BMC Biophysics最新文献

{"title":"Rheological properties of cells measured by optical tweezers.","authors":"Yareni A Ayala,&nbsp;Bruno Pontes,&nbsp;Diney S Ether,&nbsp;Luis B Pires,&nbsp;Glauber R Araujo,&nbsp;Susana Frases,&nbsp;Luciana F Romão,&nbsp;Marcos Farina,&nbsp;Vivaldo Moura-Neto,&nbsp;Nathan B Viana,&nbsp;H Moysés Nussenzveig","doi":"10.1186/s13628-016-0031-4","DOIUrl":"https://doi.org/10.1186/s13628-016-0031-4","url":null,"abstract":"<p><strong>Background: </strong>The viscoelastic properties of cells have been investigated by a variety of techniques. However, the experimental data reported in literature for viscoelastic moduli differ by up to three orders of magnitude. This has been attributed to differences in techniques and models for cell response as well as to the natural variability of cells.</p><p><strong>Results: </strong>In this work we develop and apply a new methodology based on optical tweezers to investigate the rheological behavior of fibroblasts, neurons and astrocytes in the frequency range from 1Hz to 35Hz, determining the storage and loss moduli of their membrane-cortex complex. To avoid distortions associated with cell probing techniques, we use a previously developed method that takes into account the influence of under bead cell thickness and bead immersion. These two parameters were carefully measured for the three cell types used. Employing the soft glass rheology model, we obtain the scaling exponent and the Young's modulus for each cell type. The obtained viscoelastic moduli are in the order of Pa. Among the three cell types, astrocytes have the lowest elastic modulus, while neurons and fibroblasts exhibit a more solid-like behavior.</p><p><strong>Conclusions: </strong>Although some discrepancies with previous results remain and may be inevitable in view of natural variability, the methodology developed in this work allows us to explore the viscoelastic behavior of the membrane-cortex complex of different cell types as well as to compare their viscous and elastic moduli, obtained under identical and well-defined experimental conditions, relating them to the cell functions.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":"9 ","pages":"5"},"PeriodicalIF":0.0,"publicationDate":"2016-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-016-0031-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34608699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of the coarse-grained OPEP force field for protein-protein docking.","authors":"Philipp Kynast,&nbsp;Philippe Derreumaux,&nbsp;Birgit Strodel","doi":"10.1186/s13628-016-0029-y","DOIUrl":"https://doi.org/10.1186/s13628-016-0029-y","url":null,"abstract":"<p><strong>Background: </strong>Knowing the binding site of protein-protein complexes helps understand their function and shows possible regulation sites. The ultimate goal of protein-protein docking is the prediction of the three-dimensional structure of a protein-protein complex. Docking itself only produces plausible candidate structures, which must be ranked using scoring functions to identify the structures that are most likely to occur in nature.</p><p><strong>Methods: </strong>In this work, we rescore rigid body protein-protein predictions using the optimized potential for efficient structure prediction (OPEP), which is a coarse-grained force field. Using a force field based on continuous functions rather than a grid-based scoring function allows the introduction of protein flexibility during the docking procedure. First, we produce protein-protein predictions using ZDOCK, and after energy minimization via OPEP we rank them using an OPEP-based soft rescoring function. We also train the rescoring function for different complex classes and demonstrate its improved performance for an independent dataset.</p><p><strong>Results: </strong>The trained rescoring function produces a better ranking than ZDOCK for more than 50 % of targets, rising to over 70 % when considering only enzyme/inhibitor complexes.</p><p><strong>Conclusions: </strong>This study demonstrates for the first time that energy functions derived from the coarse-grained OPEP force field can be employed to rescore predictions for protein-protein complexes.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":"9 ","pages":"4"},"PeriodicalIF":0.0,"publicationDate":"2016-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-016-0029-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34482429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A biophysical model of supercoiling dependent transcription predicts a structural aspect to gene regulation","authors":"C. Bohrer, Elijah Roberts","doi":"10.1186/s13628-016-0027-0","DOIUrl":"https://doi.org/10.1186/s13628-016-0027-0","url":null,"abstract":"","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-016-0027-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65859877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"α-synuclein-lanthanide metal ions interaction: binding sites, conformation and fibrillation","authors":"Jia Bai, Zeting Zhang, Maili Liu, Conggang Li","doi":"10.1186/s13628-016-0026-1","DOIUrl":"https://doi.org/10.1186/s13628-016-0026-1","url":null,"abstract":"","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-016-0026-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65859871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"BMC Biophysics reviewer acknowledgement 2015","authors":"Julia Simundza","doi":"10.1186/s13628-016-0028-z","DOIUrl":"https://doi.org/10.1186/s13628-016-0028-z","url":null,"abstract":"","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-016-0028-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65859883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prediction of solution properties and dynamics of RNAs by means of Brownian dynamics simulation of coarse-grained models: Ribosomal 5S RNA and phenylalanine transfer RNA","authors":"A. Benítez, J. G. Hernández Cifre, F. G. Díaz Baños, J. de la Torre","doi":"10.1186/s13628-015-0025-7","DOIUrl":"https://doi.org/10.1186/s13628-015-0025-7","url":null,"abstract":"","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-015-0025-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65859839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PDE/ODE modeling and simulation to determine the role of diffusion in long-term and -range cellular signaling.","authors":"Elfriede Friedmann","doi":"10.1186/s13628-015-0024-8","DOIUrl":"https://doi.org/10.1186/s13628-015-0024-8","url":null,"abstract":"<p><strong>Background: </strong>We study the relevance of diffusion for the dynamics of signaling pathways. Mathematical modeling of cellular diffusion leads to a coupled system of differential equations with Robin boundary conditions which requires a substantial knowledge in mathematical theory. Using our new developed analytical and numerical techniques together with modern experiments, we analyze and quantify various types of diffusive effects in intra- and inter-cellular signaling. The complexity of these models necessitates suitable numerical methods to perform the simulations precisely and within an acceptable period of time.</p><p><strong>Methods: </strong>The numerical methods comprise a Galerkin finite element space discretization, an adaptive time stepping scheme and either an iterative operator splitting method or fully coupled multilevel algorithm as solver.</p><p><strong>Results: </strong>The simulation outcome allows us to analyze different biological aspects. On the scale of a single cell, we showed the high cytoplasmic concentration gradients in irregular geometries. We found an 11 % maximum relative total STAT5-concentration variation in a fibroblast and a 70 % maximum relative pSTAT5-concentration variation in a fibroblast with an irregular cell shape. For pSMAD2 the maximum relative variation was 18 % in a hepatocyte with a box shape and 70 % in an irregular geometry. This result can be also obtained in a cell with a box shape if the molecules diffuse slowly (with D=1 μm(2)/s instead of D=15 μm(2)/s). On a scale of cell system in the lymph node, our simulations showed an inhomogeneous IL-2 pattern with an amount over three orders of magnitude (10(-3)-1 pM) and high gradients in face of its fast diffusivity. We observed that 20 out of 125 cells were activated after 9 h and 33 in the steady state. Our in-silico experiments showed that the insertion of 31 regulatory T cells in our cell system can completely downregulate the signal.</p><p><strong>Conclusions: </strong>We quantify the concentration gradients evolving from the diffusion of the molecules in several signaling pathways. For intracellular signaling pathways with nuclear accumulation the size of cytoplasmic gradients does not indicate the change in gene expression which has to be analyzed separately in future. For intercellular signaling the high cytokine concentration gradients play an essential role in the regulation of the molecular mechanism of the immune response. Furthermore, our simulation results can give the information on which signaling pathway diffusion may play a role. We conclude that a PDE model has to be considered for cells with an irregular shape or for slow diffusing molecules. Also the high gradients inside a cell or in a cell system can play an essential role in the regulation of the molecular mechanisms.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":"8 ","pages":"10"},"PeriodicalIF":0.0,"publicationDate":"2015-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-015-0024-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34160276","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Copper-free click chemistry for attachment of biomolecules in magnetic tweezers.","authors":"Jorine M Eeftens,&nbsp;Jaco van der Torre,&nbsp;Daniel R Burnham,&nbsp;Cees Dekker","doi":"10.1186/s13628-015-0023-9","DOIUrl":"https://doi.org/10.1186/s13628-015-0023-9","url":null,"abstract":"<p><strong>Background: </strong>Single-molecule techniques have proven to be an excellent approach for quantitatively studying DNA-protein interactions at the single-molecule level. In magnetic tweezers, a force is applied to a biopolymer that is anchored between a glass surface and a magnetic bead. Whereas the relevant force regime for many biological processes is above 20pN, problems arise at these higher forces, since the molecule of interest can detach from the attachment points at the surface or the bead. Whereas many recipes for attachment of biopolymers have been developed, most methods do not suffice, as the molecules break at high force, or the attachment chemistry leads to nonspecific cross reactions with proteins.</p><p><strong>Results: </strong>Here, we demonstrate a novel attachment method using copper-free click chemistry, where a DBCO-tagged DNA molecule is bound to an azide-functionalized surface. We use this new technique to covalently attach DNA to a flow cell surface. We show that this technique results in covalently linked tethers that are torsionally constrained and withstand very high forces (>100pN) in magnetic tweezers.</p><p><strong>Conclusions: </strong>This novel anchoring strategy using copper-free click chemistry allows to specifically and covalently link biomolecules, and conduct high-force single-molecule experiments. Excitingly, this advance opens up the possibility for single-molecule experiments on DNA-protein complexes and molecules that are taken directly from cell lysate.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":"8 ","pages":"9"},"PeriodicalIF":0.0,"publicationDate":"2015-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-015-0023-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34039634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The biophysical nature of cells: potential cell behaviours revealed by analytical and computational studies of cell surface mechanics.","authors":"Ramiro Magno,&nbsp;Verônica A Grieneisen,&nbsp;Athanasius Fm Marée","doi":"10.1186/s13628-015-0022-x","DOIUrl":"https://doi.org/10.1186/s13628-015-0022-x","url":null,"abstract":"<p><strong>Background: </strong>The biophysical characteristics of cells determine their shape in isolation and when packed within tissues. Cells can form regular or irregular epithelial structures, round up and form clusters, or deform and attach to substrates. The acquired shape of cells and tissues is a consequence of (i) internal cytoskeletal processes, such as actin polymerisation and cortical myosin contraction, (ii) adhesion molecules within the cell membrane that interact with substrates and neighbouring cells, and (iii) processes that regulate cell volume. Although these processes seem relatively simple, when combined they unleash a rich variety of cellular behaviour that is not readily understandable outside a theoretical framework.</p><p><strong>Methods: </strong>We perform a mathematical analysis of a commonly used class of model formalisms that describe cell surface mechanics using an energy-based approach. Predictions are then confirmed through comparison with the computational outcomes of a Vertex model and 2D and 3D simulations of the Cellular Potts model.</p><p><strong>Results: </strong>The analytical study reveals the complete possible spectrum of single cell behaviour and tissue packing in both 2D and 3D, by taking the typical core elements of cell surface mechanics into account: adhesion, cortical tension and volume conservation. We show that from an energy-based description, forces and tensions can be derived, as well as the prediction of cell behaviour and tissue packing, providing an intuitive and biologically relevant mapping between modelling parameters and experiments.</p><p><strong>Conclusions: </strong>The quantitative cellular behaviours and biological insights agree between the analytical study and the diverse computational model formalisms, including the Cellular Potts model. This illustrates the generality of energy-based approaches for cell surface mechanics and highlights how meaningful and quantitative comparisons between models can be established. Moreover, the mathematical analysis reveals direct links between known biophysical properties and specific parameter settings within the Cellular Potts model.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":"8 ","pages":"8"},"PeriodicalIF":0.0,"publicationDate":"2015-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-015-0022-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33344321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smoothed particle hydrodynamics.","authors":"Wenxiao Pan,&nbsp;Michael Daily,&nbsp;Nathan A Baker","doi":"10.1186/s13628-015-0021-y","DOIUrl":"https://doi.org/10.1186/s13628-015-0021-y","url":null,"abstract":"<p><strong>Background: </strong>The calculation of diffusion-controlled ligand binding rates is important for understanding enzyme mechanisms as well as designing enzyme inhibitors.</p><p><strong>Methods: </strong>We demonstrate the accuracy and effectiveness of a Lagrangian particle-based method, smoothed particle hydrodynamics (SPH), to study diffusion in biomolecular systems by numerically solving the time-dependent Smoluchowski equation for continuum diffusion. Unlike previous studies, a reactive Robin boundary condition (BC), rather than the absolute absorbing (Dirichlet) BC, is considered on the reactive boundaries. This new BC treatment allows for the analysis of enzymes with \"imperfect\" reaction rates.</p><p><strong>Results: </strong>The numerical method is first verified in simple systems and then applied to the calculation of ligand binding to a mouse acetylcholinesterase (mAChE) monomer. Rates for inhibitor binding to mAChE are calculated at various ionic strengths and compared with experiment and other numerical methods. We find that imposition of the Robin BC improves agreement between calculated and experimental reaction rates.</p><p><strong>Conclusions: </strong>Although this initial application focuses on a single monomer system, our new method provides a framework to explore broader applications of SPH in larger-scale biomolecular complexes by taking advantage of its Lagrangian particle-based nature.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":"8 ","pages":"7"},"PeriodicalIF":0.0,"publicationDate":"2015-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-015-0021-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33322888","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}