Annual Review of Biophysics最新文献_第8页

Analysis of Tandem Repeat Protein Folding Using Nearest-Neighbor Models. 用最近邻模型分析串联重复蛋白折叠。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 Epub Date: 2021-02-19 DOI: 10.1146/annurev-biophys-102220-083020

Mark Petersen, Doug Barrick

{"title":"Analysis of Tandem Repeat Protein Folding Using Nearest-Neighbor Models.","authors":"Mark Petersen, Doug Barrick","doi":"10.1146/annurev-biophys-102220-083020","DOIUrl":"https://doi.org/10.1146/annurev-biophys-102220-083020","url":null,"abstract":"Cooperativity is a hallmark of protein folding, but the thermodynamic origins of cooperativity are difficult to quantify. Tandem repeat proteins provide a unique experimental system to quantify cooperativity due to their internal symmetry and their tolerance of deletion, extension, and in some cases fragmentation into single repeats. Analysis of repeat proteins of different lengths with nearest-neighbor Ising models provides values for repeat folding ([Formula: see text]) and inter-repeat coupling (ΔGi-1,i). In this article, we review the architecture of repeat proteins and classify them in terms of ΔGi and ΔGi-1,i; this classification scheme groups repeat proteins according to their degree of cooperativity. We then present various statistical thermodynamic models, based on the 1D-Ising model, for analysis of different classes of repeat proteins. We use these models to analyze data for highly and moderately cooperative and noncooperative repeat proteins and relate their fitted parameters to overall structural features.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2021-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8105288/pdf/nihms-1689711.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25384572","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: 6

From Bench to Keyboard and Back Again: A Brief History of Lambda Phage Modeling. 从工作台到键盘再回来:Lambda噬菌体建模简史。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 DOI: 10.1146/annurev-biophys-082020-063558

Michael G Cortes, Yiruo Lin, Lanying Zeng, Gábor Balázsi

{"title":"From Bench to Keyboard and Back Again: A Brief History of Lambda Phage Modeling.","authors":"Michael G Cortes, Yiruo Lin, Lanying Zeng, Gábor Balázsi","doi":"10.1146/annurev-biophys-082020-063558","DOIUrl":"https://doi.org/10.1146/annurev-biophys-082020-063558","url":null,"abstract":"Cellular decision making is the process whereby cells choose one developmental pathway from multiple possible ones, either spontaneously or due to environmental stimuli. Examples in various cell types suggest an almost inexhaustible plethora of underlying molecular mechanisms. In general, cellular decisions rely on the gene regulatory network, which integrates external signals to drive cell fate choice. The search for general principles of such a process benefits from appropriate biological model systems that reveal how and why certain gene regulatory mechanisms drive specific cellular decisions according to ecological context and evolutionary outcomes. In this article, we review the historical and ongoing development of the phage lambda lysis-lysogeny decision as a model system to investigate all aspects of cellular decision making. The unique generality, simplicity, and richness of phage lambda decision making render it a constant source ofmathematical modeling-aided inspiration across all of biology. We discuss the origins and progress of quantitative phage lambda modeling from the 1950s until today, as well as its possible future directions. We provide examples of how modeling enabled methods and theory development, leading to new biological insights by revealing gaps in the theory and pinpointing areas requiring further experimental investigation. Overall, we highlight the utility of theoretical approaches both as predictive tools, to forecast the outcome of novel experiments, and as explanatory tools, to elucidate the natural processes underlying experimental data.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2021-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8590857/pdf/nihms-1746789.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38956154","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: 3

Structures and Functions of Chromatin Fibers. 染色质纤维的结构和功能。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 DOI: 10.1146/annurev-biophys-062920-063639

Ping Chen, Wei Li, Guohong Li

引用次数: 18

Review of COVID-19 Antibody Therapies. COVID-19抗体治疗综述

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 Epub Date: 2020-10-16 DOI: 10.1146/annurev-biophys-062920-063711

Jiahui Chen, Kaifu Gao, Rui Wang, Duc Duy Nguyen, Guo-Wei Wei

{"title":"Review of COVID-19 Antibody Therapies.","authors":"Jiahui Chen, Kaifu Gao, Rui Wang, Duc Duy Nguyen, Guo-Wei Wei","doi":"10.1146/annurev-biophys-062920-063711","DOIUrl":"10.1146/annurev-biophys-062920-063711","url":null,"abstract":"In the global health emergency caused by coronavirus disease 2019 (COVID-19), efficient and specific therapies are urgently needed. Compared with traditional small-molecular drugs, antibody therapies are relatively easy to develop; they are as specific as vaccines in targeting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); and they have thus attracted much attention in the past few months. This article reviews seven existing antibodies for neutralizing SARS-CoV-2 with 3D structures deposited in the Protein Data Bank (PDB). Five 3D antibody structures associated with the SARS-CoV spike (S) protein are also evaluated for their potential in neutralizing SARS-CoV-2. The interactions of these antibodies with the S protein receptor-binding domain (RBD) are compared with those between angiotensin-converting enzyme 2 and RBD complexes. Due to the orders of magnitude in the discrepancies of experimental binding affinities, we introduce topological data analysis, a variety of network models, and deep learning to analyze the binding strength and therapeutic potential of the 14 antibody-antigen complexes. The current COVID-19 antibody clinical trials, which are not limited to the S protein target, are also reviewed.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2021-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biophys-062920-063711","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38495089","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: 15

The Mechanosensory Transduction Machinery in Inner Ear Hair Cells. 内耳毛细胞的机械感觉传导机制

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 Epub Date: 2020-12-07 DOI: 10.1146/annurev-biophys-062420-081842

Wang Zheng, Jeffrey R Holt

{"title":"The Mechanosensory Transduction Machinery in Inner Ear Hair Cells.","authors":"Wang Zheng, Jeffrey R Holt","doi":"10.1146/annurev-biophys-062420-081842","DOIUrl":"10.1146/annurev-biophys-062420-081842","url":null,"abstract":"Sound-induced mechanical stimuli are detected by elaborate mechanosensory transduction (MT) machinery in highly specialized hair cells of the inner ear. Genetic studies of inherited deafness in the past decades have uncovered several molecular constituents of the MT complex, and intense debate has surrounded the molecular identity of the pore-forming subunits. How the MT components function in concert in response to physical stimulation is not fully understood. In this review, we summarize and discuss multiple lines of evidence supporting the hypothesis that transmembrane channel-like 1 is a long-sought MT channel subunit. We also review specific roles of other components of the MT complex, including protocadherin 15, cadherin 23, lipoma HMGIC fusion partner-like 5, transmembrane inner ear, calcium and integrin-binding family member 2, and ankyrins. Based on these recent advances, we propose a unifying theory of hair cell MT that may reconcile most of the functional discoveries obtained to date. Finally, we discuss key questions that need to be addressed for a comprehensive understanding of hair cell MT at molecular and atomic levels.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":10.4,"publicationDate":"2021-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8163026/pdf/nihms-1704181.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38344741","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

Biophysics of Chromatin Remodeling. 染色质重塑的生物物理学。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 Epub Date: 2021-01-04 DOI: 10.1146/annurev-biophys-082520-080201

Ilana M Nodelman, Gregory D Bowman

引用次数: 25

The Contribution of Biophysics and Structural Biology to Current Advances in COVID-19. 生物物理学和结构生物学对COVID-19当前进展的贡献。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 DOI: 10.1146/annurev-biophys-102620-080956

Francisco J Barrantes

{"title":"The Contribution of Biophysics and Structural Biology to Current Advances in COVID-19.","authors":"Francisco J Barrantes","doi":"10.1146/annurev-biophys-102620-080956","DOIUrl":"https://doi.org/10.1146/annurev-biophys-102620-080956","url":null,"abstract":"Critical to viral infection are the multiple interactions between viral proteins and host-cell counterparts. The first such interaction is the recognition of viral envelope proteins by surface receptors that normally fulfil other physiological roles, a hijacking mechanism perfected over the course of evolution. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has successfully adopted this strategy using its spike glycoprotein to dock on the membrane-bound metalloprotease angiotensin-converting enzyme 2 (ACE2). The crystal structures of several SARS-CoV-2 proteins alone or in complex with their receptors or other ligands were recently solved at an unprecedented pace. This accomplishment is partly due to the increasing availability of data on other coronaviruses and ACE2 over the past 18 years. Likewise, other key intervening actors and mechanisms of viral infection were elucidated with the aid of biophysical approaches. An understanding of the various structurally important motifs of the interacting partners provides key mechanistic information for the development of structure-based designer drugs able to inhibit various steps of the infective cycle, including neutralizing antibodies, small organic drugs, and vaccines. This review analyzes current progress and the outlook for future structural studies.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2021-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38956584","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: 12

Biomolecular Systems Engineering: Unlocking the Potential of Engineered Allostery via the Lactose Repressor Topology. 生物分子系统工程:通过乳糖抑制因子拓扑释放工程变构的潜力。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 Epub Date: 2021-02-19 DOI: 10.1146/annurev-biophys-090820-101708

Thomas M Groseclose, Ronald E Rondon, Ashley N Hersey, Prasaad T Milner, Dowan Kim, Fumin Zhang, Matthew J Realff, Corey J Wilson

{"title":"Biomolecular Systems Engineering: Unlocking the Potential of Engineered Allostery via the Lactose Repressor Topology.","authors":"Thomas M Groseclose, Ronald E Rondon, Ashley N Hersey, Prasaad T Milner, Dowan Kim, Fumin Zhang, Matthew J Realff, Corey J Wilson","doi":"10.1146/annurev-biophys-090820-101708","DOIUrl":"https://doi.org/10.1146/annurev-biophys-090820-101708","url":null,"abstract":"Allosteric function is a critical component of many of the parts used to construct gene networks throughout synthetic biology. In this review, we discuss an emerging field of research and education, biomolecular systems engineering, that expands on the synthetic biology edifice-integrating workflows and strategies from protein engineering, chemical engineering, electrical engineering, and computer science principles. We focus on the role of engineered allosteric communication as it relates to transcriptional gene regulators-i.e., transcription factors and corresponding unit operations. In this review, we (a) explore allosteric communication in the lactose repressor LacI topology, (b) demonstrate how to leverage this understanding of allostery in the LacI system to engineer non-natural BUFFER and NOT logical operations, (c) illustrate how engineering workflows can be used to confer alternate allosteric functions in disparate systems that share the LacI topology, and (d) demonstrate how fundamental unit operations can be directed to form combinational logical operations.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2021-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25384573","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: 6

Advancing Biophysics Using DNA Origami. 利用DNA折纸推进生物物理学。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 Epub Date: 2021-03-01 DOI: 10.1146/annurev-biophys-110520-125739

Wouter Engelen, Hendrik Dietz

引用次数: 17

Biophysics of Notch Signaling. 诺奇信号的生物物理学。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 Epub Date: 2021-02-03 DOI: 10.1146/annurev-biophys-101920-082204

David Sprinzak, Stephen C Blacklow

引用次数: 0