Quarterly Reviews of Biophysics最新文献

Cryo-EM reconstruction of helical polymers: Beyond the simple cases.

IF 7.2 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2024-12-11 DOI: 10.1017/S0033583524000155

Mark A B Kreutzberger, Ravi R Sonani, Edward H Egelman

{"title":"Cryo-EM reconstruction of helical polymers: Beyond the simple cases.","authors":"Mark A B Kreutzberger, Ravi R Sonani, Edward H Egelman","doi":"10.1017/S0033583524000155","DOIUrl":"https://doi.org/10.1017/S0033583524000155","url":null,"abstract":"Helices are one of the most frequently encountered symmetries in biological assemblies. Helical symmetry has been exploited in electron microscopic studies as a limited number of filament images, in principle, can provide all the information needed to do a three-dimensional reconstruction of a polymer. Over the past 25 years, three-dimensional reconstructions of helical polymers from cryo-EM images have shifted completely from Fourier-Bessel methods to single-particle approaches. The single-particle approaches have allowed people to surmount the problem that very few biological polymers are crystalline in order, and despite the flexibility and heterogeneity present in most of these polymers, reaching a resolution where accurate atomic models can be built has now become the standard. While determining the correct helical symmetry may be very simple for something like F-actin, for many other polymers, particularly those formed from small peptides, it can be much more challenging. This review discusses why symmetry determination can be problematic, and why trial-and-error methods are still the best approach. Studies of many macromolecular assemblies, such as icosahedral capsids, have usually found that not imposing symmetry leads to a great reduction in resolution while at the same time revealing possibly interesting asymmetric features. We show that for certain helical assemblies asymmetric reconstructions can sometimes lead to greatly improved resolution. Further, in the case of supercoiled flagellar filaments from bacteria and archaea, we show that the imposition of helical symmetry can not only be wrong, but is not necessary, and obscures the mechanisms whereby these filaments supercoil.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"57 ","pages":"e16"},"PeriodicalIF":7.2,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807822","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

Graph theory approaches for molecular dynamics simulations.

IF 7.2 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2024-12-10 DOI: 10.1017/S0033583524000143

Amun C Patel, Souvik Sinha, Giulia Palermo

{"title":"Graph theory approaches for molecular dynamics simulations.","authors":"Amun C Patel, Souvik Sinha, Giulia Palermo","doi":"10.1017/S0033583524000143","DOIUrl":"10.1017/S0033583524000143","url":null,"abstract":"Graph theory, a branch of mathematics that focuses on the study of graphs (networks of nodes and edges), provides a robust framework for analysing the structural and functional properties of biomolecules. By leveraging molecular dynamics (MD) simulations, atoms or groups of atoms can be represented as nodes, while their dynamic interactions are depicted as edges. This network-based approach facilitates the characterization of properties such as connectivity, centrality, and modularity, which are essential for understanding the behaviour of molecular systems. This review details the application and development of graph theory-based models in studying biomolecular systems. We introduce key concepts in graph theory and demonstrate their practical applications, illustrating how innovative graph theory approaches can be employed to design biomolecular systems with enhanced functionality. Specifically, we explore the integration of graph theoretical methods with MD simulations to gain deeper insights into complex biological phenomena, such as allosteric regulation, conformational dynamics, and catalytic functions. Ultimately, graph theory has proven to be a powerful tool in the field of molecular dynamics, offering valuable insights into the structural properties, dynamics, and interactions of molecular systems. This review establishes a foundation for using graph theory in molecular design and engineering, highlighting its potential to transform the field and drive advancements in the understanding and manipulation of biomolecular systems.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"57 ","pages":"e15"},"PeriodicalIF":7.2,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142802145","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

Atomic molecular dynamics simulation advances of de novo-designed proteins.

IF 7.2 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2024-12-05 DOI: 10.1017/S0033583524000131

Moye Wang, Anqi Ma, Hongjiang Wang, Xiaotong Lou

引用次数: 0

Review of contemporary fluorescence correlation spectroscopy method in diverse solution studies. 当代荧光相关光谱法在各种溶液研究中的应用综述。

IF 7.2 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2024-10-28 DOI: 10.1017/S003358352400012X

Snežana M Jovičić

引用次数: 0

Optical scattering methods for the label-free analysis of single biomolecules. 用于单个生物分子无标记分析的光学散射方法。

IF 7.2 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2024-10-24 DOI: 10.1017/S0033583524000088

Reuven Gordon, Matthew Peters, Cuifeng Ying

引用次数: 0

The development and applications of multidimensional biomolecular spectroscopy illustrated by photosynthetic light harvesting. 以光合作用采光为例，说明多维生物分子光谱学的发展和应用。

IF 7.2 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2024-10-22 DOI: 10.1017/S003358352400009X

Graham R Fleming, Gregory D Scholes

{"title":"The development and applications of multidimensional biomolecular spectroscopy illustrated by photosynthetic light harvesting.","authors":"Graham R Fleming, Gregory D Scholes","doi":"10.1017/S003358352400009X","DOIUrl":"https://doi.org/10.1017/S003358352400009X","url":null,"abstract":"The parallel and synergistic developments of atomic resolution structural information, new spectroscopic methods, their underpinning formalism, and the application of sophisticated theoretical methods have led to a step function change in our understanding of photosynthetic light harvesting, the process by which photosynthetic organisms collect solar energy and supply it to their reaction centers to initiate the chemistry of photosynthesis. The new spectroscopic methods, in particular multidimensional spectroscopies, have enabled a transition from recording rates of processes to focusing on mechanism. We discuss two ultrafast spectroscopies - two-dimensional electronic spectroscopy and two-dimensional electronic-vibrational spectroscopy - and illustrate their development through the lens of photosynthetic light harvesting. Both spectroscopies provide enhanced spectral resolution and, in different ways, reveal pathways of energy flow and coherent oscillations which relate to the quantum mechanical mixing of, for example, electronic excitations (excitons) and nuclear motions. The new types of information present in these spectra provoked the application of sophisticated quantum dynamical theories to describe the temporal evolution of the spectra and provide new questions for experimental investigation. While multidimensional spectroscopies have applications in many other areas of science, we feel that the investigation of photosynthetic light harvesting has had the largest influence on the development of spectroscopic and theoretical methods for the study of quantum dynamics in biology, hence the focus of this review. We conclude with key questions for the next decade of this review.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"57 ","pages":"e11"},"PeriodicalIF":7.2,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142473244","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

Protonation constants of endo- and exogenous L-amino acids and their derivatives in aqueous and mixed solution: Unraveling molecular secrets. 内源性和外源性 L-氨基酸及其衍生物在水溶液和混合溶液中的质子常数：揭开分子的秘密

IF 7.2 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2024-10-18 DOI: 10.1017/S0033583524000118

Marek Pająk, Jakub Fichna, Magdalena Woźniczka

{"title":"Protonation constants of endo- and exogenous L-amino acids and their derivatives in aqueous and mixed solution: Unraveling molecular secrets.","authors":"Marek Pająk, Jakub Fichna, Magdalena Woźniczka","doi":"10.1017/S0033583524000118","DOIUrl":"https://doi.org/10.1017/S0033583524000118","url":null,"abstract":"The aim of this review is to summarize the progress made in the determination of the protonation constants of biologically active ligands: endo- and exogenous L-amino acids and their derivatives in aqueous and mixed solutions using different experimental techniques. The knowledge of the protonation constants of the aforementioned ligands is crucial for the determination of the equilibrium constants of complex formation and thus for the understanding of complex biological reactions such as transamination, racemization, and decarboxylation. Thus, the protonation constants of ligands are a measure of their ability to form complexes with metal ions. This knowledge not only helps to understand fundamental biochemical processes, but also has practical applications in areas such as drug design, where ligands are often targeted for therapeutic purposes. The activity of the ligands tends to increase after complexation and their order is consistent with the values of the stepwise dissociation constants of the complexes formed. Understanding the properties of ligands by determining their protonation constants in different environments and their interactions with surrounding molecules is crucial to unraveling the complexity of biological systems.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"57 ","pages":"e10"},"PeriodicalIF":7.2,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142473243","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

Solution-based biophysical characterization of conformation change in structure-switching aptamers. 基于溶液的结构转换适配体构象变化生物物理表征。

IF 7.2 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2024-09-03 DOI: 10.1017/S0033583524000076

Sophie R Eisen, Philippe Dauphin-Ducharme, Philip E Johnson

{"title":"Solution-based biophysical characterization of conformation change in structure-switching aptamers.","authors":"Sophie R Eisen, Philippe Dauphin-Ducharme, Philip E Johnson","doi":"10.1017/S0033583524000076","DOIUrl":"10.1017/S0033583524000076","url":null,"abstract":"Structure-switching aptamers have become ubiquitous in several applications, notably in analytical devices such as biosensors, due to their ease of supporting strong signaling. Aside from their ability to bind specifically with their respective target, this class of aptamers also undergoes a conformational rearrangement upon target recognition. While several well-studied and early-developed aptamers (e.g., cocaine, ATP, and thrombin) have been found to have this structure-switching property, the vast majority do not. As a result, it is common to try to engineer aptamers into switches. This proves challenging in part because of the difficulty in obtaining structural and functional information about aptamers. In response, we review various readily available biophysical characterization tools that are capable of assessing structure switching of aptamers. In doing so, we delve into the fundamentals of these different techniques and detail how they have been utilized in characterizing structure-switching aptamers. While each of these biophysical techniques alone has utility, their real power to demonstrate the occurrence of structural change with ligand binding is when multiple techniques are used. We hope that through a deeper understanding of these techniques, researchers will be better able to acquire biophysical information about their aptamer-ligand systems and accelerate the translation of aptamers into biosensors.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":" ","pages":"e9"},"PeriodicalIF":7.2,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142120402","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. DNA 链在 PCR 加热循环后分子断裂的恢复力及其对 PCR 可靠性的影响。

IF 7.2 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2024-08-15 DOI: 10.1017/S0033583524000064

Roberto Serpieri, Fabio Franchi

{"title":"Resilience of DNA chains to molecular fracture after PCR heating cycles and implications on PCR reliability.","authors":"Roberto Serpieri, Fabio Franchi","doi":"10.1017/S0033583524000064","DOIUrl":"https://doi.org/10.1017/S0033583524000064","url":null,"abstract":"Soon after its introduction in 1987, polymerase chain reaction (PCR) has become a technique widely employed in diagnostic medical devices and forensic science with the intention of amplifying genetic information. PCR prescribes that each of its cycles must include a heating subprocess at 95 °C or more (denominated DNA denaturation and provided for allowing a claimed orderly separation of the two complementary nucleotides strands), which can produce significant damage to DNA, caused by high-speed collisions with surrounding molecules. Since such disruption should be prevented in order to reliably employ PCR, a study of the mechanics of such loss of structural integrity is herein presented, preceded by a review of the fundamental literature which has elucidated the effects of molecular agitation on DNA fragmentation. The main conclusion of this retrospective survey is that the body of examined theoretical and experimental evidence consistently and redundantly confirms scarce resilience and significant loss of structural integrity when DNA is heated at temperatures above 90 °C, even for 1 minute. Such conclusion contradicts the claimed paradigm of PCR fidelity and raises the concern that, at least for long sequences, if PCR can amplify some information, such amplified information may be unreliable for diagnostic or forensic applications, since it originates from sequences of nucleotides subjected to random fragmentation and reaggregation. Such a low-reliability scenario should be preventively considered in the various fields where DNA amplification methodologies are employed which provide for high-temperature heating under conditions equal to or similar to those prescribed by the PCR protocols reviewed in this study.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"57 ","pages":"e8"},"PeriodicalIF":7.2,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141983118","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

Towards the understanding of molecular motors and its relationship with local unfolding. 了解分子马达及其与局部展开的关系。

IF 7.2 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2024-05-08 DOI: 10.1017/S0033583524000052

Zahra Alavi, Nathalie Casanova-Morales, Diego Quiroga-Roger, Christian A M Wilson

{"title":"Towards the understanding of molecular motors and its relationship with local unfolding.","authors":"Zahra Alavi, Nathalie Casanova-Morales, Diego Quiroga-Roger, Christian A M Wilson","doi":"10.1017/S0033583524000052","DOIUrl":"10.1017/S0033583524000052","url":null,"abstract":"Molecular motors are machines essential for life since they convert chemical energy into mechanical work. However, the precise mechanism by which nucleotide binding, catalysis, or release of products is coupled to the work performed by the molecular motor is still not entirely clear. This is due, in part, to a lack of understanding of the role of force in the mechanical-structural processes involved in enzyme catalysis. From a mechanical perspective, one promising hypothesis is the Haldane-Pauling hypothesis which considers the idea that part of the enzymatic catalysis is strain-induced. It suggests that enzymes cannot be efficient catalysts if they are fully complementary to the substrates. Instead, they must exert strain on the substrate upon binding, using enzyme-substrate energy interaction (binding energy) to accelerate the reaction rate. A novel idea suggests that during catalysis, significant strain energy is built up, which is then released by a local unfolding/refolding event known as 'cracking'. Recent evidence has also shown that in catalytic reactions involving conformational changes, part of the heat released results in a center-of-mass acceleration of the enzyme, raising the possibility that the heat released by the reaction itself could affect the enzyme's integrity. Thus, it has been suggested that this released heat could promote or be linked to the cracking seen in proteins such as adenylate kinase (AK). We propose that the energy released as a consequence of ligand binding/catalysis is associated with the local unfolding/refolding events (cracking), and that this energy is capable of driving the mechanical work.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":" ","pages":"e7"},"PeriodicalIF":7.2,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140877192","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