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Impact of quantum and neuromorphic computing on biomolecular simulations: Current status and perspectives 量子计算和神经形态计算对生物分子模拟的影响：现状与展望
IF 6.8 2区 生物学
Current opinion in structural biology Pub Date : 2024-05-24 DOI: 10.1016/j.sbi.2024.102817
Sandra Diaz-Pier , Paolo Carloni
{"title":"Impact of quantum and neuromorphic computing on biomolecular simulations: Current status and perspectives","authors":"Sandra Diaz-Pier ,&nbsp;Paolo Carloni","doi":"10.1016/j.sbi.2024.102817","DOIUrl":"https://doi.org/10.1016/j.sbi.2024.102817","url":null,"abstract":"<div><p>New high-performance computing architectures are becoming operative, in addition to exascale computers. Quantum computers (QC) solve optimization problems with unprecedented efficiency and speed, while neuromorphic hardware (NMH) simulates neural network dynamics. Albeit, at the moment, both find no practical use in all atom biomolecular simulations, QC might be exploited in the not-too-far future to simulate systems for which electronic degrees of freedom play a key and intricate role for biological function, whereas NMH might accelerate molecular dynamics simulations with low energy consumption. Machine learning and artificial intelligence algorithms running on NMH and QC could assist in the analysis of data and speed up research. If these implementations are successful, modular supercomputing could further dramatically enhance the overall computing capacity by combining highly optimized software tools into workflows, linking these architectures to exascale computers.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"87 ","pages":"Article 102817"},"PeriodicalIF":6.8,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959440X24000447/pdfft?md5=572fde927378e84697c8378fa6377638&pid=1-s2.0-S0959440X24000447-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141090675","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
Integrative modeling meets deep learning: Recent advances in modeling protein assemblies 综合建模与深度学习的结合：蛋白质组装建模的最新进展
IF 6.8 2区 生物学
Current opinion in structural biology Pub Date : 2024-05-24 DOI: 10.1016/j.sbi.2024.102841
Ben Shor, Dina Schneidman-Duhovny
{"title":"Integrative modeling meets deep learning: Recent advances in modeling protein assemblies","authors":"Ben Shor,&nbsp;Dina Schneidman-Duhovny","doi":"10.1016/j.sbi.2024.102841","DOIUrl":"https://doi.org/10.1016/j.sbi.2024.102841","url":null,"abstract":"<div><p>Recent progress in protein structure prediction based on deep learning revolutionized the field of Structural Biology. Beyond single proteins, it also enabled high-throughput prediction of structures of protein–protein interactions. Despite the success in predicting complex structures, large macromolecular assemblies still require specialized approaches. Here we describe recent advances in modeling macromolecular assemblies using integrative and hierarchical approaches. We highlight applications that predict protein–protein interactions and challenges in modeling complexes based on the interaction networks, including the prediction of complex stoichiometry and heterogeneity.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"87 ","pages":"Article 102841"},"PeriodicalIF":6.8,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141090676","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
Nanodiscs for the study of membrane proteins 用于研究膜蛋白的纳米光盘
IF 6.8 2区 生物学
Current opinion in structural biology Pub Date : 2024-05-24 DOI: 10.1016/j.sbi.2024.102844
Ilia G. Denisov, Stephen G. Sligar
{"title":"Nanodiscs for the study of membrane proteins","authors":"Ilia G. Denisov,&nbsp;Stephen G. Sligar","doi":"10.1016/j.sbi.2024.102844","DOIUrl":"https://doi.org/10.1016/j.sbi.2024.102844","url":null,"abstract":"<div><p>Nanodiscs represent a versatile tool for studies of membrane proteins and protein-membrane interactions under native-like conditions. Multiple variations of the Nanodisc platform, as well as new experimental methods, have been recently developed to understand various aspects of structure, dynamics and functional properties of systems involved in signaling, transport, blood coagulation and many other critically important processes. In this mini-review, we focus on some of these exciting recent developments that utilize the Nanodisc platform.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"87 ","pages":"Article 102844"},"PeriodicalIF":6.8,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141090674","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
Structural biology in cellulo: Minding the gap between conceptualization and realization 细胞结构生物学：注意概念化与实现之间的差距
IF 6.8 2区 生物学
Current opinion in structural biology Pub Date : 2024-05-23 DOI: 10.1016/j.sbi.2024.102843
Fotis L. Kyrilis , Jason K.K. Low , Joel P. Mackay , Panagiotis L. Kastritis
{"title":"Structural biology in cellulo: Minding the gap between conceptualization and realization","authors":"Fotis L. Kyrilis ,&nbsp;Jason K.K. Low ,&nbsp;Joel P. Mackay ,&nbsp;Panagiotis L. Kastritis","doi":"10.1016/j.sbi.2024.102843","DOIUrl":"https://doi.org/10.1016/j.sbi.2024.102843","url":null,"abstract":"<div><p>Recent technological advances have deepened our perception of cellular structure. However, most structural data doesn't originate from intact cells, limiting our understanding of cellular processes. Here, we discuss current and future developments that will bring us towards a structural picture of the cell. Electron cryotomography is the standard bearer, with its ability to provide <em>in cellulo</em> snapshots. Single-particle electron microscopy (of purified biomolecules and of complex mixtures) and covalent crosslinking combined with mass spectrometry also have significant roles to play, as do artificial intelligence algorithms in their many guises. To integrate these multiple approaches, data curation and standardisation will be critical – as is the need to expand efforts beyond our current protein-centric view to the other (macro)molecules that sustain life.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"87 ","pages":"Article 102843"},"PeriodicalIF":6.8,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959440X24000708/pdfft?md5=2564ad9745ce4e2e12c2449aef7b7814&pid=1-s2.0-S0959440X24000708-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141083832","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
Small spaces, big problems: The abnormal nucleoplasm of micronuclei and its consequences 小空间，大问题：微核的异常核质及其后果
IF 6.8 2区 生物学
Current opinion in structural biology Pub Date : 2024-05-18 DOI: 10.1016/j.sbi.2024.102839
Molly G. Zych , Emily M. Hatch
{"title":"Small spaces, big problems: The abnormal nucleoplasm of micronuclei and its consequences","authors":"Molly G. Zych ,&nbsp;Emily M. Hatch","doi":"10.1016/j.sbi.2024.102839","DOIUrl":"10.1016/j.sbi.2024.102839","url":null,"abstract":"<div><p>Micronuclei (MN) form from missegregated chromatin that recruits its own nuclear envelope during mitotic exit and are a common consequence of chromosomal instability. MN are unstable due to errors in nuclear envelope organization and frequently rupture, leading to loss of compartmentalization, loss of nuclear functions, and major changes in genome stability and gene expression. However, recent work found that, even prior to rupture, nuclear processes can be severely defective in MN, which may contribute to rupture-associated defects and have lasting consequences for chromatin structure and function. In this review we discuss work that highlights nuclear function defects in intact MN, including their mechanisms and consequences, and how biases in chromosome missegregation into MN may affect the penetrance of these defects. Illuminating the nuclear environment of MN demonstrates that MN formation alone has major consequences for both the genome and cell and provides new insight into how nuclear content is regulated.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"87 ","pages":"Article 102839"},"PeriodicalIF":6.8,"publicationDate":"2024-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141064415","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
Nucleic acids in modern molecular therapies: A realm of opportunities for strategic drug design 现代分子疗法中的核酸：战略性药物设计的机遇领域
IF 6.8 2区 生物学
Current opinion in structural biology Pub Date : 2024-05-16 DOI: 10.1016/j.sbi.2024.102838
Vito Genna , Laura Reyes-Fraile , Javier Iglesias-Fernandez , Modesto Orozco
{"title":"Nucleic acids in modern molecular therapies: A realm of opportunities for strategic drug design","authors":"Vito Genna ,&nbsp;Laura Reyes-Fraile ,&nbsp;Javier Iglesias-Fernandez ,&nbsp;Modesto Orozco","doi":"10.1016/j.sbi.2024.102838","DOIUrl":"https://doi.org/10.1016/j.sbi.2024.102838","url":null,"abstract":"<div><p>RNA vaccines have made evident to society what was already known by the scientific community: nucleic acids will be the “drugs of the future.” By modifying the genome, interfering in transcription or translation, and by introducing new catalysts into the cell or by mimicking antibody effects, nucleic acids can generate therapeutic activities that are not accessible by any other therapeutic agents. There are, however, challenges that need to be solved in the next few years to make nucleic acids usable in a wide range of therapeutic scenarios. This review illustrates how simulation methods can help achieve this goal.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"87 ","pages":"Article 102838"},"PeriodicalIF":6.8,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140950023","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
Context-dependent, fuzzy protein interactions: Towards sequence-based insights 与上下文相关的模糊蛋白质相互作用：基于序列的洞察力
IF 6.8 2区 生物学
Current opinion in structural biology Pub Date : 2024-05-16 DOI: 10.1016/j.sbi.2024.102834
Monika Fuxreiter
{"title":"Context-dependent, fuzzy protein interactions: Towards sequence-based insights","authors":"Monika Fuxreiter","doi":"10.1016/j.sbi.2024.102834","DOIUrl":"https://doi.org/10.1016/j.sbi.2024.102834","url":null,"abstract":"<div><p>Predicting protein interactions in the cellular environment still remains a challenge in the AlphaFold era. Protein interactions, similarly to their structures, sample a continuum from ordered to disordered states, with specific partners in many bound configurations. A multiplicity of binding modes (MBM) enables transition between these states under different cellular conditions. This review focuses on how the cellular environment affects protein interactions, highlighting the molecular mechanisms, biophysical origin, and sequence-based principles of context-dependent, fuzzy interactions. It summarises experimental and computational approaches to address the challenge of interaction heterogeneity and its contribution to a wide range of biological functions. These insights will help in understanding complex cellular processes, involving conversions between protein assembly states, such as from liquid-like droplet state to the amyloid state.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"87 ","pages":"Article 102834"},"PeriodicalIF":6.8,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959440X24000617/pdfft?md5=a14b460350f485fc4164d4d417000fb7&pid=1-s2.0-S0959440X24000617-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140950022","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
Updated understanding of the protein–DNA recognition code used by C2H2 zinc finger proteins 对 C2H2 锌指蛋白使用的蛋白质-DNA 识别代码的最新了解
IF 6.8 2区 生物学
Current opinion in structural biology Pub Date : 2024-05-15 DOI: 10.1016/j.sbi.2024.102836
Xing Zhang , Robert M. Blumenthal , Xiaodong Cheng
{"title":"Updated understanding of the protein–DNA recognition code used by C2H2 zinc finger proteins","authors":"Xing Zhang ,&nbsp;Robert M. Blumenthal ,&nbsp;Xiaodong Cheng","doi":"10.1016/j.sbi.2024.102836","DOIUrl":"https://doi.org/10.1016/j.sbi.2024.102836","url":null,"abstract":"<div><p>C2H2 zinc-finger (ZF) proteins form the largest family of DNA-binding transcription factors coded by mammalian genomes. In a typical DNA-binding ZF module, there are twelve residues (numbered from −1 to −12) between the last zinc-coordinating cysteine and the first zinc-coordinating histidine. The established C2H2-ZF “recognition code” suggests that residues at positions −1, −4, and −7 recognize the 5′, central, and 3′ bases of a DNA base-pair triplet, respectively. Structural studies have highlighted that additional residues at positions −5 and −8 also play roles in specific DNA recognition. The presence of bulky and either charged or polar residues at these five positions determines specificity for given DNA bases: guanine is recognized by arginine, lysine, or histidine; adenine by asparagine or glutamine; thymine or 5-methylcytosine by glutamate; and unmodified cytosine by aspartate. This review discusses recent structural characterizations of C2H2-ZFs that add to our understanding of the principles underlying the C2H2-ZF recognition code.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"87 ","pages":"Article 102836"},"PeriodicalIF":6.8,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959440X24000630/pdfft?md5=814979783ac30da15c2c02fce3e63764&pid=1-s2.0-S0959440X24000630-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140948475","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
Modeling membranes in situ 原位膜建模
IF 6.8 2区 生物学
Current opinion in structural biology Pub Date : 2024-05-13 DOI: 10.1016/j.sbi.2024.102837
Chelsea M. Brown, Siewert J. Marrink
{"title":"Modeling membranes in situ","authors":"Chelsea M. Brown,&nbsp;Siewert J. Marrink","doi":"10.1016/j.sbi.2024.102837","DOIUrl":"https://doi.org/10.1016/j.sbi.2024.102837","url":null,"abstract":"<div><p>Molecular dynamics simulations of cellular membranes have come a long way—from simple model lipid bilayers to multicomponent systems capturing the crowded and complex nature of real cell membranes. In this opinionated minireview, we discuss the current challenge to simulate the dynamics of membranes in their native environment, <em>in situ</em>, with the prospect of reaching the level of whole cells and cell organelles using an integrative modeling framework.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"87 ","pages":"Article 102837"},"PeriodicalIF":6.8,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959440X24000642/pdfft?md5=026395d37fb0de7a34e4d200ac44929f&pid=1-s2.0-S0959440X24000642-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140918569","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
Structures, dynamics, complexes, and functions: From classic computation to artificial intelligence 结构、动力学、复合体和函数：从经典计算到人工智能
IF 6.8 2区 生物学
Current opinion in structural biology Pub Date : 2024-05-13 DOI: 10.1016/j.sbi.2024.102835
Elena Frasnetti , Andrea Magni , Matteo Castelli , Stefano A. Serapian , Elisabetta Moroni , Giorgio Colombo
{"title":"Structures, dynamics, complexes, and functions: From classic computation to artificial intelligence","authors":"Elena Frasnetti ,&nbsp;Andrea Magni ,&nbsp;Matteo Castelli ,&nbsp;Stefano A. Serapian ,&nbsp;Elisabetta Moroni ,&nbsp;Giorgio Colombo","doi":"10.1016/j.sbi.2024.102835","DOIUrl":"https://doi.org/10.1016/j.sbi.2024.102835","url":null,"abstract":"<div><p>Computational approaches can provide highly detailed insight into the molecular recognition processes that underlie drug binding, the assembly of protein complexes, and the regulation of biological functional processes. Classical simulation methods can bridge a wide range of length- and time-scales typically involved in such processes. Lately, automated learning and artificial intelligence methods have shown the potential to expand the reach of physics-based approaches, ushering in the possibility to model and even design complex protein architectures. The synergy between atomistic simulations and AI methods is an emerging frontier with a huge potential for advances in structural biology. Herein, we explore various examples and frameworks for these approaches, providing select instances and applications that illustrate their impact on fundamental biomolecular problems.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"87 ","pages":"Article 102835"},"PeriodicalIF":6.8,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959440X24000629/pdfft?md5=8a2ddd4bf65be6e833cf2b31b35625d6&pid=1-s2.0-S0959440X24000629-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140918570","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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