Prediction protein interaction domains and motifs. Medical search. Frequent questions

METHODS AND RESULTS: Amino acid sequence alignments, protein structure prediction analysis, and protein: nucleic acid interaction assays were used to show that the Leishmania major RT domain preserves the canonical structural elements found in higher eukaryotes, including the canonical motifs and the aspartic acid residues that stabilize the Mg2+ ion cofactor. (bvsalud.org)
CONCLUSION: Our results highlight that the telomerase catalysis mechanism is conserved in a pathogen of medical importance despite the structural peculiarities present in the parasite's RT domain. (bvsalud.org)
However, analogous proteins may have structural homology although this is not a prerequisite. (hindawi.com)
Triangle network motifs predict complexes by complementing high-error interactomes with structural information. (leibniz-fli.de)
As is shown in Table 1 , these methods mostly employ RNA sequence and structural information to predict protein-RNA interactions. (biomedcentral.com)
The pathogen protein and host interactor protein with a common interacting host protein are compared for similar domains indicating global structural similarity and motifs indicating local sequence similarity to determine Domain Mimicry Pairs (DMPs) and Motif Mimicry Pair (MMPs) respectively (depicted in Figure 1). (sblab-nsit.net)
Structural analysis showed that effector proteins were small in size (50AA to 422AA) and of diverse sequences, and the conserved sequential elements or clear common elements were not involved, regardless of their secretion from the pathogen to the host. (figshare.com)
Predicting protein function using structure: structural alignments, structural motifs, annotation transfer via structure similarity. (tum.de)
The translated polyprotein consists of three structural [capsid (C), membrane (M) and envelope (E)] and seven non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5). (spandidos-publications.com)
Using tools developed in our lab, SamCC Turbo and DeepCoil we revealed peculiar structural features of these domains that may be essential for the functioning of KfrA proteins. (edu.pl)
Coiled coils are widespread, highly-regular, protein domains involved in diverse processes ranging from providing structural rigidity to the transduction of conformational changes. (edu.pl)
Mauno Vihinen is well-known for his experience and interest in investigating variations and their effects whether they emerge at molecular levels (DNA, RNA protein), in structural context or in the cellular networks and pathways. (lu.se)

Chia-Tzu Ho, Yu-Wei Huang, Chia-Hua Lo, Wei-Cheng Lo * (2021, Nov). Discovering the ultimate limits of protein secondary structure prediction. (nctu.edu.tw)
A secondary structure-based position-specific scoring matrix applied to the improvement in protein secondary structure prediction. (nctu.edu.tw)
The influence of dataset homology and a rigorous evaluation strategy on protein secondary structure prediction. (nctu.edu.tw)
A simple strategy to enhance the speed of protein secondary structure prediction without sacrificing accuracy. (nctu.edu.tw)
Exploring the effects of sparse restraints on protein structure prediction. (ncbs.res.in)
Ranjan, D. "ABI Innovation: Advanced Informatics and Eective Algorithms for Improved CryoEM Protein Structure Prediction and Density Analysis" $589,703. (odu.edu)
Ranjan, D. "Improving Protein Secondary Structure Prediction using 3-dimensional Spatial Constraints of the Protein" $122,000. (odu.edu)

Two highly positive sequences exist towards the N terminus of PRP36 while a highly negative sequence exists within the DUF4596 domains towards the C terminus. (wikipedia.org)
The purified recombinant Leishmania RT protein is biochemically active and interacts with the G-rich telomeric strand and the TER template sequence. (bvsalud.org)
A signature motif in the N-terminus domain of THSD7A (T28mer) with sequence homology to the major PLA2R epitope (P28mer) was identified. (manchester.ac.uk)
B-cell epitope prediction analysis and homology modelling revealed this sequence to be antigenic and surface available suggesting it is accessible for the antibody to bind. (manchester.ac.uk)
Real time interaction analyses and antibodies off-rate could be reliably determined using bio-layer interferometry.A signature motif in the N-terminus domain of THSD7A (T28mer) with sequence homology to the major PLA2R epitope (P28mer) was identified. (manchester.ac.uk)
Chi-Chun Chen, Yu-Wei Huang, Hsuan-Cheng Huang, Wei-Cheng Lo *, Ping-Chiang Lyu* (2022, Nov). SeqCP: A sequence-based algorithm for searching circularly permuted proteins. (nctu.edu.tw)
The study of MscL, a highly convenient model system, will give us basic understanding and the first example of what type of intramolecular interactions, sequence motifs, and conformations make membrane proteins sensitive to a physiologically relevant mechanical stimulation. (usda.gov)
The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods. (embl.de)
Phyletic distributions of eukaryotic signalling domains were studied using recently developed sensitive methods for protein sequence analysis, with an emphasis on the detection and accurate enumeration of homologues in bacteria and archaea. (embl.de)
Prediction of the effect of single point mutations (sequence variants) on protein function and the organism. (tum.de)
Students understand the principle concepts in protein sequence analysis with focus on protein function and protein function prediction and are able to evaluate these. (tum.de)
The method, named Predikin, identifies key conserved substrate-determining residues in the kinase catalytic domain that contact the substrate in the region of the phosphorylation site and so determine the sequence surrounding the phosphorylation site. (biomedcentral.com)
The heptapeptide sequence from -3 to +3 that best binds to the pocket is determined by the physicochemical nature of the residues in the catalytic domain that line the pocket and contact the substrate. (biomedcentral.com)
Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. (embl.de)
There are many superfamilies of Znf motifs, varying in both sequence and structure. (embl.de)

PRP36 is 1346 amino acids long and is proline rich, meaning that a greater proportion of proline residues exist throughout the protein, including the DUF4596 domain, in comparison with other human proteins. (wikipedia.org)
Furthermore, amino acid substitutions specific to the Leishmania genus and partial conservation of the residues involved with nucleic acid interactions are shown. (bvsalud.org)
VH is derived from a single protein domain of 35 residues [ 9 ]. (hindawi.com)
There were 427 candidate effector proteins that contain more than or equal to 4 cysteine residues, and 339 candidate effector proteins contained the known motifs. (figshare.com)
Predikin now consists of two components: (i) PredikinDB, a database of phosphorylation sites that links substrates to kinase sequences and (ii) a Perl module, which provides methods to classify protein kinases, reliably identify substrate-determining residues, generate scoring matrices and score putative phosphorylation sites in query sequences. (biomedcentral.com)
New features in Predikin include the use of SQL queries to PredikinDB to generate predictions, scoring of predictions, more reliable identification of substrate-determining residues and putative phosphorylation sites, extended options to handle protein kinase and substrate data and an improved web interface. (biomedcentral.com)
The post-translational modification of proteins by phosphorylation of serine, threonine or tyrosine residues is a ubiquitous process in cellular regulation. (biomedcentral.com)
The second factor, termed peptide specificity, describes the interaction between amino acid residues in the catalytic domain of the protein kinase and the substrate residues that surround the phosphorylated residue. (biomedcentral.com)
Crystal structures of protein kinases with bound substrate peptides show that substrate residues at positions -3 to +3 relative to the phosphorylated serine, threonine or tyrosine residue adopt an extended conformation and bind to a pocket in the catalytic domain of the protein kinase [ 8 ]. (biomedcentral.com)
However, it is recognised that for many protein kinase families, particularly those that phosphorylate Ser/Thr residues, peptide specificity is the major factor that determines substrate specificity. (biomedcentral.com)
Following the evaluation of the model and the identification of motifs characteristic of the Flaviviridae family, data from previous publications on the treatment of HCV were incorporated, with the aim of detecting the ideal residues in the Spondweni model, which are similar to those of the HCV structure and are inhibitor targets. (spandidos-publications.com)
Protein Domain-Swapping Can Be a Consequence of Functional Residues. (ncbs.res.in)
They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. (embl.de)

We examined each of the individual SARS-CoV-2 proteins for their cytotoxicity in HEK 293 T cells and their subcellular localization in COS-7 cells. (biomedcentral.com)
Purification of individual SARS-CoV-2 proteins from human cells have identified a potential interaction between a catalytic-inactive version of Nsp5 with human tRNA methyltransferase 1 (TRMT1) ( Gordon et al , 2020b ). (elifesciences.org)

The paper "DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses" was officially accepted by Bioinformatics . (osumc.edu)
The paper "DMINDA 2.0: integrated and systematic views of regu-latory DNA motif identification and analyses" was submitted to Bioinformatics . (osumc.edu)
Jinyu Yang, Xin Chen, Adam McDermaid, and Qin Ma$, DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses, Bioinformatics , DOI: 10.1093/bioinformatics/btx223, 2017. (osumc.edu)
Bioinformatics analysis depicted the cytoplasmic localization of TPD52 and the high conservation of its coiled-coil domains. (biomedcentral.com)
Especially, deep learning is increasingly used in the bioinformatics field by virtue of its ability to learn generalized representations from DNA and protein sequences. (biomedcentral.com)
The results showed that the prediction of P. triticina effector proteins based on transcriptomic analysis and multiple bioinformatics software is effective and more accurate, laying the foundation of revealing the pathogenic mechanism of Pt and controlling disease. (figshare.com)

The gene spans between base pair numbers 7868719 and 7874441 on chromosome 19 and is located between two other genes-LYPLA2P2, a pseudogene, and EVI5L, a gene which produces a protein that regulates Rab GTPase activity. (wikipedia.org)
Studies of human genome demonstrate that protein-coding genes only occupy less than 2% of the entire genome [ 1 ]. (ijbs.com)
Forkhead box protein M1 (FOXM1) is a key transcription factor (TF) that regulates a common set of genes related to the cell cycle in various cell types. (mdpi.com)
Protein kinases, the enzymes responsible for protein phosphorylation, make up almost 2% of protein-encoding genes in the human genome [ 1 ] and an estimated 30-50% of human proteins are phosphorylated [ 2 ]. (biomedcentral.com)
The Arabidopsis genome contains an estimated 340,000 potential MADS binding sites ( de Folter and Angenent, 2006 ), leading to the intriguing question: What is the biological significance of the large number of potential MADS binding sites, and how many target genes do MADS proteins really regulate? (frontiersin.org)
Based on these studies, it appears that MADS proteins may directly regulate thousands of target genes (Figure 1 A), and may serve to integrate different biological processes. (frontiersin.org)
(A) Network representation (Cytoscape) of the reported target genes (represented by blue lines) of the four MADS proteins (yellow circles). (frontiersin.org)
The four MADS proteins share 70 target genes. (frontiersin.org)
Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. (embl.de)
Ranjan, D. "Cellular and Molecular Interactions among Genes in Cerebellar Development over Time and Space" $22,000. (odu.edu)
The major part of his production relates to variations ranging from protein engineering to effects and mechanisms of variations in protein structures, genes and diseases. (lu.se)
Although many data sources for genes and diseases are in the public domain, finding published results with potential implications for understanding gene-disease relationships and gene-environment interactions is not a trivial task. (cdc.gov)
Gene Prospector is a Web-based application designed to help researchers prioritize and evaluate evidence for genes related to human disease or interactions with non-genetic risk factors. (cdc.gov)
Like Rb protein, many of the proteins encoded by tumor suppressor genes act at specific points in the cell cycle. (medscape.com)

Protein design methods use trial and error or more sophisticated methods like directed evolution or inverse folding to generate novel scaffolds or to find novel protein sequences folding into a defined scaffold, respectively. (hindawi.com)
Given the intimate relationship between a protein's structure and function, a way to design proteins with targeted properties is to start from a desired structure and find sequences able to fold into it, imposing additional constraints in the process [ 1 ]. (hindawi.com)
co-occurrence analysis of query motifs in given promoter sequences in support co-factor identification and the co-regulation mechanism (PMID:23846744) . (osumc.edu)
Computer programs can predict PPIs based on similar interactions found in other proteins by comparing protein sequences and three-dimensional structures. (jove.com)
We showed how this machine learning-ready data set can be used in focused and global analyses, such as the development of a new version of DeepCoil , a tool for the detection of coiled-coil domains in sequences. (edu.pl)

The long-term research goal of the lab is to apply computer modeling to gain insight into cellular signal transduction pathways, specifically to provide deeper insight into both the normal and aberrant subcellular targeting of domains contained in proteins which are part of macromolecular complexes and function in various biological processes. (cuny.edu)
The subcellular localization of EZH2 protein was predicted by using different predictors (CELLO, Euk-mPLoc, WoLF PSORT, and TargetP). (hindawi.com)

2016). In addition, Vihinen has introduced widely followed guidelines, recommendations and policies, he has founded a new sub-discipline of immunome, and introduced systematics to biological prediction methods and their assessment. (lu.se)

The 3',5'-cyclic adenosine monophosphate (cAMP) and protein kinase A (PKA) are known to play a role in disease progression as they mediate downstream signalling pathways that can promote cell growth and disease progression. (gla.ac.uk)
Hatzis P, Kyrmizi I, Talianidis I. (2006) Mitogen-activated protein kinase-mediated disruption of enhancer-promoter communication inhibits hepatocyte nuclear factor 4alpha expression. (forth.gr)
Recessively inherited deletions/duplications and point mutations in the parkin gene are the most common cause of early-onset parkinsonism known so far, but in an increasing number of studies, genetic variations in the serine/threonine kinase domain of the PINK1 gene are found to explain early-onset parkinsonism. (biomedcentral.com)
In the PINK1 gene we identified two novel putative pathogenic substitutions, P416R and S419P, located in a conserved motif of the serine/threonine kinase domain. (biomedcentral.com)
In general, a protein kinase acts on a discrete set of substrates to ensure that signalling fidelity is maintained. (biomedcentral.com)
How a particular protein kinase recognises its substrate protein(s) is therefore a key question. (biomedcentral.com)
Two major factors determine the formation of a protein kinase-substrate complex [ 4 ]. (biomedcentral.com)
The first, termed substrate recruitment, encompasses any process that increases the effective concentration of the protein kinase substrate. (biomedcentral.com)
The relative contribution of substrate recruitment and peptide specificity to protein kinase substrate specificity varies between protein kinases. (biomedcentral.com)
For instance, many enzymes, such as protein kinase A here, form a cleft that can recognize and bind polypeptide loops of their binding partners. (jove.com)

Previously undetected bacterial homologues were identified for# plant pathogenesis-related proteins, Pad1, von Willebrand factor type A, src homology 3 and YWTD repeat-containing domains. (embl.de)

We also used Mass-Spec Affinity purification to identify the host proteins interacting with SARS-CoV-2 Orf6 protein and tested a drug that could inhibit a specific Orf6 and host protein interaction. (biomedcentral.com)
For example, HIV-1 Vpr protein interacts with host proteins to modify host cell energy metabolism, oxidative status and proteasome function. (biomedcentral.com)
A pathogen protein interacts with many host proteins that in turn interacts with many other host proteins. (sblab-nsit.net)

DMINDA 2 is an updated version of our previous motif analysis webserver, DMINDA (regulatory DNA motif identification and analysis), which was published in Nucleic Acids Research in April, 2014 (PMID: 24753419) . (osumc.edu)
We believe that DMINDA 2 , as a new and comprehensive web server for cis-regulatory motif finding and analysis, will benefit the genomic research community in general and prokaryotic genome researchers in particular, in terms of elucidating the mechanism of transcriptional regulation at a system level. (osumc.edu)
Originally discovered as a chief regulatory protein of glucose and lipid metabolism and cell differentiation, the peroxisome proliferator-activated receptor gamma (PPARγ) is a ligand-activated transcription factor of the nuclear hormone receptor superfamily 8 . (nature.com)
Protein kinases and their substrates regulate essentially all cellular processes through complex regulatory networks, in which phosphorylated proteins act as switches that tune the response of the cell to environmental stimuli. (biomedcentral.com)
(C) Wire diagram (BioTapestry) showing the complex regulatory network between the four MADS proteins themselves. (frontiersin.org)
The differential regulation of aos and btd domains by dri occurs at a time when Dri is found in all somatic nuclei of the embryo, so that Dri must be acting to permit the proper function of other developmental regulatory factors. (sdbonline.org)
Several agents have been developed to target these key regulatory proteins that are essential for HIV replication. (biomedcentral.com)
Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. (embl.de)

Yun-Tzai Lee, Wei-Cheng Lo *, and Shih-Che Sue* (2017, Jan). Computational prediction of new intein split sites. (nctu.edu.tw)

2006) Senseless physically interacts with proneural proteins and functions as a transcriptional co-activator. (forth.gr)
Proteomics revealed Orf6 interacts with nucleopore proteins (RAE1, XPO1, RANBP2 and nucleoporins). (biomedcentral.com)

PPI spider: a tool for the interpretation of proteomics data in the context of protein-protein interaction networks. (leibniz-fli.de)

Systematic characterization of the protein interaction network and protein complexes in Saccharomyces cerevisiae using tandem affinity purification and mass spectrometry. (leibniz-fli.de)
We, therefore, follow the stepwise assembly of the SNARE complex and target individual SNAREs, binary sub-complexes, the ternary SNARE complex as well as interactions with Complexin-1. (nature.com)
In fact, a large number of proteins need to form protein complexes or oligomers to carry out their functions. (jove.com)
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. (jove.com)
The p16INK4A protein is a cell-cycle inhibitor that acts by inhibiting activated cyclin D:CDK4/6 complexes, which play a crucial role in the control of the cell cycle by phosphorylating Rb protein. (medscape.com)

GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects. (nctu.edu.tw)

Glittenberg M, Pitsouli C, Garvey C, Delidakis C, Bray S. (2006) Role of conserved intracellular motifs in Serrate signalling, cis-inhibition and endocytosis. (forth.gr)
Intracellular VWA domains and homologues in prokaryotes have recently been identified. (embl.de)
Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome. (embl.de)
Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. (embl.de)

Specific domains or motifs mimicked commonly by a large number of pathogens are likely to be responsible for microbial virulence suitable for drug/vaccine targeting. (sblab-nsit.net)
Plant pathogens secrete effector proteins that alter the structure of the host cell, interfere plant defenses, or modify the physiology of plant cells. (figshare.com)

Another type of interface, known as helix-helix, or coiled-coil interaction, forms when helices of two proteins wrap around each other. (jove.com)
We have recently taken part in a study that focused on the structure and function of coiled-coil domains of two KfrA proteins. (edu.pl)
Further molecular dynamics and modeling simulations have shown that these specific non-canonical regions are constantly present, suggesting that they are an inherent feature of KfrA coiled-coil domains. (edu.pl)
By applying SamCC Turbo to the whole Protein Data Bank served via localpdb , we built a comprehensive library of coiled-coil domains. (edu.pl)
29. Rämisch S, Lizatović R, André I. Automated de novo phasing and model building of coiled-coil proteins. (lu.se)

However, functions of individual SARS-CoV-2 viral proteins, particularly how they affect human cells, remain largely unknown. (biomedcentral.com)
The SARS-CoV-2 viral genome encodes 28 confirmed proteins. (biomedcentral.com)
Nonstructural protein 5 (Nsp5) is the main protease of SARS-CoV-2 that cleaves viral polyproteins into individual polypeptides necessary for viral replication. (elifesciences.org)
The most crucial NS proteins are the viral helicase and the viral RNA-dependent RNA polymerase (RdRp) ( 2 ). (spandidos-publications.com)
Entry of HIV-1 into human lymphoid requires activities of viral envelope glycoproteins gp120 and gp41, and two host-cell proteins, the primary receptor CD4 and a chemokine co-receptor. (biomedcentral.com)

Scarpati M, Heavner ME, Wiech E, Singh S. Proteomic Tools for the Analysis of Cytoskeleton Proteins.Methods Mol Biol. (cuny.edu)

The Ma lab has recently published one de-novo motif prediction algorithm (PMID: 27507169) based on the phylogenetic footprinting technology (Function I) , and one regulon identification method (PMID: 26975728) (Function II) based on our motif analysis tools and an orthologous gene mapping algorithm (PMID: 21965536) (Function III) . (osumc.edu)
26. Rämisch S, Lizatovic and Andre I. "Exploring alternate states and oligomerization preferences of coiled-coils by de novo structure modeling" Proteins, 2014. (lu.se)

The analysis of mutations now allows us to narrow the search for functionally important regions to the short N-terminal helix, two transmembrane domains of the protein, and the loop between them. (usda.gov)
Following these data, in collaboration with Dr. H. R. Guy (NIH), we built molecular models for the E. coli MscL in the closed, closed-expanded and open conformations and found that the channel can not be gated solely with gate that is placed within the transmembrane domain as was previously proposed (Spencer et al. (usda.gov)
Instead, we propose that the gating is accomplished by unresolved N-terminal domains (S1) connected to the transmembrane barrel via flexible linkers. (usda.gov)
18. Sanowar S, Singh P, Pfuetzner RA, Andre I, Zheng H, Spreter T, Strynadka NC, Baker D, Goodlett DR and Miller S. Interactions of the Transmembrane Polymeric Rings of the Salmonella enterica Serovar Typhimurium Type III Secretion System. (lu.se)
This new approach has been shown to preserve mobility and enzymatic activity of transmembrane proteins in the resulting nSLB. (lu.se)

Polycomb Group (PcG) proteins are a family of protein complex that regulate gene expression, especially repressing gene transcription [ 1 ]. (hindawi.com)
Alternative splicing of gene can generate multiple transcripts and proteins to regulate tissue and organ development [ 17 ]. (hindawi.com)

de Marcos-Lousa C, P Sideris D, Tokatlidis K. (2006) Translocation of mitochondrial inner-membrane proteins: conformation matters. (forth.gr)
Native membrane derived polymer-supported lipid bilayers (nSLBs) are poised to bridge the gap between live cell experiments and traditional model membrane architectures that by offering a combination of accessibility by surface sensitive analytical instrumentation and a composition which more closely resembles cellular membranes by displaying a diversity of endogenous membrane proteins, lipids, and carbohydrates. (lu.se)

RNA binding proteins (RBPs) play a vital role in post-transcriptional processes in all eukaryotes, such as splicing regulation, mRNA transport, and modulation of mRNA translation and decay. (biomedcentral.com)
Comparisons of the domain distributions in eukaryotes and prokaryotes enabled distinctions to be made between the domains originating prior to the last common ancestor of all known life forms and those apparently originating as consequences of horizontal gene transfer events. (embl.de)

Yun-Tzai Lee, Tz-Hsiang Su, Wei-Cheng Lo , Ping-Chiang Lyu* and Shih-Che Sue* (2012, Aug). Circular permutation prediction reveals a viable backbone disconnection for split proteins: an approach in identifying a new functional split intein. (nctu.edu.tw)
Sixteen families, 9 domains, and 53 other known functional types were found in 186 candidate effector proteins using the Pfam search. (figshare.com)
Identification, modeling, and characterization studies of Tetrahymena thermophila myosin FERM domains suggests a conserved core fold but functional differences.Cytoskeleton, 72: 585-596. (cuny.edu)
In other cases, different proteins or polypeptides come together to form a functional unit. (jove.com)
[ 1 ] His prediction was subsequently supported by the cloning of the retinoblastoma tumor suppressor gene ( RB1 ) and by functional studies of the retinoblastoma protein, Rb. (medscape.com)

In convergent evolution, nonhomologous proteins evolve in separate biological contexts to catalyze the same or similar reactions. (hindawi.com)
In the exam the participants demonstrate their ability to devise and discuss an appropriate computational approach for a solution for a biological problem in the area of function prediction. (tum.de)
Many biological processes depend on protein-protein interactions. (jove.com)
Current studies are devoted into analysis of variations and their effects, including prediction method development, and systems biological studies. (lu.se)

2023. Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity. . (ncbs.res.in)

The quantitative reverse transcription PCR (qRT-PCR) analysis of 14 candidate effector proteins secreted after P. triticina inoculation showed that the tested effectors displayed different expression patterns in different stages, suggesting that they may be involved in the wheat-P. triticina interaction. (figshare.com)
This interface is observed frequently in proteins that contain leucine zipper domains such as eukaryotic transcription factors. (jove.com)
MADS domain transcription factors are key regulators in yeast, animals, and plants. (frontiersin.org)
We demonstrate that a direct interaction between the methyl-CpG-dependent transcription repressor Kaiso and xTcf3, a transducer of the Wnt signalling pathway, results in their mutual disengagement from their respective DNA-binding sites. (biologists.com)
The CDK4-cyclinD complex normally phosphorylates the retinoblastoma protein (Rb protein), leading to release of the E2F transcription factor and cell cycle progression. (medscape.com)

The functions of these accessory proteins remain largely unresolved since they lack well-defined domain structures. (biomedcentral.com)
A Method for Assessing the Robustness of Protein Structures by Randomizing Packing Interactions. (ncbs.res.in)
We are particularly interested in understanding how protein folds have emerged and how protein structures and functions are encoded by the alphabet of 20 amino acids. (edu.pl)
Overall, performed studies allowed us to postulate the hypothesis that KfrA type proteins have moonlighting activity - they not only act as transcriptional auto-regulators but form cytoskeletal structures, which might facilitate plasmid DNA delivery and its position in the cells. (edu.pl)
Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. (embl.de)
20. Sgourakis NG, Lange OF, DiMaio F, André I, Fitzkee NC, Rossi P, Montelione GT, Bax A, Baker D. Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings. (lu.se)

We set out to identify the SARS-CoV-2 pathogenic proteins that through host interactions cause the cellular damages underlying COVID-19 symptomatology. (biomedcentral.com)
Our study revealed Orf6 as a highly pathogenic protein from the SARS-CoV-2 genome, identified its key host interacting proteins, and Selinexor as a drug candidate for directly targeting Orf6 host protein interaction that leads to cytotoxicity. (biomedcentral.com)
Studies of the human immune deficiency virus (HIV-1) over the past 30 years have demonstrated the presence of prime pathogenic proteins that contribute to virulence and host disease progression, and the potential of targeting these proteins for effective therapeutic intervention [ 9 ]. (biomedcentral.com)
Therefore, the identification of effector proteins is critical to reveal the pathogenic mechanism. (figshare.com)

The physical shape of the interfaces determines the way two proteins interact. (jove.com)
Co-immunoprecipitation of proteins and yeast two-hybrid screening are widely used to provide evidence on whether two proteins interact in vitro . (jove.com)
After CD4 binding, various gp120 domains interact with the enzyme PDI and the chemokine co-receptors forms a PDI-CD4-gp120-chemokine complex. (biomedcentral.com)
All of them employ a conserved region, termed the core motif, to interact with nucleotide-based cofactors (NAD, NADP, FAD, and SAM) that are essential for their functioning. (edu.pl)
Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. (embl.de)
This initial interaction (platelet adhesion) sets the stage for other adhesive reactions that allow the platelets to interact with other agonists in the vicinity of vessel injury, such as adenosine 5'-diphosphate (ADP), subendothelial collagen, and thrombin. (medscape.com)

PRP36 secondary structure has not been explicitly determined, but predictions based on the PRR36 mRNA give some possibilities. (wikipedia.org)
Additionally, circRNAs modulate pre-mRNA alternative splicing and possess protein-coding capacity. (ijbs.com)
Subsequently, we detected the expression of EZH2 on mRNA level and protein level in two different embryonic development stages (65-dpc and 90-dpc) via qRT-PCR and western blots. (hindawi.com)

Alpha-helixes, beta sheets, and other structure characteristics fail to be conserved across PRP36 orthologs with the exception of an alpha-helix alpha-helix beta-strand beta-strand motif that was highly conserved across mammals. (wikipedia.org)
The interaction of Kaiso with xTcf3 is highly conserved and is dependent on its zinc-finger domains (ZF1-3) and the corresponding HMG DNA-binding domain of TCF3/4 factors. (biologists.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)
A major difference was found between the distributions of enzyme families that are typically found in all three divisions of cellular life and non-enzymatic domain families that are usually eukaryote-specific. (embl.de)

Deciphering soluble and membrane protein function using yeast systems. (leibniz-fli.de)
Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. (embl.de)

Discovery and optimization of chromenotriazolopyrimidines as potent inhibitors of the mouse double minute 2-tumor protein 53 protein-protein interaction. (leibniz-fli.de)
Small molecule protein-protein interaction inhibitors as CNS therapeutic agents: current progress and future hurdles. (leibniz-fli.de)

NASCENT: An automatic protein interaction network generation tool for non-model organisms. (leibniz-fli.de)
It is present mostly in the endoplasmic reticulum and act as oxidase to forms disulfide bonds in nascent proteins and assists in protein folding [ 4 ]. (biomedcentral.com)

PRR36 Transcript Variant 2 theoretically encodes a protein 260 amino acids in length. (wikipedia.org)
This locus, however, also encodes a protein from an alternative reading frame, designated p19ARF. (medscape.com)

PRP36 (Proline Rich Protein 36) is an extracellular protein in Homo sapiens that is encoded by the PRR36 (Proline Rich Region 36) gene that contains a domain of unknown function, DUF4596, towards the C terminus of the protein. (wikipedia.org)
However, according to Phobius, PRP36 is predicted to be a non-cytoplasmic protein existing the extracellular space. (wikipedia.org)
VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). (embl.de)

PRR36 (FLJ22184) Transcript Variant 1, seen in the image below, is 4518 base pairs long and consists of six exons, of which the last five are utilized in protein coding. (wikipedia.org)

Classification of nonenzymatic homologues of protein kinases. (leibniz-fli.de)
We have previously described an approach to predicting the substrate specificity of serine-threonine protein kinases. (biomedcentral.com)
The new features significantly enhance the ability of Predikin to analyse protein kinases and their substrates. (biomedcentral.com)
Defects in these networks result in a variety of disease states making protein kinases important targets for drug design [ 3 ]. (biomedcentral.com)
The prediction of peptide specificity is therefore the basis for most of the available computational methods aimed at predicting substrates of protein kinases. (biomedcentral.com)
Vertebrate protein kinases LIMK-1 and LIMK-2. (embl.de)

One of the methods that have been proposed is a multiobjective optimization, in which protein stability and catalytic activity are simultaneously optimized [ 4 , 5 ]. (hindawi.com)
The first residue of the PWWP motif modulates HATH domain binding, stability, and protein-protein interaction. (nctu.edu.tw)
2006) Cdc42 regulates adherens junction stability and endothelial permeability by inducing alpha-catenin interaction with the vascular endothelial cadherin complex. (forth.gr)

in an operon with an upstream PurR/LacI-type transcriptional regulator gene, named amlR ( ACSP50_2475 ), and a gene downstream ( ACSP50_2473 ) encoding a GGDEF-EAL-domain-containing protein putatively involved in c-di-GMP signaling. (frontiersin.org)

Amino-acid composition after loop deletion drives domain swapping. (ncbs.res.in)
Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. (embl.de)

I was able to further validate these binding sites by designing cell permeable peptides designed to disrupt protein binding in vitro. (gla.ac.uk)

In PRP36 the amino acids isoleucine, tyrosine, and asparagine are present at a decreased proportion compared to a typical human protein. (wikipedia.org)
Some LIM domains bind protein partners via tyrosine-containing motifs. (embl.de)

Anti-THSD7A positive sera were further characterized by western blotting and slot blotting on THSD7A protein fragments and peptides. (manchester.ac.uk)

They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. (embl.de)

By applying deep-learning techniques we created a computational tool that enables the prediction and re-design of cofactor specificity in Rossmann fold enzymes. (edu.pl)
Adriana's BSc work entitled "Ancestral state reconstruction approach in investigating Rossmann fold evolution" focused on deciphering the evolution of regions responsible for the cofactor binding, whereas Kamil's MSc work entitled "Re-engineering cofactor specificity of the Rossmann fold proteins using graph neural networks" describes a new method for predicting the cofactor specificity in Rossmann enzymes. (edu.pl)

Predicting protein-protein interfaces as clusters of optimal docking area points. (leibniz-fli.de)
Continued development of an empirical function for predicting and rationalizing protein-protein binding affinities. (leibniz-fli.de)

The platelet GP IIb/IIIa complex mediates platelet-to-platelet interactions (platelet aggregation). (medscape.com)

The optimization was guided by directed evolution based on hydrophobicity scores, molecular weight, and secondary structure predictions. (hindawi.com)
However, molecular weight is also important due to potential steric incompatibilities within protein cores. (hindawi.com)
ImitateDB is a comprehensive database for information about molecular mimicry candidates represented as DMPs and MMPs for each experimentally validated unique host pathogen protein-protein interaction. (sblab-nsit.net)
The methodology will include site-directed mutagenesis, covalent protein modifications, patch- clamp measurements, thermodynamic and kinetic analysis of dose-response curves and rates of transitions, videomicroscopy, and molecular modeling. (usda.gov)
Molecular modeling and computational analyses suggests that the Sinorhizobium meliloti periplasmic regulator protein ExoR adopts a superhelical fold and is controlled by a unique mechanism of proteolysis. (cuny.edu)

An effective computational method incorporating multiple secondary structure predictions in topology determination for cryo-EM images. (odu.edu)

Comparative analysis and unification of domain-domain interaction networks. (leibniz-fli.de)
Arguelles J, Lee J, Cardenas LV, Govind S, Singh S. In Silico Analysis of a Drosophila Parasitoid Venom Peptide Reveals Prevalence of the Cation-Polar-Cation Clip Motif in Knottin Proteins. (cuny.edu)

This motif begins slightly before and carries into the DUF4596 region, suggesting a high importance for this domain in PRP36 function. (wikipedia.org)
PRP36 has medium scores for predicted interaction with two other proteins of unknown function, OVCH1 and FAM179A. (wikipedia.org)
What is protein function? (tum.de)
Overview over prediction of protein function. (tum.de)
As opposed to the first part (Protein Prediction I), protein structure has only played a minor role: it has been introduced if it has been helpful to further our understanding of function. (tum.de)
Lectures, Seminars, Exercises, Problems for individual and team study: The students apply the theory presented in the lecture by writing a protein function prediction method in the exercise starting from data in varying form (depending on the problem at hand). (tum.de)
Using the folding landscapes of proteins to understand protein function. (ncbs.res.in)
While many studies have been focused on the membrane structure, the dynamics of such systems are crucial for the function of the membrane including membrane bound proteins. (lu.se)

Proline rich proteins are often observed to be intrinsically unstructured and have been connected with protein-protein interactions in signaling pathways. (wikipedia.org)
Intrinsically disordered regions (IDRs) lacking a fixed three-dimensional protein structure are widespread and play a central role in cell regulation. (iucr.org)

Purification and mutagenesis studies of TANC1 ankyrin repeats domain provide clues to understand mis-sense variants from diseases. (nih.gov)
Laboratory methods, such as affinity purification, mass spectrometry, and protein microarrays, can be used to identify new interactions. (jove.com)

The evolutionary origin of slipknot topology in proteins remains a mystery. (edu.pl)

Genetic association studies, such as recent genome-wide association studies (GWAS), have provided a springboard for exploring the contribution of inherited genetic variation and gene/environment interactions in relation to disease. (cdc.gov)

Anatomy14

Organisms13

Chemicals and Drugs80

Analytical, Diagnostic and Therapeutic Techniques and Equipment42

Phenomena and Processes91

Disciplines and Occupations5

Anthropology, Education, Sociology and Social Phenomena1

Information Science20

Health Care8

Structural12

Structure prediction7

Sequence15

Residues13

Individual SARS-CoV-2 proteins2

Bioinformatics6

Genes14

Sequences5

Subcellular2

20161

Kinase10

Homology1

Host proteins3

Regulatory8

20171

Interacts2

Proteomics1

Complexes5

Annotation1

Intracellular4

Pathogens2

Coiled-coil5

Viral5

Methods Mol1

Novo2

Transmembrane5

Regulate2

Membrane proteins2

Eukaryotes2

Functional5

Biological4

20231

Transcription5

Structures6

Pathogenic4

Interact6

MRNA3

Highly conserved2

Cellular2

Yeast2

Inhibitors2

NASCENT2

Encodes a protein2

Extracellular3

Pairs1

Kinases6

Stability3

Transcriptional1

Amino acid2

Vitro1

Tyrosine2

Peptides1

Scaffolds1

Specificity2

Predicting2

Mediates1

Molecular5

Secondary structure1

Analysis2

Function8

Intrinsically2

Purification2

Topology1

Genome1