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On the Rational Design of Cooperative Receptors. 论合作受体的合理设计。
IF 10.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 Epub Date: 2023-02-03 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, Alejandro Chamorro-Garcia, Francesco Ricci, Kevin W Plaxco","doi":"10.1146/annurev-biophys-091222-082247","DOIUrl":"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":10.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11824748/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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 10.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 Epub Date: 2023-01-10 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, Marlene Adlhart, Thomas H Kapral","doi":"10.1146/annurev-biophys-090622-102329","DOIUrl":"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":10.4,"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: 0
Variable-Temperature Native Mass Spectrometry for Studies of Protein Folding, Stabilities, Assembly, and Molecular Interactions. 变温天然质谱法研究蛋白质折叠，稳定性，组装和分子相互作用。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2022-05-09 DOI: 10.1146/annurev-biophys-102221-101121
Arthur Laganowsky, David E Clemmer, David H Russell
{"title":"Variable-Temperature Native Mass Spectrometry for Studies of Protein Folding, Stabilities, Assembly, and Molecular Interactions.","authors":"Arthur Laganowsky,&nbsp;David E Clemmer,&nbsp;David H Russell","doi":"10.1146/annurev-biophys-102221-101121","DOIUrl":"https://doi.org/10.1146/annurev-biophys-102221-101121","url":null,"abstract":"<p><p>The structures and conformational dynamics of proteins, protein complexes, and their noncovalent interactions with other molecules are controlled specifically by the Gibbs free energy (entropy and enthalpy) of the system. For some organisms, temperature is highly regulated, but the majority of biophysical studies are carried out at room, nonphysiological temperature. In this review, we describe variable-temperature electrospray ionization (vT-ESI) mass spectrometry (MS)-based studies with unparalleled sensitivity, dynamic range, and selectivity for studies of both cold- and heat-induced chemical processes. Such studies provide direct determinations of stabilities, reactivities, and thermodynamic measurements for native and non-native structures of proteins and protein complexes and for protein-ligand interactions. Highlighted in this review are vT-ESI-MS studies that reveal 40 different conformers of chymotrypsin inhibitor 2, a classic two-state (native → unfolded) unfolder, and thermochemistry for a model membrane protein system binding lipid and its regulatory protein.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"51 ","pages":"63-77"},"PeriodicalIF":12.4,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9086101/pdf/nihms-1785165.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9802732","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: 12
Chiral Induced Spin Selectivity and Its Implications for Biological Functions. 手性诱导自旋选择性及其对生物功能的影响。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2022-05-09 Epub Date: 2021-12-21 DOI: 10.1146/annurev-biophys-083021-070400
Ron Naaman, Yossi Paltiel, David H Waldeck
{"title":"Chiral Induced Spin Selectivity and Its Implications for Biological Functions.","authors":"Ron Naaman,&nbsp;Yossi Paltiel,&nbsp;David H Waldeck","doi":"10.1146/annurev-biophys-083021-070400","DOIUrl":"https://doi.org/10.1146/annurev-biophys-083021-070400","url":null,"abstract":"<p><p>Chirality in life has been preserved throughout evolution. It has been assumed that the main function of chirality is its contribution to structural properties. In the past two decades, however, it has been established that chiral molecules possess unique electronic properties. Electrons that pass through chiral molecules, or even charge displacements within a chiral molecule, do so in a manner that depends on the electron's spin and the molecule's enantiomeric form. This effect, referred to as chiral induced spin selectivity (CISS), has several important implications for the properties of biosystems. Among these implications, CISS facilitates long-range electron transfer, enhances bio-affinities and enantioselectivity, and enables efficient and selective multi-electron redox processes. In this article, we review the CISS effect and some of its manifestations in biological systems. We argue that chirality is preserved so persistently in biology not only because of its structural effect, but also because of its important function in spin polarizing electrons.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"99-114"},"PeriodicalIF":12.4,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39745245","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: 33
ATP-Independent Chaperones. ATP-Independent陪伴。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2022-05-09 Epub Date: 2022-02-15 DOI: 10.1146/annurev-biophys-090121-082906
Rishav Mitra, Kevin Wu, Changhan Lee, James C A Bardwell
{"title":"ATP-Independent Chaperones.","authors":"Rishav Mitra,&nbsp;Kevin Wu,&nbsp;Changhan Lee,&nbsp;James C A Bardwell","doi":"10.1146/annurev-biophys-090121-082906","DOIUrl":"https://doi.org/10.1146/annurev-biophys-090121-082906","url":null,"abstract":"<p><p>The folding of proteins into their native structure is crucial for the functioning of all biological processes. Molecular chaperones are guardians of the proteome that assist in protein folding and prevent the accumulation of aberrant protein conformations that can lead to proteotoxicity. ATP-independent chaperones do not require ATP to regulate their functional cycle. Although these chaperones have been traditionally regarded as passive holdases that merely prevent aggregation, recent work has shown that they can directly affect the folding energy landscape by tuning their affinity to various folding states of the client. This review focuses on emerging paradigms in the mechanism of action of ATP-independent chaperones and on the various modes of regulating client binding and release.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"409-429"},"PeriodicalIF":12.4,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39926411","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: 9
Native Mass Spectrometry: Recent Progress and Remaining Challenges. 原生质谱:最近的进展和仍然存在的挑战。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2022-05-09 Epub Date: 2022-01-04 DOI: 10.1146/annurev-biophys-092721-085421
Kelly R Karch, Dalton T Snyder, Sophie R Harvey, Vicki H Wysocki
{"title":"Native Mass Spectrometry: Recent Progress and Remaining Challenges.","authors":"Kelly R Karch, Dalton T Snyder, Sophie R Harvey, Vicki H Wysocki","doi":"10.1146/annurev-biophys-092721-085421","DOIUrl":"10.1146/annurev-biophys-092721-085421","url":null,"abstract":"<p><p>Native mass spectrometry (nMS) has emerged as an important tool in studying the structure and function of macromolecules and their complexes in the gas phase. In this review, we cover recent advances in nMS and related techniques including sample preparation, instrumentation, activation methods, and data analysis software. These advances have enabled nMS-based techniques to address a variety of challenging questions in structural biology. The second half of this review highlights recent applications of these technologies and surveys the classes of complexes that can be studied with nMS. Complementarity of nMS to existing structural biology techniques and current challenges in nMS are also addressed.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"51 ","pages":"157-179"},"PeriodicalIF":12.4,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10700022/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9699529","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: 36
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