Quarterly Reviews of Biophysics最新文献_第2页

Structural biology inside multicellular specimens using electron cryotomography. 利用电子冷冻成像技术进行多细胞标本内部结构生物学研究。

IF 7.2 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2025-01-13 DOI: 10.1017/S0033583525000010

Ido Caspy, Zhexin Wang, Tanmay A M Bharat

{"title":"Structural biology inside multicellular specimens using electron cryotomography.","authors":"Ido Caspy, Zhexin Wang, Tanmay A M Bharat","doi":"10.1017/S0033583525000010","DOIUrl":"10.1017/S0033583525000010","url":null,"abstract":"The electron cryomicroscopy (cryo-EM) resolution revolution has shifted structural biology into a new era, enabling the routine structure determination of macromolecular complexes at an unprecedented rate. Building on this, electron cryotomography (cryo-ET) offers the potential to visualise the native three-dimensional organisation of biological specimens, from cells to tissues and even entire organisms. Despite this huge potential, the study of tissue-like multicellular specimens via cryo-ET still presents numerous challenges, wherein many steps in the workflow are being developed or in urgent need of improvement. In this review, we outline the latest techniques currently utilised for in situ imaging of multicellular specimens, while clearly enumerating their associated limitations. We consider every step in typical workflows employed by various laboratories, including sample preparation, data collection and image analysis, to highlight recent progress and showcase prominent success stories. By considering the entire structural biology workflow for multicellular specimens, we identify which future exciting developments in hardware and software could enable comprehensive in situ structural biology investigations, bringing forth a new age of discovery in molecular structural and cell biology.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":" ","pages":"e6"},"PeriodicalIF":7.2,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7617309/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142972090","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

Life and death of Yfh1: how cool is cold denaturation. Yfh1的生与死：冷变性有多冷？

IF 7.2 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2025-01-13 DOI: 10.1017/S0033583524000180

Piero Andrea Temussi, Stephen R Martin, Annalisa Pastore

引用次数: 0

Single-molecule orientation-localization microscopy: Applications and approaches. 单分子定向定位显微镜：应用和方法。

IF 7.2 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2024-12-23 DOI: 10.1017/S0033583524000167

Oumeng Zhang, Matthew D Lew

{"title":"Single-molecule orientation-localization microscopy: Applications and approaches.","authors":"Oumeng Zhang, Matthew D Lew","doi":"10.1017/S0033583524000167","DOIUrl":"10.1017/S0033583524000167","url":null,"abstract":"Single-molecule orientation-localization microscopy (SMOLM) builds upon super-resolved localization microscopy by imaging orientations and rotational dynamics of individual molecules in addition to their positions. This added dimensionality provides unparalleled insights into nanoscale biophysical and biochemical processes, including the organization of actin networks, movement of molecular motors, conformations of DNA strands, growth and remodeling of amyloid aggregates, and composition changes within lipid membranes. In this review, we discuss recent innovations in SMOLM and cover three key aspects: (1) biophysical insights enabled by labeling strategies that endow fluorescent probes to bind to targets with orientation specificity; (2) advanced imaging techniques that leverage the physics of light-matter interactions and estimation theory to encode orientation information with high fidelity into microscope images; and (3) computational methods that ensure accurate and precise data analysis and interpretation, even in the presence of severe shot noise. Additionally, we compare labeling approaches, imaging hardware, and publicly available analysis software to aid the community in choosing the best SMOLM implementation for their specific biophysical application. Finally, we highlight future directions for SMOLM, such as the development of probes with improved photostability and specificity, the design of “smart” adaptive hardware, and the use of advanced computational approaches to handle large, complex datasets. This review underscores the significant current and potential impact of SMOLM in deepening our understanding of molecular dynamics, paving the way for future breakthroughs in the fields of biophysics, biochemistry, and materials science.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"57 ","pages":"e17"},"PeriodicalIF":7.2,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11771422/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142877763","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

Cryo-EM reconstruction of helical polymers: Beyond the simple cases. 螺旋聚合物的低温电镜重建：超越简单的情况。

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":"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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11730170/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Graph theory approaches for molecular dynamics simulations. 分子动力学模拟的图论方法。

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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11853848/pdf/","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":"OA","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. 新设计蛋白的原子分子动力学模拟研究进展。

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