• We found that overall the residue contact pattern can distinguish protein folds best when contacts are defined for residue pairs whose Cβ atoms are at 7.0 Å or closer to each other. (biomedcentral.com)
  • For capturing contacts between neighboring β strands, considering the distance between Cα atoms is better than the Cβ−based distance because the side-chain of interacting residues on β strands sometimes point to opposite directions. (biomedcentral.com)
  • 3. Definition of contacts (residue centers and distance thresholds) (i) The definition historically used in CASP: a pair of residues is defined to be in contact when the distance between their Cβ atoms (Cα in case of glycine) is smaller than 8.0 Å. (predictioncenter.org)
  • The neuron connections or synapses are composed of membrane, proteins, ions and transmitters, each of which are composed on many atoms. (scienceforums.net)
  • The identification of similar three-dimensional (3D) amino acid patterns among different proteins might be helpful to explain the polypharmacological profile of many currently used drugs. (frontiersin.org)
  • The hOAT3 cDNA consisted of 2179 base pairs that encoded a 543-amino-acid residue protein with 12 putative transmembrane domains. (aspetjournals.org)
  • I was wondering, therefore, if there's a way in rosetta-scripts to just assign a penalty for residues at the i and i+2 position based on their amino acids. (rosettacommons.org)
  • This is in contrast with the exponential complexity of the amino acid-level configuration space of proteins. (biomedcentral.com)
  • The number of degrees of freedom needed for the description, comparison and classification of the macroscopic, biologically-relevant features of proteins is necessarily much smaller than that associated with the collection of amino acids. (biomedcentral.com)
  • A disadvantage of the rmsd -based measures is that it assumes a strict one-to-one correspondence between at least the C alpha (C α ) atom coordinates of the compared proteins, i.e., it requires an alignment at the amino acid level of detail. (biomedcentral.com)
  • The residue contact information can be incorporated in structure prediction in several different ways: It can be incorporated as statistical potentials or it can be also used as constraints in ab initio structure prediction. (biomedcentral.com)
  • I know there are residue type constraints where I can assign a penalty/bonus to individual residue types at a position, but is there a way to set up constraints for pairs of residues at specific positions? (rosettacommons.org)
  • Methods of correlation analysis allow for the identification of pairs of residue positions, whose occupancy is mutually dependent due to constraints imposed by protein structure or function. (uni-regensburg.de)
  • Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry, 2010, Protein Science) and was able to set constraints for one metal binding site in residue_pair_jump_cst file and run AbinitioRelax without any issues. (rosettacommons.org)
  • You'll likely also have to update any other references to zinc (e.g. in the -constraints:cst_file and -constraints:cst_fa_file) so that you have a set of references to each zinc atom (each to their own CYS residue). (rosettacommons.org)
  • core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file 2L62_03_05.200_v1_3 core.scoring.constraints.util: Constraint choice: 2L62.cen_cst core.io.constraints: read constraints from 2L62.cen_cst core.io.constraints: Read in 8 constraints core.fragment: compute strand/loop fractions for 28 residues. (rosettacommons.org)
  • Evolutionary analysis comparing mitoribosomes from different species with bacterial counterparts, illustrates that the exit tunnel evolves via deletions in the rRNA and extensions of mitoribosomal proteins. (nature.com)
  • The very premise of using model organisms to inform human biology relies on the fact that many biological processes, and the underlying genomic elements that encode them, are frequently conserved across large evolutionary distances, especially for protein-coding genes. (biorxiv.org)
  • sRNAs usually work by pairing with target mRNAs, often with the assistance of protein partners called RNA chaperones. (nature.com)
  • Conceptual parallels exist between bacterial and eukaryotic small-RNA (sRNA) pathways, yet relatively little is known about which protein may recognize and recruit bacterial sRNAs to interact with targets. (biomedcentral.com)
  • Trans- encoded sRNAs form imperfect base-pairing interactions with complementary sequences in their mRNA targets, which are often located at or near ribosome binding sites (RBS), but can also be located upstream of the translation start site as well as deep in the coding regions (CDS) [ 2 ]. (biomedcentral.com)
  • Like microRNAs (miRNAs) in eukaryotes, trans -acting bacterial sRNAs appear to recognize their targets by a seed-pairing mechanism using seeds as small as 6-7 nucleotides. (biomedcentral.com)
  • To provide a representative reference for studying protein synthesis in the mitochondria of fungi, and to reveal how the mitoribosome functions in coordination with its translation partners, we determined structures of the translating mitoribosome from the representative fungal model organism Neurospora crassa . (nature.com)
  • As compared with the original version, substantial improvements that have been incorporated to our software allow: (i) to compare quaternary structures, (ii) to deal with a list of pairs of structures, (iii) to know how druggable is the zone where similar 3D patterns are detected and (iv) to significantly reduce the execution time. (frontiersin.org)
  • Unfortunately, the design of drugs with multiple activities on a selected handful of different protein structures remains a significant experimental and computational challenge ( Konc, 2019 ). (frontiersin.org)
  • Although protein structures have been solved by experiments at an increasing rate, a flood of new sequences have been determined even more rapidly due to the advance of sequencing technologies[ 6 , 7 ]. (biomedcentral.com)
  • We demonstrate that the multipoles can be used for the quantitative description of the protein shape and for the comparison of protein structures at various levels of detail. (biomedcentral.com)
  • Despite this, however, when it comes to quantitatively measure the difference between protein structures, in most cases, the measure of choice remains the root mean square deviation ( rmsd ) between aligned atomic coordinates. (biomedcentral.com)
  • Analysis of non-redundant SCOP structures from Y. Zhang's group shows that the average number of short, medium, and long-range contacts of a well folded protein domain is 0.3*L, 0.4*L, and 1.2*L, respectively. (predictioncenter.org)
  • The models of the active mitoribosome explain how mRNA binds through a dedicated protein platform on the small subunit, tRNA is translocated with the help of the protein mL108, bridging it with L1 stalk on the large subunit, and nascent polypeptide paths through a newly shaped exit tunnel involving a series of structural rearrangements. (nature.com)
  • Binding of mRNA requires extended mitoribosomal proteins of the small subunit, and movement of tRNA is realized through additional proteins of the large subunit. (nature.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)
  • Likewise, the ProQ/FinO domain-containing protein RocC of Legionella pneumophila interacts with only one trans -acting sRNA (RocR) to repress post-transcriptionally multiple mRNA targets 6 . (nature.com)
  • Such interactions generally result in a decrease in protein synthesis, either by stimulating mRNA degradation or by inhibiting translation. (biomedcentral.com)
  • It is believed that the functional space of all proteins can be spanned by combining a rather small number of structural units, termed folds. (biomedcentral.com)
  • The number of different folds is small compared to the total number of proteins, of the order of 1000 for globular, water-soluble proteins [ 1 ]. (biomedcentral.com)
  • Effective encoding of residue contact information is crucial for protein structure prediction since it has a unique role to capture long-range residue interactions compared to other commonly used scoring terms. (biomedcentral.com)
  • To seek the most effective definition of residue contacts for template-based protein structure prediction, we evaluated 45 different contact definitions, varying bases of contacts and distance cutoffs, in terms of their ability to identify proteins of the same fold. (biomedcentral.com)
  • A proper encoding of residue contact information is crucial for structure prediction because in principle, a full distance map or a residue contact map has sufficient information for reconstructing the tertiary structure of a protein[ 25 ]. (biomedcentral.com)
  • Assessment is concentrated on the long-range contacts (separation of the interacting residues of at least 24 positions along the sequence) as these are the most valuable for structure prediction. (predictioncenter.org)
  • Mitoribosomes are specialized protein synthesis machineries in mitochondria. (nature.com)
  • Protein synthesis in mitochondria supports bioenergetics of eukaryotic cells and is executed by dedicated mitoribosomes. (nature.com)
  • Therefore, to provide a reference for the process of protein synthesis in mitochondria, we set out to investigate the functional translation apparatus from the model organism N. crassa . (nature.com)
  • 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)
  • The involvement of viral DNA-binding proteins in the regulation of virulence genes, transcription, DNA replication, and repair make them significant targets. (mdpi.com)
  • An in-house analysis shows that the three definitions on CASP targets agree in 80+ % of cases (i.e., contact between two residues according to measure x is also a contact according to measure y). (predictioncenter.org)
  • Insight into how these proteins recognize their cognate RNAs initiated with FinO. (nature.com)
  • Consequently, such approaches do not consider the similarity of residue pairs, which may degrade the algorithm's performance. (uni-regensburg.de)
  • Similarly, a minimal ProQ/FinO domain protein, NMB1681, has been shown to bind a range of structured RNAs in Neisseria meningitidis 15 . (nature.com)
  • To these numbers, you should add the charge of the minimal QM system, as well as other metals or non-standard residues. (lu.se)
  • The ProQ/FinO family of RNA binding proteins mediate sRNA-directed gene regulation throughout gram-negative bacteria. (nature.com)
  • For your residue_pair_jump_cst file, simply give a block (each block starts with a BEGIN line and ends with an END line) for each zinc atom you want to model. (rosettacommons.org)
  • The presence of aberrant hypermethylation was associated with loss of MGMT protein, in contrast to retention of protein in the majority of tumors without aberrant hypermethylation. (aacrjournals.org)
  • A pair of genes from the same gene family is said to be homologous to each other, and the assumption is that homologous genes are likely to have similar biological functions. (biorxiv.org)
  • The tertiary structure of proteins provides crucial information for understanding molecular mechanisms of biological functions. (biomedcentral.com)
  • Alkylation of DNA at the O 6 position of guanine is an important step in the formation of mutations in cancer, primarily due to the tendency of the O 6 -methylguanine to pair with thymine during replication, resulting in a conversion of guanine-cytosine to adenine-thymine pairs in DNA (2) . (aacrjournals.org)
  • L. Hu, P. Söderhjelm, U. Ryde "Accurate reaction energies in proteins obtained by combining QM/MM and large QM calculations" J. Chem. (lu.se)
  • Check all residue that do not form such ionic pairs or are not part of the QM system or binds to a metal site with a pdb viewer. (lu.se)
  • In our present view, these areas are found for systems where several types of macromolecules (proteins, polysaccharides or polyelectrolytes) and/or amphiphiles interact to form a functional or destructive unit. (lu.se)
  • When results of fold recognition were examined for individual proteins, we found that the effective contact definition depends on the fold of the proteins. (biomedcentral.com)
  • One typical algorithm is H2r, which characterizes each individual residue position k by the conn(k)-value, which is the number of significantly correlated pairs it belongs to. (uni-regensburg.de)
  • To decide on significance, the algorithm calculates a p-value by performing a randomization test for each individual pair of residue positions. (uni-regensburg.de)
  • The reason for asking this is that I have set up my own custom function in pyrosetta to penalize residues at positions i and i+2 (as in the original question), and this function makes use of the ContextIndependentTwoBodyEnergy term. (rosettacommons.org)
  • The outcome of H2rs and of a method that predicts contacting residue positions (PSICOV) overlapped only marginally. (uni-regensburg.de)
  • Considering substitution frequencies for residue pairs by means of the von Neumann entropy and a p-value improved the success rate in identifying important residue positions. (uni-regensburg.de)
  • Created 9281 residue types core.scoring.ScoreFunctionFactory: SCOREFUNCTION: score13_env_hb core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. (rosettacommons.org)
  • We prove that, when the biologically relevant portions of the proteins are retained, it can robustly discriminate between the various families in the set in a way not possible through sequence or conventional structural representations alone. (biomedcentral.com)
  • This works, but it's REALLY slow in pyrosetta (even using a trivial test scoring function), with repacking of a small protein taking about 10X as long as without the pyrosetta function. (rosettacommons.org)
  • The largest deterioration of the fold recognition was observed for β-class proteins when the threading methods were used because the average alignment accuracy was worst for this fold class. (biomedcentral.com)
  • In the case of threading, alignment accuracy strongly influences the fraction of common contacts identified among proteins of the same fold, which eventually affects the fold recognition accuracy. (biomedcentral.com)
  • protocols.jumping: read ResiduePair jump-definitions from 2L62.residue_pair_jump_cst core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. (rosettacommons.org)
  • core.chemical.ResidueTypeSet: Finished initializing centroid residue type set. (rosettacommons.org)
  • 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)
  • 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)
  • Among various structure-based terms, residue-residue contact potentials[ 21 - 23 ] are unique in that they capture long-range interactions in a protein structure[ 24 ]. (biomedcentral.com)
  • That the structure determines the function of proteins is a central paradigm in biology. (biomedcentral.com)
  • The results described here demonstrate how a granular description of the protein structure can be achieved using multipolar coefficients. (biomedcentral.com)
  • The functions of a protein are determined by its three dimensional structure. (biomedcentral.com)
  • We determined A by deducing substitution frequencies from contacting residue pairs observed in the homologs of 35 809 proteins, whose structure is known. (uni-regensburg.de)
  • The hOAT3 protein was shown to be localized in the basolateral membrane of renal proximal tubules and the hOAT3 gene was determined to be located on the human chromosome 11q12-q13.3 by fluorescent in situ hybridization analysis. (aspetjournals.org)
  • For each residue in the list of buried charges, add a note if it forms an ionic pair with another residue in the protein (also given in the output). (lu.se)
  • The DNA repair protein O 6 -methylguanine DNA methyltransferase (MGMT) removes alkyl adducts from the O 6 position of guanine. (aacrjournals.org)
  • We then test the parameterization on a benchmark set of the protein kinase-like superfamily. (biomedcentral.com)
  • All this should in principle be done already when the MD simulation is set up (to get proper protonation state of all residues). (lu.se)
  • Lower fold recognition accuracy was observed when inaccurate threading alignments were used to identify common residue contacts between protein pairs. (biomedcentral.com)
  • Also, previous assessments evaluated predictions on medium + long-range contacts (12+ residues separation). (predictioncenter.org)
  • Finally, we describe a bL9m-lacking assembly intermediate complexed with the maturation factor Atp25 that is formed as a result of protein splitting. (nature.com)
  • Specifically, we construct a (dis)similarity measure in multipolar configuration space, and show how such a function can be used for the comparison of a pair of proteins. (biomedcentral.com)
  • Typing Tool, it uses the most recent norovirus and sapovirus reference arrangement of the pair. (cdc.gov)