Annual Review of Biophysics最新文献_第7页

A Life of Biophysics. 《生命物理学》

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-120121-074034

Bertil Hille

引用次数: 0

Enzymology and Dynamics by Cryogenic Electron Microscopy. 低温电子显微镜下的酶学和动力学。

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-100121-075228

Ming-Daw Tsai, Wen-Jin Wu, Meng-Chiao Ho

引用次数: 10

Nanomechanics of Blood Clot and Thrombus Formation. 血凝块和血栓形成的纳米力学。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2022-05-09 Epub Date: 2022-01-06 DOI: 10.1146/annurev-biophys-111821-072110

Marco M Domingues, Filomena A Carvalho, Nuno C Santos

引用次数: 2

Rules of Physical Mathematics Govern Intrinsically Disordered Proteins. 物理数学规则支配内在无序的蛋白质。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2022-05-09 DOI: 10.1146/annurev-biophys-120221-095357

Kingshuk Ghosh, Jonathan Huihui, Michael Phillips, Austin Haider

{"title":"Rules of Physical Mathematics Govern Intrinsically Disordered Proteins.","authors":"Kingshuk Ghosh, Jonathan Huihui, Michael Phillips, Austin Haider","doi":"10.1146/annurev-biophys-120221-095357","DOIUrl":"https://doi.org/10.1146/annurev-biophys-120221-095357","url":null,"abstract":"In stark contrast to foldable proteins with a unique folded state, intrinsically disordered proteins and regions (IDPs) persist in perpetually disordered ensembles. Yet an IDP ensemble has conformational features-even when averaged-that are specific to its sequence. In fact, subtle changes in an IDP sequence can modulate its conformational features and its function. Recent advances in theoretical physics reveal a set of elegant mathematical expressions that describe the intricate relationships among IDP sequences, their ensemble conformations, and the regulation of their biological functions. These equations also describe the molecular properties of IDP sequences that predict similarities and dissimilarities in their functions and facilitate classification of sequences by function, an unmet challenge to traditional bioinformatics. These physical sequence-patterning metrics offer a promising new avenue for advancing synthetic biology at a time when multiple novel functional modes mediated by IDPs are emerging.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9190209/pdf/nihms-1811710.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10441271","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: 16

Orientation of Cell Polarity by Chemical Gradients. 用化学梯度研究细胞极性取向。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2022-05-09 Epub Date: 2022-02-07 DOI: 10.1146/annurev-biophys-110821-071250

Debraj Ghose, Timothy Elston, Daniel Lew

{"title":"Orientation of Cell Polarity by Chemical Gradients.","authors":"Debraj Ghose, Timothy Elston, Daniel Lew","doi":"10.1146/annurev-biophys-110821-071250","DOIUrl":"https://doi.org/10.1146/annurev-biophys-110821-071250","url":null,"abstract":"Accurate decoding of spatial chemical landscapes is critical for many cell functions. Eukaryotic cells decode local chemical gradients to orient growth or movement in productive directions. Recent work on yeast model systems, whose gradient sensing pathways display much less complexity than those in animal cells, has suggested new paradigms for how these very small cells successfully exploit information in noisy and dynamic pheromone gradients to identify their mates. Pheromone receptors regulate a polarity circuit centered on the conserved Rho-family GTPase, Cdc42. The polarity circuit contains both positive and negative feedback pathways, allowing spontaneous symmetry breaking and also polarity site disassembly and relocation. Cdc42 orients the actin cytoskeleton, leading to focused vesicle traffic that promotes movement of the polarity site and also reshapes the cortical distribution of receptors at the cell surface. In this article, we review the advances from work on yeasts and compare them with the excitable signaling pathways that have been revealed in chemotactic animal cells.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9549416/pdf/nihms-1839523.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39600081","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: 11

Molecular Shape Solution for Mesoscopic Remodeling of Cellular Membranes. 膜介观重塑的分子形态溶液。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2022-05-09 Epub Date: 2022-03-03 DOI: 10.1146/annurev-biophys-011422-100054

Pavel V Bashkirov, Peter I Kuzmin, Javier Vera Lillo, Vadim A Frolov

{"title":"Molecular Shape Solution for Mesoscopic Remodeling of Cellular Membranes.","authors":"Pavel V Bashkirov, Peter I Kuzmin, Javier Vera Lillo, Vadim A Frolov","doi":"10.1146/annurev-biophys-011422-100054","DOIUrl":"10.1146/annurev-biophys-011422-100054","url":null,"abstract":"Cellular membranes self-assemble from and interact with various molecular species. Each molecule locally shapes the lipid bilayer, the soft elastic core of cellular membranes. The dynamic architecture of intracellular membrane systems is based on elastic transformations and lateral redistribution of these elementary shapes, driven by chemical and curvature stress gradients. The minimization of the total elastic stress by such redistribution composes the most basic, primordial mechanism of membrane curvature-composition coupling (CCC). Although CCC is generally considered in the context of dynamic compositional heterogeneity of cellular membrane systems, in this article we discuss a broader involvement of CCC in controlling membrane deformations. We focus specifically on the mesoscale membrane transformations in open, reservoir-governed systems, such as membrane budding, tubulation, and the emergence of highly curved sites of membrane fusion and fission. We reveal that the reshuffling of molecular shapes constitutes an independent deformation mode with complex rheological properties.This mode controls effective elasticity of local deformations as well as stationary elastic stress, thus emerging as a major regulator of intracellular membrane remodeling.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10787580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44784378","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

Insights into the Thermodynamics and Kinetics of Amino-Acid Radicals in Proteins. 蛋白质中氨基酸自由基的热力学和动力学研究。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2022-05-09 DOI: 10.1146/annurev-biophys-100521-103031

Cecilia Tommos

{"title":"Insights into the Thermodynamics and Kinetics of Amino-Acid Radicals in Proteins.","authors":"Cecilia Tommos","doi":"10.1146/annurev-biophys-100521-103031","DOIUrl":"https://doi.org/10.1146/annurev-biophys-100521-103031","url":null,"abstract":"Some oxidoreductase enzymes use redox-active tyrosine, tryptophan, cysteine, and/or glycine residues as one-electron, high-potential redox (radical) cofactors. Amino-acid radical cofactors typically perform one of four tasks-they work in concert with a metallocofactor to carry out a multielectron redox process, serve as storage sites for oxidizing equivalents, activate the substrate molecules, or move oxidizing equivalents over long distances. It is challenging to experimentally resolve the thermodynamic and kinetic redox properties of a single-amino-acid residue. The inherently reactive and highly oxidizing properties of amino-acid radicals increase the experimental barriers further still. This review describes a family of stable and well-structured model proteins that was made specifically to study tyrosine and tryptophan oxidation-reduction. The so-called α3X model protein system was combined with very-high-potential protein film voltammetry, transient absorption spectroscopy, and theoretical methods to gain a comprehensive description of the thermodynamic and kinetic properties of protein tyrosine and tryptophan radicals.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9922538/pdf/nihms-1869088.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9802743","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: 2

Mapping Enzyme Landscapes by Time-Resolved Crystallography with Synchrotron and X-Ray Free Electron Laser Light. 用同步加速器和x射线自由电子激光绘制酶的时间分辨晶体图谱。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2022-05-09 DOI: 10.1146/annurev-biophys-100421-110959

Mark A Wilson

{"title":"Mapping Enzyme Landscapes by Time-Resolved Crystallography with Synchrotron and X-Ray Free Electron Laser Light.","authors":"Mark A Wilson","doi":"10.1146/annurev-biophys-100421-110959","DOIUrl":"https://doi.org/10.1146/annurev-biophys-100421-110959","url":null,"abstract":"Directly observing enzyme catalysis in real time at the molecular level has been a long-standing goal of structural enzymology. Time-resolved serial crystallography methods at synchrotron and X-ray free electron laser (XFEL) sources have enabled researchers to follow enzyme catalysis and other nonequilibrium events at ambient conditions with unprecedented time resolution. X-ray crystallography provides detailed information about conformational heterogeneity and protein dynamics, which is enhanced when time-resolved approaches are used. This review outlines the ways in which information about the underlying energy landscape of a protein can be extracted from X-ray crystallographic data, with an emphasis on new developments in XFEL and synchrotron time-resolved crystallography. The emerging view of enzyme catalysis afforded by these techniques can be interpreted as enzymes moving on a time-dependent energy landscape. Some consequences of this view are discussed, including the proposal that irreversible enzymes or enzymes that use covalent catalytic mechanisms may commonly exhibit catalysis-activated motions.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9132212/pdf/nihms-1804778.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9802734","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: 8

Morphology and Transport in Eukaryotic Cells. 真核细胞的形态和运输。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2022-05-09 Epub Date: 2022-01-19 DOI: 10.1146/annurev-biophys-111121-103956

Anamika Agrawal, Zubenelgenubi C Scott, Elena F Koslover

引用次数: 6

Macromolecular Crowding Is More than Hard-Core Repulsions. 大分子拥挤不仅仅是核心排斥。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2022-02-03 DOI: 10.1146/annurev-biophys-091321-071829

Shannon L. Speer, C. Stewart, Liel Sapir, D. Harries, G. Pielak

{"title":"Macromolecular Crowding Is More than Hard-Core Repulsions.","authors":"Shannon L. Speer, C. Stewart, Liel Sapir, D. Harries, G. Pielak","doi":"10.1146/annurev-biophys-091321-071829","DOIUrl":"https://doi.org/10.1146/annurev-biophys-091321-071829","url":null,"abstract":"Cells are crowded, but proteins are almost always studied in dilute aqueous buffer. We review the experimental evidence that crowding affects the equilibrium thermodynamics of protein stability and protein association and discuss the theories employed to explain these observations. In doing so, we highlight differences between synthetic polymers and biologically relevant crowders. Theories based on hard-core interactions predict only crowding-induced entropic stabilization. However, experiment-based efforts conducted under physiologically relevant conditions show that crowding can destabilize proteins and their complexes. Furthermore, quantification of the temperature dependence of crowding effects produced by both large and small cosolutes, including osmolytes, sugars, synthetic polymers, and proteins, reveals enthalpic effects that stabilize or destabilize proteins. Crowding-induced destabilization and the enthalpic component point to the role of chemical interactions between and among the macromolecules, cosolutes, and water. We conclude with suggestions for future studies. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2022-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45672140","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: 36