Quarterly Reviews Of Biophysics[JOURNAL]
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200 papers
Lasing emission spectroscopy for bioanalytics and biomedicine.
Szwachta G, Jalonicka E, Rygiel T … +1 more , Hanczyc P
Q Rev Biophys · 2026 Jun · PMID 42252744 · Publisher ↗
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 genera...
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.
Elementary processes and mechanisms of nanopore formation induced by antimicrobial peptides and other membrane-active peptides.
Billah MM, Tamba Y, Islam MZ … +1 more , Yamazaki M
Q Rev Biophys · 2026 Jun · PMID 42237812 · Publisher ↗
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, a...
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.
Biomineralization: Perspectives on control of crystal polymorphism, order-disorder and solvation states.
Addadi L, Weiner S
Q Rev Biophys · 2026 May · PMID 42112551 · Publisher ↗
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 issue...
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.
The pivotal roles of cellular biophysics and mechanobiology in the development of Human Organs-on-Chips.
Ingber DE
Q Rev Biophys · 2026 May · PMID 42076914 · Publisher ↗
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...
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.
Biophysics meets fungal biology: Characterising the fungal cell envelope and its interactions with drug-like molecules.
Obeng-Gyasi O, Deplazes E
Q Rev Biophys · 2026 Apr · PMID 42046897 · Publisher ↗
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....
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.
Energy landscapes in molecular biology: History, principles, and perspectives.
Nussinov R, Regev C, Jang H
Q Rev Biophys · 2026 Apr · PMID 42015616 · Publisher ↗
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 havin...
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, 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.
The influence of structure, dissociation constants, and an aqueous environment on the physicochemical properties of L-α-amino acids.
Pająk M, Woźniczka M, Kamysz E … +2 more , Banach M, Fichna J
Q Rev Biophys · 2026 Apr · PMID 41944360 · Publisher ↗
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...
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 (). 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.
Crystallographic binding modes of octahedral transition metal complexes to duplex DNA.
Prieto Otoya TD, Cardin CJ
Q Rev Biophys · 2026 Mar · PMID 41909942 · Publisher ↗
Octahedral transition metal complexes are increasingly recognised as useful tools for the development of complex cations that recognise and interact with specific DNA sequences and higher-order DNA topologies. The versat...
Octahedral transition metal complexes are increasingly recognised as useful tools for the development of complex cations that recognise and interact with specific DNA sequences and higher-order DNA topologies. The versatility and diversity of these complexes is particularly due to their rich photophysical and electrochemical properties at the octahedral metal centre, which can be modulated by changing the surrounding ligands. While X-ray crystallography provides uniquely direct structural information on metal-DNA binding, it is one of several essential approaches; solution-state methods such as NMR and complementary biophysical studies are critical for defining predominant binding modes in solution and in biologically relevant environments. Here, we present an overview of the different binding modes of some of these octahedral transition metal complexes with DNA, emphasising the structural and biophysical studies employed to understand metal complex-DNA interactions.
Cryo-EM of endogenous membrane proteins in their native lipid bilayer.
Rubinstein JL
Q Rev Biophys · 2026 Mar · PMID 41789471 · Publisher ↗
Single-particle electron cryomicroscopy (cryo-EM) has enabled rapid advances in our understanding of membrane protein structure and function. The primary goal during the development of cryo-EM was to perform experiments...
Single-particle electron cryomicroscopy (cryo-EM) has enabled rapid advances in our understanding of membrane protein structure and function. The primary goal during the development of cryo-EM was to perform experiments equivalent to X-ray crystallography, but without needing to crystallize the protein of interest first. However, exciting recent progress in single-particle cryo-EM has come from relaxing assumptions and constraints related to the homogeneity of samples. These assumptions and constraints, which were necessary for crystallization, include that all molecules imaged have the same composition and are in the same conformation, that the specimen consists of only one species, and that the specimen is derived from a solution of isolated protein particles. Here, I discuss the study of membrane protein complexes within lipid bilayers by single-particle cryo-EM. I point out the value and recently achieved capability of studying membrane proteins in lipid vesicles, and in particular endogenous membrane proteins in vesicles prepared from their native lipid bilayer.
Revealing protein dynamics with high-pressure NMR.
Roche J, Roumestand C, Royer CA
Q Rev Biophys · 2026 Feb · PMID 41742810 · Publisher ↗
While the structure of proteins can now be predicted from sequence with high certainty, the prediction of protein functional dynamics remains to be achieved. Progress towards this goal will require a much larger experime...
While the structure of proteins can now be predicted from sequence with high certainty, the prediction of protein functional dynamics remains to be achieved. Progress towards this goal will require a much larger experimental database of the relationships among sequence, dynamics, and function than currently available. Dynamic transitions that are key to protein function and turnover remain difficult to access and characterize because they have significantly higher free energy than the folded states of proteins and hence are not populated. To access these higher free energy states, proteins must be perturbed. High temperatures often lead to aggregation, while chemical denaturants, because they interact with the entire protein backbone, tend to smooth protein conformational landscapes. In contrast, high hydrostatic pressure represents a continuous and reversible variable that can perturb protein structure locally around internal cavities, leading to partial structural disruption, populating these higher energy states sufficiently for their characterization.
The energy barrier model in membrane biophysics: Ion flow, current-voltage relations, and Donnan osmosis.
Manning G
Q Rev Biophys · 2026 Feb · PMID 41736698 · Publisher ↗
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...
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.
The multifaceted character of water as solvent for proteins: From poor for folded proteins to good for (some) intrinsically disordered proteins and protein segments.
Schweitzer-Stenner R
Q Rev Biophys · 2026 Feb · PMID 41725507 · Publisher ↗
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 enable...
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.
Delivery of macromolecular drugs: An update.
Langer R
Q Rev Biophys · 2025 Nov · PMID 41249147 · Publisher ↗
In 2019, in this journal, I discussed approaches for controlling the movement of molecules, in particular macromolecules, with an emphasis on how this enabled advances in the field of drug delivery - a field that has imp...
In 2019, in this journal, I discussed approaches for controlling the movement of molecules, in particular macromolecules, with an emphasis on how this enabled advances in the field of drug delivery - a field that has impacted billions of people worldwide. Since 2019, there have been advances in our work and this field including a striking demonstration in which drug delivery nanoparticles were crucial to the success of mRNA therapies and the Covid-19 vaccine. In this paper, I provide updates in such areas as i) developing new methods for oral drug delivery systems, ii) delivery of molecules to specific sites of the body, iii) new types of delivery systems, and iv) examples of machine learning/artificial intelligence in these areas. I also discuss advances in mRNA technology as it relates to drug delivery and the development of nanoparticles to protect and deliver vaccines, which saved and improved the lives of hundreds of millions of people throughout the world.
Allostery: allosteric networks and allosteric signaling bias.
Nussinov R, Yavuz BR, Jang H
Q Rev Biophys · 2025 Nov · PMID 41249142 · Publisher ↗
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 m...
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 and are graphs specified by nodes (residues) and edges (their connections). Allosteric 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 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 Within this framework, we further consider signaling strength and duration as key determinants of cell fate: eak and sustained, it may induce differentiation; bursts of strong and short, proliferation.
Time-resolved fluorescence of tryptophan in biophysical chemistry and pharmaceutical research - the pleasures and nightmares dealing with nature's own fluorophore.
Carabadjac I, Heerklotz H
Q Rev Biophys · 2025 Nov · PMID 41177528 · Publisher ↗
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 membran...
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.
Resilience of DNA chains to molecular fracture after PCR heating cycles and implications on PCR reliability - EXPRESSION OF CONCERN.
Serpieri R, Franchi F
Q Rev Biophys · 2025 Aug · PMID 40755072 · Publisher ↗
Abstract loading — click title to view on PubMed.
How reliable is PCR? A mini review.
Konrad H, Beyer A
Q Rev Biophys · 2025 Jul · PMID 40637419 · Publisher ↗
The question of whether PCR is reliable sounds strange at first. However, looking at the scientific literature from the 1950s and 60s, one will find many publications on the physicochemistry of DNA that have been forgott...
The question of whether PCR is reliable sounds strange at first. However, looking at the scientific literature from the 1950s and 60s, one will find many publications on the physicochemistry of DNA that have been forgotten meanwhile. Quite a few of these studies have shown that DNA is thermolabile, which consequently raises the question of whether this thermolability is relevant in the context of PCR, namely in the denaturation phase. However, it can be shown that this is not the case: losses due to thermal hydrolysis are irrelevant for the performance of contemporary PCR protocols and their specificity as well as for the significance of their results. There is now a huge amount of scientifically verified and published data on technical and molecular aspects of PCR, a small selection of which we quote here. In addition, we present some primary data that also clearly demonstrate the reliability of PCR.
Using multiscale molecular dynamics simulations to explore the fusion machinery underlying neurotransmitter release.
An D, Sharma S, Lindau M
Q Rev Biophys · 2025 Jun · PMID 40574507 · Full text
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). Whil...
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.
Some general principles of riboswitch structure and interactions with small-molecule ligands.
Huang L, Lilley DMJ
Q Rev Biophys · 2025 May · PMID 40432402 · Publisher ↗
Riboswitches are RNA elements with a defined structure found in noncoding sections of genes that allow the direct control of gene expression by the binding of small molecules functionally related to the gene product. In...
Riboswitches are RNA elements with a defined structure found in noncoding sections of genes that allow the direct control of gene expression by the binding of small molecules functionally related to the gene product. In most cases, this is a metabolite in the same (typically biosynthetic) pathway as an enzyme (or transporter) encoded by the gene that is controlled. The structures of many riboswitches have been determined and this provides a large database of RNA structure and ligand binding. In this review, we extract general principles of RNA structure and the manner or ligand binding from this resource.
From resting potential to dynamics: advances in membrane voltage indicators and imaging techniques - ERRATUM.
Shakibi R, Yazdipour F, Abadijoo H … +9 more , Manoochehri N, Rostami Pouria F, Bajooli T, Simaee H, Abdolmaleki P, Khatibi A, Abdolahad M, Moosavi-Movahhedi AA, Khayamian MA
Q Rev Biophys · 2025 Mar · PMID 40162525 · Publisher ↗
Abstract loading — click title to view on PubMed.
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