Proteins-Structure Function and Bioinformatics最新文献_第9页

Retraction: Citius, Altius, Fortius. J. Lange, G. Vriend. Proteins: Structure, Function, and Bioinformatics. 2020. https://doi.org/10.1002/prot.12345. 撤回：Citius, Altius, Fortius.J. Lange, G. Vriend.蛋白质：结构、功能和生物信息学》。2020. https://doi.org/10.1002/prot.12345.

IF 2.9 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2024-05-01 Epub Date: 2023-12-18 DOI: 10.1002/prot.26649

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Dynamically driven correlations in elastic net models reveal sequence of events and causality in proteins 弹性网模型中的动态相关性揭示了蛋白质中的事件序列和因果关系

IF 2.9 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2024-04-30 DOI: 10.1002/prot.26697

Albert Erkip, Burak Erman

{"title":"Dynamically driven correlations in elastic net models reveal sequence of events and causality in proteins","authors":"Albert Erkip, Burak Erman","doi":"10.1002/prot.26697","DOIUrl":"https://doi.org/10.1002/prot.26697","url":null,"abstract":"An explicit analytic solution is given for the Langevin equation applied to the Gaussian Network Model of a protein subjected to both a random and a deterministic periodic force. Synchronous and asynchronous components of time correlation functions are derived and an expression for phase differences in the time correlations of residue pairs is obtained. The synchronous component enables the determination of dynamic communities within the protein structure. The asynchronous component reveals causality, where the time correlation function between residues i and j differs depending on whether i is observed before j or vice versa, resulting in directional information flow. Driver and driven residues in the allosteric process of cyclophilin A and human NAD‐dependent isocitrate dehydrogenase are determined by a perturbation‐scanning technique. Factors affecting phase differences between fluctuations of residues, such as network topology, connectivity, and residue centrality, are identified. Within the constraints of the isotropic Gaussian Network Model, our results show that asynchronicity increases with viscosity and distance between residues, decreases with increasing connectivity, and decreases with increasing levels of eigenvector centrality.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140830716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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P1′ specificity of the S219V/R203G mutant tobacco etch virus protease S219V/R203G 突变体烟草蚀变病毒蛋白酶的 P1′特异性

IF 2.9 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2024-04-26 DOI: 10.1002/prot.26693

Mária Golda, Gyula Hoffka, Scott Cherry, Joseph E. Tropea, George T. Lountos, David S. Waugh, Alexander Wlodawer, József Tőzsér, János András Mótyán

{"title":"P1′ specificity of the S219V/R203G mutant tobacco etch virus protease","authors":"Mária Golda, Gyula Hoffka, Scott Cherry, Joseph E. Tropea, George T. Lountos, David S. Waugh, Alexander Wlodawer, József Tőzsér, János András Mótyán","doi":"10.1002/prot.26693","DOIUrl":"https://doi.org/10.1002/prot.26693","url":null,"abstract":"Proteases that recognize linear amino acid sequences with high specificity became indispensable tools of recombinant protein technology for the removal of various fusion tags. Due to its stringent sequence specificity, the catalytic domain of the nuclear inclusion cysteine protease of tobacco etch virus (TEV PR) is also a widely applied reagent for enzymatic removal of fusion tags. For this reason, efforts have been made to improve its stability and modify its specificity. For example, P1′ autoproteolytic cleavage‐resistant mutant (S219V) TEV PR was found not only to be nearly impervious to self‐inactivation, but also exhibited greater stability and catalytic efficiency than the wild‐type enzyme. An R203G substitution has been reported to further relax the P1′ specificity of the enzyme, however, these results were obtained from crude intracellular assays. Until now, there has been no rigorous comparison of the P1′ specificity of the S219V and S219V/R203G mutants in vitro, under carefully controlled conditions. Here, we compare the P1′ amino acid preferences of these single and double TEV PR mutants. The in vitro analysis was performed by using recombinant protein substrates representing 20 P1′ variants of the consensus TENLYFQ*SGT cleavage site, and synthetic oligopeptide substrates were also applied to study a limited set of the most preferred variants. In addition, the enzyme–substrate interactions were analyzed in silico. The results indicate highly similar P1′ preferences for both enzymes, many side‐chains can be accommodated by the S1′ binding sites, but the kinetic assays revealed lower catalytic efficiency for the S219V/R203G than for the S219V mutant.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140803482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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The study of iron‐ and copper‐binding proteome of Fusarium oxysporum and its effector candidates 草孢子菌的铁和铜结合蛋白质组及其效应物候选研究

IF 2.9 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2024-04-26 DOI: 10.1002/prot.26696

Ankita Singh Kushwah, Himisha Dixit, Vipin Upadhyay, Shailender Kumar Verma, Ramasare Prasad

{"title":"The study of iron‐ and copper‐binding proteome of Fusarium oxysporum and its effector candidates","authors":"Ankita Singh Kushwah, Himisha Dixit, Vipin Upadhyay, Shailender Kumar Verma, Ramasare Prasad","doi":"10.1002/prot.26696","DOIUrl":"https://doi.org/10.1002/prot.26696","url":null,"abstract":"Fusarium oxysporum f.sp. lycopersici is a phytopathogen which causes vascular wilt disease in tomato plants. The survival tactics of both pathogens and hosts depend on intricate interactions between host plants and pathogenic microbes. Iron‐binding proteins (IBPs) and copper‐binding proteins (CBPs) play a crucial role in these interactions by participating in enzyme reactions, virulence, metabolism, and transport processes. We employed high‐throughput computational tools at the sequence and structural levels to investigate the IBPs and CBPs of F. oxysporum. A total of 124 IBPs and 37 CBPs were identified in the proteome of Fusarium. The ranking of amino acids based on their affinity for binding with iron is Glu > His> Asp > Asn > Cys, and for copper is His > Asp > Cys respectively. The functional annotation, determination of subcellular localization, and Gene Ontology analysis of these putative IBPs and CBPs have unveiled their potential involvement in a diverse array of cellular and biological processes. Three iron‐binding glycosyl hydrolase family proteins, along with four CBPs with carbohydrate‐binding domains, have been identified as potential effector candidates. These proteins are distinct from the host Solanum lycopersicum proteome. Moreover, they are known to be located extracellularly and function as enzymes that degrade the host cell wall during pathogen–host interactions. The insights gained from this report on the role of metal ions in plant–pathogen interactions can help develop a better understanding of their fundamental biology and control vascular wilt disease in tomato plants.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140806428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploiting protein language models for the precise classification of ion channels and ion transporters 利用蛋白质语言模型对离子通道和离子转运体进行精确分类

IF 2.9 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2024-04-24 DOI: 10.1002/prot.26694

Hamed Ghazikhani, Gregory Butler

{"title":"Exploiting protein language models for the precise classification of ion channels and ion transporters","authors":"Hamed Ghazikhani, Gregory Butler","doi":"10.1002/prot.26694","DOIUrl":"https://doi.org/10.1002/prot.26694","url":null,"abstract":"This study introduces TooT‐PLM‐ionCT, a comprehensive framework that consolidates three distinct systems, each meticulously tailored for one of the following tasks: distinguishing ion channels (ICs) from membrane proteins (MPs), segregating ion transporters (ITs) from MPs, and differentiating ICs from ITs. Drawing upon the strengths of six Protein Language Models (PLMs)—ProtBERT, ProtBERT‐BFD, ESM‐1b, ESM‐2 (650M parameters), and ESM‐2 (15B parameters), TooT‐PLM‐ionCT employs a combination of traditional classifiers and deep learning models for nuanced protein classification. Originally validated on an existing dataset by previous researchers, our systems demonstrated superior performance in identifying ITs from MPs and distinguishing ICs from ITs, with the IC‐MP discrimination achieving state‐of‐the‐art results. In light of recommendations for additional validation, we introduced a new dataset, significantly enhancing the robustness and generalization of our models across bioinformatics challenges. This new evaluation underscored the effectiveness of TooT‐PLM‐ionCT in adapting to novel data while maintaining high classification accuracy. Furthermore, this study explores critical factors affecting classification accuracy, such as dataset balancing, the impact of using frozen versus fine‐tuned PLM representations, and the variance between half and full precision in floating‐point computations. To facilitate broader application and accessibility, a web server (https://tootsuite.encs.concordia.ca/service/TooT-PLM-ionCT) has been developed, allowing users to evaluate unknown protein sequences through our specialized systems for IC‐MP, IT‐MP, and IC‐IT classification tasks.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140803557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural basis for the recognition of α‐1,6‐branched α‐glucan by GH13_47 α‐amylase from Rhodothermus marinus 海红藻 GH13_47 α-淀粉酶识别 α-1,6-支链 α-葡聚糖的结构基础

IF 2.9 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2024-04-20 DOI: 10.1002/prot.26695

Yuki Miyasaka, Kohei Yokoyama, Takuma Kozono, Yoshikazu Kitano, Takatsugu Miyazaki, Masayoshi Sakaguchi, Atsushi Nishikawa, Takashi Tonozuka

{"title":"Structural basis for the recognition of α‐1,6‐branched α‐glucan by GH13_47 α‐amylase from Rhodothermus marinus","authors":"Yuki Miyasaka, Kohei Yokoyama, Takuma Kozono, Yoshikazu Kitano, Takatsugu Miyazaki, Masayoshi Sakaguchi, Atsushi Nishikawa, Takashi Tonozuka","doi":"10.1002/prot.26695","DOIUrl":"https://doi.org/10.1002/prot.26695","url":null,"abstract":"Glycoside hydrolase (GH) family 13 is among the main families of enzymes acting on starch; recently, subfamily 47 of GH13 (GH13_47) has been established. The crystal structure and function of a GH13_47 enzyme from Bacteroides ovatus has only been reported to date. This enzyme has α‐amylase activity, while the GH13_47 enzymes comprise approximately 800–900 amino acid residues which are almost double those of typical α‐amylases. It is important to know how different the GH13_47 enzymes are from other α‐amylases. Rhodothermus marinus JCM9785, a thermophilic bacterium, possesses a gene for the GH13_47 enzyme, which is designated here as RmGH13_47A. Its structure has been predicted to be composed of seven domains: N1, N2, N3, A, B, C, and D. We constructed a plasmid encoding Gly266‐Glu886, which contains the N3, A, B, and C domains and expressed the protein in Escherichia coli. The enzyme hydrolyzed starch and pullulan by a neopullulanase‐type action. Additionally, the enzyme acted on maltotetraose, and saccharides with α‐1,6‐glucosidic linkages were observed in the products. Following the replacement of the catalytic residue Asp563 with Ala, the crystal structure of the variant D563A in complex with the enzymatic products from maltotetraose was determined; as a result, electron density for an α‐1,6‐branched pentasaccharide was observed in the catalytic pocket, and Ile762 and Asp763 interacted with the branched chain of the pentasaccharide. These findings suggest that RmGH13_47A is an α‐amylase that prefers α‐1,6‐branched parts of starch to produce oligosaccharides.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140625921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Graphical models for identifying pore‐forming proteins 识别孔形成蛋白质的图形模型

IF 2.9 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2024-04-15 DOI: 10.1002/prot.26687

Nan Xu, Theodore W. Kahn, Theju Jacob, Yan Liu

{"title":"Graphical models for identifying pore‐forming proteins","authors":"Nan Xu, Theodore W. Kahn, Theju Jacob, Yan Liu","doi":"10.1002/prot.26687","DOIUrl":"https://doi.org/10.1002/prot.26687","url":null,"abstract":"Pore‐forming toxins (PFTs) are proteins that form lesions in biological membranes. Better understanding of the structure and function of these proteins will be beneficial in a number of biotechnological applications, including the development of new pest control methods in agriculture. When searching for new pore formers, existing sequence homology‐based methods fail to discover truly novel proteins with low sequence identity to known proteins. Search methodologies based on protein structures would help us move beyond this limitation. As the number of known structures for PFTs is very limited, it's quite challenging to identify new proteins having similar structures using computational approaches like deep learning. In this article, we therefore propose a sample‐efficient graphical model, where a protein structure graph is first constructed according to consensus secondary structures. A semi‐Markov conditional random fields model is then developed to perform protein sequence segmentation. We demonstrate that our method is able to distinguish structurally similar proteins even in the absence of sequence similarity (pairwise sequence identity < 0.4)—a feat not achievable by traditional approaches like HMMs. To extract proteins of interest from a genome‐wide protein database for further study, we also develop an efficient framework for UniRef50 with 43 million proteins.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140565831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Cover Image, Volume 92, Issue 5 封面图片，第 92 卷第 5 期

IF 2.9 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2024-04-12 DOI: 10.1002/prot.26691

Irena Roterman, Katarzyna Stapor, Leszek Konieczny

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Issue Information ‐ Table of Content 发行信息 - 目录

IF 2.9 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2024-04-12 DOI: 10.1002/prot.26520

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Thermodynamic consequences of stapling side‐chains on a peptide ligand using a lactam‐bridge: A theoretical study on anti‐angiogenic peptides targeting VEGF 使用内酰胺桥在多肽配体上订合侧链的热力学后果：针对血管内皮生长因子的抗血管生成肽的理论研究

IF 2.9 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2024-04-11 DOI: 10.1002/prot.26692

Mahroof Kalathingal, Young Min Rhee

{"title":"Thermodynamic consequences of stapling side‐chains on a peptide ligand using a lactam‐bridge: A theoretical study on anti‐angiogenic peptides targeting VEGF","authors":"Mahroof Kalathingal, Young Min Rhee","doi":"10.1002/prot.26692","DOIUrl":"https://doi.org/10.1002/prot.26692","url":null,"abstract":"Peptides are promising therapeutic agents for various biological targets due to their high efficacy and low toxicity, and the design of peptide ligands with high binding affinity to the target of interest is of utmost importance in peptide‐based drug design. Introducing a conformational constraint to a flexible peptide ligand using a side‐chain lactam‐bridge is a convenient and efficient method to improve its binding affinity to the target. However, in general, such a small structural modification to a flexible ligand made with the intent of lowering the configurational entropic penalty for binding may have unintended consequences in different components of the binding enthalpy and entropy, including the configurational entropy component, which are still not clearly understood. Toward probing this, we examine different components of the binding enthalpy and entropy as well as the underlying structure and dynamics, for a side‐chain lactam‐bridged peptide inhibitor and its flexible analog forming complexes with vascular endothelial growth factor (VEGF), using all‐atom molecular dynamics simulations. It is found that introducing a side‐chain lactam‐bridge constraint into the flexible peptide analog led to a gain in configurational entropy change but losses in solvation entropy, solute internal energy, and solvation energy changes upon binding, pinpointing the opportunities and challenges in drug design. The present study features an interplay between configurational and solvation entropy changes, as well as the one between binding enthalpy and entropy, in ligand‐target binding upon imposing a conformational constraint into a flexible ligand.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140565834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0