Journal of Biological Physics最新文献

{"title":"Pushing the limits of luminescence thermometry: probing the temperature of proteins in cells","authors":"Glauco S. Maciel","doi":"10.1007/s10867-021-09600-w","DOIUrl":"10.1007/s10867-021-09600-w","url":null,"abstract":"<div><p>Proteins are involved in numerous cellular activities such as transport and catalysis. Misfolding during biosynthesis and malfunctioning as a molecular machine may lead to physiological disorders and metabolic problems. Protein folding and mechanical work may be viewed as thermodynamic energetically favorable processes in which stochastic nonequilibrium intermediate states may be present with conditions such as thermal fluctuations. In my opinion, measuring those thermal fluctuations may be a way to access the energy exchange between the protein and the physiological environment and to better understand how those nonequilibrium states may influence the misfolding/folding process and the efficiency of the molecular engine cycle. Here, I discuss luminescence thermometry as a possible way to measure those temperature fluctuations from a single-molecule experimental perspective with its current technical limitations and challenges.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 2","pages":"167 - 175"},"PeriodicalIF":1.8,"publicationDate":"2022-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-021-09600-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4298400","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The identifiability of gene regulatory networks: the role of observation data","authors":"Xiao-Na Huang,&nbsp;Wen-Jia Shi,&nbsp;Zuo Zhou,&nbsp;Xue-Jun Zhang","doi":"10.1007/s10867-021-09595-4","DOIUrl":"10.1007/s10867-021-09595-4","url":null,"abstract":"<div><p>Identifying gene regulatory networks (GRN) from observation data is significant to understand biological systems. Conventional studies focus on improving the performance of identification algorithms. However, besides algorithm performance, the GRN identification is strongly depended on the observation data. In this work, for three GRN S-system models, three observation data collection schemes are used to perform the identifiability test procedure. A modified genetic algorithm-particle swarm optimization algorithm is proposed to implement this task, including the multi-level mutation operation and velocity limitation strategy. The results show that, in scheme 1 (starting from a special initial condition), the GRN systems are of identifiability using the sufficient transient observation data. In scheme 2, the observation data are short of sufficient system dynamic. The GRN systems are not of identifiability even though the state trajectories can be reproduced. As a special case of scheme 2, i.e., the steady-state observation data, the equilibrium point analysis is given to explain why it is infeasible for GRN identification. In schemes 1 and 2, the observation data are obtained from zero-input GRN systems, which will evolve to the steady state at last. The sufficient transient observation data in scheme 1 can be obtained by changing the experimental conditions. Additionally, the valid observation data can be also obtained by means of adding impulse excitation signal into GRN systems (scheme 3). Consequently, the GRN systems are identifiable using scheme 3. Owing to its universality and simplicity, these results provide a guide for biologists to collect valid observation data for identifying GRNs and to further understand GRN dynamics.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 1","pages":"93 - 110"},"PeriodicalIF":1.8,"publicationDate":"2022-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-021-09595-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4249441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Predictive landscapes hidden beneath biological cellular automata","authors":"Lars Koopmans,&nbsp;Hyun Youk","doi":"10.1007/s10867-021-09597-2","DOIUrl":"10.1007/s10867-021-09597-2","url":null,"abstract":"","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 1","pages":"127 - 127"},"PeriodicalIF":1.8,"publicationDate":"2021-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-021-09597-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4890255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Perspectives on the landscape and flux theory for describing emergent behaviors of the biological systems","authors":"Jin Wang","doi":"10.1007/s10867-021-09586-5","DOIUrl":"10.1007/s10867-021-09586-5","url":null,"abstract":"<div><p>We give a review on the landscape theory of the equilibrium biological systems and landscape-flux theory of the nonequilibrium biological systems as the global driving force. The emergences of the behaviors, the associated thermodynamics in terms of the entropy and free energy and dynamics in terms of the rate and paths have been quantitatively demonstrated. The hierarchical organization structures have been discussed. The biological applications ranging from protein folding, biomolecular recognition, specificity, biomolecular evolution and design for equilibrium systems as well as cell cycle, differentiation and development, cancer, neural networks and brain function, and evolution for nonequilibrium systems, cross-scale studies of genome structural dynamics and experimental quantifications/verifications of the landscape and flux are illustrated. Together, this gives an overall global physical and quantitative picture in terms of the landscape and flux for the behaviors, dynamics and functions of biological systems.\u0000</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 1","pages":"1 - 36"},"PeriodicalIF":1.8,"publicationDate":"2021-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-021-09586-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4980704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Shape transformations of red blood cells in the capillary and their possible connections to oxygen transportation","authors":"Caiqun Wang,&nbsp;Jianfeng Li,&nbsp;Liutao Zhao,&nbsp;Ping Qian","doi":"10.1007/s10867-021-09594-5","DOIUrl":"10.1007/s10867-021-09594-5","url":null,"abstract":"<div><p>In this work, a series of numerical simulations have been performed to obtain the steady shapes of red blood cells under a shear force field in the capillary. Two possible classes of steady shapes, the axisymmetric parachute and the non-axisymmetric parachute, are found. If we assume that oxygen diffusion across the red cell membrane is mediated by membrane curvature, it is found that the non-axisymmetric parachute will be more favorable due to its special shape which enables it to have a larger portion of membrane patch capable of releasing oxygen to tissues.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 1","pages":"79 - 92"},"PeriodicalIF":1.8,"publicationDate":"2021-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-021-09594-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4766302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Energy landscapes and dynamics of ion translocation through membrane transporters: a meeting ground for physics, chemistry, and biology","authors":"Sunil Nath","doi":"10.1007/s10867-021-09591-8","DOIUrl":"10.1007/s10867-021-09591-8","url":null,"abstract":"<div><p>The dynamics of ion translocation through membrane transporters is visualized from a comprehensive point of view by a Gibbs energy landscape approach. The Δ<i>G</i> calculations have been performed with the Kirkwood–Tanford–Warshel (KTW) electrostatic theory that properly takes into account the self-energies of the ions. The Gibbs energy landscapes for translocation of a single charge and an ion pair are calculated, compared, and contrasted as a function of the order parameter, and the characteristics of the frustrated system with bistability for the ion pair are described and quantified in considerable detail. These calculations have been compared with experimental data on the Δ<i>G</i> of ion pairs in proteins. It is shown that, under suitable conditions, the adverse Gibbs energy barrier can be almost completely compensated by the sum of the electrostatic energy of the charge–charge interactions and the solvation energy of the ion pair. The maxima in Δ<i>G</i>_KTW with interionic distance in the bound <i>H</i>⁺ – <i>A</i>⁻ charge pair on the enzyme is interpreted in thermodynamic and molecular mechanistic terms, and biological implications for molecular mechanisms of ATP synthesis are discussed. The timescale at which the order parameter moves between two stable states has been estimated by solving the dynamical equations of motion, and a wealth of novel insights into energy transduction during ATP synthesis by the membrane-bound F_OF₁-ATP synthase transporter is offered. In summary, a unifying <i>analytical</i> framework that integrates physics, chemistry, and biology has been developed for ion translocation by membrane transporters for the first time by means of a Gibbs energy landscape approach.</p><h3>Graphical abstract</h3>\u0000 <figure><div><div><div><picture><source><img></source></picture></div></div></div></figure>\u0000 </div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"47 4","pages":"401 - 433"},"PeriodicalIF":1.8,"publicationDate":"2021-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-021-09591-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4733656","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of Conformational Substates and Energy Landscapes on Understanding Hemoglobin Kinetics and Function","authors":"William A. Eaton","doi":"10.1007/s10867-021-09588-3","DOIUrl":"10.1007/s10867-021-09588-3","url":null,"abstract":"<div><p>Hans Frauenfelder’s discovery of conformational substates in studies of myoglobin carbon monoxide geminate rebinding kinetics at cryogenic temperatures (Austin RH, Beeson KW, Eisenstein L, Frauenfelder H, &amp; Gunsalus IC (1975) Dynamics of Ligand Binding to Myoglobin. <i>Biochemistry</i> 14(24):5355–5373) followed by his introduction of energy landscape theory with Peter Wolynes (Frauenfelder H, Sligar SG, &amp; Wolynes PG (1991) The Energy Landscapes and Motions of Proteins. <i>Science</i> 254(5038):1598–1603) marked the beginning of a new era in the physics and physical chemistry of proteins. Their work played a major role in demonstrating the power and importance of dynamics and of Kramers reaction rate theory for understanding protein function. The biggest impact of energy landscape theory has been in the protein folding field, which is well-known and has been documented in numerous articles and reviews, including a recent one of my own (Eaton WA (2021) Modern Kinetics and Mechanism of Protein Folding: a Retrospective. <i>J. Phys. Chem. B.</i> 125(14):3452–3467). Here I will describe the much less well-known impact of their modern view of proteins on both experimental and theoretical studies of hemoglobin kinetics and function. I will first describe how Frauenfelder’s experiments motivated and influenced my own research on myoglobin, which were key ingredients to my work on understanding hemoglobin.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"47 4","pages":"337 - 353"},"PeriodicalIF":1.8,"publicationDate":"2021-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-021-09588-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4473489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Learning the local landscape of protein structures with convolutional neural networks","authors":"Anastasiya V. Kulikova,&nbsp;Daniel J. Diaz,&nbsp;James M. Loy,&nbsp;Andrew D. Ellington,&nbsp;Claus O. Wilke","doi":"10.1007/s10867-021-09593-6","DOIUrl":"10.1007/s10867-021-09593-6","url":null,"abstract":"<div><p>One fundamental problem of protein biochemistry is to predict protein structure from amino acid sequence. The inverse problem, predicting either entire sequences or individual mutations that are consistent with a given protein structure, has received much less attention even though it has important applications in both protein engineering and evolutionary biology. Here, we ask whether 3D convolutional neural networks (3D CNNs) can learn the local fitness landscape of protein structure to reliably predict either the wild-type amino acid or the consensus in a multiple sequence alignment from the local structural context surrounding site of interest. We find that the network can predict wild type with good accuracy, and that network confidence is a reliable measure of whether a given prediction is likely going to be correct or not. Predictions of consensus are less accurate and are primarily driven by whether or not the consensus matches the wild type. Our work suggests that high-confidence mis-predictions of the wild type may identify sites that are primed for mutation and likely targets for protein engineering.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"47 4","pages":"435 - 454"},"PeriodicalIF":1.8,"publicationDate":"2021-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-021-09593-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4402480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predictive landscapes hidden beneath biological cellular automata","authors":"Lars Koopmans,&nbsp;Hyun Youk","doi":"10.1007/s10867-021-09592-7","DOIUrl":"10.1007/s10867-021-09592-7","url":null,"abstract":"<div><p>To celebrate Hans Frauenfelder’s achievements, we examine energy(-like) “landscapes” for complex living systems. Energy landscapes summarize all possible dynamics of some physical systems. Energy(-like) landscapes can explain some biomolecular processes, including gene expression and, as Frauenfelder showed, protein folding. But energy-like landscapes and existing frameworks like statistical mechanics seem impractical for describing many living systems. Difficulties stem from living systems being high dimensional, nonlinear, and governed by many, tightly coupled constituents that are noisy. The predominant modeling approach is devising differential equations that are tailored to each living system. This ad hoc approach faces the notorious “parameter problem”: models have numerous nonlinear, mathematical functions with unknown parameter values, even for describing just a few intracellular processes. One cannot measure many intracellular parameters or can only measure them as snapshots in time. Another modeling approach uses cellular automata to represent living systems as discrete dynamical systems with binary variables. Quantitative (Hamiltonian-based) rules can dictate cellular automata (e.g., Cellular Potts Model). But numerous biological features, in current practice, are qualitatively described rather than quantitatively (e.g., gene is (highly) expressed or not (highly) expressed). Cellular automata governed by verbal rules are useful representations for living systems and can mitigate the parameter problem. However, they can yield complex dynamics that are difficult to understand because the automata-governing rules are not quantitative and much of the existing mathematical tools and theorems apply to continuous but not discrete dynamical systems. Recent studies found ways to overcome this challenge. These studies either discovered or suggest an existence of predictive “landscapes” whose shapes are described by Lyapunov functions and yield “equations of motion” for a “pseudo-particle.” The pseudo-particle represents the entire cellular lattice and moves on the landscape, thereby giving a low-dimensional representation of the cellular automata dynamics. We outline this promising modeling strategy.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"47 4","pages":"355 - 369"},"PeriodicalIF":1.8,"publicationDate":"2021-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-021-09592-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4227684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"It doesn’t always pay to be fit: success landscapes","authors":"Trung V. Phan,&nbsp;Gao Wang,&nbsp;Tuan K. Do,&nbsp;Ioannis G. Kevrekidis,&nbsp;Sarah Amend,&nbsp;Emma Hammarlund,&nbsp;Ken Pienta,&nbsp;Joel Brown,&nbsp;Liyu Liu,&nbsp;Robert H. Austin","doi":"10.1007/s10867-021-09589-2","DOIUrl":"10.1007/s10867-021-09589-2","url":null,"abstract":"<div><p>Landscapes play an important role in many areas of biology, in which biological lives are deeply entangled. Here we discuss a form of landscape in evolutionary biology which takes into account (1) initial growth rates, (2) mutation rates, (3) resource consumption by organisms, and (4) cyclic changes in the resources with time. The long-term equilibrium number of surviving organisms as a function of these four parameters forms what we call a success landscape, a landscape we would claim is qualitatively different from fitness landscapes which commonly do not include mutations or resource consumption/changes in mapping genomes to the final number of survivors. Although our analysis is purely theoretical, we believe the results have possibly strong connections to how we might treat diseases such as cancer in the future with a deeper understanding of the interplay between resource degradation, mutation, and uncontrolled cell growth.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"47 4","pages":"387 - 400"},"PeriodicalIF":1.8,"publicationDate":"2021-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-021-09589-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5100311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}