BMC Biophysics最新文献

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Physical constraints on the establishment of intracellular spatial gradients in bacteria. 细菌胞内空间梯度建立的物理限制。
BMC Biophysics Pub Date : 2012-08-29 DOI: 10.1186/2046-1682-5-17
Carolina Tropini, Naveed Rabbani, Kerwyn Casey Huang
{"title":"Physical constraints on the establishment of intracellular spatial gradients in bacteria.","authors":"Carolina Tropini,&nbsp;Naveed Rabbani,&nbsp;Kerwyn Casey Huang","doi":"10.1186/2046-1682-5-17","DOIUrl":"https://doi.org/10.1186/2046-1682-5-17","url":null,"abstract":"<p><strong>Unlabelled: </strong></p><p><strong>Background: </strong>Bacteria dynamically regulate their intricate intracellular organization involving proteins that facilitate cell division, motility, and numerous other processes. Consistent with this sophisticated organization, bacteria are able to create asymmetries and spatial gradients of proteins by localizing signaling pathway components. We use mathematical modeling to investigate the biochemical and physical constraints on the generation of intracellular gradients by the asymmetric localization of a source and a sink.</p><p><strong>Results: </strong>We present a systematic computational analysis of the effects of other regulatory mechanisms, such as synthesis, degradation, saturation, and cell growth. We also demonstrate that gradients can be established in a variety of bacterial morphologies such as rods, crescents, spheres, branched and constricted cells.</p><p><strong>Conclusions: </strong>Taken together, these results suggest that gradients are a robust and potentially common mechanism for providing intracellular spatial cues.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2046-1682-5-17","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30867865","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}
引用次数: 9
Effects of spermine NONOate and ATP on the thermal stability of hemoglobin. 精胺NONOate和ATP对血红蛋白热稳定性的影响。
BMC Biophysics Pub Date : 2012-08-28 DOI: 10.1186/2046-1682-5-16
Rasha Bassam, Juergen Hescheler, Ayseguel Temiz-Artmann, Gerhard M Artmann, Ilya Digel
{"title":"Effects of spermine NONOate and ATP on the thermal stability of hemoglobin.","authors":"Rasha Bassam,&nbsp;Juergen Hescheler,&nbsp;Ayseguel Temiz-Artmann,&nbsp;Gerhard M Artmann,&nbsp;Ilya Digel","doi":"10.1186/2046-1682-5-16","DOIUrl":"https://doi.org/10.1186/2046-1682-5-16","url":null,"abstract":"<p><strong>Background: </strong>Minor changes in protein structure induced by small organic and inorganic molecules can result in significant metabolic effects. The effects can be even more profound if the molecular players are chemically active and present in the cell in considerable amounts. The aim of our study was to investigate effects of a nitric oxide donor (spermine NONOate), ATP and sodium/potassium environment on the dynamics of thermal unfolding of human hemoglobin (Hb). The effect of these molecules was examined by means of circular dichroism spectrometry (CD) in the temperature range between 25°C and 70°C. The alpha-helical content of buffered hemoglobin samples (0.1 mg/ml) was estimated via ellipticity change measurements at a heating rate of 1°C/min.</p><p><strong>Results: </strong>Major results were: 1) spermine NONOate persistently decreased the hemoglobin unfolding temperature Tuirrespectively of the Na + /K + environment, 2) ATP instead increased the unfolding temperature by 3°C in both sodium-based and potassium-based buffers and 3) mutual effects of ATP and NO were strongly influenced by particular buffer ionic compositions. Moreover, the presence of potassium facilitated a partial unfolding of alpha-helical structures even at room temperature.</p><p><strong>Conclusion: </strong>The obtained data might shed more light on molecular mechanisms and biophysics involved in the regulation of protein activity by small solutes in the cell.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2046-1682-5-16","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30863138","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}
引用次数: 1
Flexibility of EF-hand motifs: structural and thermodynamic studies of Calcium Binding Protein-1 from Entamoeba histolytica with Pb2+, Ba2+, and Sr2+. EF-hand基元的灵活性:Pb2+, Ba2+和Sr2+溶组织内阿米巴钙结合蛋白-1的结构和热力学研究。
BMC Biophysics Pub Date : 2012-08-20 DOI: 10.1186/2046-1682-5-15
Shivesh Kumar, Ejaz Ahmad, Sanjeev Kumar, Rizwan Hasan Khan, Samudrala Gourinath
{"title":"Flexibility of EF-hand motifs: structural and thermodynamic studies of Calcium Binding Protein-1 from Entamoeba histolytica with Pb2+, Ba2+, and Sr2+.","authors":"Shivesh Kumar,&nbsp;Ejaz Ahmad,&nbsp;Sanjeev Kumar,&nbsp;Rizwan Hasan Khan,&nbsp;Samudrala Gourinath","doi":"10.1186/2046-1682-5-15","DOIUrl":"https://doi.org/10.1186/2046-1682-5-15","url":null,"abstract":"<p><strong>Background: </strong>EF-hand proteins can be activated by the binding of various heavy metals other than calcium, and such complexes can disturb the calcium-signaling pathway and cause toxicity and disease causing state. So far, no comprehensive study has been done to understand different heavy metals binding to calcium signaling proteins.</p><p><strong>Results: </strong>In this work, the flexibility of the EF-hand motifs are examined by crystallographic and thermodynamic studies of binding of Pb2+, Ba2+ and Sr2+ to Calcium Binding Protein-1 from Entamoeba histolytica (EhCaBP1). The structures of the EhCaBP1- heavy metal complexes are found to be overall similar, nevertheless specific differences in metal coordination, and small differences in the coordination distances between the metal and the ligands in the metal binding loop. The largest such distances occur for the Ba2+- EhCaBP1 complex, where two bariums are bound with partial occupancy at the EF2 motif. Thermodynamic studies confirm that EhCaBP1 has five binding sites for Ba2+ compared to four binding sites for the other metals. These structures and thermodynamic studies reveal that the EF-hand motifs can accommodate several heavy atoms with similar binding affinities. The binding of Ca2+ to the 1st, 2nd and 4th sites and the binding of Ba2+ to the 1st, 2nd, 4th and 5th sites are both enthalpically and entropically driven, whereas the binding of Sr2+ to the 1st, 2nd and 4th sites are simply enthalpy driven, interestingly in agreement with ITC data, Sr2+ do not coordinate with water in this structure. For all the metals, binding to the 3rd site is only entropy driven.</p><p><strong>Conclusion: </strong>Energetically, Ca2+ is preferred in three sites, while in one site Ba2+ has better binding energy. The Sr2+-coordination in the EF hand motifs is similar to that of the native Ca2+ bound structure, except for the lack of water coordination. Sr2+ coordination seems to be a pre-formed in nature since all seven coordinating atoms are from the protein itself, which also correlates with entropy contributions in Sr2+ binding. These findings improve our understanding of metal association with calcium binding proteins and of metal induced conformational changes.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2046-1682-5-15","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30845848","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}
引用次数: 13
Molecular dynamics simulations on aqueous two-phase systems - Single PEG-molecules in solution. 水两相体系的分子动力学模拟。溶液中的单peg分子。
BMC Biophysics Pub Date : 2012-08-08 DOI: 10.1186/2046-1682-5-14
Stefan A Oelmeier, Florian Dismer, Jürgen Hubbuch
{"title":"Molecular dynamics simulations on aqueous two-phase systems - Single PEG-molecules in solution.","authors":"Stefan A Oelmeier,&nbsp;Florian Dismer,&nbsp;Jürgen Hubbuch","doi":"10.1186/2046-1682-5-14","DOIUrl":"https://doi.org/10.1186/2046-1682-5-14","url":null,"abstract":"<p><strong>Background: </strong>Molecular Dynamics (MD) simulations are a promising tool to generate molecular understanding of processes related to the purification of proteins. Polyethylene glycols (PEG) of various length are commonly used in the production and purification of proteins. The molecular mechanisms behind PEG driven precipitation, aqueous two-phase formation or the effects of PEGylation are however still poorly understood.</p><p><strong>Results: </strong>In this paper, we ran MD simulations of single PEG molecules of variable length in explicitly simulated water. The resulting structures are in good agreement with experimentally determined 3D structures of PEG. The increase in surface hydrophobicity of PEG of longer chain length could be explained on an atomic scale. PEG-water interactions as well as aqueous two-phase formation in the presence of PO4 were found to be correlated to PEG surface hydrophobicity.</p><p><strong>Conclusions: </strong>We were able to show that the taken MD simulation approach is capable of generating both structural data as well as molecule descriptors in agreement with experimental data. Thus, we are confident of having a good in silico representation of PEG.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2046-1682-5-14","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30818197","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}
引用次数: 68
A minimal ligand binding pocket within a network of correlated mutations identified by multiple sequence and structural analysis of G protein coupled receptors. 通过对G蛋白偶联受体的多序列和结构分析,确定了相关突变网络中的最小配体结合袋。
BMC Biophysics Pub Date : 2012-06-29 DOI: 10.1186/2046-1682-5-13
Subhodeep Moitra, Kalyan C Tirupula, Judith Klein-Seetharaman, Christopher James Langmead
{"title":"A minimal ligand binding pocket within a network of correlated mutations identified by multiple sequence and structural analysis of G protein coupled receptors.","authors":"Subhodeep Moitra,&nbsp;Kalyan C Tirupula,&nbsp;Judith Klein-Seetharaman,&nbsp;Christopher James Langmead","doi":"10.1186/2046-1682-5-13","DOIUrl":"https://doi.org/10.1186/2046-1682-5-13","url":null,"abstract":"<p><strong>Background: </strong>G protein coupled receptors (GPCRs) are seven helical transmembrane proteins that function as signal transducers. They bind ligands in their extracellular and transmembrane regions and activate cognate G proteins at their intracellular surface at the other side of the membrane. The relay of allosteric communication between the ligand binding site and the distant G protein binding site is poorly understood. In this study, GREMLIN 1, a recently developed method that identifies networks of co-evolving residues from multiple sequence alignments, was used to identify those that may be involved in communicating the activation signal across the membrane. The GREMLIN-predicted long-range interactions between amino acids were analyzed with respect to the seven GPCR structures that have been crystallized at the time this study was undertaken.</p><p><strong>Results: </strong>GREMLIN significantly enriches the edges containing residues that are part of the ligand binding pocket, when compared to a control distribution of edges drawn from a random graph. An analysis of these edges reveals a minimal GPCR binding pocket containing four residues (T1183.33, M2075.42, Y2686.51 and A2927.39). Additionally, of the ten residues predicted to have the most long-range interactions (A1173.32, A2726.55, E1133.28, H2115.46, S186EC2, A2927.39, E1223.37, G902.57, G1143.29 and M2075.42), nine are part of the ligand binding pocket.</p><p><strong>Conclusions: </strong>We demonstrate the use of GREMLIN to reveal a network of statistically correlated and functionally important residues in class A GPCRs. GREMLIN identified that ligand binding pocket residues are extensively correlated with distal residues. An analysis of the GREMLIN edges across multiple structures suggests that there may be a minimal binding pocket common to the seven known GPCRs. Further, the activation of rhodopsin involves these long-range interactions between extracellular and intracellular domain residues mediated by the retinal domain.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2046-1682-5-13","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30729235","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}
引用次数: 8
Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase. RNA 聚合酶催化和转译周期的分子动力学和突变分析。
BMC Biophysics Pub Date : 2012-06-07 DOI: 10.1186/2046-1682-5-11
Maria L Kireeva, Kristopher Opron, Steve A Seibold, Céline Domecq, Robert I Cukier, Benoit Coulombe, Mikhail Kashlev, Zachary F Burton
{"title":"Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase.","authors":"Maria L Kireeva, Kristopher Opron, Steve A Seibold, Céline Domecq, Robert I Cukier, Benoit Coulombe, Mikhail Kashlev, Zachary F Burton","doi":"10.1186/2046-1682-5-11","DOIUrl":"10.1186/2046-1682-5-11","url":null,"abstract":"<p><strong>Unlabelled: </strong></p><p><strong>Background: </strong>During elongation, multi-subunit RNA polymerases (RNAPs) cycle between phosphodiester bond formation and nucleic acid translocation. In the conformation associated with catalysis, the mobile \"trigger loop\" of the catalytic subunit closes on the nucleoside triphosphate (NTP) substrate. Closing of the trigger loop is expected to exclude water from the active site, and dehydration may contribute to catalysis and fidelity. In the absence of a NTP substrate in the active site, the trigger loop opens, which may enable translocation. Another notable structural element of the RNAP catalytic center is the \"bridge helix\" that separates the active site from downstream DNA. The bridge helix may participate in translocation by bending against the RNA/DNA hybrid to induce RNAP forward movement and to vacate the active site for the next NTP loading. The transition between catalytic and translocation conformations of RNAP is not evident from static crystallographic snapshots in which macromolecular motions may be restrained by crystal packing.</p><p><strong>Results: </strong>All atom molecular dynamics simulations of Thermus thermophilus (Tt) RNAP reveal flexible hinges, located within the two helices at the base of the trigger loop, and two glycine hinges clustered near the N-terminal end of the bridge helix. As simulation progresses, these hinges adopt distinct conformations in the closed and open trigger loop structures. A number of residues (described as \"switch\" residues) trade atomic contacts (ion pairs or hydrogen bonds) in response to changes in hinge orientation. In vivo phenotypes and in vitro activities rendered by mutations in the hinge and switch residues in Saccharomyces cerevisiae (Sc) RNAP II support the importance of conformational changes predicted from simulations in catalysis and translocation. During simulation, the elongation complex with an open trigger loop spontaneously translocates forward relative to the elongation complex with a closed trigger loop.</p><p><strong>Conclusions: </strong>Switching between catalytic and translocating RNAP forms involves closing and opening of the trigger loop and long-range conformational changes in the atomic contacts of amino acid side chains, some located at a considerable distance from the trigger loop and active site. Trigger loop closing appears to support chemistry and the fidelity of RNA synthesis. Trigger loop opening and limited bridge helix bending appears to promote forward nucleic acid translocation.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3533926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30673507","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}
引用次数: 0
Intrinsic thermodynamics of ethoxzolamide inhibitor binding to human carbonic anhydrase XIII. 乙氧唑胺抑制剂与人碳酸酐酶XIII结合的内在热力学。
BMC Biophysics Pub Date : 2012-06-07 DOI: 10.1186/2046-1682-5-12
Lina Baranauskienė, Daumantas Matulis
{"title":"Intrinsic thermodynamics of ethoxzolamide inhibitor binding to human carbonic anhydrase XIII.","authors":"Lina Baranauskienė,&nbsp;Daumantas Matulis","doi":"10.1186/2046-1682-5-12","DOIUrl":"https://doi.org/10.1186/2046-1682-5-12","url":null,"abstract":"<p><strong>Unlabelled: </strong></p><p><strong>Background: </strong>Human carbonic anhydrases (CAs) play crucial role in various physiological processes including carbon dioxide and hydrocarbon transport, acid homeostasis, biosynthetic reactions, and various pathological processes, especially tumor progression. Therefore, CAs are interesting targets for pharmaceutical research. The structure-activity relationships (SAR) of designed inhibitors require detailed thermodynamic and structural characterization of the binding reaction. Unfortunately, most publications list only the observed thermodynamic parameters that are significantly different from the intrinsic parameters. However, only intrinsic parameters could be used in the rational design and SAR of the novel compounds.</p><p><strong>Results: </strong>Intrinsic binding parameters for several inhibitors, including ethoxzolamide, trifluoromethanesulfonamide, and acetazolamide, binding to recombinant human CA XIII isozyme were determined. The parameters were the intrinsic Gibbs free energy, enthalpy, entropy, and the heat capacity. They were determined by titration calorimetry and thermal shift assay in a wide pH and temperature range to dissect all linked protonation reaction contributions.</p><p><strong>Conclusions: </strong>Precise determination of the inhibitor binding thermodynamics enabled correct intrinsic affinity and enthalpy ranking of the compounds and provided the means for SAR analysis of other rationally designed CA inhibitors.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2046-1682-5-12","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30672663","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}
引用次数: 33
Can dietary fibre help provide safer food products for sufferers of gluten intolerance? A well-established biophysical probe may help towards providing an answer. 膳食纤维能为麸质不耐症患者提供更安全的食品吗?一个成熟的生物物理探针可能有助于提供答案。
BMC Biophysics Pub Date : 2012-05-17 DOI: 10.1186/2046-1682-5-10
M Samil Kök, Richard Gillis, Shirley Ang, David Lafond, Arthur S Tatham, Gary Adams, Stephen E Harding
{"title":"Can dietary fibre help provide safer food products for sufferers of gluten intolerance? A well-established biophysical probe may help towards providing an answer.","authors":"M Samil Kök,&nbsp;Richard Gillis,&nbsp;Shirley Ang,&nbsp;David Lafond,&nbsp;Arthur S Tatham,&nbsp;Gary Adams,&nbsp;Stephen E Harding","doi":"10.1186/2046-1682-5-10","DOIUrl":"https://doi.org/10.1186/2046-1682-5-10","url":null,"abstract":"<p><p> Gluten intolerance is a condition which affects an increasing percentage of the world's population and for which the only current treatment is a restrictive gluten free diet. However could the inclusion of a particular polysaccharide, or blends of different types, help with the provision of 'safer' foods for those individuals who suffer from this condition? We review the current knowledge on the prevalence, clinical symptoms and treatment of gluten intolerance, and the use and properties of the allergens responsible. We consider the potential for dietary fibre polysaccharides to sequester peptides that are responsible for activation of the disease in susceptible individuals, and consider the potential of co-sedimentation in the analytical ultracentrifuge as a molecular probe for finding interactions strong enough to be considered as useful.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2046-1682-5-10","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30625740","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}
引用次数: 4
DelPhi: a comprehensive suite for DelPhi software and associated resources. DelPhi: DelPhi软件和相关资源的综合套件。
BMC Biophysics Pub Date : 2012-05-14 DOI: 10.1186/2046-1682-5-9
Lin Li, Chuan Li, Subhra Sarkar, Jie Zhang, Shawn Witham, Zhe Zhang, Lin Wang, Nicholas Smith, Marharyta Petukh, Emil Alexov
{"title":"DelPhi: a comprehensive suite for DelPhi software and associated resources.","authors":"Lin Li,&nbsp;Chuan Li,&nbsp;Subhra Sarkar,&nbsp;Jie Zhang,&nbsp;Shawn Witham,&nbsp;Zhe Zhang,&nbsp;Lin Wang,&nbsp;Nicholas Smith,&nbsp;Marharyta Petukh,&nbsp;Emil Alexov","doi":"10.1186/2046-1682-5-9","DOIUrl":"https://doi.org/10.1186/2046-1682-5-9","url":null,"abstract":"<p><strong>Background: </strong>Accurate modeling of electrostatic potential and corresponding energies becomes increasingly important for understanding properties of biological macromolecules and their complexes. However, this is not an easy task due to the irregular shape of biological entities and the presence of water and mobile ions.</p><p><strong>Results: </strong>Here we report a comprehensive suite for the well-known Poisson-Boltzmann solver, DelPhi, enriched with additional features to facilitate DelPhi usage. The suite allows for easy download of both DelPhi executable files and source code along with a makefile for local installations. The users can obtain the DelPhi manual and parameter files required for the corresponding investigation. Non-experienced researchers can download examples containing all necessary data to carry out DelPhi runs on a set of selected examples illustrating various DelPhi features and demonstrating DelPhi's accuracy against analytical solutions.</p><p><strong>Conclusions: </strong>DelPhi suite offers not only the DelPhi executable and sources files, examples and parameter files, but also provides links to third party developed resources either utilizing DelPhi or providing plugins for DelPhi. In addition, the users and developers are offered a forum to share ideas, resolve issues, report bugs and seek help with respect to the DelPhi package. The resource is available free of charge for academic users from URL: http://compbio.clemson.edu/DelPhi.php.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2046-1682-5-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30615532","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}
引用次数: 325
Differences in adhesion and protrusion properties correlate with differences in migration speed under EGF stimulation. 在EGF刺激下,粘附和突出特性的差异与迁移速度的差异有关。
BMC Biophysics Pub Date : 2012-05-11 DOI: 10.1186/2046-1682-5-8
Yue Hou, Sarah Hedberg, Ian C Schneider
{"title":"Differences in adhesion and protrusion properties correlate with differences in migration speed under EGF stimulation.","authors":"Yue Hou,&nbsp;Sarah Hedberg,&nbsp;Ian C Schneider","doi":"10.1186/2046-1682-5-8","DOIUrl":"https://doi.org/10.1186/2046-1682-5-8","url":null,"abstract":"<p><strong>Background: </strong>Cell migration plays an essential role in many biological processes, such as cancer metastasis, wound healing and immune response. Cell migration is mediated through protrusion and focal adhesion (FA) assembly, maturation and disassembly. Epidermal growth factor (EGF) is known to enhance migration rate in many cell types; however it is not known how FA maturation, FA dynamics and protrusion dynamics are regulated during EGF-induced migration. Here we use total internal reflection fluorescence (TIRF) microscopy and image analysis to quantify FA properties and protrusion dynamics under different doses of EGF stimulation.</p><p><strong>Results: </strong>EGF was found to broaden the distribution of cell migration rates, generating more fast and slow cells. Furthermore, groups based on EGF stimulation condition or cell migration speed were marked by characteristic signatures. When data was binned based on EGF stimulation conditions, FA intensity and FA number per cell showed the largest difference among stimulation groups. FA intensity decreased with increasing EGF concentration and FA number per cell was highest under intermediate stimulation conditions. No difference in protrusion behavior was observed. However, when data was binned based on cell migration speed, FA intensity and not FA number per cell showed the largest difference among groups. FA intensity was lower for fast migrating cells. Additionally, waves of protrusion tended to correlate with fast migrating cells.</p><p><strong>Conclusions: </strong>Only a portion of the FA properties and protrusion dynamics that correlate with migration speed, correlate with EGF stimulation condition. Those that do not correlate with EGF stimulation condition constitute the most sensitive output for identifying why cells respond differently to EGF. The idea that EGF can both increase and decrease the migration speed of individual cells in a population has particular relevance to cancer metastasis where the microenvironment can select subpopulations based on some adhesion and protrusion characteristics, leading to a more invasive phenotype as would be seen if all cells responded like an \"average\" cell.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2046-1682-5-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30611029","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}
引用次数: 16
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