BMC Biophysics最新文献

{"title":"Kinematic difference between a biological cell and an artificial vesicle in a strong DC electric field – a “shell” membrane model study","authors":"H. Ye","doi":"10.1186/S13628-017-0038-5","DOIUrl":"https://doi.org/10.1186/S13628-017-0038-5","url":null,"abstract":"","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/S13628-017-0038-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43731720","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":"Human S100A5 binds Ca²⁺ and Cu²⁺ independently.","authors":"Lucas C Wheeler,&nbsp;Michael J Harms","doi":"10.1186/s13628-017-0040-y","DOIUrl":"https://doi.org/10.1186/s13628-017-0040-y","url":null,"abstract":"<p><strong>Background: </strong>S100A5 is a calcium binding protein found in a small subset of amniote tissues. Little is known about the biological roles of S100A5, but it may be involved in inflammation and olfactory signaling. Previous work indicated that S100A5 displays antagonism between binding of Ca²⁺ and Cu²⁺ ions-one of the most commonly cited features of the protein. We set out to characterize the interplay between Ca²⁺ and Cu²⁺ binding by S100A5 using isothermal titration calorimetry (ITC), circular dichroism spectroscopy (CD), and analytical ultracentrifugation (AUC).</p><p><strong>Results: </strong>We found that human S100A5 is capable of binding both Cu²⁺ and Ca²⁺ ions simultaneously. The wildtype protein was extremely aggregation-prone in the presence of Cu²⁺ and Ca²⁺. A Cys-free version of S100A5, however, was not prone to precipitation or oligomerization. Mutation of the cysteines does not disrupt the binding of either Ca²⁺ or Cu²⁺ to S100A5. In the Cys-free background, we measured Ca²⁺ and Cu²⁺ binding in the presence and absence of the other metal using ITC. Saturating concentrations of Ca²⁺ or Cu²⁺ do not disrupt the binding of one another. Ca²⁺ and Cu²⁺ binding induce structural changes in S100A5, which are measurable using CD spectroscopy. We show via sedimentation velocity AUC that the wildtype protein is prone to the formation of soluble oligomers, which are not present in Cys-free samples.</p><p><strong>Conclusions: </strong>S100A5 can bind Ca²⁺ and Cu²⁺ ions simultaneously and independently. This observation is in direct contrast to previously-reported antagonism between binding of Cu²⁺ and Ca²⁺ ions. The previous result is likely due to metal-dependent aggregation. Little is known about the biology of S100A5, so an accurate understanding of the biochemistry is necessary to make informed biological hypotheses. Our observations suggest the possibility of independent biological functions for Cu²⁺ and Ca²⁺ binding by S100A5.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-017-0040-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35612610","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":"Kinetic and thermodynamic studies reveal chemokine homologues CC11 and CC24 with an almost identical tertiary structure have different folding pathways.","authors":"Baosheng Ge,&nbsp;Xiaoyong Jiang,&nbsp;Yao Chen,&nbsp;Tingting Sun,&nbsp;Qiuxia Yang,&nbsp;Fang Huang","doi":"10.1186/s13628-017-0039-4","DOIUrl":"https://doi.org/10.1186/s13628-017-0039-4","url":null,"abstract":"<p><strong>Background: </strong>Proteins with low sequence identity but almost identical tertiary structure and function have been valuable to uncover the relationship between sequence, tertiary structure, folding mechanism and functions. Two homologous chemokines, CCL11 and CCL24, with low sequence identity but similar tertiary structure and function, provide an excellent model system for respective studies.</p><p><strong>Results: </strong>The kinetics and thermodynamics of the two homologous chemokines were systematically characterized. Despite their similar tertiary structures, CCL11 and CCL24 show different thermodynamic stability in guanidine hydrochloride titration, with D_50% = 2.20 M and 4.96 M, respectively. The kinetics curves clearly show two phases in the folding/unfolding processes of both CCL11 and CCL24, which suggests the existence of an intermediate state in their folding/unfolding processes. The folding pathway of both CCL11 and CCL24 could be well described using a folding model with an on-pathway folding intermediate. However, the folding kinetics and stability of the intermediate state of CCL11 and CCL24 are obviously different.</p><p><strong>Conclusion: </strong>Our results suggest homologous proteins with low sequence identity can display almost identical tertiary structure, but very different folding mechanisms, which applies to homologues in the chemokine protein family, extending the general applicability of the above observation.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-017-0039-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35414341","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":"Modeling of RAS complexes supports roles in cancer for less studied partners.","authors":"H Billur Engin,&nbsp;Daniel Carlin,&nbsp;Dexter Pratt,&nbsp;Hannah Carter","doi":"10.1186/s13628-017-0037-6","DOIUrl":"https://doi.org/10.1186/s13628-017-0037-6","url":null,"abstract":"<p><strong>Background: </strong>RAS protein interactions have predominantly been studied in the context of the RAF and PI3kinase oncogenic pathways. Structural modeling and X-ray crystallography have demonstrated that RAS isoforms bind to canonical downstream effector proteins in these pathways using the highly conserved switch I and II regions. Other non-canonical RAS protein interactions have been experimentally identified, however it is not clear whether these proteins also interact with RAS via the switch regions.</p><p><strong>Results: </strong>To address this question we constructed a RAS isoform-specific protein-protein interaction network and predicted 3D complexes involving RAS isoforms and interaction partners to identify the most probable interaction interfaces. The resulting models correctly captured the binding interfaces for well-studied effectors, and additionally implicated residues in the allosteric and hyper-variable regions of RAS proteins as the predominant binding site for non-canonical effectors. Several partners binding to this new interface (SRC, LGALS1, RABGEF1, CALM and RARRES3) have been implicated as important regulators of oncogenic RAS signaling. We further used these models to investigate competitive binding and multi-protein complexes compatible with RAS surface occupancy and the putative effects of somatic mutations on RAS protein interactions.</p><p><strong>Conclusions: </strong>We discuss our findings in the context of RAS localization to the plasma membrane versus within the cytoplasm and provide a list of RAS protein interactions with possible cancer-related consequences, which could help guide future therapeutic strategies to target RAS proteins.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-017-0037-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35327194","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":"DNA secondary structure formation by DNA shuffling of the conserved domains of the Cry protein of <i>Bacillus thuringiensis</i>.","authors":"Efrain H Pinzon,&nbsp;Daniel A Sierra,&nbsp;Miguel O Suarez,&nbsp;Sergio Orduz,&nbsp;Alvaro M Florez","doi":"10.1186/s13628-017-0036-7","DOIUrl":"https://doi.org/10.1186/s13628-017-0036-7","url":null,"abstract":"<p><strong>Background: </strong>The Cry toxins, or δ-endotoxins, are a diverse group of proteins produced by <i>Bacillus thuringiensis</i>. While DNA secondary structures are biologically relevant, it is unknown if such structures are formed in regions encoding conserved domains of Cry toxins under shuffling conditions. We analyzed 5 holotypes that encode Cry toxins and that grouped into 4 clusters according to their phylogenetic closeness. The mean number of DNA secondary structures that formed and the mean Gibbs free energy [Formula: see text] were determined by an <i>in silico</i> analysis using different experimental DNA shuffling scenarios. In terms of spontaneity, shuffling efficiency was directly proportional to the formation of secondary structures but inversely proportional to ∆G.</p><p><strong>Results: </strong>The results showed a shared thermodynamic pattern for each cluster and relationships among sequences that are phylogenetically close at the protein level. The regions of the <i>cry11Aa, Ba</i> and <i>Bb</i> genes that encode domain I showed more spontaneity and thus a greater tendency to form secondary structures (<∆G). In the region of domain III; this tendency was lower (>∆G) in the <i>cry11Ba</i> and <i>Bb</i> genes. Proteins that are phylogenetically closer to Cry11Ba and Cry11Bb, such as Cry2Aa and Cry18Aa, maintained the same thermodynamic pattern. More distant proteins, such as Cry1Aa, Cry1Ab, Cry30Aa and Cry30Ca, featured different thermodynamic patterns in their DNA.</p><p><strong>Conclusion: </strong>These results suggest the presence of thermodynamic variations associated to the formation of secondary structures and an evolutionary relationship with regions that encode highly conserved domains in Cry proteins. The findings of this study may have a role in the <i>in silico</i> design of <i>cry</i> gene assembly by DNA shuffling techniques.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-017-0036-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35024604","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":"Accuracy of the detection of binding events using 3D single particle tracking.","authors":"Sara Carozza, Jamie Culkin, John van Noort","doi":"10.1186/s13628-017-0035-8","DOIUrl":"10.1186/s13628-017-0035-8","url":null,"abstract":"<p><strong>Background: </strong>Nanoparticles can be used as markers to track the position of biomolecules, such as single proteins, inside living cells. The activity of a protein can sometimes be inferred from changes in the mobility of the attached particle. Mean Square Displacement analysis is the most common method to obtain mobility information from trajectories of tracked particles, such as the diffusion coefficient <i>D</i>. However, the precision of <i>D</i> sets a limit to discriminate changes in mobility caused by biological events from changes that reflect the stochasticity inherent to diffusion. This issue is of particular importance in an experiment aiming to quantify dynamic processes.</p><p><strong>Results: </strong>Here, we present simulations and 3D tracking experiments with Gold Nanorods freely diffusing in glycerol solution to establish the best analysis parameters to extract the diffusion coefficient. We applied this knowledge to the detection of a temporary change in diffusion, as it can occur due to the transient binding of a particle to an immobile structure within the cell, and tested its dependence on the magnitude of the change in diffusion and duration of this event.</p><p><strong>Conclusions: </strong>The simulations show that the spatial accuracy of particle tracking generally does not limit the detection of short binding events. Careful analysis of the magnitude of the change in diffusion and the number of frames per binding event is required for accurate quantification of such events.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5364544/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34856906","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":"BFPTool: a software tool for analysis of Biomembrane Force Probe experiments.","authors":"Daniel Šmít,&nbsp;Coralie Fouquet,&nbsp;Mohamed Doulazmi,&nbsp;Frédéric Pincet,&nbsp;Alain Trembleau,&nbsp;Martin Zapotocky","doi":"10.1186/s13628-016-0033-2","DOIUrl":"https://doi.org/10.1186/s13628-016-0033-2","url":null,"abstract":"<p><strong>Background: </strong>The Biomembrane Force Probe is an approachable experimental technique commonly used for single-molecule force spectroscopy and experiments on biological interfaces. The technique operates in the range of forces from 0.1 pN to 1000 pN. Experiments are typically repeated many times, conditions are often not optimal, the captured video can be unstable and lose focus; this makes efficient analysis challenging, while out-of-the-box non-proprietary solutions are not freely available.</p><p><strong>Results: </strong>This dedicated tool was developed to integrate and simplify the image processing and analysis of videomicroscopy recordings from BFP experiments. A novel processing feature, allowing the tracking of the pipette, was incorporated to address a limitation of preceding methods. Emphasis was placed on versatility and comprehensible user interface implemented in a graphical form.</p><p><strong>Conclusions: </strong>An integrated analytical tool was implemented to provide a faster, simpler and more convenient way to process and analyse BFP experiments.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-016-0033-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34808850","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":"Native flexibility of structurally homologous proteins: insights from anisotropic network model","authors":"R. Sarkar","doi":"10.1186/s13628-017-0034-9","DOIUrl":"https://doi.org/10.1186/s13628-017-0034-9","url":null,"abstract":"","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-017-0034-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46735856","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":"Structure and domain dynamics of human lactoferrin in solution and the influence of Fe(III)-ion ligand binding","authors":"C. Sill, R. Biehl, B. Hoffmann, A. Radulescu, M. Appavou, B. Farago, R. Merkel, D. Richter","doi":"10.1186/s13628-016-0032-3","DOIUrl":"https://doi.org/10.1186/s13628-016-0032-3","url":null,"abstract":"","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-016-0032-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65859891","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":"Exploring in vivo cholesterol-mediated interactions between activated EGF receptors in plasma membrane with single-molecule optical tracking.","authors":"Chien Y Lin,&nbsp;Jung Y Huang,&nbsp;Leu-Wei Lo","doi":"10.1186/s13628-016-0030-5","DOIUrl":"https://doi.org/10.1186/s13628-016-0030-5","url":null,"abstract":"<p><strong>Background: </strong>The first step in many cellular signaling processes occurs at various types of receptors in the plasma membrane. Membrane cholesterol can alter these signaling pathways of living cells. However, the process in which the interaction of activated receptors is modulated by cholesterol remains unclear.</p><p><strong>Methods: </strong>In this study, we measured single-molecule optical trajectories of epidermal growth factor receptors moving in the plasma membranes of two cancerous cell lines and one normal endothelial cell line. A stochastic model was developed and applied to identify critical information from single-molecule trajectories.</p><p><strong>Results: </strong>We discovered that unliganded epidermal growth factor receptors may reside nearby cholesterol-riched regions of the plasma membrane and can move into these lipid domains when subjected to ligand binding. The amount of membrane cholesterol considerably affects the stability of correlated motion of activated epidermal growth factor receptors.</p><p><strong>Conclusions: </strong>Our results provide single-molecule evidence of membrane cholesterol in regulating signaling receptors. Because the three cell lines used for this study are quite diverse, our results may be useful to shed light on the mechanism of cholesterol-mediated interaction between activated receptors in live cells.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-016-0030-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34614244","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}