Quarterly Reviews of Biophysics最新文献

S-layer (Glyco)protein lattices: Biophysical principles of antifouling at prokaryotic interfaces. s层（Glyco）蛋白晶格：原核界面防污的生物物理原理。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2026-08-07 DOI: 10.1017/S0033583526100213

Uwe B Sleytr, Bernhard Schuster

{"title":"S-layer (Glyco)protein lattices: Biophysical principles of antifouling at prokaryotic interfaces.","authors":"Uwe B Sleytr, Bernhard Schuster","doi":"10.1017/S0033583526100213","DOIUrl":"https://doi.org/10.1017/S0033583526100213","url":null,"abstract":"Surface layer (S-layer) lattices, composed of proteins and glycoproteins, constitute one of the most abundant and conserved supramolecular structures in the prokaryotic world. These self-assembling, two-dimensional arrays represent a major evolutionary investment, often accounting for up to 10% of total cellular protein synthesis. Despite enormous sequence diversity and adaptation to widely different ecological niches, S-layers persist across phylogeny, suggesting a fundamental selective advantage. In this review, we synthesize historical ultrastructural observations with modern atomic-resolution structural data and biophysical principles to demonstrate that antifouling is a general and fundamental function of all bacterial and archaeal S-layers. We argue that antifouling arises from a sophisticated synergy of lattice dynamics, crystalline nanotopography, electrostatic mosaicity, fragmented hydrophobicity, structured hydration shells and frequently glycan-mediated steric repulsion. We specifically place S-layer antifouling into the physical framework of life at low Reynolds numbers, where even minimal surface fouling imposes severe energetic penalties on nutrient acquisition and motility. We also highlight the S-layer as a tunable interface that suppresses non-specific fouling while precisely gating specific molecular interactions and community formation. Finally, we discuss how this universal biophysical strategy provides a powerful blueprint for biomimetic surface engineering in (nano)biotechnology, synthetic biology, and materials science.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"59 ","pages":"e14"},"PeriodicalIF":6.1,"publicationDate":"2026-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148685660","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

Lasing emission spectroscopy for bioanalytics and biomedicine. 用于生物分析和生物医学的激光发射光谱。

IF 5.3 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2026-06-08 DOI: 10.1017/S0033583526100183

Grzegorz Szwachta, Ewelina Jalonicka, Tomasz Rygiel, Piotr Hanczyc

{"title":"Lasing emission spectroscopy for bioanalytics and biomedicine.","authors":"Grzegorz Szwachta, Ewelina Jalonicka, Tomasz Rygiel, Piotr Hanczyc","doi":"10.1017/S0033583526100183","DOIUrl":"10.1017/S0033583526100183","url":null,"abstract":"Lasing spectroscopy (LS) is emerging as a powerful extension of conventional fluorescence methods for highly sensitive bioanalytical detection. By exploiting stimulated emission and optical feedback mechanisms, LS generates narrow spectral linewidths, threshold-dependent emission, and highly directional radiation, enabling enhanced signal-to-noise ratios and improved sensitivity compared with traditional fluorescence spectroscopy. In bioanalytical systems, subtle molecular events such as biomolecular binding, conformational transitions, or local refractive-index changes can significantly modify lasing thresholds, emission intensity, or spectral position, providing sensitive optical readouts of biochemical processes. This review presents a comprehensive overview of LS methodologies and their emerging applications in biomedical research. The discussion is structured according to a graded framework of increasing optical and methodological complexity, beginning with mirrorless amplified spontaneous emission (ASE) and random lasing (RL) in solid-state biomolecular matrices, followed by engineered photonic architectures, including distributed-feedback gratings and nanoporous anodic alumina (NAA) structures. More advanced resonator-based configurations in liquids, such as Fabry–Pérot (FP) cavities, whispering-gallery-mode microresonators, and optofluidic droplet lasers, are also examined. Across these platforms, LS is shown to enable ultrasensitive bioanalytical detection and novel diagnostic strategies, including early detection of protein aggregation, monitoring nucleic-acid conformational states, tissue- and single-cell laser diagnostics, and label-free refractometric biosensing. Finally, the review highlights current technical challenges, including dye photostability, cavity engineering, and measurement standardization, and discusses future perspectives for translating lasing-based bioanalytics toward clinically relevant diagnostics in neurodegenerative diseases, oncology, metabolic disorders, and infectious diseases.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"59 ","pages":"e12"},"PeriodicalIF":5.3,"publicationDate":"2026-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148199795","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

Elementary processes and mechanisms of nanopore formation induced by antimicrobial peptides and other membrane-active peptides. 抗菌肽和其他膜活性肽诱导纳米孔形成的基本过程和机制。

IF 5.3 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2026-06-04 DOI: 10.1017/S0033583526100195

Md Masum Billah, Yukihiro Tamba, Md Zahidul Islam, Masahito Yamazaki

{"title":"Elementary processes and mechanisms of nanopore formation induced by antimicrobial peptides and other membrane-active peptides.","authors":"Md Masum Billah, Yukihiro Tamba, Md Zahidul Islam, Masahito Yamazaki","doi":"10.1017/S0033583526100195","DOIUrl":"10.1017/S0033583526100195","url":null,"abstract":"The activity of membrane-active peptides/proteins (MAPs) involves interactions with lipid bilayer regions of cell membranes. For example, antimicrobial peptides, lytic peptides, pore-forming toxins, lipidated peptides, and cell-penetrating peptides are all MAPs. Most MAPs induce damage in cell membranes/lipid bilayers, such as nanopore formation. Various methods have been employed to examine the interactions between MAPs and lipid bilayers, as well as MAP-induced membrane damage. Methods using giant unilamellar vesicles (GUVs) are particularly versatile techniques because they provide useful information regarding both MAP-lipid bilayer interactions and MAP activities such as membrane damage. GUV studies have revealed many aspects of elementary processes of MAP-induced membrane damage and their correlations, thus clarifying the mechanisms of MAPs-induced membrane damage. Here, we focus on GUV-based studies of MAP-induced nanopore formation in lipid bilayers. First, we review the binding of MAPs to the lipid bilayers. Second, we review the rate of MAP-induced nanopore formation and the rate of membrane permeation of fluorescent probes through the nanopores. Third, we review the relationships between several elementary processes involved in MAP-induced nanopore formation (i.e., binding of MAPs, nanopore formation, translocation of MAPs across lipid bilayers) and factors that induce membrane instability to facilitate nanopore formation. The pre-pore model of translocation of MAPs across lipid bilayers is also reviewed. Fourth, we review the effects of membrane tension, membrane potential, and lipid composition on MAP-induced formation of nanopores and their stability. Finally, we describe our perspectives on future GUV-based studies of MAP-induced nanopore formation.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"59 ","pages":"e11"},"PeriodicalIF":5.3,"publicationDate":"2026-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148157818","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

Biomineralization: Perspectives on control of crystal polymorphism, order-disorder and solvation states. 生物矿化：晶体多态性、有序-无序和溶剂化状态控制的观点。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2026-05-11 DOI: 10.1017/S0033583526100171

Lia Addadi, Steve Weiner

{"title":"Biomineralization: Perspectives on control of crystal polymorphism, order-disorder and solvation states.","authors":"Lia Addadi, Steve Weiner","doi":"10.1017/S0033583526100171","DOIUrl":"10.1017/S0033583526100171","url":null,"abstract":"Some of the most challenging issues in biomineralization relate to understanding how organisms control the properties of the minerals and molecular crystals that they form. Here, we examine these largely unresolved issues by considering factors that could be involved in determining the specific crystal polymorph formed. We also focus on the interplay between control over the properties of transient disordered precursor phases and control exerted by crystal nucleation on pre-positioned structured surfaces. In most cases, the polymorph and/or mineral types used are clearly under genetic control, yet in only very few cases are we aware of an obvious functional benefit. This is exemplified by many molecular crystals in vision and production of structural colors, where polymorph type and function do not correlate. There are many common underlying control mechanisms common to the formation of carbonate and phosphate minerals, and molecular crystals. We conclude that in many cases control is being exerted both at the precursor phase stage, as well as at the nucleation stage, and suggest that this possible redundancy could be responsible for the high fidelity that organisms exhibit over crystal polymorph and molecular crystal types formed. Finally cholesterol crystal formation, provides good insights into polymorph choice and substrate control. We wonder whether this occurs because this is a pathological process that perhaps 'obeys' better the chemical laws that we understand, as opposed to the normal biological control exhibited through cells that appear to be far more complex.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"59 ","pages":"e10"},"PeriodicalIF":6.1,"publicationDate":"2026-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147869440","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 pivotal roles of cellular biophysics and mechanobiology in the development of Human Organs-on-Chips. 细胞生物物理学和机械生物学在人体器官芯片发展中的关键作用。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2026-05-04 DOI: 10.1017/S003358352610016X

Donald E Ingber

{"title":"The pivotal roles of cellular biophysics and mechanobiology in the development of Human Organs-on-Chips.","authors":"Donald E Ingber","doi":"10.1017/S003358352610016X","DOIUrl":"10.1017/S003358352610016X","url":null,"abstract":"The development of Human Organs-on-Chips (Organ Chips) - microfluidic culture devices lined by living human tissues that recapitulate organ-level pathophysiology and offer a new approach to replace animal testing in drug development and advance personalized medicine - is often viewed through the lens of bioengineering and microfabrication. However, the origin of this technology lies deeply rooted in pursuit of a fundamental understanding of cellular biophysics and human mechanobiology. This review is written primarily from a personal perspective, and it traces work beginning 50 years ago, which describes how the need for new experimental tools to test a novel tensegrity model of cellular mechanics and mechanotransduction led to the melding of cell biology, engineering, and computer microchip manufacturing approaches, and eventually to the birth of Organ Chip technology. The initial driving force was the need to artificially control the shape of living cells to demonstrate the central role that mechanical forces play in biological control. This led to the adoption of soft lithography to create tailored cell culture environments and later to the development of mechanically active, microfluidic Organ Chip culture systems. By recapitulating tissue-tissue interfaces and the dynamic mechanical microenvironments of living organs, Organ Chips enable understanding of mechanobiological phenomena that are unattainable with traditional static cell cultures or animal models. This path of research has confirmed the indispensable importance of physical forces for physiological control, in addition to accelerating drug discovery, enhancing toxicity assessment, and deepening our comprehension of disease pathogenesis.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"59 ","pages":"e9"},"PeriodicalIF":6.1,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147820097","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

Biophysics meets fungal biology: Characterising the fungal cell envelope and its interactions with drug-like molecules. 生物物理学与真菌生物学：表征真菌细胞包膜及其与药物样分子的相互作用。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2026-04-28 DOI: 10.1017/S0033583526100158

Obed Obeng-Gyasi, Evelyne Deplazes

{"title":"Biophysics meets fungal biology: Characterising the fungal cell envelope and its interactions with drug-like molecules.","authors":"Obed Obeng-Gyasi, Evelyne Deplazes","doi":"10.1017/S0033583526100158","DOIUrl":"10.1017/S0033583526100158","url":null,"abstract":"The fungal cell envelope, consisting of the cell wall and plasma membrane, is a dynamic structure crucial for cell shape, viability, pathogenicity, and the cell's ability to interact with and respond to its environment. Most antifungal drug development target components of the fungal plasma membrane and cell wall, thus understanding its composition and interactions with small molecules is vital for biomedical research and drug development. However, studying cell walls and membranes is challenging due to their high degree of complexity, their heterogeneous and dynamic structure and their sensitivity to environmental conditions. Our review provides a unique exploration of how biophysical techniques have advanced our understanding of the cell envelope's structure, its role in fungal pathogenicity, and drug resistance, which are critical issues for global health and food security. We highlight recent advances in microscopy and spectroscopy approaches, combined with analytical techniques and lipidomics, that have enabled detailed study of fungal cell walls and plasma membranes at unprecedented spatial and temporal resolutions. These studies have helped provide structural models of fungal cell walls and plasma membranes, including important differences between clinically relevant fungal species that are critical for antifungal drug development. Our review also summarises commonly used model membranes systems and discusses challenges and considerations in bridging gaps between simplified models and cellular systems, and why they are lacking compared to bacterial and mammalian systems and what is required to improve these systems.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"59 ","pages":"e8"},"PeriodicalIF":6.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147779500","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

Energy landscapes in molecular biology: History, principles, and perspectives. 分子生物学中的能量景观：历史、原理和观点。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2026-04-22 DOI: 10.1017/S0033583526100134

Ruth Nussinov, Clil Regev, Hyunbum Jang

{"title":"Energy landscapes in molecular biology: History, principles, and perspectives.","authors":"Ruth Nussinov, Clil Regev, Hyunbum Jang","doi":"10.1017/S0033583526100134","DOIUrl":"10.1017/S0033583526100134","url":null,"abstract":"In an editorial for a Special Issue, Nussinov and Wolynes explored the energy landscapes of biomolecular function, questioning whether they constituted a second molecular biology revolution. With more than a decade having passed and science having progressed significantly, we revisit this question. Statistical energy landscapes not only visualize folding funnels but also quantify the likelihoods of different states, embodying the foundational physical-chemical principles of protein actions. Building upon the theory of energy landscapes, the conformational selection and population shift paradigm posited that since all functional conformations already pre-exist in a dynamic equilibrium, a ligand 'selects' and stabilizes a state from this pre-existing pool, resulting in re-equilibration, or shift, of the population. The principle that it established - that function harnesses transitions between pre-existing conformations - revolutionized the understanding of allostery and, broadly, regulation. This paradigm challenged and superseded the decades-old, albeit persisting, belief of only one (or two; 'open' and 'closed') protein conformations. It also indicates that for engineered proteins to exert effective function, we must account for the timescales of flipping between energy landscape states, for example, by tuning the barrier heights. Returning to the question of whether landscapes constituted a second biomolecular biology revolution, we consider their bedrock contributions, which are far beyond the original protein folding funnels. They established the principle of multiple dynamic conformational states 'jumping' over barriers during population shifts. By leveraging core concepts like conformational ensembles, modern molecular biology has achieved breakthroughs such as next-generation allosteric drugs, indeed leading to a transformative era in molecular science.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"59 ","pages":"e7"},"PeriodicalIF":6.1,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147779503","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 influence of structure, dissociation constants, and an aqueous environment on the physicochemical properties of L-α-amino acids. 结构、解离常数和水环境对L-α-氨基酸理化性质的影响。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2026-04-07 DOI: 10.1017/S0033583526100146

Marek Pająk, Magdalena Woźniczka, Elżbieta Kamysz, Marcin Banach, Jakub Fichna

{"title":"The influence of structure, dissociation constants, and an aqueous environment on the physicochemical properties of L-α-amino acids.","authors":"Marek Pająk, Magdalena Woźniczka, Elżbieta Kamysz, Marcin Banach, Jakub Fichna","doi":"10.1017/S0033583526100146","DOIUrl":"10.1017/S0033583526100146","url":null,"abstract":"L-α-amino acids are the fundamental building blocks of proteins and play a pivotal role in the biochemistry of living organisms. The behavior of these molecules in an aqueous solution – the primary medium for biological reactions – is contingent on their physicochemical properties, including molecular structure and dissociation constants (Ka). The objective of this article is to provide a comprehensive description of the chemical significance of amino acids in an aqueous environment. This encompasses their ionization states at varying pH, interactions with water molecules, environmental effects (e.g., ionic strength, temperature, the presence of other ions, and pressure), and the implications of these factors for the stability and biological function of the example peptides and proteins. The article also presents a discussion of contemporary experimental and computational methodologies employed in the study of the physicochemical properties of amino acids in an aqueous solution. It is imperative that these relationships are comprehended if advancements in the fields of drug design, protein engineering, and biotechnology are to be facilitated.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"59 ","pages":"e6"},"PeriodicalIF":6.1,"publicationDate":"2026-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147628299","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

Crystallographic binding modes of octahedral transition metal complexes to duplex DNA. 八面体过渡金属配合物与双链DNA的结晶结合模式。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2026-03-30 DOI: 10.1017/S0033583526100122

Tayler D Prieto Otoya, Christine Janet Cardin

引用次数: 0

Cryo-EM of endogenous membrane proteins in their native lipid bilayer. 内源性膜蛋白在其天然脂质双分子层中的低温电镜观察。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2026-03-06 DOI: 10.1017/S0033583526100109

John L Rubinstein

引用次数: 0