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Annual Review of Biophysics最新文献

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Free Energy Methods for the Description of Molecular Processes. 描述分子过程的自由能方法。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-062722-093258
Christophe Chipot
{"title":"Free Energy Methods for the Description of Molecular Processes.","authors":"Christophe Chipot","doi":"10.1146/annurev-biophys-062722-093258","DOIUrl":"https://doi.org/10.1146/annurev-biophys-062722-093258","url":null,"abstract":"<p><p>Efforts to combine theory and experiment to advance our knowledge of molecular processes relevant to biophysics have been considerably enhanced by the contribution of statistical-mechanics simulations. Key to the understanding of such molecular processes is the underlying free-energy change. Being able to accurately predict this change from first principles represents an appealing prospect. Over the past decades, the synergy between steadily growing computational resources and unrelenting methodological developments has brought free-energy calculations into the arsenal of tools commonly utilized to tackle important questions that experiment alone has left unresolved. The continued emergence of new options to determine free energies has also bred confusion amid the community of users, who may find it difficult to choose the best-suited algorithm to address the problem at hand. In an attempt to clarify the current landscape, this review recounts how the field has been shaped and how the broad gamut of methods available today is rooted in a few foundational principles laid down many years ago.Three examples of molecular processes central to biophysics illustrate where free-energy calculations stand and what are the conceptual and practical obstacles that we must overcome to increase their predictive power.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"113-138"},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9444040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 8
Graphene and Two-Dimensional Materials for Biomolecule Sensing. 用于生物分子传感的石墨烯和二维材料。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-111622-091121
Deependra Kumar Ban, Prabhakar R Bandaru
{"title":"Graphene and Two-Dimensional Materials for Biomolecule Sensing.","authors":"Deependra Kumar Ban,&nbsp;Prabhakar R Bandaru","doi":"10.1146/annurev-biophys-111622-091121","DOIUrl":"https://doi.org/10.1146/annurev-biophys-111622-091121","url":null,"abstract":"<p><p>An ideal biosensor material at room temperature, with an extremely large surface area per unit mass combined with the possibility of harnessing quantum mechanical attributes, would be comprised of graphene and other two-dimensional (2D) materials. The sensing of a variety of sizes and types of biomolecules involves modulation of the electrical charge density of (current through) the 2D material and manifests through specific components of the capacitance (resistance). While sensitive detection at the single-molecule level, i.e., at zeptomolar concentrations, may be achieved, specificity in a complex mixture is more demanding. Attention should be paid to the influence of inevitably present defects in the 2D materials on the sensing, as well as calibration of obtained results with acceptable standards. The consequent establishment of a roadmap for the widespread deployment of 2D material-based biosensors in point-of-care platforms has the potential to revolutionize health care.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"487-507"},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9444170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 2
Quantitative Single-Molecule Localization Microscopy. 定量单分子定位显微镜。
IF 10.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-111622-091212
Siewert Hugelier, P L Colosi, Melike Lakadamyali
{"title":"Quantitative Single-Molecule Localization Microscopy.","authors":"Siewert Hugelier, P L Colosi, Melike Lakadamyali","doi":"10.1146/annurev-biophys-111622-091212","DOIUrl":"10.1146/annurev-biophys-111622-091212","url":null,"abstract":"<p><p>Super-resolution fluorescence microscopy allows the investigation of cellular structures at nanoscale resolution using light. Current developments in super-resolution microscopy have focused on reliable quantification of the underlying biological data. In this review, we first describe the basic principles of super-resolution microscopy techniques such as stimulated emission depletion (STED) microscopy and single-molecule localization microscopy (SMLM), and then give a broad overview of methodological developments to quantify super-resolution data, particularly those geared toward SMLM data. We cover commonly used techniques such as spatial point pattern analysis, colocalization, and protein copy number quantification but also describe more advanced techniques such as structural modeling, single-particle tracking, and biosensing. Finally, we provide an outlook on exciting new research directions to which quantitative super-resolution microscopy might be applied.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"139-160"},"PeriodicalIF":10.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11268362/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9500938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Bringing Structure to Cell Biology with Cryo-Electron Tomography. 利用低温电子断层扫描技术为细胞生物学提供结构。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-111622-091327
Lindsey N Young, Elizabeth Villa
{"title":"Bringing Structure to Cell Biology with Cryo-Electron Tomography.","authors":"Lindsey N Young, Elizabeth Villa","doi":"10.1146/annurev-biophys-111622-091327","DOIUrl":"10.1146/annurev-biophys-111622-091327","url":null,"abstract":"<p><p>Recent advances in cryo-electron microscopy have marked only the beginning of the potential of this technique. To bring structure into cell biology, the modality of cryo-electron tomography has fast developed into a bona fide in situ structural biology technique where structures are determined in their native environment, the cell. Nearly every step of the cryo-focused ion beam-assisted electron tomography (cryo-FIB-ET) workflow has been improved upon in the past decade, since the first windows were carved into cells, unveiling macromolecular networks in near-native conditions. By bridging structural and cell biology, cryo-FIB-ET is advancing our understanding of structure-function relationships in their native environment and becoming a tool for discovering new biology.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"573-595"},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10763975/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9501370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 7
On the Rational Design of Cooperative Receptors. 论合作受体的合理设计。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-091222-082247
Gabriel Ortega, Alejandro Chamorro-Garcia, Francesco Ricci, Kevin W Plaxco
{"title":"On the Rational Design of Cooperative Receptors.","authors":"Gabriel Ortega,&nbsp;Alejandro Chamorro-Garcia,&nbsp;Francesco Ricci,&nbsp;Kevin W Plaxco","doi":"10.1146/annurev-biophys-091222-082247","DOIUrl":"https://doi.org/10.1146/annurev-biophys-091222-082247","url":null,"abstract":"<p><p>Cooperativity (homotropic allostery) is the primary mechanism by which evolution steepens the binding curves of biomolecular receptors to produce more responsive input-output behavior in biomolecular systems. Motivated by the ubiquity with which nature employs this effect, over the past 15 years we, together with other groups, have engineered this mechanism into several otherwise noncooperative receptors. These efforts largely aimed to improve the utility of such receptors in artificial biotechnologies, such as synthetic biology and biosensors, but they have also provided the first quantitative, experimental tests of longstanding ideas about the mechanisms underlying cooperativity. In this article, we review the literature on the design of this effect, paying particular attention to the design strategies involved, the extent to which each can be rationally applied to (and optimized for) new receptors, and what each teaches us about the origins and optimization of this important phenomenon.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"319-337"},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9871542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 4
Interaction Dynamics of Intrinsically Disordered Proteins from Single-Molecule Spectroscopy. 从单分子光谱分析内在无序蛋白的相互作用动力学。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-101122-071930
Aritra Chowdhury, Daniel Nettels, Benjamin Schuler
{"title":"Interaction Dynamics of Intrinsically Disordered Proteins from Single-Molecule Spectroscopy.","authors":"Aritra Chowdhury,&nbsp;Daniel Nettels,&nbsp;Benjamin Schuler","doi":"10.1146/annurev-biophys-101122-071930","DOIUrl":"https://doi.org/10.1146/annurev-biophys-101122-071930","url":null,"abstract":"<p><p>Many proteins contain large structurally disordered regions or are entirely disordered under physiological conditions. The functions of these intrinsically disordered proteins (IDPs) often involve interactions with other biomolecules. An important emerging effort has thus been to identify the molecular mechanisms of IDP interactions and how they differ from the textbook notions of biomolecular binding for folded proteins. In this review, we summarize how the versatile tool kit of single-molecule fluorescence spectroscopy can aid the investigation of these conformationally heterogeneous and highly dynamic molecular systems. We discuss the experimental observables that can be employed and how they enable IDP complexes to be probed on timescales from nanoseconds to hours. Key insights include the diverse structural and dynamic properties of bound IDPs and the kinetic mechanisms facilitated by disorder, such as fly-casting; disorder-mediated encounter complexes; and competitive substitution via ternary complexes, which enables rapid dissociation even for high-affinity complexes. We also discuss emerging links to aggregation, liquid-liquid phase separation, and cellular processes, as well as current technical advances to further expand the scope of single-molecule spectroscopy.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"433-462"},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9499389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 7
Cryo-Electron Tomography: The Resolution Revolution and a Surge of In Situ Virological Discoveries. 冷冻电子断层扫描:分辨率革命和原位病毒学发现的激增。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-092022-100958
Ye Hong, Yutong Song, Zheyuan Zhang, Sai Li
{"title":"Cryo-Electron Tomography: The Resolution Revolution and a Surge of In Situ Virological Discoveries.","authors":"Ye Hong,&nbsp;Yutong Song,&nbsp;Zheyuan Zhang,&nbsp;Sai Li","doi":"10.1146/annurev-biophys-092022-100958","DOIUrl":"https://doi.org/10.1146/annurev-biophys-092022-100958","url":null,"abstract":"<p><p>The recent proliferation of cryo-electron tomography (cryo-ET) techniques has led to the cryo-ET resolution revolution. Meanwhile, significant efforts have been made to improve the identification of targets in the cellular context and the throughput of cryo-focused ion beam (FIB) milling. Together, these developments led to a surge of in situ discoveries on how enveloped viruses are assembled and how viruses interact with cells in infected hosts. In this article, we review the recent advances in cryo-ET, high-resolution insights into virus assembly, and the findings from inside infected eukaryotic and prokaryotic cells.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"339-360"},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9505450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 4
Mechanism of Activation of the Visual Receptor Rhodopsin. 视受体视紫红质的激活机制。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-083122-094909
Steven O Smith
{"title":"Mechanism of Activation of the Visual Receptor Rhodopsin.","authors":"Steven O Smith","doi":"10.1146/annurev-biophys-083122-094909","DOIUrl":"https://doi.org/10.1146/annurev-biophys-083122-094909","url":null,"abstract":"<p><p>Rhodopsin is the photoreceptor in human rod cells responsible for dim-light vision. The visual receptors are part of the large superfamily of G protein-coupled receptors (GPCRs) that mediate signal transduction in response to diverse diffusible ligands. The high level of sequence conservation within the transmembrane helices of the visual receptors and the family A GPCRs has long been considered evidence for a common pathway for signal transduction. I review recent studies that reveal a comprehensive mechanism for how light absorption by the retinylidene chromophore drives rhodopsin activation and highlight those features of the mechanism that are conserved across the ligand-activated GPCRs.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"301-317"},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9798907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 2
Mitochondrial Ion Channels. 线粒体离子通道。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-092622-094853
Ildiko Szabo, Adam Szewczyk
{"title":"Mitochondrial Ion Channels.","authors":"Ildiko Szabo,&nbsp;Adam Szewczyk","doi":"10.1146/annurev-biophys-092622-094853","DOIUrl":"https://doi.org/10.1146/annurev-biophys-092622-094853","url":null,"abstract":"<p><p>Mitochondria are involved in multiple cellular tasks, such as ATP synthesis, metabolism, metabolite and ion transport, regulation of apoptosis, inflammation, signaling, and inheritance of mitochondrial DNA. The majority of the correct functioning of mitochondria is based on the large electrochemical proton gradient, whose component, the inner mitochondrial membrane potential, is strictly controlled by ion transport through mitochondrial membranes. Consequently, mitochondrial function is critically dependent on ion homeostasis, the disturbance of which leads to abnormal cell functions. Therefore, the discovery of mitochondrial ion channels influencing ion permeability through the membrane has defined a new dimension of the function of ion channels in different cell types, mainly linked to the important tasks that mitochondrial ion channels perform in cell life and death. This review summarizes studies on animal mitochondrial ion channels with special focus on their biophysical properties, molecular identity, and regulation. Additionally, the potential of mitochondrial ion channels as therapeutic targets for several diseases is briefly discussed.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"229-254"},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9500937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 4
Coding From Binding? Molecular Interactions at the Heart of Translation. 从绑定中编码?翻译核心的分子相互作用。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-090622-102329
Bojan Zagrovic, Marlene Adlhart, Thomas H Kapral
{"title":"Coding From Binding? Molecular Interactions at the Heart of Translation.","authors":"Bojan Zagrovic,&nbsp;Marlene Adlhart,&nbsp;Thomas H Kapral","doi":"10.1146/annurev-biophys-090622-102329","DOIUrl":"https://doi.org/10.1146/annurev-biophys-090622-102329","url":null,"abstract":"<p><p>The mechanism and the evolution of DNA replication and transcription, the key elements of the central dogma of biology, are fundamentally well explained by the physicochemical complementarity between strands of nucleic acids. However, the determinants that have shaped the third part of the dogma-the process of biological translation and the universal genetic code-remain unclear. We review and seek parallels between different proposals that view the evolution of translation through the prism of weak, noncovalent interactions between biological macromolecules. In particular, we focus on a recent proposal that there exists a hitherto unrecognized complementarity at the heart of biology, that between messenger RNA coding regions and the proteins that they encode, especially if the two are unstructured. Reflecting the idea that the genetic code evolved from intrinsic binding propensities between nucleotides and amino acids, this proposal promises to forge a link between the distant past and the present of biological systems.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"69-89"},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10399293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 1
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