• Modeling suggests that access to these titratable residues is blocked by a ladder of hydrophobic residues, and ATP-driven conformational changes open and close this hydrophobic seal to permit metal binding and release. (nih.gov)
  • The conservation of this arrangement of titratable and hydrophobic residues among ABC transporters of transition metals suggests a common mechanism. (nih.gov)
  • 1992), A cluster of hydrophobic amino acid residues re. (xenbase.org)
  • A cluster of hydrophobic amino acid residues required for fast Na(+)-channel inactivation. (xenbase.org)
  • The model has only two types of residues, hydrophobic and hydrophilic. (lu.se)
  • We invoke various groups as potential proton acceptors-namely, the phosphate and leucyl amino groups of leucyl-adenylate, the A76 base of tRNA, and the Asp80 and Glu532 residues of the protein-and consider both metal-assisted and metal-free reactions. (nih.gov)
  • We also analyzed the distance of functional amino acids to the general center of mass (GCM) of the structure, relative solvent accessibility (RSA), and the use of relative entropy as a measure of sequence conservation. (elsevierpure.com)
  • Here, we set out to identify amino acid residues responsible for glucosinolate transport activity of the main seed glucosinolate exporter UMAMIT29 in Arabidopsis thaliana . (frontiersin.org)
  • Transport activity assays of mutant variants with a single point amino acid substitution in each site UMAMIT29 suggest that five of these residues are critical for glucosinolate transport. (frontiersin.org)
  • Cysteines are one of the most rarely used amino acids, but when conserved in proteins they often play critical roles in structure, function, or regulation. (hindawi.com)
  • Amino acid residues required for fast Na(+)-channel inactivation: charge neutralizations and deletions in the III-IV linker. (xenbase.org)
  • Amino acid residues are. (cdc.gov)
  • We execute short timescale (30 ps) molecular dynamics simulations with high sampling frequency (0.01 ps), to identify amino acid residue hubs whose global connectivity dynamics are characteristic of the ligand or mutation associated with the target protein. (nference.com)
  • SEB consists of 239 amino acid residues and has a molecular weight of 28 kd. (medscape.com)
  • Gamma-glutamyl carboxylase catalyzes carboxylation of Gla residues in the amino-terminal portion of the molecule. (medscape.com)
  • Meanwhile sequence conservation remains by far the most influential feature in identifying functional residues. (elsevierpure.com)
  • To test this, we aligned 97 protein sequences consisting of homologs of UMAMIT clade I from 27 plant species and created sequence logos containing the 51 residues identified in the structural analysis ( Supplementary Figure 1 ). (frontiersin.org)
  • In GeomNet, the co-evolutionary features extracted from MSA that search from the sequence databases are sent to an improved residual neural network to predict the inter-residue geometric constraints. (sciencegate.app)
  • In addition to angles, we make use of sequence properties like secondary structure at each time-step, without using any database. (sciencegate.app)
  • Despite low levels of sequence identity (often 10-30%), the three-dimensional structures display a highly similar alpha/beta folding pattern. (ox.ac.uk)
  • object, for the residue in that sequence which is aligned with this residue. (salilab.org)
  • This virtual residue then makes the sequence length different between the input and native poses, causing the assertion that the length must match (in order to calculate RMSD) to fail. (rosettacommons.org)
  • Here, we report the X-ray structure of Thermobifida fusca AA10A (TfAA10A), investigate mutational characterization of key surface residues near its active site, and explore the importance of the various domains of Thermobifida fusca AA10B (TfAA10B). (biomedcentral.com)
  • This protocol describes the requirements for a pesticide residue study in food collected from local markets. (springer.com)
  • In Africa where traditional agriculture is widely practiced, pesticides pose serious health hazards and environmental contamination, due to the increasing pesticide use in agricultural production and limited capacity for pesticide residue testing and monitoring (Fuhrimann et al. (springer.com)
  • Additionally, it has been difficult to target interventions without understanding if presumed residues are actually exceeding legal maximum residue limits (MRLs), if they are the result of illegal pesticide use (knowingly or unknowingly by farmers), if they are the result of poor product quality or counterfeit products, or if other factors are involved, such as poor efficacy testing and label establishment during the registration of the products. (springer.com)
  • GLP is generally a guideline or a requirement for pesticide residue studies and MRL. (springer.com)
  • Recently, studies of fraudulent pesticides in Africa suggested that the use of illegal pesticides may lead to significant health concerns due to severe environmental contamination and pesticide residues in food crops (Haggblade et al. (springer.com)
  • 2020 ). A more recent study assessed concentrations of pesticide residues in fruits and vegetables in Uganda and observed multiple pesticide residues occurred in commonly consumed fruit and vegetables (Ssemugabo et al. (springer.com)
  • Crop residue on the soil surface reduces erosion and adds to soil organic matter. (sare.org)
  • With conservation systems, increased crop residue and soil moisture reduce soil temperatures when compared with conventional practices. (sare.org)
  • Crop residue management in arable cropping systems under temperate climate. (ac.be)
  • This review highlights the challenges in establishing definitive evidence regarding the effects of crop residue management on soil organisms and nutrient dynamics. (ac.be)
  • In EmaNet, the 1D and 2D features are extracted from the folded model and sent to the deep residual neural network to estimate the inter-residue distance deviation and per-residue lDDT of the model, which will be fed back to GeomNet as dynamic features to correct the geometries prediction and progressively improve model accuracy. (sciencegate.app)
  • This approach could be used to identify and promote micro-organisms with beneficial effects against residue-borne pathogens, and more broadly, to decipher the complex interactions between multi-species pathosystems and other microbial components in crop residues. (biorxiv.org)
  • All these micro-organisms are grouped into structured communities that can be defined in terms of their composition and interactions. (biorxiv.org)
  • Effective encoding of residue contact information is crucial for protein structure prediction since it has a unique role to capture long-range residue interactions compared to other commonly used scoring terms. (biomedcentral.com)
  • Among various structure-based terms, residue-residue contact potentials[ 21 - 23 ] are unique in that they capture long-range interactions in a protein structure[ 24 ]. (biomedcentral.com)
  • The data also demonstrate essential interactions of Asn-111 with active site residues. (ox.ac.uk)
  • Second, cytochromes act on greasy substrates, there are few if any polar interactions generally, so constraining to polymer residues may not be that useful. (stackexchange.com)
  • These results suggest that the first transmembrane glycine residue on the β 2 subunit may be important for conformational or allosteric interactions of channel gating by both GABA and anesthetics. (aspetjournals.org)
  • We have investigated the involvement of these five residues in the interactions with heme. (lu.se)
  • In absence of local interactions, native structure formation does not occur for the temperatures considered. (lu.se)
  • All or other nearby charged groups, the pKa shift of a buried pH-dependent properties of proteins are ultimately governed residue is dominated by the large electrostatic self-energy by the electrostatic interactions of ionizable side chains. (lu.se)
  • Because this is for the whole system RMSD calculation, and antibody residue indexes are renumbered by chothia scheme, so I have to find interface RMSD function and change chothia scheme back to normal index numbers. (rosettacommons.org)
  • Using CDR shuffling, residues important for the assembly of mucin-1 specific paratopes were defined by random recombination of the complementarity determining regions derived from a set of mucin-1 specific clones, previously selected from an antibody fragment library. (lu.se)
  • The importance of several of these conserved residues was supported by their presence in a mouse monoclonal antibody with a known structure and the same epitope specificity. (lu.se)
  • Several of these corresponding residues in the mouse monoclonal antibody are known to interact with the antigen. (lu.se)
  • In conclusion, critical residues important for maintaining a human antigen-specific binding site during the process of in vitro antibody evolution were defined. (lu.se)
  • Both the structure of the PGs and the GAG chains, and the expression of the enzymes involved in their biosynthesis and degradation, vary between normal cells and tumor cells. (lu.se)
  • The biosynthesis of GAG chains is initiated by xylosylation of a serine residue of the core protein, followed by galactosylation by beta 4GalT7. (lu.se)
  • The C-terminal domain of NleG2-3 (residues 90 to 191) is the most conserved region in NleG proteins and was solved by NMR. (rcsb.org)
  • Background: Worldwide structural genomics projects continue to release new protein structures at an unprecedented pace, so far nearly 6000, but only about 60% of these proteins have any sort of functional annotation.Results: We explored a range of features that can be used for the prediction of functional residues given a known three-dimensional structure. (elsevierpure.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)
  • Residue contacts defined by Cβ−Cβ distance of 7.0 Å work best overall among tested to identify proteins of the same fold. (biomedcentral.com)
  • The tertiary structure of proteins provides crucial information for understanding molecular mechanisms of biological functions. (biomedcentral.com)
  • Based on a predicted model of UMAMIT29, we propose that the substrate transporting cavity consists of 51 residues, of which four are highly conserved residues across all the analyzed homologs of UMAMIT29. (frontiersin.org)
  • Based on our model, we proposed a substrate-transporting cavity of UMAMIT29 defined by helix I to IV and VI-IX and selected 51 residues as putative substrate binding sites based on solvent accessibility ( Figure 1 ). (frontiersin.org)
  • Although the chemicals used in this way in the past may have decomposed or dissipated into the environment, it is usually possible to detect significant levels of the compounds used in previous chemical remedial treatments, their contaminants or decay residues, in the dust and debris of treated buildings. (buildingconservation.com)
  • Special Issue 9701 - Monograph on Residues and Contaminants in Milk and Milk Products. (fil-idf.org)
  • by IDF Group of Experts A4 - Residues and contaminants in milk and milk products The current monograph is th. (fil-idf.org)
  • The transcription of COX-1 yields a 2.7-kilobase (kb) messenger ribonucleic acid (mRNA) that encodes a 576-residue, 65-kd protein. (medscape.com)
  • The aim of this study was to characterise the impact of a resistance gene against L. maculans infection on residue microbial communities and to identify micro-organisms interacting with this pathogen during residue degradation. (biorxiv.org)
  • 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)
  • 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)
  • How to use model quality assessment to further improve the accuracy of protein structure prediction, especially not reliant on the existing templates, is helpful for unraveling the folding mechanism. (sciencegate.app)
  • Here, we investigate whether model quality assessment can be introduced into structure prediction to form a closed-loop feedback, and iteratively improve the accuracy of de novo protein structure prediction. (sciencegate.app)
  • Results: In this study, we propose a de novo protein structure prediction method called RocketX. (sciencegate.app)
  • AbstractQuality Assessment (QA) plays an important role in protein structure prediction. (sciencegate.app)
  • Our experiment points out new directions for QA problem and our method could be widely used for protein structure prediction problem. (sciencegate.app)
  • The NMR-assisted modeling challenge in CASP13 provided a blind test to explore the capabilities and limitations of current modeling techniques in leveraging NMR data which had high sparsity, ambiguity and error rate for protein structure prediction. (sciencegate.app)
  • Solved crystal structures of P450 BM3 variants in complex with styrene provide on the molecular level a first explanation of how a positively charged surface residue inverts the enantiopreference of styrene epoxidation. (lincoln.ac.uk)
  • What is the correct method of identifying the interacting residues for specific molecular docking? (stackexchange.com)
  • Based on enzymatic studies, that is galactosylation and its inhibition, conformational analysis and molecular modeling using the crystal structure, we propose that the binding pocket of beta 4GalT7 is very narrow, with a precise set of important hydrogen bonds. (lu.se)
  • We find that despite its broad metal-recognition profile, MntBC-A imports only manganese, whereas zinc can function as a high-affinity inhibitor of MntBC-A. Computational analysis shows that the transmembrane metal permeation pathway is lined with six titratable residues that can coordinate the positively charged metal, and mutagenesis studies show that they are essential for manganese transport. (nih.gov)
  • Pharmaceutical residues in freshwater systems are a potential risk to human health and our ecosystems. (mn-net.com)
  • 1) OECD POLICY HIGHLIGHTS Pharmaceutical residues in freshwater:Hazards and policy responses (2019). (mn-net.com)
  • We suggest incorporation of structure-guided genetic inference assays into pharmaceutical and healthcare Oncology workflows. (nference.com)
  • Proposal for regulatory risk mitigation measures for human pharmaceutical residues in the environment. (janusinfo.se)
  • This extends the previously recognized catalytic triad of Ser-Tyr-Lys residues to form a tetrad of Asn-Ser-Tyr-Lys in the majority of characterized short-chain dehydrogenases/reductase enzymes. (ox.ac.uk)
  • On the other hand, the MRD data are consistent with a local conformational change in response to ionization of the internal residues. (lu.se)
  • Primary structure and functional expression of the beta 1 subunit of the rat brain sodium channel. (xenbase.org)
  • SEB has 2 distinct tightly "packed" domains that have a very complex tertiary structure. (medscape.com)
  • A combination of site-directed mutagenesis and electron paramagnetic resonance was used to explore the differences observed in the structure and redox properties of the Rieske cluster. (ucl.ac.uk)
  • Site-directed mutagenesis of the γ-aminobutyric acid type A (GABA A ) receptor β 2 subunit has demonstrated that conversion of a conserved glycine residue located at the entrance to the first transmembrane domain into the homologous ρ 1 residue phenylalanine alters the modulating effects of four different i.v. anesthetics: pentobarbital, alphaxalone, etomidate, and propofol. (aspetjournals.org)
  • Fungal community structure differed between the two lines at harvest, but not subsequently, suggesting that the presence/absence of the resistance gene influences the microbiome at the base of the stem whilst the plant is alive, but that this does not necessarily lead to differential colonisation of the residues by fungi. (biorxiv.org)
  • It is also involved in the maintenance of chromatin structure, the regulation of gene expression, and the stress response. (wikipedia.org)
  • The diagram at the top shows the structure of gene 62. (cdc.gov)
  • Vegetable crop residues take a particular position relative to arable crops due to often large amounts of biomass with a N content up to 200 kg N ha −1 left behind on the field. (mdpi.com)
  • Structural analysis of this structure revealed the presence of a RING finger/U-box motif. (rcsb.org)
  • We previously analyzed the IM-MS spectra of WT Aβ 1-40 and found that the population of oligomers of a given order (e.g. trimers, tetramers, pentamers, etc.) splits into two distinct structural variants, differing in their collisional cross section and, therefore, their structure 17 . (nature.com)
  • These structure-based terms are commonly derived from statistics of structural properties observed in representative structures (knowledge-based statistical potentials). (biomedcentral.com)
  • With the rapid progress and improvements in the fields of macromolecular crystallography, Cryo-EM, small angle scattering, electron diffraction and use of XFELs, the new LINXS theme INTEGRATIVE STRUCTURAL BIOLOGY is formed to advance cutting-edge research and to encourage new users to utilize integrative structure biology to address key scientific questions. (lu.se)
  • 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)
  • Also, in contrast to earlier studies using lattice models, our results convincingly demonstrate that one does not need more than two types of residues to generate sequences with good thermodynamic folding properties in three dimensions. (lu.se)
  • As a result, moldboard plowing or other soil inversion to bury crop residues and restructure the soil is traditionally recommended to control some soil insects. (sare.org)
  • To examine the role of water penetration, we have measured the 17O and 2H magnetic relaxation dis- persions (MRD) for the V66E and V66K mutants of staphylococcal nuclease, where glutamic acid and lysine residues are buried in predominantly apolar environments. (lu.se)
  • Earthworms and microorganisms play a range of beneficial roles in agricultural systems, including increased organic matter mineralization, nutrient cycling, and soil structure stabilization. (ac.be)
  • These results suggest that CedA has multiple roles and residues with different functions are positioned in the two regions. (elsevierpure.com)
  • When each of the 11 residues of UMAMIT29 was individually mutated into the corresponding residue in UMAMIT32, five mutant variants (UMAMIT29#V27F, UMAMIT29#M86V, UMAMIT29#L109V, UMAMIT29#Q263S, and UMAMIT29#T267Y) reduced glucosinolate transport activity over 75% compared to wild-type UMAMIT29. (frontiersin.org)
  • This represents an approximately 14-fold enrichment of catalytic residues on the entire input set (corresponding to a sensitivity of 63% and a precision of 17%), a performance competitive with that of other state-of-the-art methods.Conclusions: We found that several of the graph based measures utilize the same underlying feature of protein structures, which can be simply and more effectively captured with the distance to GCM definition. (elsevierpure.com)
  • We selected the Escherichia coli nitro/quinone reductase NfsA for chloramphenicol detoxification by simultaneously randomising eight active-site residues and interrogating ~250,000,000 reconfigured variants. (elifesciences.org)
  • We have analyzed the role of several conserved residues regarding folding, stability, steady-state kinetics, and coenzyme binding using bacterial 3beta/17beta-hydroxysteroid dehydrogenase and selected mutants. (ox.ac.uk)
  • Seedbed preparation can range from complete burial of plant residue to no-till. (sare.org)
  • however, the preserved material ranges from three-dimensional, predominantly phosphatized structures to dark films of mainly organic matter. (lu.se)
  • From the selected features, neural networks were trained to identify catalytic residues. (elsevierpure.com)
  • Soil residue incorporation of mineral particles can maintain P and N levels, however returning soil also increases aeration and the activation of microbial activity. (ac.be)
  • 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)
  • We propose a novel protein single-model QA method which is built on a new representation that converts raw atom information into a series of carbon-alpha (Cα) atoms with side-chain information, defined by their dihedral angles and bond lengths to the prior residue. (sciencegate.app)
  • In the log file, check that residues are discarded because of missing backbone atoms. (rosettacommons.org)
  • Rosetta requires that all backbone atoms are present in order to build the residue. (rosettacommons.org)
  • This suggests that these residues are key for UMAMIT29-mediated glucosinolate transport activity and thus potential targets for blocking the transport of glucosinolates to the seeds. (frontiersin.org)
  • A1M binds heme and the crystal structure suggests that C34 and H123 participate in a heme binding site. (lu.se)
  • Evidence suggests that COX-1 and COX-2 are similar in structure and function but that they exist as 2 distinct enzymatic entities. (medscape.com)
  • At neutral pH, where these residues are uncharged, we find no evidence of buried water molecules near the mutation site. (lu.se)
  • However, my native structure shares the same residue number and same residue / atom names with input structure. (rosettacommons.org)
  • AbstractComputational methods that produce accurate protein structure models from limited experimental data, e.g. from nuclear magnetic resonance (NMR) spectroscopy, hold great potential for biomedical research. (sciencegate.app)
  • State the theorem of quadratic reciprocity and use it to determine whether a given integer is a quadratic residue modulo a given prime. (manchester.ac.uk)
  • Check that you have got integer charges of all residue with changepdb command cc. (lu.se)
  • Crystal structures of an NH2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions. (neb.com)
  • By comparing differentially conserved residues within the predicted cavities between glucosinolate-transporting and non-glucosinolate-transporting UMAMITs, we identify 11 candidate residues. (frontiersin.org)
  • Lower fold recognition accuracy was observed when inaccurate threading alignments were used to identify common residue contacts between protein pairs. (biomedcentral.com)
  • After searching online, I found out that I should identify the interacting residues of that ligand. (stackexchange.com)
  • Those responsible for buildings in the UK should therefore take all reasonable measures to identify and control the potential risks from residues of previous chemical remedial treatments to control woodworm and other decay organisms. (buildingconservation.com)
  • The soil structure is preserved under no-till, with increased moisture and aeration [29]. (sare.org)
  • Residue covering the soil surface decreases soil temperature, which may slow the growth of plants that are susceptible to insect damage in their seedling stages, such as corn. (sare.org)
  • Because many conservation tillage systems involve multiple cropping practices and because shading by residue can slow the warming of soil in the spring, the crop is often planted later than in conventional systems. (sare.org)
  • However, chlordane residue is still present from prior use in many homes and other structures, as well as the surrounding soil. (cdc.gov)
  • The structure of TfAA10A is similar to other bacterial LPMOs (lytic polysaccharide monooxygenases), including signs of photo-reduction and a distorted active site, with mixed features showing both type I and II copper coordination. (biomedcentral.com)
  • However, at the same time vegetable crop residues are a vital link in closing the nutrient and organic matter cycle of soils. (mdpi.com)
  • The results indicate that certain residues that are not frequently considered in structure-aided kinase inhibitor design have an important role to play. (rcsb.org)