Journal of Molecular Biology最新文献

{"title":"From Extreme Environments in Nature to Molecular and Cellular Adaptation and Functional Regulation","authors":"Igor N. Berezovsky , Ruth Nussinov","doi":"10.1016/j.jmb.2026.169639","DOIUrl":"10.1016/j.jmb.2026.169639","url":null,"abstract":"","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 4","pages":"Article 169639"},"PeriodicalIF":4.5,"publicationDate":"2026-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145984203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrating Sequence, Structure, and Graph-based Features for Elucidating the Stability of Thermophilic Proteins","authors":"P. Ramakrishna Reddy,&nbsp;Fathima Ridha,&nbsp;M. Michael Gromiha","doi":"10.1016/j.jmb.2025.169593","DOIUrl":"10.1016/j.jmb.2025.169593","url":null,"abstract":"<div><div>Proteins from thermophilic organisms exhibit remarkable stability under extreme thermal conditions. Understanding the molecular mechanisms underlying thermostability is essential for studying protein evolution and engineering robust enzymes. In this study, we systematically analyzed four sets of mesophilic–thermophilic protein pairs to investigate the molecular basis of thermal adaptation. We have constructed independent datasets of mesophilic–thermophilic protein pairs defined by sequence identity and optimal growth temperature (OGT): (a) &gt;90% identity and 60–80 °C OGT, (b) 50–90% identity and &gt;80 °C OGT, (c) 50–90% identity and 60–80 °C OGT, and (d) 50–90% identity and 40–60 °C OGT. Mutational analysis revealed that thermophilic proteins consistently reduced polar, uncharged residues while enriching charged, hydrophobic, and aromatic residues, particularly in extreme thermophiles (&gt;80 °C). Further, by integrating multiple known protein features into a hierarchical rule-based classifier, we identified the thermostable protein from a pair of sequences and also assessed the relative importance of features across datasets to provide interpretable insights into protein thermostability. The hierarchical rule-based method identified stabilizing residues as the primary distinguishing factor, followed by electrostatic energy, volume, and localized electrical effects, which correctly classified 99% of thermophilic proteins. A bagging model trained on the same features achieved a balanced accuracy of 92% in 5-fold cross-validation and 91% on the 20% hold-out test set. Furthermore, independent validation using multiple mutations in proteins accurately identified 94% of stabilizing and destabilizing mutations. The results obtained in this work provide valuable insights to understand the thermal adaptation of proteins and reliably identify thermostable proteins.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 4","pages":"Article 169593"},"PeriodicalIF":4.5,"publicationDate":"2026-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145754843","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On the Molecular Basis of the Hypersaline Adaptation of Halophilic Proteins","authors":"Gabriel Ortega-Quintanilla ,&nbsp;Oscar Millet","doi":"10.1016/j.jmb.2025.169439","DOIUrl":"10.1016/j.jmb.2025.169439","url":null,"abstract":"<div><div>Halophilic organisms have adapted to survive in environments with extremely high salinity, such as saline lakes. To achieve this, they modify their proteome to withstand salt concentrations that inactivate non-adapted mesophilic proteins. The surfaces of halophilic proteins feature a very characteristic amino acid composition, favoring short, polar, and acidic amino acids—such as aspartate, glutamate, and threonine—while disfavoring bulky, hydrophobic amino acids—such as lysine, methionine, and leucine. In this work, we review our understanding of the molecular basis of haloadaptation. We critically examine the role of electrostatic interactions in stabilizing halophilic proteins, while underlining the importance of other contributions from hydrophobic solvation and preferential ion exclusion. Finally, we describe the mechanistic link by which the halophilic amino acid composition optimizes function in hypersaline environments, balancing the trade-off between stability, solubility, and catalytic function.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 4","pages":"Article 169439"},"PeriodicalIF":4.5,"publicationDate":"2026-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145068836","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PERCEPTRON-PTMKB: A Web Server for Residue-Based Post-Translational Modification Analysis and Propensity Scoring.","authors":"Abdullah Bin Faiz, Muhammad Shoaib, Safee Ullah Chaudary","doi":"10.1016/j.jmb.2026.169709","DOIUrl":"10.1016/j.jmb.2026.169709","url":null,"abstract":"<p><p>The identification of post-translational modifications (PTMs) of protein residues is vital for understanding protein functions and their subsequent role in cellular processes. Researchers have collected substantial experimental data on PTMs along with their validation and assortment into online databases. However, these databases do not offer integration with protein search and identification tools which then prevent researchers from seamlessly employing them in deciphering PTMs in biological samples. Additionally, there is a lack of tools that evaluate protein residues in light of their neighborhoods for the variety of PTMs found in PTM databases. Here, we propose PERCEPTRON-PTMKB, a web server designed for the analysis and evaluation of PTM sites using empirical datasets. PERCEPTRON-PTMKB provides a quantitative evaluation of per-residue PTM site through its propensity scoring algorithm. The search and propensity calculation pipelines are also served via a secure RESTful API, which enables their seamless integration into protein sequence search engines. PERCEPTRON-PTMKB is available freely at https://perceptronptmkb.lums.edu.pk.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169709"},"PeriodicalIF":4.5,"publicationDate":"2026-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146197163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CLISGen: A Comprehensive Resource of SNP Genotypes for Human Cell Lines.","authors":"Matteo Marchesin, Davide Dalfovo, Alessandro Romanel","doi":"10.1016/j.jmb.2026.169681","DOIUrl":"10.1016/j.jmb.2026.169681","url":null,"abstract":"<p><p>Selecting cell lines with specific Single Nucleotide Polymorphism (SNP) genotypes is a critical bottleneck in functional genomics, often requiring advanced bioinformatic skills. To address this, we developed CLISGen (Cell LInes SNP Genotypes), a database with a user-friendly web application that simplifies access to SNP genotypes in over 1000 cancer cell lines from the Cancer Cell Line Encyclopedia. CLISGen integrates and harmonizes data from Whole-Genome, Whole-Exome, and RNA sequencing, enriching it with contextual information like copy number alterations and genetic ancestry. The platform allows users to search for specific variants or variants in specific genes or genomic regions and filter results by tissue type or data quality, providing intuitive graphical and tabular outputs. By eliminating a major experimental bottleneck, CLISGen offers researchers a powerful resource to efficiently select suitable cell models for studying the link between genetic variation and cancer. CLISGen is freely available at https://bcglab.cibio.unitn.it/clisgen.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169681"},"PeriodicalIF":4.5,"publicationDate":"2026-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146140727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"KBase: Open-source Platform for Collaborative Biological Data Analysis and Publication.","authors":"Elisha M Wood-Charlson, Christopher S Henry, Paramvir S Dehal, Gazi Mahmud, Benjamin H Allen, Kathleen Beilsmith, D Dakota Blair, Shane Canon, Mikaela Cashman, Dylan Chivian, Robert Cottingham, Zachary Crockett, Ellen G Dow, Meghan Drake, Janaka N Edirisinghe, José P Faria, Andrew Freiburger, Tianhao Gu, Prachi Gupta, A J Ireland, Sean Jungbluth, Roy Kamimura, Keith Keller, Ahmed Khan, Dileep Kishore, Dan Klos, Filipe Liu, David Lyon, Christopher Neely, Katherine L O'Grady, Gavin Price, Priya Ranjan, William J Riehl, Boris Sadkhin, Sam Seaver, Gwyneth A Terry, Yue Wang, Pamela Weisenhorn, Ziming Yang, Shinjae Yoo, Adam P Arkin","doi":"10.1016/j.jmb.2026.169676","DOIUrl":"10.1016/j.jmb.2026.169676","url":null,"abstract":"<p><p>The U.S. Department of Energy's Systems Biology Knowledgebase (KBase; www.kbase.us) is an open, collaborative platform that integrates data, models, and analysis tools to accelerate discovery in microbiology, plant biology, and environmental systems. Recently, KBase expanded as a comprehensive, multi-omics ecosystem. KBase enables representation of scientific samples, long-read sequence analysis, protein structure integration, and scalable modeling of microbial communities across diverse environments. KBase also generates digital notebooks as citable, executable research objects that link data, methods, and interpretation. KBase also supports a global education community focused on training the next generation of scientists to use high-performance computational tools. Together, these advances position KBase as a central hub for open, reproducible systems biology. In turn, this enables us to integrate many of the emerging advances in data federation, semantic interoperability, and agent-assisted analysis, paving the way for KBase to support the next generation of AI-driven discovery tools.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169676"},"PeriodicalIF":4.5,"publicationDate":"2026-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146130788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ABSEIL: A polypeptide helicity and ensemble prediction tool.","authors":"Hannah Hortman, Ruiling A Zhang, Roy G Hughes, Marco Castillo, Eric Chen, Samia Evans, Jonathan Ortega, Jeremy Bandini, Mark McCahill, Scott C Schmidler, Terrence G Oas","doi":"10.1016/j.jmb.2026.169675","DOIUrl":"10.1016/j.jmb.2026.169675","url":null,"abstract":"<p><p>Nascent helicity in polypeptides and unfolded proteins arises from local structure formation and represents one of the earliest events in a protein folding reaction. Nascent helicity may also influence the physical properties of intrinsically disordered regions. For this reason, there has been great interest in statistical mechanical models that describe the coil→helix transitions that lead to nascent helicity. These models, collectively called helix-coil models, have been empirically parameterized using an extensive data set of circular dichroism (CD) measurements of natural and designed peptides that form various degrees of nascent helicity. The purpose of A Bayesian Statistical Engine to Infer HeLicity (ABSEIL) (https://abseil.oit.duke.edu/) is to allow users to submit polypeptide sequences to: (1) predict the overall helicity of the sequence; (2) predict the helicity of each residue; and (3) enumerate the ensemble of helix-coil configurations in order of their relative populations. The tool also allows users to search the database of peptide CD experiments on which the predictive model was trained. The website architecture allows for anonymous usage and enables administrative management. The web application server is managed by the Duke Office of Information Technology (OIT) system administrators and conforms to OIT's security and operational best practices.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169675"},"PeriodicalIF":4.5,"publicationDate":"2026-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13003202/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146137075","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"mCSM-metal: A Deep Learning Resource to Predict Effect of Mutations on Metal Ion Binding.","authors":"Akshita Kumar, Ashar J Malik, David B Ascher","doi":"10.1016/j.jmb.2026.169678","DOIUrl":"10.1016/j.jmb.2026.169678","url":null,"abstract":"<p><p>Metal ions play critical structural, regulatory, and enzymatic roles in proteins, making their binding essential for biological processes. Experimental identification of metal-binding sites is resource-intensive and limited in scalability. Recent advances in protein language models have transformed computational predictions, yet current tools do not address how residue-level metal-binding probabilities change upon mutation. To fill this gap, mCSM-metal leverages embeddings from ESMBind with our graph-based structural signatures to accurately predict the effects of single or multiple point mutations on the binding of seven essential ions (Zn²⁺, Ca²⁺, Mg²⁺, Mn²⁺, Fe³⁺, Co²⁺, Cu²⁺). Our model achieves accuracies, F1-scores, and Matthews Correlation Coefficient values up to 0.97, 0.97, and 0.95, outperforming other approaches. The webserver provides an interactive platform to assess and visualise local and long-range impacts of mutations on metal-ion binding, offering new avenues for applications in structural biology, disease modelling, and protein engineering. The web application is freely available at: https://biosig.lab.uq.edu.au/mcsm_metal/.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169678"},"PeriodicalIF":4.5,"publicationDate":"2026-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146130753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sequence Engineering at Non-motif Modulator Residues Yields a Peptide That Effectively Targets a Single PDZ Protein in a Disease-relevant Cellular Context","authors":"Jeanine F. Amacher ,&nbsp;Patrick R. Cushing ,&nbsp;Lars Vouilleme ,&nbsp;Sierra N. Cullati ,&nbsp;Bin Deng ,&nbsp;Scott A. Gerber ,&nbsp;Prisca Boisguerin ,&nbsp;Dean R. Madden","doi":"10.1016/j.jmb.2025.169597","DOIUrl":"10.1016/j.jmb.2025.169597","url":null,"abstract":"<div><div>PDZ interaction networks are finely-tuned products of evolution. These widespread binding domains recognize short linear motifs (SLiMs), usually at the C-terminus of their interacting partners, and are involved in trafficking and signaling pathways, the formation of tight junctions, and scaffolding of the post-synaptic density of neurons, amongst other roles. Typically, a single PDZ domain binds multiple targets; conversely, each PDZ-binding protein engages several PDZ domains, dependent on cellular conditions. Historical PDZ binding motifs rely on two key positions for binding. However, previous insights on modulator, or non-motif, selectivity preferences reveal that these limited motifs are insufficient to describe PDZ-mediated interactomes, consistent with the observation that the degree of promiscuity is much more limited than predicted by defined binding classes. Here, we use these principles to engineer and test a peptide-based inhibitor capable of interacting with a single PDZ domain-containing protein in a disease-relevant cellular system. We first interrogate a previously developed sequence selective for cystic fibrosis transmembrane conductance regulator (CFTR)-Associated Ligand (CAL), one of five PDZ domains known to bind the CFTR C-terminus, probing for off-target PDZ partners. Once identified, we use parallel biochemical and structural refinement to eliminate these interactions and introduce a CAL PDZ inhibitor with unprecedented PDZ domain selectivity. We test and verify specificity using relevant cellular PDZ target networks in a mass spectrometry-based approach. Our resultant selective inhibitor enhances chloride efflux when applied to polarized patient bronchial epithelial cells, as well as confirms that engineering an effectively single-PDZ peptide is possible when modulator preferences are applied.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 3","pages":"Article 169597"},"PeriodicalIF":4.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145792920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural and Biochemical Insights into the Broad-Spectrum TET Enzyme From Methanocaldococcus jannaschii Reveal the Basis of Substrate Specificity in M42 Aminopeptidases","authors":"Joaquin Atalah ,&nbsp;Hind Basbous ,&nbsp;Gregory Effantin ,&nbsp;Sylvie Kieffer-Jaquinod ,&nbsp;Guy Schoehn ,&nbsp;Eric Girard ,&nbsp;Bruno Franzetti","doi":"10.1016/j.jmb.2025.169596","DOIUrl":"10.1016/j.jmb.2025.169596","url":null,"abstract":"<div><div>TET peptidases of the M42 family are ∼500 kDa hollow dodecameric complexes ubiquitous in prokaryotes. These enzymes act as strict aminopeptidases, catalyzing the removal of N-terminal amino acids from peptides. A common feature of M42 TET aminopeptidases characterized to date is their marked substrate preference for a limited subset of amino acids. Unlike other hyperthermophilic archaea studied so far, the autotrophic archaeon <em>Methanocaldococcus jannaschii</em> possesses only a single gene encoding an M42 peptidase. This enzyme, named MjTET, is the first reported M42 peptidase to exhibit broad amino acid specificity, including activity on aromatic residues. To assess their peptide degradation efficiencies, the catalytic constants of MjTET were compared to those of its close analogs from <em>Pyrococcus horikoshii</em>. The specialized TETs from <em>P. horikoshii</em> displayed higher catalytic efficiencies than the generalist MjTET, likely reflecting the reliance of Thermococcales on peptide fermentation for energy. Additionally, the structure of MjTET was resolved to 3 Å using cryo-EM and compared with the available models of the four <em>P. horikoshii</em> TETs to identify features underlying substrate specificity. This analysis, combined with mutagenesis studies, revealed a previously uncharacterized loop in the catalytic domain that contributes to substrate discrimination. Collectively, these findings show that substrate specificity in TET enzymes arises from a complex interplay of tertiary structure, oligomeric assembly, and electrostatic surface potential.</div></div><div><h3>Importance</h3><div>This study first reported a novel TET peptidase from Methanogenic hyperthermophilic archaea. Its enzymatic properties compared to the specialized TET enzyme characterized so far from heterotrophic archaea suggest a link with autotrophy. It also represents an important step in explaining the structural features guiding substrate specificity.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 3","pages":"Article 169596"},"PeriodicalIF":4.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145792970","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}