AIMS Biophysics最新文献

{"title":"The effects of temperature on streptavidin-biotin binding using affinity isothermal titration calorimetry","authors":"K. Mpye, S. Gildenhuys, Salerwe Mosebi","doi":"10.3934/biophy.2020018","DOIUrl":"https://doi.org/10.3934/biophy.2020018","url":null,"abstract":"An entropically-driven binding interaction at a certain temperature may change to an enthalpically-driven process at another temperature, depending on the polarization state of the groups that are involved in binding. The streptavidin-biotin complex has been extensively studied across biological, medical, chemical and material science fields using various techniques, however, not much has been reported on this interaction across a broad temperature range, between 2 °C and 40 °C using biophysical techniques. In this study, we determined how the forces involved in the streptavidin-biotin complex formation are affected by the reaction temperature using the Affinity ITC (TA Instruments). We observed that this complex formation is a spontaneous binding process, indicated by a negative Gibbs energy (ΔG) at all temperatures tested. The observed negative heat capacity (ΔCp) ~ −459.9 cal/mol K highlights the polar solvation of the interaction that corresponds to a decreasing enthalpy (more negative) (ΔH) with increasing reaction temperature. The stoichiometry (n) of 0.98 was estimated at 25 °C. An increase in reaction temperature resulted in an almost two-fold increase or more in n, notably from 1.59 to 3.41 between 30 °C and 40 °C. Whereas, at lower reaction temperatures, 2 °C to 10 °C, higher molar binding ratios were recorded, i.e. 2.74 to 5.76. We report an enthalpically-driven interaction between 30 °C and 40 °C whereas, an entropically-favourable interaction is observed at lower temperatures, suggestive of an interaction dominated by nonpolar interactions at lower temperatures and polar interactions at higher temperatures. Consequently, alterations in the polarisation state of streptavidin result in moderate binding affinity of biotin to streptavidin at higher reaction temperatures, K D 10-4 ≤ 10-5 M.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"1 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2020-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41929788","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":"Calorimetry and FTIR reveal the ability of URG7 protein to modify the aggregation state of both cell lysate and amylogenic α-synuclein","authors":"J. Dandurand, A. Ostuni, M. Armentano, M. Crudele, V. Dolce, Federica Marra, V. Samouillan, F. Bisaccia","doi":"10.3934/biophy.2020015","DOIUrl":"https://doi.org/10.3934/biophy.2020015","url":null,"abstract":"Differential scanning calorimetry and FITR analyses allowed to investigate the role of URG7 (up-regulated gene clone 7) protein involved in the development of hepatocellular carcinoma induced by hepatitis B virus infection, on the physical structure both of lysates of human hepatoblastoma cells (HepG2) stressed with tunicamycin and α-synuclein, one of the proteins associated with neurogenerative diseases. The protein-water interfacial region was identified and correlated with protein structure. DSC results confirm through the interfacial water behavior that URG7 is able to act in two ways: it maintains the interfacial water stability and controls the mobile fraction level, thereby the flexibility and the protein folding. The mobile water phase increases strongly for cells exposed to α-synuclein, demonstrating an important influence on water hydration. FTIR results evidenced an increase of about 30% of cross β structures in cells exposed to α-synuclein, associated with aggregated proteins. In stress conditions, URG7 was able to maintain the same fraction of mobile water as untreated cells. URG7 was able to restore the water reorientation ability around the complex lysate system and reduced abnormal protein folding.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2020-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48476262","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":"Towards virtual surgery planning: the modified Blalock-Taussig Shunt","authors":"Stephen J. Haller, R. Gerrah, S. Rugonyi","doi":"10.3934/biophy.2020014","DOIUrl":"https://doi.org/10.3934/biophy.2020014","url":null,"abstract":"A modified Blalock-Taussig shunt (MBTS) is an aortopulmonary shunt to establish or augment pulmonary perfusion in congenital cardiac defects with limited pulmonary blood flow. Proper function of this shunt is of utmost importance. In clinical practice, prediction of flow in an MBTS relies on previous experience. In the research field, computational modeling techniques have been developed to simulate flow in an MBTS and predict its performance. These techniques are promising but also time consuming and prone to uncertainties; therefore not yet suitable for clinical practice. Here we present a simplified, patient-based computational model to predict mean circulatory flow characteristics after MBTS insertion. Simulations performed over a range of pulmonary vascular resistances, were compared to data from: i) previous modeling studies; ii) data from the specific patient modeled, and iii) a cohort of patients with MBTS. Model predictions were within one standard deviation from cohort data; and within 1% from results of previous (more complex) computational models. In comparison to previous studies, our model is computationally stable with significantly shorter computational time to perform simulations. We envision that our approach could be used in the future to perform virtual surgeries, quickly testing different surgical scenarios using the patient own geometrical and physiological characteristics, to aid surgeons in decision making.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2020-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45506114","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":"Analysis of a normal and aero helmet on an elite cyclist in the dropped position","authors":"Pedro Forte, D. Marinho, T. Barbosa, J. Morais","doi":"10.3934/biophy.2020005","DOIUrl":"https://doi.org/10.3934/biophy.2020005","url":null,"abstract":"Cyclists use to wear different helmets and adopt different body positions on the bicycle to minimize resistance. The aim of this study was to compare a standard helmet with the new aero road helmets in a bicycle-cyclist system by CFD on the dropped position. An elite level road cyclist volunteered to this research. The cyclist was scanned on his racing bicycle on the dropped position wearing competition gear and a standard helmet and an aero road helmet. A three-dimensional domain around the cyclist with 7 m of length, 2.5 m of width and 2.5 m of height and meshed with more than 43 million of prismatic and tetrahedral elements. The numerical simulations were conducted at 11.11 m/s. The numerical simulations outputs were viscous, pressure and total drag and coefficient of drag. The standard helmet presented a viscous drag of 10.52 N, a pressure drag of 16.51 N and a total drag of 21.98 N. The aero road helmet presented a pressure drag of 7.40 N, a viscous drag of 12.56 N and a total drag of 19.96 N. Moreover, the aero road helmet presented a lower viscous, pressure and total drag coefficient in comparison to the standard helmet. It is possible to conclude that an aero road helmet imposes less drag in comparison to a standard helmet.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2020-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44220849","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":"Structural changes in thyroid hormone receptor-beta by T3 binding and L330S mutational interactions","authors":"T. R. Lamichhane, H. P. Lamichhane","doi":"10.3934/biophy.2020003","DOIUrl":"https://doi.org/10.3934/biophy.2020003","url":null,"abstract":"The point mutations like L330S in the ligand binding domain (LBD) of thyroid hormone receptor-beta (THR-β) make the structural changes as reflected by Ramachandran plots, solvent accessible surface area, radial distribution functions, root mean square deviations and fluctuations, and interaction and internal energies of the LBD residues. By using nanoscale molecular dynamics (NAMD) simulations, the structural features of T3 liganded, unliganded and mutated THR-β LBD are compared to explore the molecular insights in euthyroid, hypothyroid and resistance to thyroid hormones (RTH) states, respectively. The L330S-mutant causes steric hindrance while binding T3 into THR-β LBD causing RTH in the thyroid patients.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2020-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42188785","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":"The potential of lipid soluble thiamine in the treatment of cancer","authors":"D. Lonsdale, C. Marrs","doi":"10.3934/biophy.2020002","DOIUrl":"https://doi.org/10.3934/biophy.2020002","url":null,"abstract":"The resurgence of interest in cancer metabolism has linked alterations in the regulation and exploitation of metabolic pathways with an anabolic phenotype that increases biomass production for the replication of new daughter cells. To support the increase in the metabolic rate of cancer cells, a coordinated increase in the supply of nutrients, such as glucose, as well as micronutrients functioning as enzyme cofactors is required. The majority of co-enzymes are derivatives of water-soluble vitamins such as niacin, folate, pantothenic acid, pyridoxine, biotin, riboflavin and thiamine (Vitamin B1). Continuous dietary intake of these micronutrients is essential for maintaining normal health. How cancer cells adaptively regulate cellular homeostasis of cofactors and how they can regulate expression and function of metabolic enzymes in cancer is under-appreciated. Exploitation of cofactor-dependent metabolic pathways with the advent of anti-folates highlights the potential vulnerabilities and importance of vitamins in cancer biology. Vitamin supplementation products are easily accessible and patients often perceive them as safe and beneficial without full knowledge of their effects. Thus, understanding the significance of enzyme cofactors in cancer cell metabolism will provide for important dietary strategies and new molecular targets to reduce disease progression. Recent studies have demonstrated the significance of thiamine-dependent enzymes in cancer cell metabolism. Therefore, this hypothesis discusses the current knowledge in the alterations in thiamine availability, homeostasis, and exploitation of thiamine-dependent pathways by cancer cells.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2020-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44419090","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":"Peptide AEDL alters chromatin conformation via histone binding","authors":"Larisa I. Fedoreyeva, Boris F. Vanyushin, Ekaterina N. Baranova","doi":"10.3934/biophy.2020001","DOIUrl":"https://doi.org/10.3934/biophy.2020001","url":null,"abstract":"Eukaryotic DNA is tightly packed into chromatin, a DNA–protein structure that exists as transcriptionally permissive euchromatin or repressive heterochromatin. Post-translational modification of histones plays a key role in regulating chromatin dynamics. Short peptides derived from various sources are known to function as epigenetic modulators; however, their mechanisms of action are poorly understood. We addressed this issued by investigating the effect of peptide AEDL on chromatin structure in tobacco (Nicotiana tabacum L.), a commercially important plant species. The chromatin of tobacco interphase cells is characterized by the presence of zones of transcriptionally active domains and particular domains of condensed chromatin of cells that partially coincide with heterochromatin zones. Chromatin decondensation and the formation of euchromatin, accompanied by the activation of genes expression activity, are a determining factor in responses to stressful effects. Our results show that plants grown in the presence of 10 −7 M peptide AEDL transformed condensed chromatin domains from 45% in control cells to 25%. Histone modifications, which constitute the so-called histone code, play a decisive role in the control of chromatin structure. Fluorescence quenching experiments using fluorescein isothiocyanate-labeled histones revealed that the linker histone H1 and complexes of core H3 and H1 histones with DNA bound to peptide AEDL in a 1: 1 molar ratio. The peptide was found to bind to the N-terminal lysine residue of H1 and the lysine residue at position 36 of the H3 C terminus. These interactions of histones H1 and H3 with AEDL peptide loosened the tightly packed chromatin structure, getting transcriptionally active euchromatin. Our findings provide novel insight into the mechanism of gene regulation by short peptides and have implications for breeding more resistant or productive varieties of tobacco and other crops.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2020-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43092450","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":"A generalization of the Shell Theorem.Electric potential of charged spheres and charged vesicles surrounded by electrolyte","authors":"Istv'an P. Sug'ar","doi":"10.3934/biophy.2020007","DOIUrl":"https://doi.org/10.3934/biophy.2020007","url":null,"abstract":"<jats:p xml:lang=\"fr\" />","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2020-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49312548","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":"Imaging flow cytometry methods for quantitative analysis of label-free crystalline silica particle interactions with immune cells.","authors":"Bradley Vis,&nbsp;Jonathan J Powell,&nbsp;Rachel E Hewitt","doi":"10.3934/biophy.2020012","DOIUrl":"https://doi.org/10.3934/biophy.2020012","url":null,"abstract":"<p><p>Exposure to respirable fractions of crystalline silica quartz dust particles is associated with silicosis, cancer and the development of autoimmune conditions. Early cellular interactions are not well understood, partly due to a lack of suitable technological methods. Improved techniques are needed to better quantify and study high-level respirable crystalline silica exposure in human populations. Techniques that can be applied to complex biological matrices are pivotal to understanding particle-cell interactions and the impact of particles within real, biologically complex environments. In this study, we investigated whether imaging flow cytometry could be used to assess the interactions between cells and crystalline silica when present within complex biological matrices. Using the respirable-size fine quartz crystalline silica dust Min-u-sil® 5, we first validated previous reports that, whilst associating with cells, crystalline silica particles can be detected solely through their differential light scattering profile using conventional flow cytometry. This same property reliably identified crystalline silica in association with primary monocytic cells <i>in vitro</i> using an imaging flow cytometry assay, where darkfield intensity measurements were able to detect crystalline silica concentrations as low as 2.5 μg/mL. Finally, we ultilised fresh whole blood as an exemplary complex biological matrix to test the technique. Even after the increased sample processing required to analyse cells within whole blood, imaging flow cytometry was capable of detecting and assessing silica-association to cells. As expected, in fresh whole blood exposed to crystalline silica, neutrophils and cells of the monocyte/macrophage lineage phagocytosed the particles. In addition to the use of this technique in <i>in vitro</i> exposure models, this method has the potential to be applied directly to <i>ex vivo</i> diagnostic studies and research models, where the identification of crystalline silica association with cells in complex biological matrices such as bronchial lavage fluids, alongside additional functional and phenotypic cellular readouts, is required.</p>","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"7 3","pages":"144-166"},"PeriodicalIF":1.5,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7343534/pdf/EMS86720.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38140152","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":"Data formats for modelling the spatial structure of chromatin based on experimental positions of nucleosomes","authors":"M. Mörl, Tilo Zülske, R. Schöpflin, G. Wedemann","doi":"10.3934/BIOPHY.2019.3.83","DOIUrl":"https://doi.org/10.3934/BIOPHY.2019.3.83","url":null,"abstract":"In the nucleus of eukaryotic cells, DNA is wrapped around histone proteins, forming units termed nucleosomes. Nucleosome chains fold into chromatin. Despite extensive experimental advancement, many fundamental features of chromatin remain uncertain. Since all cell types and states cannot be profiled experimentally, especially in solution and in vivo, computer simulations are valuable tools for research. Most computer simulation models of chromatin are coarse-grained and describe the main characteristics of 3D chromatin packing. Newer models include experimentally derived positions of nucleosomes. While it is common practice in other disciplines, such as systems biology, to make experimental data publicly available, data from computer simulations of chromatin models are not usually published. Thus, data standard exchange formats are lacking, and we address this issue in the present work. We analysed the workflow, from experimental determination of the positions of nucleosomes through to analysis of outputs from simulated computer models. We defined standardized formats based on Extensible Markup Language (XML) for artefacts generated by steps in this workflow. We found that XML is useful since it is easy to transform XML-based-files by applying Extensible Stylesheet Language Transformations (XSLT) to other formats. We demonstrate the viability of this approach and the associated file formats using a complete example of computer simulation of chromatin domains based on experimentally determined nucleosome positions. The XML schemas and examples are published in an open source repository.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2019-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47594543","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}