Quarterly Reviews of Biophysics最新文献_第2页

Revealing protein dynamics with high-pressure NMR. 用高压核磁共振揭示蛋白质动力学。

IF 5.3 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2026-02-26 DOI: 10.1017/S0033583526100092

Julien Roche, Christian Roumestand, Catherine A Royer

引用次数: 0

The energy barrier model in membrane biophysics: Ion flow, current-voltage relations, and Donnan osmosis. 膜生物物理学中的能量势垒模型：离子流、电流-电压关系和唐南渗透。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2026-02-25 DOI: 10.1017/S0033583526100110

Gerald Manning

{"title":"The energy barrier model in membrane biophysics: Ion flow, current-voltage relations, and Donnan osmosis.","authors":"Gerald Manning","doi":"10.1017/S0033583526100110","DOIUrl":"10.1017/S0033583526100110","url":null,"abstract":"Theoretical analysis of an energy barrier model for the electrical properties of a biological membrane yields new results. Discontinuities at the membrane-solution interfaces are crucial and receive careful attention, as does the polarization charge density due to electroneutral but polarized ion distributions. The topics explored include the equilibrium and time-dependent Nernst potential, the resting potential, the capacitance-resistance equation for membrane voltage, and large electrical effects on osmosis (bulk volume flow). The generalization of Nernst-Hartley salt diffusion to the diffusion of mixed salts as a necessary tool is accomplished. The electric field inside the membrane is especially strong at the membrane-solution interfaces. The analysis of the resting potential differs from the Goldman-Hodgkin-Katz formulation but predicts realistic numerical values for animal cells and also captures the effect of switching sodium and potassium ion permeabilities. An analysis of the physical basis of bulk water flow in the presence of impermeant and permeant ions, that is, Donnan osmosis, reveals large ion charge effects that have not previously been considered. The equation derived here for Donnan osmotic flow helps to explain why the action of the sodium pump is essential for the prevention of excessive osmotic stress on cellular membranes.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"59 ","pages":"e1"},"PeriodicalIF":6.1,"publicationDate":"2026-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147284876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

The multifaceted character of water as solvent for proteins: From poor for folded proteins to good for (some) intrinsically disordered proteins and protein segments. 水作为蛋白质溶剂的多面性：从对折叠蛋白质的不利到对（某些）内在无序的蛋白质和蛋白质片段的有利。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2026-02-23 DOI: 10.1017/S0033583526100080

Reinhard Schweitzer-Stenner

{"title":"The multifaceted character of water as solvent for proteins: From poor for folded proteins to good for (some) intrinsically disordered proteins and protein segments.","authors":"Reinhard Schweitzer-Stenner","doi":"10.1017/S0033583526100080","DOIUrl":"10.1017/S0033583526100080","url":null,"abstract":"Intrinsically disordered proteins (IDPs) and disordered regions of folded proteins (IDRs) perform a plethora of cellular functions involving interactions with a variety of proteins, DNA, and RNA. Their flexibility enables them to interact with different cellular components. They can adopt molten globule as well as extended statistical coil structures depending on their amino acid residue sequence. They are generally more enriched in polar and charged residues, which generally facilitate solvation. This review article asks to what extent water as a solvent affects local (on a residue level) and global properties (size, Flory exponents) of IDPs. It introduces various aspects of protein hydration in the folded state as a benchmark and reference. The results of experimental and computational studies on short model peptides reveal how local structural propensities of residues are determined by water-backbone and water-side chain interactions. Ramachandran plots of individual amino acid residues are side-chain and neighbor-dependent. For unfolded oligo-peptides and IDPs (IDRs) the article discusses the intricated relationship between IDP hydration and global parameters (i.e., radius of gyration), which involves multiple parameters such as net charge, charge distribution, hydrophobicity, and the ionic strength of the aqueous solution. A review of experimental work that explored the strength of water-protein interactions and their influence on water dynamics reveals significant differences between water binding to folded and disordered proteins. Finally, The role of water in liquid-liquid mixing of short peptides and IDPs is delineated, which can lead to gelation and the formation of membrane-less droplets.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":" ","pages":"e5"},"PeriodicalIF":6.1,"publicationDate":"2026-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147271882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Delivery of macromolecular drugs: An update. 大分子药物的递送：最新进展。

IF 5.3 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2025-11-18 DOI: 10.1017/S0033583525100073

Robert Langer

引用次数: 0

Allostery: allosteric networks and allosteric signaling bias. 变构：变构网络和变构信号偏倚。

IF 5.3 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2025-11-18 DOI: 10.1017/S0033583525100061

Ruth Nussinov, Bengi R Yavuz, Hyunbum Jang

{"title":"Allostery: allosteric networks and allosteric signaling bias.","authors":"Ruth Nussinov, Bengi R Yavuz, Hyunbum Jang","doi":"10.1017/S0033583525100061","DOIUrl":"10.1017/S0033583525100061","url":null,"abstract":"Allosteric communication is established by networks through which strain energy generated at the allosteric site by an allosteric event, such as ligand binding, can propagate to the functional site. Exerted on multiple molecules in the cell, it can wield a biased function. Here, we discuss allosteric networks and allosteric signaling bias. Networks are graphs specified by nodes (residues) and edges (their connections). Allosteric bias is a property of a population. It is described by allosteric effector-specific dynamic distributions of conformational ensembles, as classically exemplified by G protein-coupled receptors (GPCRs). An ensemble describes the likelihood of a specific (strong/weak) allosteric signal propagating to a specific functional site. A network description provides the propagation route in a specific conformation, pinpointing key residues whose mutations could promote drug resistance. Efficiency is influenced by path length, relative stabilities and allosteric transitions. Through specific contacts, specific ligands can bias signaling in proteins, for example, in receptor tyrosine kinases (RTKs) toward specific phosphorylation sites and cell signaling activation. Thus, rather than the two - active and inactive - states, and a single pathway, we consider multiple states and favored pathways. This allows us to consider biased allosteric switches among minor, invisible states and observable outcomes. Within this framework, we further consider signaling strength and duration as key determinants of cell fate: If weak and sustained, it may induce differentiation; If bursts of strong and short, proliferation.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":" ","pages":"e17"},"PeriodicalIF":5.3,"publicationDate":"2025-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145542113","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Time-resolved fluorescence of tryptophan in biophysical chemistry and pharmaceutical research - the pleasures and nightmares dealing with nature's own fluorophore. 生物物理化学和药物研究中色氨酸的时间分辨荧光——处理大自然自身荧光团的乐趣和噩梦。

IF 5.3 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2025-11-03 DOI: 10.1017/S003358352510005X

Iulia Carabadjac, Heiko Heerklotz

{"title":"Time-resolved fluorescence of tryptophan in biophysical chemistry and pharmaceutical research - the pleasures and nightmares dealing with nature's own fluorophore.","authors":"Iulia Carabadjac, Heiko Heerklotz","doi":"10.1017/S003358352510005X","DOIUrl":"10.1017/S003358352510005X","url":null,"abstract":"Time-resolved (TR) intrinsic fluorescence of tryptophan (Trp) provides a wealth of information on the structure and localization of proteins and peptides and their interactions with one another, with drugs, lipid membranes, lipid- and surfactant-based drug delivery systems, et cetera. Intrinsic Trp eliminates the need for labeling and avoids the perturbation of the system by the label; introduced Trp is a rather conservative and small label compared to others. Whereas custom-tailored fluorophores are often optimized for a special technique, Trp can be employed to monitor a wide variety of effects. We address interactions of Trp with surrounding molecules, dynamic quenchers and Förster resonance energy transfer (FRET) acceptors that affect the fluorescence decay. Speed and range of angular motion of Trp are characterized by TR anisotropy. Electrostatic interactions of Trp with charged and polar molecules, including water, are monitored by decay-associated spectra (DAS) or TR emission spectra (TRES) and quantified in terms of TR shifts of the spectral center of gravity. This versatility is a great advantage and, at the same time, comes with a complexity of the behavior that can render it a challenge to interpret the data in detail properly. This review provides an overview of applications of TR fluorescence of Trp bulk samples in biomolecular, biophysical, and pharmaceutical studies. The aim is not only to point out the diversity of the read-out of these techniques, but also critically examine their current use. Therefore, we identify most common technical pitfalls and evaluate the degree of reliability of the interpretational approaches. This should aid a more extensive and meaningful use of TR fluorescence of Trp.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":" ","pages":"e18"},"PeriodicalIF":5.3,"publicationDate":"2025-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145431828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Resilience of DNA chains to molecular fracture after PCR heating cycles and implications on PCR reliability - EXPRESSION OF CONCERN. PCR加热循环后DNA链对分子断裂的弹性及其对PCR可靠性的影响——表达关注。

IF 5.3 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2025-08-04 DOI: 10.1017/S0033583525100036

Roberto Serpieri, Fabio Franchi

引用次数: 0

How reliable is PCR? A mini review. PCR有多可靠？一个小回顾。

IF 5.3 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2025-07-10 DOI: 10.1017/S0033583525100024

Helen Konrad, Andreas Beyer

引用次数: 0

Using multiscale molecular dynamics simulations to explore the fusion machinery underlying neurotransmitter release. 利用多尺度分子动力学模拟探索神经递质释放背后的融合机制。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2025-06-27 DOI: 10.1017/S0033583525100048

Dong An, Satyan Sharma, Manfred Lindau

{"title":"Using multiscale molecular dynamics simulations to explore the fusion machinery underlying neurotransmitter release.","authors":"Dong An, Satyan Sharma, Manfred Lindau","doi":"10.1017/S0033583525100048","DOIUrl":"10.1017/S0033583525100048","url":null,"abstract":"Neurotransmitter release via synaptic vesicle fusion with the plasma membrane is driven by SNARE proteins (Synaptobrevin, Syntaxin, and SNAP-25) and accessory proteins (Synaptotagmin, Complexin, Munc13, and Munc18). While extensively studied experimentally, the precise mechanisms and dynamics remain elusive due to spatiotemporal limitations. Molecular dynamics (MD) simulations-both all-atom (AA) and coarse-grained (CG)-bridge these gaps by capturing fusion dynamics beyond experimental resolution. This review explores the use of these simulations in understanding SNARE-mediated membrane fusion and its regulation by Synaptotagmin and Complexin. We first examine two competing hypotheses regarding the driving force of fusion: (1) SNARE zippering transducing energy through rigid juxtamembrane domains (JMDs) and (2) SNAREs generating entropic forces via flexible JMDs. Despite different origins of forces, the conserved fusion pathway - from membrane adhesion to stalk and fusion pore (FP) formation - emerges across models. We also highlight the critical role of SNARE transmembrane domains (TMDs) and their regulation by post-translational modifications like palmitoylation in fast fusion. Further, we review Ca²⁺-dependent interactions of Synaptotagmin's C2 domains with lipids and SNAREs at the primary and tripartite interfaces, and how these interactions regulate fusion timing. Complexin's role in clamping spontaneous fusion while facilitating evoked release via its central and accessory helices is also discussed. We present a case study leveraging AA and CG simulations to investigate ion selectivity in FPs, balancing timescale and accuracy. We conclude with the limitations in current simulations and using AI tools to construct complete fusion machinery and explore isoform-specific functions in fusion machinery.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":" ","pages":"e14"},"PeriodicalIF":6.1,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13092361/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144507967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Some general principles of riboswitch structure and interactions with small-molecule ligands. 核开关结构和与小分子配体相互作用的一般原理。

IF 5.3 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2025-05-28 DOI: 10.1017/S0033583525100012

Lin Huang, David M J Lilley

引用次数: 0