基于图像分析技术的红细胞膜力学特性多参数动态测定的研究

探索以图像分析技术,在无扰、在位、实时的情况下,对单个活态红细胞的多个力学参量：弯曲模量KC、剪切模量μ及切向与弯曲模量之比ε等进行非侵入性连续动态测定的新方法。以该技术对红细胞在不同外部条件（温度、氧分压、渗透压）下的力学参量进行动态监测,不但揭示出有关变量条件对细胞各个力学参量的影响。还证明了本技术适于对细胞的各种生理和病理过程进行连续监测。     

抗菌肽BLFcin6与不同磷脂膜之间相互作用的分子动力学模拟研究

抗菌肽具有广谱抗菌特性,有望成为抗生素较好的替代产品.研究抗菌肽的抗菌机制,可以为新型抗菌肽的设计提供指导.无论抗菌肽采用哪种抗菌机制,其首先要稳定地吸附到细胞膜之上.因此,本文利用分子动力学模拟方法比较了抗菌小肽BLFcin6与5种不同细胞膜之间的相互作用.对这5种细胞膜而言,小肽会很快结合在POPG膜和DPPC-CHOL膜的表面,倾向于进入DPPC膜的疏水内部,与POPC膜和POPC-CHOL膜的接触很少.考察相互作用能,小肽与POPG膜的相互作用最强,主要是小肽与细胞膜亲水头部存在静电相互作用;小肽与DPPC膜的疏水尾部的相互作用较强,但受胆固醇影响,小肽只结合在DPPC-CHOL膜表面.在结合过程中,小肽N端的Arg会先结合到细胞膜上,静电相互作用在小肽锚定细胞膜的过程中起关键作用.以上研究从原子水平上解释了为什么BLFcin6小肽具有抗菌作用,哪些残基起关键作用,也为进一步开展BLFcin6小肽及其衍生小肽的研究奠定基础.     

Ydj1p锌指结构突变体对底物结合影响的分子动力学模拟分析

Ydj1p是酵母细胞质中一种主要的I型Hsp40分子伴侣,Ydj1p锌指结构在传递底物给Hsp70时发挥重要的作用,锌指结构域的两个锌离子结合位点区域(ZBDⅠ和ZBDⅡ)与半胱氨酸形成配位键对底物传递中维持结构稳定非常重要。本研究通过分子动力学手段对Ydj1p与各锌指结构突变体进行了模拟,分析ZBDⅠ突变体关键残基C143S、C201S,ZBDⅡ突变体关键残基C162S、C185S的突变影响Hsp40与Hsp70的底物传递。分析结果表明,当锌指部位的氨基酸发生突变,不仅能影响Ydj1p的结构稳定性,也能影响底物的传递,并且锌指结构Ⅰ突变体和锌指结构Ⅱ突变体之间也具有明显差异。通过结合能量的分析以及构象变化比对,揭示了Ydj1p以及各锌指结构突变体底物结合能力的强弱,这与生化实验研究了Ydj1p锌指结构与Hsp70合作,帮助多肽传递的功能是至关重要的结果较为相近。     

分子动力学模拟尿素对水溶液中蛋白质构象转变的影响

采用分子动力学方法和全原子模型研究尿素和水分子对模型蛋白S-肽链结构转化的影响。模拟结果显示S-肽链的变性速率常数k值随着尿素浓度的增加而先降低后升高,在尿素浓度为2.9 mol/L时达到最低值。模拟了不同尿素浓度下尿素-肽链、水-肽链以及肽链分子氢键的形成状况。结果表明:尿素浓度较低时,尿素分子与S-肽链的极性氨基酸侧链形成氢键,但不破坏其分子内的骨架氢键,尿素在S-肽链水化层外形成限制性空间,增强了S-肽链的稳定性。随着尿素的升高,尿素分子进入S-肽链内部并与其内部氨基酸残基形成氢键,导致S-肽链的骨架氢键丧失,S-肽链发生去折叠。上述模拟结果与文献报道的实验结果一致,从分子水平上揭示了尿素对蛋白质分子结构变化的影响机制,对于研究和发展蛋白质折叠及稳定化技术具有指导意义。     

胸部物理治疗对呼吸机相关性肺炎的效果分析

为探究胸部物理治疗对呼吸机相关性肺炎(VAP)治疗的效果及呼吸力学参数指标的影响作用,本研究选取90例确诊VAP患者作为研究对象,其中45例患者仅采取基础治疗(对照组),另外45例患者采用基础治疗+胸部物理治疗(研究组),对比两组临床治疗效果及呼吸力学参数指标变化。研究结果显示,治疗前,两组患者的MAP、HR、氧合指数、SpO2、CPIS评分差异无统计学意义(p0.05);治疗5 d后,研究组的MAP、氧合指数、SpO2显著的高于对照组(p0.05),研究组的CPIS评分显著低于对照组(p0.05);治疗前,两组患者的PIP、Cdyn、Raw、WOB指标差异无统计学意义(p0.05);治疗5 d后,研究组的Cdyn高于对照组(p0.05),研究组的PIP、Raw、WOB显著低于对照组(p0.05);研究组的ICU住院时间和机械通气时间都显著低于对照组(p0.05),研究组的救治成功率为95.56%,高于对照组的91.11%,但是差异无统计学意义(p0.05)。研究结果表明,胸部物理治疗对于VAP患者而言,有利于改善肺功能、呼吸力学参数以及缩短治疗时间。     

Val55点突变对鸡胱抑素I66Q结构稳定性影响的分子动力学研究

Val55是鸡胱抑素(Chicken cystatin,cC)铰链环状区的重要位点。本文采用分子动力学模拟的方法研究了V55位点突变对cC典型的淀粉样突变体I66Q结构稳定性的影响情况,并深入探讨了其分子机制。研究表明V55N和V55D对I66Q突变体都有稳定其结构的作用,但V55N的稳定作用更显著。进一步研究发现V55N和V55D对I66Q的这种稳定作用是由于突变后的55位残基与邻近残基形成了较多稳定的氢键,从而增加了自身位点及Loop1、β2-β3的稳定性,并进一步稳定了I66Q的α-螺旋和疏水核心结构。这可能最终阻碍胱抑素淀粉样突变体I66Q结构域交换的发生。     

Val55点突变对鸡胱抑素I66Q结构稳定性影响的分子动力学研究

Val55是鸡胱抑素(Chicken cystatin,cC)铰链环状区的重要位点.本文采用分子动力学模拟的方法研究了V55位点突变对cC典型的淀粉样突变体I66Q结构稳定性的影响情况,并深入探讨了其分子机制.研究表明V55N和V55D对I66Q突变体都有稳定其结构的作用,但V55N的稳定作用更显著.进一步研究发现V55N和V55D对I66Q的这种稳定作用是由于突变后的55位残基与邻近残基形成了较多稳定的氢键,从而增加了自身位点及Loop1、β2 - β3的稳定性,并进一步稳定了I66Q的α-螺旋和疏水核心结构.这可能最终阻碍胱抑素淀粉样突变体I66Q结构域交换的发生.     

相互作用对纳米颗粒跨生物膜输运的影响

纳米颗粒与生物膜之间的相互作用,对于纳米颗粒在细胞成像、生物传感器设计、药物输送及疾病诊断和治疗等方面的应用有着重要的影响.本文采用自洽场理论,考察了不同相互作用条件下,纳米颗粒跨膜输运过程中生物膜的形变情况,以及系统自由能的变化情况.结果表明,在纳米颗粒跨膜输运的过程中,随着纳米颗粒与生物膜之间相互作用的改变,生物膜...     

老年高血压患者颈动脉内膜中膜厚度与动态血压参数的相关性

目的:探究老年高血压患者颈动脉内膜中膜厚度(IMT)与动态血压参数间的相关关系,为老年高血压患者的临床治疗提供理论基础。方法:选取2015年1月至2016年1月在我院接受治疗的老年高血压患者204例,根据超声检查结果分为A、B、C三组,每组68例。24 h无创检测患者动态血压参数,包括24h平均收缩压(24h SBP),24 h平均舒张压(24h DBP)、白天平均收缩压(d SBP)、白天平均舒张压(d DBP)、夜间平均收缩压(n SBP)、夜间平均舒张压(n DBP),24h脉压(24h PP)及白天脉压(d PP)、夜间脉压(n PP),记录冠心病的发生率、杓型与非杓型高血压比例,利用Person相关性分析IMT与冠心病发生率及动态血压参数的相关性。结果:收缩压和脉压比较差异均有统计学意义(P0.05),其中B组、C组高于A组,C组高于B组,差异具有统计学意义(P0.05)。非杓型高血压在A组占54.41%,B组占60.29%,C组占79.41%,各组间差异有统计学意义(P0.05);A组、B组、C组冠心病发病率分别为41.18%、54.41%和91.18%,组间比较差异有统计学意义(P0.05)。IMT同冠心病发生率和24h SBP、d SBP、n SBP、24h PP、d PP、n PP呈正相关(r=0.876,0.448,0.378,0.476,0.443,0.491,0.438,P0.05)。结论:老年高血压患者收缩压,脉压升高以及非杓型高血压是造成颈动脉内膜中膜厚度增加的主要原因,同时,IMT与冠心病发病率和动态血压参数间呈正相关关系。     

Molecular Dynamics Investigation of Bond Ordering of Unsaturated Lipids in Monolayers

Molecular dynamics simulations of three model lipid monolayers of 2,3-diacyl-D-glycerolipids, that contained stearoyl (18:0) in the position 3 and oleoyl (18:9cis), linoleoyl (18:26cis), or linolenoyl (18:33cis) in the position 2, have been carried out. The simulation systems consisted of 24 lipid molecules arranged in a rectangular simulation cell, with periodic boundary conditions in the surface plane. 1 nanosecond simulations were performed at T = 295 K. C-C and C-H bond order parameter profiles and the bond orientation distributions about the monolayer normal have been calculated. The relation of the distributions to the order parameters was analyzed in terms of maxima and widths of the distributions. The cis double bond order parameter is found to be higher than those of adjacent single C-C bonds. The widths of the two distributions of C-H bonds of the cis double bond segment in di- and triunsaturated molecules are much smaller than that obtained for methylene group located between the double bonds. The bond orientation distribution function widths depend on both the segment location in the chain and the segment chemical structure.     

Correlation between the order parameter and the steady-state fluorescence anisotropy of 1,6-diphenyl-1,3,5-hexatriene and an evaluation of membrane fluidity

In this paper it is shown that for 1,6-diphenyl-1,3,5-hexatriene there exists a simple analytical relation between the orientational order parameter and the steady-state fluorescence anisotropy. This relation is derived on semi-empirical grounds. The order parameter and the true microviscosity for membranes as calculated from steady-state measurements are evaluated. For biological membranes the estimation of the order parameter from steady-state experiments is feasible, but the evaluation of the true microviscosity is not reliable. Also, the physiological relevance of the order parameter is discussed.     

Force field comparisons of the heat capacity of carbon nanotubes

The force fields Tersoff, CHARMM, COMPASS, CVFF and PCFF are compared using molecular calculations and simulations of SWNT thermal properties. The heat capacity results from the force fields vary significantly in the low (room) temperature range. The COMPASS force field best reproduces the phonon frequencies calculated from density functional theory and is consistent with the Raman scattering results. The temperature dependent behavior of SWNT heat capacity is investigated using harmonic and quasi-harmonic dynamics theories. The impact of quasi-harmonic analysis is not significant in the low and intermediate temperature range (below 500 K). Thus, force field comparisons based on the harmonic approximation are valid in that temperature range. Above 500 K, heat capacity results based on the Tersoff force field using a quasi-harmonic approximation are further investigated.     

Combinatorial microscopy for the study of protein–membrane interactions in supported lipid bilayers: Order parameter measurements by combined polarized TIRFM/AFM

Understanding the mechanisms of peptide-induced membrane disorder is critical to the design of novel antimicrobial and cell-penetrating peptides. One means of quantifying local structure and order/disorder is through the orientational order parameter, typically obtained using various spectroscopic approaches. We report here on the use of an image-based means of tracking the order parameter in supported lipid bilayers during peptide-induced disordering. By coupling polarized total internal reflection fluorescence microscopy with in situ atomic force microscopy, it is now possible to track changes in order parameter associated with peptide binding and insertion, as well as lipid headgroup and acyl chain reordering, while simultaneously resolving molecular-scale topographical changes. Interactions between the model antimicrobial peptide, indolicidin, and its fluorescent analog, TAMRA-indolicidin, with model eukaryotic (DOPC:DSPC:cholesterol) and prokaryotic (DOPE/DOPG) membranes were tracked using the fluorescent lipid reporters, DiI-C₂₀ and BODIPY-PC. Changes in the order parameter upon membrane binding and insertion provided insights into the orientation of the peptide and the role of membrane chemistry and composition on insertion dynamics and membrane restructuring.     

Interaction between dihydropyridines and phospholipid bilayers: a molecular dynamics simulation

Interaction of the calcium-channel antagonist dihydropyridines (DHPs), lacidipine and nifedipine, with a phospholipid bilayer was studied using 600 ps molecular dynamic simulations. We have constructed a double layer membrane model composed of 42 dimirystoyl-phosphatidylcholine molecules. The DHP molecules locate at about 7 Å from the centre of the membrane, inducing an asymmetry in the bilayer. While lacidipine did not induce significant local perturbations as judged by the gauche-trans isomerisation rate, nifedipine significantly decreased this rate, probably by producing a local rigidity of the membrane in the vicinity of the DHP.     

Modeling of Platinum Clusters in H-Mordenite

The size, location and structure of Pt clusters in H-mordenite have been investigated by molecular mechanics energy minimization and molecular dynamics simulation techniques using the Catalysis software of Molecular Simulations (MSI). Lattice energy minimizations are performed to study the effects of the specific framework aluminum positions on the location and stability of monoatomic Pt sites in H-mordenite. The lattice energies relative to the siliceous platinum-aluminosilicate structure reveal that the stability of a single Pt atom in H-mordenite is remarkably influenced by the specific location of the Al atoms in the lattice. At the studied Si/Al ratio of two Al ions per unit cell, a stabilization of the H-mordenite lattice upon Pt deposition is obtained. Moreover, lattice energy calculations on Pt/aluminosilicate mordenites of different metal contents per unit cell have been performed. An optimum size for the aggregate confined to the 12-ring main channel that is almost independent of the Pt content per mordenite unit cell has been found. The structural features of the resulting clusters at the end of molecular dynamics simulations on Pt/alumina-mordenites reflect a strong metal-zeolite interaction. The present results are consistent with a previous molecular dynamics simulation study on the structure of platinum deposited on SiO₂ surfaces.     

Molecular dynamics (MD) simulations for the prediction of chiral discrimination of N-acetylphenylalanine enantiomers by cyclomaltoheptaose (beta-cyclodextrin, beta-CD) based on the MM-PBSA (molecular mechanics-Poisson-Boltzmann surface area) approach

Molecular dynamics (MD) simulations were performed for the prediction of chiral discrimination of N-acetylphenylalanine enantiomers by cyclomaltoheptaose (beta-cyclodextrin, beta-CD). Binding free energies and various conformational properties were obtained using by the MM-PBSA (molecular mechanics Poisson-Boltzmann/surface area) approach. The calculated relative difference (DeltaDeltabinding) of binding free energy was in fine agreement with the experimentally determined value. The difference of rotameric distributions of guest N-acetylphenylalanine enantiomers complexed with the host, beta-CD, was observed after the conformational analyses, suggesting that the conformational changes of guest captured within host cavity would be a decisive factor for enantiodifferentiation at a molecular level.     

Setting up and running molecular dynamics simulations of membrane proteins

Molecular dynamics simulations have become a popular and powerful technique to study lipids and membrane proteins. We present some general questions and issues that should be considered prior to embarking on molecular dynamics simulation studies of membrane proteins and review common simulation methods. We suggest a practical approach to setting up and running simulations of membrane proteins, and introduce two new (related) methods to embed a protein in a lipid bilayer. Both methods rely on placing lipids and the protein(s) on a widely spaced grid and then 'shrinking' the grid until the bilayer with the protein has the desired density, with lipids neatly packed around the protein. When starting from a grid based on a single lipid structure, or several potentially different lipid structures (method 1), the bilayer will start well-packed but requires more equilibration. When starting from a pre-equilibrated bilayer, either pure or mixed, most of the structure of the bilayer stays intact, reducing equilibration time (method 2). The main advantages of these methods are that they minimize equilibration time and can be almost completely automated, nearly eliminating one time consuming step in MD simulations of membrane proteins.     

Backbone dynamics of oxidized and reduced D. vulgaris flavodoxin in solution

Recombinant Desulfovibrio vulgaris flavodoxin was produced inEscherichia coli. A complete backbone NMR assignment for the two-electronreduced protein revealed significant changes of chemical shift valuescompared to the oxidized protein, in particular for the flavinemononucleotide (FMN)-binding site. A comparison of homo- and heteronuclearNOESY spectra for the two redox states led to the assumption that reductionis not accompanied by significant changes of the global fold of the protein.The backbone dynamics of both the oxidized and reduced forms of D. vulgarisflavodoxin were investigated using two-dimensional¹⁵N-¹H correlation NMR spectroscopy.T₁, T₂ and NOE data are obtained for 95%of the backbone amide groups in both redox states. These values wereanalysed in terms of the model-free approach introduced by Lipari andSzabo [(1982) J. Am. Chem. Soc., 104, 4546-;4559, 4559-;4570]. Acomparison of the two redox states indicates that in the reduced speciessignificantly more flexibility occurs in the two loop regions enclosing FMN.Also, a higher amplitude of local motion could be found for the N(3)H groupof FMN bound to the reduced protein compared to the oxidized state.