the most preferred targets against SARS-CoV-2. (biorxiv.org)

Accurate prediction of protein structure is fundamentally important to understand biological function of proteins. (biomedcentral.com)

ThreaderAI first employs deep learning to predict residue-residue aligning probability matrix by integrating sequence profile, predicted sequential structural features, and predicted residue-residue contacts, and then builds template-query alignment by applying a dynamic programming algorithm on the probability matrix. (biomedcentral.com)
Based on distance-based protein folding tools, we predict the substrate-transporting cavity of UMAMIT29. (frontiersin.org)
Here we predict the binding residues of such interprotein complexes. (ox.ac.uk)
We have developed a suite of methods, i-Patch, which predict the interprotein contact sites by considering the two proteins as a network, with residues as nodes and contacts as edges. (ox.ac.uk)
i-Patch then uses the propensities of patches of residues to interact, to predict interprotein contact sites. (ox.ac.uk)

Despite the fact that the biological relevance of those defensins for the respective fungi remains unclear, their antibacterial activity and protein structure have been properly characterized, which led to their recognition as genuine CS defensins (291). (hivinhibitor.com)

An in-house analysis shows that the three definitions on CASP targets agree in 80+ % of cases (i.e., contact between two residues according to measure x is also a contact according to measure y). (predictioncenter.org)

Although the general identity involving the three proteins was rather low (25 to 40 ), protein sequence alignment revealed that VdAMP3 contains the six very conserved cysteine residues that happen to be considered important for the structure of CS defensins (Fig. 1B) (27). (hivinhibitor.com)
B) Protein sequence alignment with CS defensins plectasin and eurocin (E. amstelodami) supports the structure prediction of VdAMP3. (hivinhibitor.com)
Plant defensins exhibit a conserved tertiary structure that consists of a triple-stranded antiparallel β-sheet and one α-helix that are stabilized into a compact shape by the disulfide bridges. (frontiersin.org)

Proteolytic events included removal of a peptide from the surface of the precursor molecule that connected the NH2- and COOH-termini of the mature protein. (rupress.org)
The viral particle is composed of a protein capsid that contains a positive-sense RNA molecule of about 8,500 nucleotides that is infectious and encodes a single polyprotein, which is processed in infected cells by cis - and trans -acting viral proteases ( 55 ) to yield different polypeptide precursors and the mature viral proteins ( 9 , 62 ). (asm.org)

When results of fold recognition were examined for individual proteins, we found that the effective contact definition depends on the fold of the proteins. (biomedcentral.com)
The model accuracy of TBM method critically depends on protein features and the scoring functions that integrate these features. (biomedcentral.com)
Sequence-based protein tertiary structure prediction is of fundamental importance because the function of a protein ultimately depends on its 3D structure. (sciopen.com)

The list of homologues is the result of a database search in SwissProt using a position-weighted dynamic programming method for sequence profile alignment (MaxHom). (tu-muenchen.de)
The listed homologues are very likely to have the same 3-D structure as the PDB protein to which they have been aligned. (tu-muenchen.de)

Based on our model, we proposed a substrate-transporting cavity of UMAMIT29 defined by helix I to IV and VI-IX and selected 51 residues as putative substrate binding sites based on solvent accessibility ( Figure 1 ). (frontiersin.org)

My results indicate that KCNK3 internalizes in response to Protein Kinase C (PKC) activation, using a novel pathway that requires the phosphoserine binding protein, 14-3-3β, and demonstrates for the first time regulated KCNK3 channel trafficking in neurons. (umassmed.edu)

NH2-terminal sequencing of the abundant precursors confirmed that the intact subunit of concanavalin A was formed by the reannealing of two fragments, since the alignment of residues 1-118 and 119-237 was reversed in the final form of the lectin identified in the chase and the precursor first labeled. (rupress.org)

Possible prospects for applications of designed proteins with modified activities or other new properties are very high,in the areas of pharmacology, enzyme applications in food industry', waste treatment and chemical synthesis, vaccine design, biosensors etc. (helmholtz-hzi.de)

In only one family of cysteine peptidases, is the role of the general base assigned to a residue other than a histidine: in peptidases from family C89 (acid ceramidase) an arginine is the general base. (embl.de)
Recombinant Mpn HPRT was expressed as an N-terminal fusion protein with a 6 × histidine tag and a tobacco etch virus (TEV) cleavage site at the N-terminus, and was purified to >98% purity by metal affinity chromatography, see more as assessed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis (data not shown). (bcl-2protein.com)

The APC protein, which comprises of 2843 amino acids, plays an important role in the β-catenin nuclear localization ( 8 ). (spandidos-publications.com)
Protein structure is fundamentally important to understand protein functions. (biomedcentral.com)
Manyclinically important human proteins are posttranslationally modified. (helmholtz-hzi.de)
Foot-and-mouth disease virus (FMDV) nonstructural protein 3A plays important roles in virus replication, virulence, and host range. (asm.org)

Using chimeric proteins in which CD4 is fused to the large intracellular loop of each of the AChR subunits we found that agrin induced clustering of only chimeras containing the β subunit loop. (jneurosci.org)
The S1 subunit (PDB I.D-6VSB) of the spike protein being reported to acts as receptor binding domain (RBD), binding to ACE-2 receptor with higher affinity. (ijpsonline.com)

Structural alignment is a valuable tool for the comparison of proteins with low sequence similarity, where evolutionary relationships between proteins cannot be easily detected by standard sequence alignment techniques. (wikipedia.org)
Structural alignment can therefore be used to imply evolutionary relationships between proteins that share very little common sequence. (wikipedia.org)
The present study unveils the structure-function and evolutionary aspects of 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD) proteins of fungal origin. (springeropen.com)

Desensitization of p21(ras) after stimulation of cells by growth factors and phorbol 12-myristate 13-acetate (PMA) correlates with hyperphosphorylation of the guanine nucleotide exchange factor Son-of-sevenless (Sos) and its dissociation from the adaptor protein Grb2 (Cherniack, A., Klarlund, J. K., Conway, B. R., and Czech, M. P. (1995) J. Biol. (umassmed.edu)

Protein structure comparison also helps to improve tools for identifying gene functions in genome databases by defining the essential sequence-structure features of a protein family16. (researchsquare.com)

This suggests that these residues are key for UMAMIT29-mediated glucosinolate transport activity and thus potential targets for blocking the transport of glucosinolates to the seeds. (frontiersin.org)

ancestor of animals, plants, and fungi that generate these proteins now (247). (hivinhibitor.com)

This review describes recent advances in the role of human HMGB proteins and other proteins interacting with them, in cancerous processes related to oxidative stress, with special reference to ovarian and prostate cancer. (hindawi.com)

The protein kinase activity of these JNK isoforms was measured using the transcription factors ATF2, Elk-1 and members of the Jun family as substrates. (umassmed.edu)
Programmable DNA binding proteins have emerged as an exciting platform for engineering synthetic transcription factors for modulating endogenous gene expression 5 - 11 . (cdc.gov)

1. The V. dahliae effector VdAMP3 evolved from an ancient fungal protein. (hivinhibitor.com)

We further propose a novel assessment of the derived alignments using the measurements of the structural variations and the percentage secondary structural equivalences. (researchsquare.com)
Percentage points are related to the number of proteins with EGF_Lam domain which could be assigned to a KEGG orthologous group, and not all proteins containing EGF_Lam domain. (embl.de)

The RNA chain is decoded and translated by ribosomes to produce a polypeptide sequence, otherwise known as a protein. (ainews.one)

Anatomy12

Organisms10

Diseases8

Chemicals and Drugs71

Analytical, Diagnostic and Therapeutic Techniques and Equipment49

Phenomena and Processes89

Disciplines and Occupations3

Technology, Industry, Agriculture2

Information Science27

Health Care12

Structures38

Sequences13

Highly conserved6

Reconstructing the tertiary structure1

Homology4

Mutation2

Bioinformatics6

Cysteine residue1

Molecular8

Mutations6

Amino acid seq2

Contact prediction2

Multifunctional1

Phylogenetic1

Membrane10

Interactions6

Homologs3

Catalytic3

Glycine2

Asparagine1

Interaction2

Peptides3

Atoms3

Homologous1

Conformational changes1

Genes8

Multiple sequence3

Pairs4

Domains4

Crucial5

Prediction of protein structure1

Predict5

Biological1

CASP1

Defensins3

Molecule2

Depends3

Homologues2

Substrate1

Pathway1

Fragments1

Synthesis1

Histidine2

Important4

Subunit2

Evolutionary3

Nucleotide1

Features of a protein1

Suggests1

Generate1

Ovarian1

Transcription2

Fungal1

Percentage2

Polypeptide1