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Solution NMR goes big: Atomic resolution studies of protein components of molecular machines and phase-separated condensates 溶液核磁共振大：分子机器和相分离凝聚物的蛋白质组分的原子分辨率研究。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-02-01 DOI: 10.1016/j.sbi.2024.102976
Alexander I.M. Sever , Rashik Ahmed , Philip Rößler , Lewis E. Kay
{"title":"Solution NMR goes big: Atomic resolution studies of protein components of molecular machines and phase-separated condensates","authors":"Alexander I.M. Sever ,&nbsp;Rashik Ahmed ,&nbsp;Philip Rößler ,&nbsp;Lewis E. Kay","doi":"10.1016/j.sbi.2024.102976","DOIUrl":"10.1016/j.sbi.2024.102976","url":null,"abstract":"<div><div>The tools of structural biology have undergone remarkable advances in the past decade. These include new computational and experimental approaches that have enabled studies at a level of detail – and ease – that were not previously possible. Yet, significant deficiencies in our understanding of biomolecular function remain and new challenges must be overcome to go beyond static pictures towards a description of function in terms of structural dynamics. Solution Nuclear Magnetic Resonance (NMR) spectroscopy has emerged as a powerful technique for atomic resolution studies of the dynamics of a wide range of biomolecules, including molecular machines and the components of phase-separated condensates. Here we highlight some of the very recent advances in these areas that have been driven by NMR.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"90 ","pages":"Article 102976"},"PeriodicalIF":6.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143001536","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}
引用次数: 0
Traversing the drug discovery landscape using native mass spectrometry 使用原生质谱法遍历药物发现景观。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-02-01 DOI: 10.1016/j.sbi.2025.102993
Hannah M. Britt , Carol V. Robinson
{"title":"Traversing the drug discovery landscape using native mass spectrometry","authors":"Hannah M. Britt ,&nbsp;Carol V. Robinson","doi":"10.1016/j.sbi.2025.102993","DOIUrl":"10.1016/j.sbi.2025.102993","url":null,"abstract":"<div><div>As health needs in our society evolve, the field of drug discovery must undergo constant innovation and improvement to identify novel targets and drug candidates. Owing to its ability to simultaneously capture biological interactions and provide in-depth molecular characterisation of the species involved, native mass spectrometry is starting to play an important role in this endeavour. Here, we discuss recent contributions that native mass spectrometry has made to drug discovery including deciphering protein-small molecule interactions, unravelling biochemical pathways, and integrating with complementary structural approaches.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"91 ","pages":"Article 102993"},"PeriodicalIF":6.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078796","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}
引用次数: 0
Computational advances in discovering cryptic pockets for drug discovery 发现药物发现的隐口袋的计算进展。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-02-01 DOI: 10.1016/j.sbi.2024.102975
Martijn P. Bemelmans , Zoe Cournia , Kelly L. Damm-Ganamet , Francesco L. Gervasio , Vineet Pande
{"title":"Computational advances in discovering cryptic pockets for drug discovery","authors":"Martijn P. Bemelmans ,&nbsp;Zoe Cournia ,&nbsp;Kelly L. Damm-Ganamet ,&nbsp;Francesco L. Gervasio ,&nbsp;Vineet Pande","doi":"10.1016/j.sbi.2024.102975","DOIUrl":"10.1016/j.sbi.2024.102975","url":null,"abstract":"<div><div>A number of promising therapeutic target proteins have been considered “undruggable” due to the lack of well-defined ligandable pockets. Substantial research in protein dynamics has elucidated the existence of “cryptic” pockets that only exist transiently and become favorable for binding in the presence of a ligand. These pockets provide an avenue to target challenging proteins, inspiring the development of multiple computational methods. This review highlights established cryptic pocket modeling approaches like mixed solvent molecular dynamics and recent applications of enhanced sampling and AI-based methods in therapeutically relevant proteins.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"90 ","pages":"Article 102975"},"PeriodicalIF":6.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142946100","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}
引用次数: 0
Molecular basis of conjugation-mediated DNA transfer by gram-negative bacteria 革兰氏阴性菌偶联介导DNA转移的分子基础。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-02-01 DOI: 10.1016/j.sbi.2024.102978
Gabriel Waksman
{"title":"Molecular basis of conjugation-mediated DNA transfer by gram-negative bacteria","authors":"Gabriel Waksman","doi":"10.1016/j.sbi.2024.102978","DOIUrl":"10.1016/j.sbi.2024.102978","url":null,"abstract":"<div><div>Bacterial conjugation is the unidirectional transfer of DNA (often plasmids, but also other mobile genetic elements, or even entire genomes), from a donor cell to a recipient cell. In Gram-negative bacteria, it requires the formation of three complexes in the donor cell: i-a large, double-membrane-embedded transport machinery called the Type IV Secretion System (T4SS), ii-a long extracellular tube, the conjugative pilus, and iii-a DNA-processing machinery termed the relaxosome. While knowledge has expanded regarding molecular events in the donor cell, very little is known about the machinery involved in DNA transfer into the recipient cell. Here, focusing on systems principally involved in DNA transfer, we provide an update on progress made on various mechanistic aspects of conjugation.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"90 ","pages":"Article 102978"},"PeriodicalIF":6.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143001518","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}
引用次数: 0
Protein binding and folding through an evolutionary lens 从进化的角度看蛋白质的结合和折叠。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-02-01 DOI: 10.1016/j.sbi.2024.102980
Per Jemth
{"title":"Protein binding and folding through an evolutionary lens","authors":"Per Jemth","doi":"10.1016/j.sbi.2024.102980","DOIUrl":"10.1016/j.sbi.2024.102980","url":null,"abstract":"<div><div>Protein–protein associations are often mediated by an intrinsically disordered protein region interacting with a folded domain in a coupled binding and folding reaction. Classic physical organic chemistry approaches together with structural biology have shed light on mechanistic aspects of such reactions. Further insight into general principles may be obtained by interpreting the results through an evolutionary lens. This review attempts to provide an overview on how the analysis of binding and folding reactions can benefit from an evolutionary approach, and is aimed at protein scientists without a background in evolution. Evolution constantly reshapes existing proteins by sampling more or less fit variants. Most new variants are weeded out as generations and new species come and go over hundreds to hundreds of millions of years. The huge ongoing genome sequencing efforts have provided us with a snapshot of existing adapted fit-for-purpose protein homologs in thousands of different organisms. Comparison of present-day orthologs and paralogs highlights general principles of the evolution of coupled binding and folding reactions and demonstrate a great potential for evolution to operate on disordered regions and modulate affinity and specificity of the interactions.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"90 ","pages":"Article 102980"},"PeriodicalIF":6.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143001533","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}
引用次数: 0
Protein-nucleic acid complexes: Docking and binding affinity 蛋白质-核酸复合物：对接和结合亲和力
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-11-30 DOI: 10.1016/j.sbi.2024.102955
M. Michael Gromiha, K. Harini
{"title":"Protein-nucleic acid complexes: Docking and binding affinity","authors":"M. Michael Gromiha,&nbsp;K. Harini","doi":"10.1016/j.sbi.2024.102955","DOIUrl":"10.1016/j.sbi.2024.102955","url":null,"abstract":"<div><div>Protein-nucleic interactions play essential roles in several biological processes, such as gene regulation, replication, transcription, repair and packaging. The knowledge of three-dimensional structures of protein-nucleic acid complexes and their binding affinities helps to understand these functions. In this review, we focus on two major aspects namely, (i) deciphering the three-dimensional structures of protein-nucleic acid complexes and (ii) predicting their binding affinities. The first part is devoted to the state-of-the-art methods for predicting the native structures and their performances including recent CASP targets. The second part is focused on different aspects of investigating the binding affinity of protein-nucleic acid complexes: (i) databases for thermodynamic parameters to understand the binding affinity, (ii) important features determining protein-nucleic acid binding affinity, (iii) predicting the binding affinity of protein-nucleic acid complexes using sequence and structure-based parameters and (iv) change in binding affinity upon mutation. It includes the latest developments in protein-nucleic acid docking algorithms and binding affinity predictions along with a list of computational resources for understanding protein-DNA and protein-RNA interactions.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"90 ","pages":"Article 102955"},"PeriodicalIF":6.1,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142748010","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}
引用次数: 0
Protein data bank: From two epidemics to the global pandemic to mRNA vaccines and Paxlovid 蛋白质数据库：从两次流行病到全球大流行，再到 mRNA 疫苗和 Paxlovid
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-11-24 DOI: 10.1016/j.sbi.2024.102954
Stephen K. Burley
{"title":"Protein data bank: From two epidemics to the global pandemic to mRNA vaccines and Paxlovid","authors":"Stephen K. Burley","doi":"10.1016/j.sbi.2024.102954","DOIUrl":"10.1016/j.sbi.2024.102954","url":null,"abstract":"<div><div>Structural biologists and the open-access Protein Data Bank (PDB) played decisive roles in combating the COVID-19 pandemic. Global biostructure data were turned into global knowledge, allowing scientists and engineers to understand the inner workings of coronaviruses and develop effective countermeasures. Two mRNA vaccines, initially designed with guidance from PDB structures of the SARS-CoV-1 and MERS-CoV spike proteins, prevented infections entirely or reduced the likelihood of morbidity and mortality for more than five billion individual recipients worldwide. Structure-guided drug discovery by Pfizer, Inc (facilitated by PDB structures), initiated in the 2000s in response to SARS-CoV-1 and resumed in 2020, yielded nirmatrelvir (the active ingredient of Paxlovid) -- a potent, orally-bioavailable inhibitor of the SARS-CoV-2 main protease. You've got to love the Protein Data Bank!</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"90 ","pages":"Article 102954"},"PeriodicalIF":6.1,"publicationDate":"2024-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142699731","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}
引用次数: 0
Characterizing heterogeneity in amyloid formation processes 淀粉样蛋白形成过程中的异质性特征。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-11-19 DOI: 10.1016/j.sbi.2024.102951
Hoi Sung Chung
{"title":"Characterizing heterogeneity in amyloid formation processes","authors":"Hoi Sung Chung","doi":"10.1016/j.sbi.2024.102951","DOIUrl":"10.1016/j.sbi.2024.102951","url":null,"abstract":"<div><div>Protein aggregation is a complex process, consisting of a large number of pathways connecting monomers and mature amyloid fibrils. Recent advances in structure determination techniques, such as solid-state NMR and cryoEM, have allowed the determination of atomic resolution structures of fibril polymorphs, but most of the intermediate stages of the process including oligomer formation remain unknown. Proper characterization of the heterogeneity of the process is critical not only for physical and chemical understanding of the aggregation process but also for elucidation of the disease mechanisms and identification of therapeutic targets. This article reviews recent developments in the characterization of heterogeneity in amyloid formation processes.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102951"},"PeriodicalIF":6.1,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681273","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}
引用次数: 0
Biochemistry and genetics are coming together to improve our understanding of genotype to phenotype relationships 生物化学和遗传学正在结合在一起，以提高我们对基因型与表型关系的理解。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-11-12 DOI: 10.1016/j.sbi.2024.102952
Judith Notbohm , Tina Perica
{"title":"Biochemistry and genetics are coming together to improve our understanding of genotype to phenotype relationships","authors":"Judith Notbohm ,&nbsp;Tina Perica","doi":"10.1016/j.sbi.2024.102952","DOIUrl":"10.1016/j.sbi.2024.102952","url":null,"abstract":"<div><div>Since genome sequencing became accessible, determining how specific differences in genotypes lead to complex phenotypes such as disease has become one of the key goals in biomedicine. Predicting effects of sequence variants on cellular or organismal phenotype faces several challenges. First, variants simultaneously affect multiple protein properties and predicting their combined effect is complex. Second, effects of changes in a single protein propagate through the cellular network, which we only partially understand. In this review, we emphasize the importance of both biochemistry and genetics in addressing these challenges. Moreover, we highlight work that blurs the distinction between biochemistry and genetics fields to provide new insights into the genotype-to-phenotype relationships.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102952"},"PeriodicalIF":6.1,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616396","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}
引用次数: 0
Deep learning for intrinsically disordered proteins: From improved predictions to deciphering conformational ensembles 内在无序蛋白质的深度学习：从改进预测到解密构象组合。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-11-12 DOI: 10.1016/j.sbi.2024.102950
Gábor Erdős, Zsuzsanna Dosztányi
{"title":"Deep learning for intrinsically disordered proteins: From improved predictions to deciphering conformational ensembles","authors":"Gábor Erdős,&nbsp;Zsuzsanna Dosztányi","doi":"10.1016/j.sbi.2024.102950","DOIUrl":"10.1016/j.sbi.2024.102950","url":null,"abstract":"<div><div>Intrinsically disordered proteins (IDPs) lack a stable three-dimensional structure under physiological conditions, challenging traditional structure-based prediction methods. This review explores how modern deep learning approaches, which have revolutionized structure prediction for globular proteins, have impacted protein disorder predictions. We highlight the role of community-driven efforts in curating data and assessing state-of-the-art, which have been crucial in advancing the field. We also review state-of-the-art methods utilizing deep learning techniques, highlighting innovative approaches. We also address advancements in characterizing protein conformational ensembles directly from sequence data using novel machine learning methods.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102950"},"PeriodicalIF":6.1,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616402","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}
引用次数: 0
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