Structural motif protein structure secondary. Medical search. Frequent questions

it can be represented by different and completely unrelated sequences in different proteins or RNA. (wikipedia.org)
G-quadruplex G-quadruplex secondary structures (G4) are formed in nucleic acids by sequences that are rich in guanine. (wikipedia.org)
Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical shape (e.g. the "B-form" DNA double helix). (wikipedia.org)
Within a sequence or database of sequences, researchers search and find motifs using computer-based techniques of sequence analysis, such as BLAST. (wikipedia.org)
They develop methods that can learn conserved structures, functions, features, and motifs from known protein and DNA sequences and use them to predict the function and structures of novel genes and proteins from the genomic efforts. (nationalacademies.org)
Their research approach uses a variety of different representations of sequences and structures. (nationalacademies.org)
Multiple representations of sequences include simple motif consensus sequence patterns, parametric representations, probabilistic techniques, graph theoretic approaches, and computer simulations. (nationalacademies.org)
However, the accuracy of the native structure derivation of ncRNAs is still not satisfactory, especially on sequences containing pseudoknots. (biomedcentral.com)
Extensive analysis of RNA properties based on SVM allows us to identify important properties of sequences and structures related to their shapes. (biomedcentral.com)
Many types of ncRNAs perform their functions through both their sequences and secondary structures, which are defined by the interacting base pairs. (biomedcentral.com)
By now you get the idea that cells generate proteins, which are sequences of amino acids. (ainews.one)
On one hand, codon redundancy (i.e. that 61 codons specify 20 amino acids [ 21 ]) potentially allows a wide variety of mRNA sequences carrying different codons to specify the same protein product. (biomedcentral.com)
alignment - A comparison of two or more gene or protein sequences in order to determine their degree of similarity in amino acid or bases, respectively. (rcsb.org)
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)
First, the sequences carrying point mutations are modeled on a given template structure, and subsequently, molecular dynamics simulations are carried out for 10 ns. (hindawi.com)
In this chapter, we report on high-resolution structures of single and multi RRM-RNA complexes to explain the numerous strategies used by these domains to interact specifically with a large repertoire of RNA sequences. (nih.gov)
Importantly, these structures also reveal with very high accuracy the RNA motifs bound specifically by RRM-containing proteins, which correspond very often to consensus sequences identified with genome-wide approaches. (nih.gov)
AMINO ACID MOTIFS are often composed of conserved sequences. (lookformedical.com)
Many SAND domain-containing proteins, including NUDR, DEAF-1 (Deformed epidermal autoregulatory factor-1) and GMEB, have been shown to bind DNA sequences specifically. (embl-heidelberg.de)
A straight richer way to obtain recognition motifs are available at the supplementary structure level, especially considering that details content in protein/peptides is normally evolutionary even more conserved through threedimensional buildings instead of through linear amino acidity sequences [55]. (biotechpatents.org)
This machinery recognizes pre-mRNA sequences at several motifs - the 5′ and 3′ splice sites, the branch point, and polypyrimidine tracts - positioned at exon-intron boundaries [ 4 ]. (biomedcentral.com)
The seven conserved helicase motifs, the point mutations of BLM protein as well as the insertion and deletions are displayed above the sequences, the ATP-binding (Ã Â ) and DNA-binding residues (Ã Â¤) of PcrA helicase are shown (24-26). (lu.se)
The structure elucidation was facilitated by utilizing long-range heteronuclear single quantum multiple bond correlation (LR-HSQMBC) and heteronuclear multiple bond correlation (HMBC) nuclear magnetic resonance (NMR) pulse sequences optimized to detect four- and five-bond 1 H- 13 C heteronuclear correlations. (cancer.gov)

Furthermore, we argue that such patterns can capture both local and global structural topology in a 3D protein conformation, thereby facilitating effective structural comparison amongst conformations. (biomedcentral.com)
It is of fundamental importance in determining PROTEIN CONFORMATION. (lookformedical.com)
Identification of convert motifs generally just involves interactions from the spatially-orientated aspect chain residues from the ligand using the receptor plus they can as a result be looked at as scaffolds, that could theoretically end up being substituted by choice rigid (+)-Camphor non-peptidic scaffolds that keep up with the useful aspect chains in the proper conformation. (biotechpatents.org)
We model structural rearrangements that lead to an open pre-snRNA conformation compatible with Sm protein interaction. (bvsalud.org)
PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). (bvsalud.org)

The mechanism of DNA recognition by this motif has beensuggested based on conserved residues, surface electrostatic potentialsand chemical shift changes. (embl.de)
The UV-C photoinduced cleavage of disulfide bonds in β-Lactoglobulin, as promoted by excitation of tryptophan residues (Trp), is shown to induce changes in the protein's secondary structure, significantly reducing the protein's resistance to pepsin digestion. (ku.dk)
VH is derived from a single protein domain of 35 residues [ 9 ]. (hindawi.com)
The protein-DNA interaction is stabilized by nonspecific contacts between the DNA backbone and residues in α 2 and the turn between α 2 and α 3. (vigyansarovar.com)
The motif comprises two α helices, E and F that flank a loop of 12 contiguous residues. (vigyansarovar.com)
Multiple hydrophobic residues pack between these regions to form a structural core. (embl-heidelberg.de)
This view is supported by mutagenesis studies indicating a critical role for particular residues in the turns of some proteins. (cloudfront.net)
In the trivalent Phactr1 complex, each G-actin⋅RPEL unit makes secondary contacts with its downstream actin involving distinct RPEL residues. (rcsb.org)
Furthermore, actin-mediated inhibition of Phactr1 nuclear import requires secondary contact residues in the Phactr1 N-terminal RPEL-N motif, suggesting that it involves interaction of RPEL-N with the C-terminal assembly. (rcsb.org)
We extended the boundary by 5 residues which lead to expression of highly stable RBMS1 protein. (neelsb.com)
Structure-guided mutagenesis reveals key RNA contact residues that are critical for RocC/RocR to repress the uptake of environmental DNA in L. pneumophila . (nature.com)

Rotational spectroscopy provides the highest resolution structures of amino acids and peptides - the building blocks of life. (kent.edu)
When compared to the native protein, the peptide mass fingerprint profile of digested UV-C-treated β-Lg shows a higher content and variety of peptides, including the production of some exclusive bioactive peptides such as PMHIRL and EKFDKALKALPMH. (ku.dk)
There are 20 different alpha amino acids commonly found in nature that can covalently link with each other to form short peptides or longer proteins. (rcsb.org)
Chances are that a assortment of brand-new ligands will emerge because high-throughput assays have already been developed to display screen for peptides that bind selectively to different conformations of G proteins subunits [50] or focus on the user interface with a particular subset of RGS protein [51]. (biotechpatents.org)
Desk 2 G Protein-Coupled Receptors for Protein and Peptides molecular modeling. (biotechpatents.org)
Compounds of interest include not only classical "drug-like" organic small molecules, but also peptides, proteins, and other bioactive chemical classes. (cancer.gov)

The size of the complex, its oligomeric state and the structures of its periplasmic N-terminal domains vary considerably between organisms. (elifesciences.org)
The N-terminal domains of secretins consist of copies of stacked rings which form a periplasmic channel that connects to IM-associated proteins, forming a multi-component secretion system. (elifesciences.org)
There are 12193 ARID domains in 12162 proteins in SMART's nrdb database. (embl.de)
A novel class of DNA-binding domains has been established from at leastsixteen recently identified DNA-binding proteins. (embl.de)
We show that dri encodes a nuclear protein that contains asequence-specific DNA-binding domain that bears no similarity to knownDNA-binding domains. (embl.de)
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. (lookformedical.com)
Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure. (lookformedical.com)
There are 2977 SAND domains in 2833 proteins in SMART's nrdb database. (embl-heidelberg.de)
There are 585506 PbH1 domains in 92548 proteins in SMART's nrdb database. (embl.de)
The FF domain: a novel motif that often accompanies WW domains. (embl.de)
Turns are sometimes found within flexible linkers or loops connecting protein domains . (cloudfront.net)
Flexible linkers allow connecting domains to freely twist and rotate to recruit their binding partners via protein domain dynamics . (cloudfront.net)
Motifs are typically the most conserved regions of PROTEIN DOMAINS and are critical for domain function. (edu.au)
The Phactr family of PP1-binding proteins and the myocardin-related transcription factor family of transcriptional coactivators contain regulatory domains comprising three copies of the RPEL motif, a G-actin binding element. (rcsb.org)
Both histone/histone and histone/DNA interactions depend on the histone fold domains and additional, well ordered structure elements extending from this motif. (nature.com)
Structural analysis and RNA binding studies reveal that other ProQ/FinO domains also recognize related transcriptional terminators with different specificities for the length of the 3' ssRNA tail. (nature.com)
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. (bvsalud.org)

Note that, while the spatial sequence of elements may be identical in all instances of a motif, they may be encoded in any order within the underlying gene. (wikipedia.org)
Helix-turn-helix Two α helices joined by a short strand of amino acids and found in many proteins that regulate gene expression. (wikipedia.org)
Outside of gene exons, there exist regulatory sequence motifs and motifs within the "junk", such as satellite DNA. (wikipedia.org)
This study demonstrates the role of codon usage bias and mRNA secondary structure in TE of T. vaginalis mRNAs, contributing to a better understanding of the factors that influence, and possibly regulate, gene expression in this human pathogen. (biomedcentral.com)
Characterization of the dead ringer gene identifies a novel, highlyconserved family of sequence-specific DNA-binding proteins. (embl.de)
Leucine zipper motifs are usually found as part of a DNA-binding domain in many transcription factors , and are therefore these motifs are involved in regulating gene expression . (vigyansarovar.com)
FHM type 4 is attributed to mutations in the PRRT2 gene, which encodes a proline-rich transmembrane protein of as yet unknown function. (frontiersin.org)
Recently, we described the characterisation of a parasite gene (TashAT2), whose polypeptide product bears AT hook DNA-binding motifs and may be transported from the parasite to the host nucleus. (lookformedical.com)
NEW YORK (GenomeWeb) - Duke University researchers reported today in a new study that they were able to increase the specificity of CRISPR-based gene editing by several orders of magnitude by engineering a hairpin secondary structure onto the spacer region of single guide RNAs (hp-sgRNAs) and combining them with various CRISPR effectors. (genomeweb.com)
The researchers also showed that hp-sgRNAs increased the specificity of gene editing using five different Cas9 or Cas12a variants, demonstrating that RNA secondary structures can tune the activity of diverse CRISPR systems. (genomeweb.com)
The researchers also found that hp-sgRNAs increased the specificity of gene editing with SaCas9 and AsCas12a proteins as well. (genomeweb.com)
First, histones collaborate with transcription factors to provide for their own removal or structural modification, resulting in gene derepression. (nature.com)
Recognition of c-myc gene promoter by human RBMS1 protein. (neelsb.com)
In this background we have worked on human RBMS1 protein that has been shown to directly regulate the c-myc gene expression levels in cancerous cells. (neelsb.com)
The ProQ/FinO family of RNA binding proteins mediate sRNA-directed gene regulation throughout gram-negative bacteria. (nature.com)
Protein name, gene name, organism and status are also stated. (projectguru.in)
Phylogenetic and amino acid comparison of highly and less neuroinvasive lineage 2 strains demonstrated that the nonstructural genes, especially the nonstructural protein 5 gene, were most variable. (cdc.gov)

An individual motif usually consists of only a few elements, e.g., the 'helix-turn-helix' motif which has just three. (wikipedia.org)
Hydrogen bonds between the carbonyl oxygen and the amido hydrogen four a.a. upstream, toward the C-Terminus of the helix, stabilize the helical structure. (flashcardmachine.com)
Large polypeptides that form a-helix or ß-sheet structures are currently beyond the reach of rotational spectroscopists, but the recent ion-drift experiments [13-15] on acetyl-(alanine)7-lysine suggest that the first direct observations of the structural motifs found in protein and peptide secondary structure using high resolution spectroscopy may not be far off. (kent.edu)
It is recently shown that using the abstract shapes, which retain adjacency and nesting of structural features but disregard the length details of helix and loop regions, can improve the performance of structure prediction. (biomedcentral.com)
One recent attempt is to first predict the abstract shapes (or shapes for short), which retain adjacency and nesting of structural features but disregard the length details of helix and loop regions [ 9 ]. (biomedcentral.com)
The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. (embl.de)
The UV-C light-induced changes in the protein secondary structure are marked by an increase in the contribution of β-sheet and α-helix structures with a concomitantly smaller contribution of the β-turn structural motif. (ku.dk)
3-10 helix - A type of protein secondary structural element that is more tightly coiled than the alpha helix (3 amino acids per turn with 10 atoms in the ring completed by each intra-helical hydrogen bond). (rcsb.org)
alpha helix - A secondary structural motif of a protein. (rcsb.org)
These helix-turn-helix structure found in many proteins(transcription factors). (vigyansarovar.com)
Its major function is in DNA recognition, as α 3 helix is involved in the recognition and is known as " recognization helix " while another one stabilizes the interaction between DNA and Protein. (vigyansarovar.com)
Helix-turn-helix motif are involved in many processes that includes DNA repair, RNA metabolism, and protein-protein interaction . (vigyansarovar.com)
Large number of prokaryotic repressors belong to the helix-turn-helix family of proteins. (vigyansarovar.com)
Helix loop helix are eukaryotic homolog of the HTH motif and are characterized by two ampipathic α -helices (60-90 amino acids) connected by a loop (10-25 amino acids). (vigyansarovar.com)
Types of helices in proteins (v. O. N. U.): 3 10 -helix, α-helix, π-helix. (zxc.wiki)
The tertiary structures of pectate lyases and rhamnogalacturonase A show a stack of parallel beta strands that are coiled into a large helix. (embl.de)
Each coil of the helix represents a structural repeat that, in some homologues, can be recognised from sequence information alone. (embl.de)
Structure and evolution of parallel beta-helix proteins. (embl.de)
Three bacterial pectate lyases, a pectin lyase from Aspergillus niger, thestructures of rhamnogalacturonase A from Aspergillus aculeatus, RGase A,and the P22-phage tailspike protein, TSP, display the right-handedparallel beta-helix architecture first seen in pectate lyase. (embl.de)
This is the first structure of a polygalacturonase andcomprises a 10 turn right-handed parallel beta-helix domain with two loopregions forming a "tunnel like" substrate-binding cleft. (embl.de)
The structure reveals specific recognition of the 3' nucleotide of the terminator by a conserved pocket involving a β-turn-α-helix motif, while the hairpin portion of the terminator is recognized by a conserved α-helical N-cap motif. (nature.com)

Cruciform DNA Cruciform DNA is a form of non-B DNA that requires at least a 6 nucleotide sequence of inverted repeats to form a structure consisting of a stem, branch point and loop in the shape of a cruciform, stabilized by negative DNA supercoiling. (wikipedia.org)
In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. (wikipedia.org)
Chen, R & Lee, JC 2003, ' Functional roles of loops 3 and 4 in the cyclic nucleotide binding domain of cyclic AMP receptor protein from Escherichia coli ', Journal of Biological Chemistry , vol. 278, no. 15, pp. 13235-13243. (utmb.edu)
Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO. (lookformedical.com)
They took into account all the variables they could use to create different structures with similar stability profiles, including placement of the stem along any area of the 20-nucleotide spacer, stem lengths, and tetraloop utilization. (genomeweb.com)

The function consequences of mutation in loop 3 of CRP are similar to that of site A and site B in the regulatory subunits of cyclic AMP-dependent protein kinases. (utmb.edu)

Sequence motif Short linear motif Protein tandem repeats Johansson, M.U. (23 July 2012). (wikipedia.org)
A conserved KDWK sequence motif is found within the alpha-helical, positively charged surface patch. (embl-heidelberg.de)

Accurate secondary structure prediction provides important information to undefirstafinding the tertiary structures and thus the functions of ncRNAs. (biomedcentral.com)
As knowing the secondary structure provides important information to undefirstafinding the tertiary structures and thus the functions of ncRNAs, deriving the secondary structures of ncRNAs remains an important research topic in RNA informatics. (biomedcentral.com)
Supersecondary structures can also be considered as an intermediate between secondary and tertiary structures. (vigyansarovar.com)

In addition to secondary structural elements, protein structural motifs often include loops of variable length and unspecified structure. (wikipedia.org)
The protein structural motif that binds cAMP is highly conserved with the exception of loops 3 and 4, whose structure and length are variable. (utmb.edu)
The cAMP receptor protein of Escherichia coli, CRP, was employed as a model system to elucidate the functional roles of these loops. (utmb.edu)
With the exception of the beta loops and random coils , these areas are characterized by the fact that the only two possible angles of rotation ψ and φ of the peptide backbone are fixed in them and repeat themselves periodically over the length of the secondary structural element. (zxc.wiki)
The RNA hairpin is a fundamental structural unit in many RNA molecules and is composed of stems and loops. (genomeweb.com)
Many disordered proteins reveal areas without any common secondary structure These regions could be termed as flexible, in comparability with structured loops. (aromaroa.com)

The tertiary structure and the quaternary structure represent superordinate structural levels. (zxc.wiki)

The RNA chain is decoded and translated by ribosomes to produce a polypeptide sequence, otherwise known as a protein. (ainews.one)
Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. (lookformedical.com)
A turn is an element of secondary structure in proteins where the polypeptide chain reverses its overall direction. (cloudfront.net)

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)
Protein-coding genes in T. vaginalis are largely controlled by two core promoter elements, producing mRNAs with short 5′ UTRs. (biomedcentral.com)
Characterisation of a cluster of genes encoding Theileria annulata AT hook DNA-binding proteins and evidence for localisation to the host cell nucleus. (lookformedical.com)
Mutations leading to loss of envelope (E) protein glycosylation together with mutations in the nonstructural (NS) protein genes may be associated with attenuation of these viruses ( 6 ). (cdc.gov)

In this work, we use SVM-based feature selection to derive the consensus abstract shape of homologous ncRNAs and apply the predicted shape to structure prediction including pseudoknots. (biomedcentral.com)
The idea of abstract shapes has long been used to characterize different types of structures. (biomedcentral.com)
abstract = "Cyclic AMP is a ubiquitous secondary message that regulates a large variety of functions. (utmb.edu)

A homology model of the PilQ protein was fitted into the cryo-EM map. (elifesciences.org)
A novel DNA-binding motif shares structural homology to DNA replicationand repair nucleases and polymerases. (embl.de)
This new DNA-binding motif shares structuralhomology with T4 RNase H, E. coli endonuclease III and Bacillus subtilisDNA polymerase I. The structural homology suggests a mechanism forsubstrate recognition by these enzymes. (embl.de)
However, analogous proteins may have structural homology although this is not a prerequisite. (hindawi.com)

In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a common three-dimensional structure that appears in a variety of different, evolutionarily unrelated molecules. (wikipedia.org)

They are also interested in predicting the interactions between ligands and proteins and between two interacting macromolecules and are actively studying the mechanisms of ligand-protein and protein-protein docking. (nationalacademies.org)

One example is the conserved bacterial ribosome silencing factor (RsfS) that binds to uL14 protein onto the large ribosomal subunit and prevents its association with the small subunit. (nih.gov)
Early studies showed that FinO specifically binds the 3' transcriptional terminator structure of FinP in a manner that critically relies on both the GC-rich hairpin and 3' polypyrimidine tail that define the terminator 16 , and further work showed that the base of the hairpin and 3' tail are both strongly protected from ribonuclease degradation by FinO 17 . (nature.com)

long range interactions within the protein molecule. (flashcardmachine.com)
Allostery - This is a type of effect seen in proteins where the binding of a molecule, ion etc. to one location can have an impact of the structure and interactions at another location. (rcsb.org)
Hydrophobicity was one of the most important physicochemical properties, due to the fact that it is involved in protein interactions, for example, by forming hydrophobic cores. (hindawi.com)
In one view, turns play a critical role in folding by bringing together and enabling or allowing interactions between regular secondary structure elements. (cloudfront.net)
Nonpolar and ionic interactions in histone-like nucleoid-structuring (H-NS) site1 and site2 dimers. (elifesciences.org)
Understanding specificity of protein-DNA interactions is a long-standing question that has been attempted to understand many times by scientists all over the world. (neelsb.com)
The work has implications for understanding general mechanism of protein-DNA interactions that involves sliding, hopping and diffusion during stochastic target search process in a dense nucleus. (neelsb.com)
The eponymous FinO protein was discovered as a regulator of F plasmid conjugation nearly 50 years ago, and acts to bind a single partner sRNA called FinP to stabilize FinP and facilitate its interactions with its antisense partner, the mRNA encoding the major F plasmid transcription factor, TraJ 5 . (nature.com)

Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure ( PUBMED:10838570 ). (embl.de)
The SAND domain (named after Sp100, AIRE-1, NucP41/75, DEAF-1) is a conserved ~80 residue region found in a number of nuclear proteins, many of which function in chromatin-dependent transcriptional control. (embl-heidelberg.de)
Here, we investigate the structural basis for RNA recognition by ProQ/FinO proteins, through the crystal structure of the ProQ/FinO domain of the Legionella pneumophila DNA uptake regulator, RocC, bound to the transcriptional terminator of its primary partner, the sRNA RocR. (nature.com)

Proteins containing these repeats most often are enzymes with polysaccharide substrates. (embl.de)

D-loop A displacement loop or D-loop is a DNA structure where the two strands of a double-stranded DNA molecule are separated for a stretch and held apart by a third strand of DNA. (wikipedia.org)
ROA spectroscopy is able to probe the chiral peptide backbone of proteins, and as such the ROA spectrum of a protein contains a wealth of structural information from within the whole molecule, across the whole vibrational spectrum. (gla.ac.uk)
As well as containing detailed information from specific structural elements such as sections of secondary structure and motifs, the ability of ROA to see the molecule as a whole also enables the global fold of the protein to be deduced from the ROA spectrum. (gla.ac.uk)
allosteric protein - A protein that changes among two or more structural conformations upon binding to a small molecule called an effector. (rcsb.org)
During or after the translation of an RNA molecule, the secondary structure and the higher structural levels of the protein are formed. (zxc.wiki)

1-7] Molecular moments of inertia, derived from spectra fitting, are used to determine conformational structures, and atomic coordinates can be determined to within a picometer or less. (kent.edu)
The group uses statistical methods and machine learning to discover first principles of molecular and structural biology from known examples. (nationalacademies.org)
In addition, these studies provide useful information about expression abundance at the mRNA and protein levels, allowing further investigations into the molecular mechanisms of translational control in this evolutionarily divergent protist. (biomedcentral.com)
The protein folding problem is therefore one of the most fundamental yet unsolved problems in computational molecular biology. (biomedcentral.com)
state that performing a Molecular Dynamics (MD) simulation on a mini-protein for just 10 μ s would require decades of computation time on a typical CPU [ 1 ]. (biomedcentral.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)
DNA in chromatin is organized in arrays of nucleosomes 1 .Two copies of each histone protein, H2A, H2B, H3 and H4, are assembled into an octamer that has 145?147 base pairs (bp) of DNA wrapped around it to form a nucleosome core (of relative molecular mass 206K). (nature.com)
Loss of METTL16 and SNRNP27K orthologs, or a single SNRNP27K methionine residue, was associated with a preference for +4 U. These findings are consistent with splicing analyses of mutants defective in either METTL16 or SNRNP27K orthologs and models derived from spliceosome structures, demonstrating that inter-species association mapping is a powerful orthogonal approach to molecular studies. (bvsalud.org)
B ) Table showing observed molecular weight and calculated molecular weight for monomeric protein of H-NS 1-57. (elifesciences.org)

Depending upon the sequence and other conditions, nucleic acids can form a variety of structural motifs which is thought to have biological significance. (wikipedia.org)
The ease with which the ROA spectra of biological molecules can be successfully measured lends itself perfectly to the ever-growing demand for biomolecular structural information, especially in the context of proteomics and the Human Genome Project. (gla.ac.uk)
In convergent evolution, nonhomologous proteins evolve in separate biological contexts to catalyze the same or similar reactions. (hindawi.com)
It is characteristic of every protein and is essential for biological function. (zxc.wiki)
This FOA encourages applications to establish partnerships between researchers interested in a biological problem of significant scope and researchers providing high-throughput structure determination capabilities through the NIGMS PSI:Biology network. (nih.gov)
Applicants to this FOA should propose work to solve a substantial biological problem for which the determination of many protein structures is necessary. (nih.gov)
It is expected that these awards will lead to new collaborations between researchers emphasizing biological function and researchers emphasizing biological structure. (nih.gov)
The teachers will become familiar with the structure of biological polymers and the relationship between structure and function. (weizmann.ac.il)
It was on that occasion that in a conversation with David Moss, Professor of Biomolecular Structures, and his co-worker Dr. Clare Sansom, the idea was conceived to organize the postgraduate course in bioinformatics, this newly emerging interdisciplinary research area as the interface between biological and computational sciences, primarily aimed at research students from Central and Eastern Europe. (iospress.nl)
More recently, the application of RNA-seq technologies has enabled the elucidation of the biological partners and targets of several ProQ/FinO family proteins. (nature.com)
Our results are the first to tubes (SWCNT) suggest the potential to interact report disruption of the mitotic spindle by with critical biological structures. (cdc.gov)

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)

Secondary actin contacts by actin-bound RPEL motifs thus govern formation of multivalent actin⋅RPEL assemblies. (rcsb.org)
Flexibility in structured proteins is bound to an equilibrium state, whereas it isn't so in IDPs. (aromaroa.com)
The surface view of the crystal structure of RBMS1 protein is shown bound with the bases of nucleotides of c-myc promoter. (neelsb.com)
We determined the 2.57 Å crystal structure of RBMS1 in its promoter DNA bound state that provided atomic-resolution insight into specific binding of individual nucleotides of DNA with the protein. (neelsb.com)
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)

This results in a vast number of conformational possibilities for each protein. (zxc.wiki)
Also, nonnative isomers of X− Pro peptide bonds in turns can completely block the conformational folding of some proteins. (cloudfront.net)
One critical step involves recruitment of the pre-assembled U4/U6.U5 tri-snRNP to Complex A, which engages 5′ and 3′ splice sites, to form the pre-catalytic Complex B. Complex B then undergoes profound structural and conformational changes that lead to catalytic activation and conversion to Complex B act , which initiates catalysis and nucleates the formation of Complex C, which completes the splicing reaction [ 3 , 4 ]. (biomedcentral.com)

The backbone atoms of the peptide in this region forms a right handed helical structure, hence the name. (rcsb.org)
In proteins, the secondary structure is determined by hydrogen bonds between the CO and NH groups of the peptide backbone. (zxc.wiki)
A hairpin is a special case of a turn, in which the direction of the protein backbone reverses and the flanking secondary structure elements interact. (cloudfront.net)
This rigidity with the protein backbone limits the folding potential and patterns of the ensuing protein. (aromaroa.com)

Important in DNA binding proteins. (wikipedia.org)
For example, many DNA binding proteins that have affinity for specific DNA binding sites bind DNA in only its double-helical form. (wikipedia.org)
This process is favored by the reversible binding of small stress-induced proteins to the ribosome to prevent unnecessary translation. (nih.gov)
Here we describe the binding mode of Staphylococcus aureus RsfS to the large ribosomal subunit and present a 3.2 Å resolution cryo-EM reconstruction of the 50S-RsfS complex together with the crystal structure of uL14-RsfS complex solved at 2.3 Å resolution. (nih.gov)
Members of the recently discovered ARID (AT-rich interaction domain) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. (embl.de)
Other proteins containing the conserved motifinclude yeast SWI1, two human retinoblastoma binding proteins, and othermammalian regulatory proteins. (embl.de)
Gelretardation and optimal binding site screens revealed that the in vitrosequence specificity of DRI is strikingly similar to that of manyhomeodomain proteins, although the sequence and predicted secondarystructure do not resemble a homeodomain. (embl.de)
Understanding such structures enables us to explore the function of a protein, explain substrate and ligand binding, perform realistic drug design and potentially cure diseases caused by protein misfolding. (biomedcentral.com)
This binding occurs at a site different from the proteins active site and enhances or reduces the protein's reactivity towards its normal ligand. (rcsb.org)
We have successfully combined two unrelated naturally occurring binding sites, the immunoglobin Fc-binding site of the Z domain and the DNA-binding motif of MyoD bHLH, into a novel stable protein. (hindawi.com)
Furthermore, we describe the consequences on RNA binding of the different structural arrangements found in tandem RRMs and higher order RNPs. (nih.gov)
DNA binding), and others can be the part of larger structural assemblies. (vigyansarovar.com)
Unlike HTH proteins, the actual DNA-binding motif of the HLH proteins is a stretch of about 13 "basic" amino acids adjacent to the HLH whose main role is in protein dimerization. (vigyansarovar.com)
Therefore, entire motif comprising the DNA-binding basic region and the HLH is termed bHLH . (vigyansarovar.com)
DNA-binding motifs, first described in one of the HMGA PROTEINS: HMG-I(Y) PROTEIN. (lookformedical.com)
Specific protein-binding measures are often used as assays in diagnostic assessments. (lookformedical.com)
These include proteins linked to various human diseases, such as the Sp100 (Speckled protein 100kDa), NUDR (Nuclear DEAF-1 related), GMEB (Glucocorticoid Modulatory Element Binding) proteins and AIRE-1 (Autoimmune regulator 1) proteins. (embl-heidelberg.de)
Lots of the known endogenous ligands have already been examined and common structural binding motifs have already been discovered [18 thoroughly, 52, 53]. (biotechpatents.org)
The team then tested the effect of predicted hp-sgRNAs structures on Cas9 binding to DNA. (genomeweb.com)
Because of significant biochemical and structural variations between valine and phenylalanine, a G to T mutation may alter the local structural architecture, facilitate secondary structure stabilization, or introduce preferential binding motifs. (news-medical.net)
Here, we provide evidence that these pre-snRNA substrates contain compact, evolutionarily conserved secondary structures that overlap with the Sm binding site. (bvsalud.org)
The figure shows RBMS1 protein scanning the DNA in search of its target sequence and binding to the sequence's nucleotides in a specific manner. (neelsb.com)
Decoding involves reading the correct code at a right time by DNA binding proteins. (neelsb.com)
The X-ray structure of RBMS1- c-myc promoter DNA complex and solution NMR structure of RBMS1 protein helped us to delineate the non-canonical binding mode of RBMS1 with the promoter DNA. (neelsb.com)
Further it defines functions which refer to co-factor binding sites or non-protein binding sites. (projectguru.in)
The chemi- appear to interact with the structural elements of the cell, cal analysis was assessed at DATA CHEM Laboratories using plasma- with apparent binding to the cytoskeleton [Porter et al. (cdc.gov)

A diagram in the paper introducing the term illustrated the D-loop with a shape resembling a capital "D", where the displaced strand formed the loop of the "D". In proteins, a structural motif describes the connectivity between secondary structural elements. (wikipedia.org)
The term 'motif' is also describes a consensus sequence of amino acids, i.e. a partial sequence common to a number of different proteins, which may or may not adopt similar conformations in the different proteins. (vigyansarovar.com)
The term flexibility can additionally be used for well-structured proteins, however describes a special phenomenon within the context of disordered proteins. (aromaroa.com)

The structure is also known as a hairpin or hairpin loop. (wikipedia.org)
They hypothesized that engineering the sgRNA might serve to regulate diverse CRISPR systems, and they specifically engineered an RNA secondary structure onto the spacer by extending a designed hairpin on the 5' end of the sgRNA. (genomeweb.com)
The resulting hairpin structure could then serve as a steric and energetic barrier to R-loop formation," senior author Charles Gersbach and his colleagues wrote. (genomeweb.com)

The spherical structure is induced by the protein's tertiary construction. (aromaroa.com)

The structural comparison of proteins has become increasingly important as a means to identify protein motifs and fold families. (aaai.org)
The resolution of the 3D structure of the SAND domain from Sp100b has revealed that it consists of a novel alpha/beta fold. (embl-heidelberg.de)

En effet, la mutation de la valine engendre une diminution de la fonction de la molécule et des expériences de BRET ont démontré une modification de l'orientation spatiale des queues cytoplasmiques. (umontreal.ca)
Some of these mutations, such as the D614G mutation in the viral spike protein, have been found to increase the infectivity and transmissibility of SARS-CoV-2. (news-medical.net)
The mutation at 25088bp occurred in the S2 subunit of the viral spike protein, which plays a vital role in virus-host membrane fusion and viral entry. (news-medical.net)
Specifically, the mutation occurred in non-structural protein 7 (NSP7), which mediates the formation of RNA polymerase complex necessary for viral replication and transcription. (news-medical.net)
Mounting evidence suggests that the genetic disorders/mutation and diseases change not only the protein expression patterns but also membranes themselves. (lu.se)

Such simulation often produces a large number of folding trajectories, each consisting of a series of 3D conformations of the protein under study. (biomedcentral.com)

Of the characterized secondary structures of ncRNAs, Watson-Crick (C-G and A-U) and wobble base p airs (G-U) are most commonly seen. (biomedcentral.com)
Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. (reference.md)
A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE. (reference.md)
Multiple turns (up to sevenfold) occur commonly in proteins. (cloudfront.net)

The second step in our algorithm is based on the atomic coordinates of the protein structures and improves the initial vector alignment by iteratively minimizing the RMSD between pairs of nearest atoms from the two proteins. (aaai.org)

Computational design of novel proteins with well-defined functions is an ongoing topic in computational biology. (hindawi.com)

regular repeating structures that occur over short localized regions. (flashcardmachine.com)
As a consequence, the frequent use of codons matching common (i.e. 'preferred codons') or rare aminoacyl-tRNA species can lead to different levels of protein production, as delays or pauses in translation are likely to occur at rare codon sites. (biomedcentral.com)
All four occur frequently in proteins but I is most common, followed by II, I′ and II′ in that order. (cloudfront.net)

Understanding the protein folding mechanism remains a grand challenge in structural biology. (biomedcentral.com)
Finally, we show how structural and cellular biology can benefit from each other and pave a way for understanding, defining, and predicting a code of RNA recognition by the RRMs. (nih.gov)
The project should involve both studies of protein function by the applicant researchers and structural studies by the PSI:Biology network. (nih.gov)

A native structure is a structure that forms conformationally folding in native state before forming the tertiary structure. (biomedcentral.com)

Dr. Brutlag's group works in functional genomics, structural genomics, and bioinformatics. (nationalacademies.org)
A secondary goal that should be sought by a bioinformatics facility is to make algorithms and analysis methods accessible for non-computational biologists. (lu.se)

of orthosteric ligands, (ii) the discussion surface area that recruits G protein and arrestins, (iii) the discussion sites of extra protein (GIPs, GPCR interacting protein that control G proteins signaling or bring about G protein-independent indicators). (biotechpatents.org)
They recognize extracellular signaling substances (ligands) of varied nature (as well as the canonical signaling pathway, the G-protein activation/inactivation routine. (biotechpatents.org)

For this reason, two or more patterns are often associated with a single motif: the defining pattern, and various typical patterns. (wikipedia.org)
As the database of ROA spectra of polypeptides and proteins has grown, it has been possible to tighten up the assignment of ROA spectral bands and band patterns to aspects of known structural content. (gla.ac.uk)
However, the bonds connected to the α-carbon can freely rotate and contribute to the flexibleness and distinctive folding patterns seen inside proteins. (aromaroa.com)

This requires an efficient and highly specific interaction between protein and DNA that control some of the most important processes pertaining to cell survival and growth. (neelsb.com)
The work provides the first structural and dynamics characterization of human RBMS1 protein, that controls the expression of c-myc proto-oncogene inside the human cell by its interaction with 7 base pair consensus sequence within the 21 bp promoter/ autonomous origin of replication region 2 kb upstream of c-myc proto-oncogene. (neelsb.com)

a. supported by chaperones , but sometimes also happens spontaneously with small proteins. (zxc.wiki)
sRNAs usually work by pairing with target mRNAs, often with the assistance of protein partners called RNA chaperones. (nature.com)
Hsp70, Hsp90, and their co-chaperones are crucial members of the proteostasis network that are able to recognize misfolded proteins, aberrant condensates and protein aggregates, triaging proteins for refolding or degradation. (encyclopedia.pub)
Indeed, Hsp70, Hsp90 and their co-chaperones are increasingly recognized as therapeutic targets for the development of treatments against prevalent protein misfolding diseases. (encyclopedia.pub)
Hsp40/DNAJ proteins interact differently with Hsp70 chaperones [ 13 ] . (encyclopedia.pub)

In a comparison of our method to Holm and Sander's DALI algorithm, our program was able to detect structural similarity at the same level as DALI. (aaai.org)
We also performed searches of a representative set of the Protein Data Bank (PDB) using our program and detected structurally similarity between several distantly related proteins. (aaai.org)
The early general expression ofdri and the similarity of DRI and homeodomain in vitro DNA-bindingspecificity compound the problem of understanding the in vivo specificityof action of these proteins. (embl.de)
on the other hand, there are many cases of nearly identical structures known, sharing no sequence similarity at all [ 3 ]. (hindawi.com)
The region PB2-T2-PB3 is the best conserved region in the lyases andshows the clearest structural similarity. (embl.de)

Their functions are closely related to their mode of RNA recognition, which has been studied by structural biologists for more than 20 years. (nih.gov)
X-ray crystallographic analysis led to the identification of the crucial structural elements involved in substrate recognition by the evolved synthetase. (cipsm.de)

Our technique represents alpha-helices and beta-strands as vectors and uses a set of seven scoring functions to compare pairs of vectors from different proteins. (aaai.org)

Les résultats obtenus montrent la fonctionnalité des motifs de localisation de la portion C-terminale de MARCH1 ainsi que la présence d'autres éléments de localisation dans la portion N-terminale de la protéine. (umontreal.ca)

Many computational methods have been used to determine the native structure of ncRNAs. (biomedcentral.com)

active site - A region in proteins and nucleic acids (that participate in chemical reactions), where reacting molecules (substrates) bind and make specific contacts necessary for chemical catalysis. (rcsb.org)
Proteins search and bind specific sequence in the background of billions of bases in the genome. (neelsb.com)
The protein undergoes a hinge-like motion in order to bind with the specific DNA which facilitated by flexibility in the linker region. (neelsb.com)
Similarly, a minimal ProQ/FinO domain protein, NMB1681, has been shown to bind a range of structured RNAs in Neisseria meningitidis 15 . (nature.com)

This process is carried out by the human spliceosome machinery, in which over 300 proteins sequentially assemble with uridine-rich small nuclear RNA molecules (U snRNAs) to form distinct small nuclear ribonucleoprotein complexes (snRNPs). (biomedcentral.com)
Developing machine and deep learning models to predict properties of molecules and identify their most important structural characteristics. (helmholtz-hzi.de)

The large ~280-kDa U5 snRNP protein PRPF8 is central to the dynamics of spliceosome assembly [ 11 ]. (biomedcentral.com)
The NMR structure of free RBMS1 was solved, as the protein did not crystallize, most likely due to its inherent flexibility, which we confirmed through NMR relaxation dynamics. (neelsb.com)

Usually, however, the first letter is I, and both [RK] choices resolve to R. Since the last choice is so wide, the pattern IQxxxRGxxxR is sometimes equated with the IQ motif itself, but a more accurate description would be a consensus sequence for the IQ motif. (wikipedia.org)

involves formation of a multimeric protein. (flashcardmachine.com)

This hydrophobic region provides an area for dimerization, allowing the motifs to "zip" together. (vigyansarovar.com)

Anatomy5

Organisms8

Chemicals and Drugs78

Analytical, Diagnostic and Therapeutic Techniques and Equipment51

Phenomena and Processes95

Disciplines and Occupations9

Technology, Industry, Agriculture3

Information Science30

Health Care10

Sequences24

Conformation5

Residues11

Peptides6

Domains17

Gene17

Helix21

Nucleotide5

Subunits1

Sequence motif2

Tertiary structures3

Loops6

Quaternary Structure1

Polypeptide3

Genes4

Abstract3

Homology4

Common three-dimensional1

Macromolecules1

Binds2

Interactions8

Transcriptional3

Enzymes1

Molecule5

Molecular10

Biological11

Membrane proteins1

Bound5

Conformational3

Backbone4

Binding26

Describes3

Hairpin3

Protein's1

Fold2

Mutation5

Conformations1

Commonly4

Atoms1

Novel proteins1

Occur3

Biology3

Forming the tertiary structure1

Bioinformatics2

Ligands2

Patterns3

Interaction2

Chaperones5

Similarity5

Recognition2

Beta strands1

Localisation1

Computational1

Bind4

Molecules2

Dynamics2

Consensus1

Multimeric1

Hydrophobic1