Annual Review of Biophysics最新文献_第8页

Protein Sequencing, One Molecule at a Time. 蛋白质测序，一次一个分子。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2022-05-09 DOI: 10.1146/annurev-biophys-102121-103615

Brendan M Floyd, Edward M Marcotte

{"title":"Protein Sequencing, One Molecule at a Time.","authors":"Brendan M Floyd, Edward M Marcotte","doi":"10.1146/annurev-biophys-102121-103615","DOIUrl":"https://doi.org/10.1146/annurev-biophys-102121-103615","url":null,"abstract":"Despite tremendous gains over the past decade, methods for characterizing proteins have generally lagged behind those for nucleic acids, which are characterized by extremely high sensitivity, dynamic range, and throughput. However, the ability to directly characterize proteins at nucleic acid levels would address critical biological challenges such as more sensitive medical diagnostics, deeper protein quantification, large-scale measurement, and discovery of alternate protein isoforms and modifications and would open new paths to single-cell proteomics. In response to this need, there has been a push to radically improve protein sequencing technologies by taking inspiration from high-throughput nucleic acid sequencing, with a particular focus on developing practical methods for single-molecule protein sequencing (SMPS). SMPS technologies fall generally into three categories: sequencing by degradation (e.g., mass spectrometry or fluorosequencing), sequencing by transit (e.g., nanopores or quantum tunneling), and sequencing by affinity (as in DNA hybridization-based approaches). We describe these diverse approaches, which range from those that are already experimentally well-supported to the merely speculative, in this nascent field striving to reformulate proteomics.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"51 ","pages":"181-200"},"PeriodicalIF":12.4,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9809159/pdf/nihms-1856919.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10471656","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: 13

Phospholipid Scrambling by G Protein-Coupled Receptors. G蛋白偶联受体的磷脂混乱。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2022-05-09 DOI: 10.1146/annurev-biophys-090821-083030

George Khelashvili, Anant K Menon

{"title":"Phospholipid Scrambling by G Protein-Coupled Receptors.","authors":"George Khelashvili, Anant K Menon","doi":"10.1146/annurev-biophys-090821-083030","DOIUrl":"https://doi.org/10.1146/annurev-biophys-090821-083030","url":null,"abstract":"Rapid flip-flop of phospholipids across the two leaflets of biological membranes is crucial for many aspects of cellular life. The transport proteins that facilitate this process are classified as pump-like flippases and floppases and channel-like scramblases. Unexpectedly, Class A G protein-coupled receptors (GPCRs), a large class of signaling proteins exemplified by the visual receptor rhodopsin and its apoprotein opsin, are constitutively active as scramblases in vitro. In liposomes, opsin scrambles lipids at a unitary rate of >100,000 per second. Atomistic molecular dynamics simulations of opsin in a lipid membrane reveal conformational transitions that expose a polar groove between transmembrane helices 6 and 7. This groove enables transbilayer lipid movement, conceptualized as the swiping of a credit card (lipid) through a card reader (GPCR). Conformational changes that facilitate scrambling are distinct from those associated with GPCR signaling. In this review, we discuss the physiological significance of GPCR scramblase activity and the modes of its regulation in cells.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"51 ","pages":"39-61"},"PeriodicalIF":12.4,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9521775/pdf/nihms-1837184.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9433752","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: 13

Molecular Mechanisms Underlying Neurotransmitter Release. 神经递质释放的分子机制。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2022-05-09 DOI: 10.1146/annurev-biophys-111821-104732

Josep Rizo

{"title":"Molecular Mechanisms Underlying Neurotransmitter Release.","authors":"Josep Rizo","doi":"10.1146/annurev-biophys-111821-104732","DOIUrl":"https://doi.org/10.1146/annurev-biophys-111821-104732","url":null,"abstract":"Major recent advances and previous data have led to a plausible model of how key proteins mediate neurotransmitter release. In this model, the soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptor (SNARE) proteins syntaxin-1, SNAP-25, and synaptobrevin form tight complexes that bring the membranes together and are crucial for membrane fusion. NSF and SNAPs disassemble SNARE complexes and ensure that fusion occurs through an exquisitely regulated pathway that starts with Munc18-1 bound to a closed conformation of syntaxin-1. Munc18-1 also binds to synaptobrevin, forming a template to assemble the SNARE complex when Munc13-1 opens syntaxin-1 while bridging the vesicle and plasma membranes. Synaptotagmin-1 and complexin bind to partially assembled SNARE complexes, likely stabilizing them and preventing fusion until Ca2+ binding to synaptotagmin-1 causes dissociation from the SNARE complex and induces interactions with phospholipids that help trigger release. Although fundamental questions remain about the mechanism of membrane fusion, these advances provide a framework to investigate the mechanisms underlying presynaptic plasticity.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"51 ","pages":"377-408"},"PeriodicalIF":12.4,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9490555/pdf/nihms-1835467.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9435069","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: 54

Waves in Embryonic Development. 胚胎发育中的波浪

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2022-05-09 Epub Date: 2022-02-04 DOI: 10.1146/annurev-biophys-111521-102500

Stefano Di Talia, Massimo Vergassola

{"title":"Waves in Embryonic Development.","authors":"Stefano Di Talia, Massimo Vergassola","doi":"10.1146/annurev-biophys-111521-102500","DOIUrl":"10.1146/annurev-biophys-111521-102500","url":null,"abstract":"Embryonic development hinges on effective coordination of molecular events across space and time. Waves have recently emerged as constituting an ubiquitous mechanism that ensures rapid spreading of regulatory signals across embryos, as well as reliable control of their patterning, namely, for the emergence of body plan structures. In this article, we review a selection of recent quantitative work on signaling waves and present an overview of the theory of waves. Our aim is to provide a succinct yet comprehensive guiding reference for the theoretical frameworks by which signaling waves can arise in embryos. We start, then, from reaction-diffusion systems, both static and time dependent; move to excitable dynamics; and conclude with systems of coupled oscillators. We link these theoretical models to molecular mechanisms recently elucidated for the control of mitotic waves in early embryos, patterning of the vertebrate body axis, micropattern cultures, and bone regeneration. Our goal is to inspire experimental work that will advance theory in development and connect its predictions to quantitative biological observations.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"51 ","pages":"327-353"},"PeriodicalIF":10.4,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10122827/pdf/nihms-1890571.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9396868","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

The Effects of Temperature on Cellular Physiology. 温度对细胞生理的影响。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2022-05-09 DOI: 10.1146/annurev-biophys-112221-074832

Benjamin D. Knapp, K. C. Huang

引用次数: 23

Super-Resolution Microscopy for Structural Cell Biology. 结构细胞生物学的超分辨率显微镜。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2022-05-09 Epub Date: 2022-02-04 DOI: 10.1146/annurev-biophys-102521-112912

Sheng Liu, Philipp Hoess, Jonas Ries

引用次数: 44

Large Chaperone Complexes Through the Lens of Nuclear Magnetic Resonance Spectroscopy. 核磁共振波谱透镜下的大型伴侣配合物。

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2022-05-09 Epub Date: 2022-01-19 DOI: 10.1146/annurev-biophys-090921-120150

Theodoros K Karamanos, G Marius Clore

{"title":"Large Chaperone Complexes Through the Lens of Nuclear Magnetic Resonance Spectroscopy.","authors":"Theodoros K Karamanos, G Marius Clore","doi":"10.1146/annurev-biophys-090921-120150","DOIUrl":"10.1146/annurev-biophys-090921-120150","url":null,"abstract":"Molecular chaperones are the guardians of the proteome inside the cell. Chaperones recognize and bind unfolded or misfolded substrates, thereby preventing further aggregation; promoting correct protein folding; and, in some instances, even disaggregating already formed aggregates. Chaperones perform their function by means of an array of weak protein-protein interactions that take place over a wide range of timescales and are therefore invisible to structural techniques dependent upon the availability of highly homogeneous samples. Nuclear magnetic resonance (NMR) spectroscopy, however, is ideally suited to study dynamic, rapidly interconverting conformational states and protein-protein interactions in solution, even if these involve a high-molecular-weight component. In this review, we give a brief overview of the principles used by chaperones to bind their client proteins and describe NMR methods that have emerged as valuable tools to probe chaperone-substrate and chaperone-chaperone interactions. We then focus on a few systems for which the application of these methods has greatly increased our understanding of the mechanisms underlying chaperone functions.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"223-246"},"PeriodicalIF":10.4,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9358445/pdf/nihms-1826902.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39832390","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

Lipid-Protein Interactions in Plasma Membrane Organization and Function. 质膜组织和功能中的脂质-蛋白相互作用。

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2022-05-09 Epub Date: 2022-01-04 DOI: 10.1146/annurev-biophys-090721-072718

Taras Sych, Kandice R Levental, Erdinc Sezgin

引用次数: 0

Chaperonin Mechanisms: Multiple and (Mis)Understood? 伴侣蛋白机制:多重和(误解)理解?

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-082521-113418

Amnon Horovitz, Tali Haviv Reingewertz, Jorge Cuéllar, José María Valpuesta

引用次数: 16

A Life of Biophysics. 《生命物理学》