光谱法研究尿素对水溶液中血红蛋白构象的影响

应用荧光猝灭法和动态光散射法测定尿素-水混合溶剂中血红蛋白(Hb)与联苯胺的结合距离和Hb的流体动力学半径. 结合Hb的荧光光谱和吸收光谱, 探讨尿素与蛋白质分子在水溶液中相互作用的机理及其对蛋白质构象的影响. 结果显示, 尿素分子取代水分子在蛋白质周围形成溶剂化层, 并与骨架肽链和亲水侧链形成氢键, 从而积聚在蛋白质分子表面. 尿素分子与蛋白质分子之间的直接相互作用对蛋白质的构象具有复杂的影响, 高浓度的尿素-水混合溶剂破坏蛋白质的构象, 而低浓度的混合溶剂则有利于蛋白质形成更紧密的构象. 在高浓度的尿素-水混合溶剂中, Hb血红素疏水空穴失去原有的三级结构后形成一个与熔球态相类似的结构.     

正丙醇水溶液准弹性中子散射光谱的分子动力学模拟

准弹性中子散射(QENS)光谱是获取溶液分子动力学性质的重要方法,但光谱解析模型的有效性和去耦合近似的合理性仍存在争议.本文利用分子动力学模拟方法获取纯水和正丙醇水溶液中羟基氢原子的自相关中间散射函数FS(Q,t)和去耦合近似函数FP(Q,t),以及相关性质来评价它们的合理性.结果表明,在低动量转移范围内平-转去耦合近似相对合理,水分子的平-转耦合贡献较小,混合溶液中水分子的平-转耦合项和转动项随动量转移Q值增大而增大,二者显现相互抵消趋势.对于混合溶液中的正丙醇羟基氢原子,由于FS(Q,t)和质心自相关中间散射函数FCM(Q,t)偏差较大,利用实验光谱直接拟合分子平动扩散系数是不合适的.三种平动模型获取的纯水和正丙醇水溶液分子平动扩散系数与实验结果一致,略高于Einstein均方位移方法所得结果.水分子在纯水和混合溶液中表现为跳跃转动,而不是连续转动.正丙醇分子存在转动各向异性,羟基氢原子沿羟基向量为跳跃转动,沿相对质心向量可近似为连续转动.模拟结果显示,高动量转移范围平-转耦合项贡献较大,直接拟合实验光谱获取分子转动扩散系数或弛豫时间是不合适的.鉴于低动量转移范围内转动和平转耦合贡献较小,以及二者的抵消作用,在此范围内获取水分子平动信息是现实可行的.     

铵根离子在水溶液中的跳跃转动机理

铵根离子的动力学行为与生命体内的生物和化学过程密切相关.依据流体力学理论,由于铵根离子与水分子之间存在多个强氢键,其转动应较慢,但实验结果并非如此,其转动的微观机理尚不清晰.本文分子动力学模拟研究表明,水溶液中铵根离子主要以快速、大角度的跳跃方式进行转动,像水分子一样遵从扩展分子跳跃转动模型.通过微观转动模式的分解和两种转动弛豫时间的比较发现,相对其氢键骨架的扩散转动,跳跃转动对其转动速率贡献更大,并随浓度增大不断强化.与水分子氢键交换方式相比,铵根离子更倾向于在非氢键相连的水分子间发生交换.     

水溶液中氢键寿命的定义和弛豫机理

氢键弛豫过程决定水溶液中分子的动力学行为,氢键寿命作为理论和实验结果中一个重要的参数通常用以描述溶液中的氢键动力学性质.本文采用SPC/E-P2和SPC/E-OPLS两种力场方法对二甲基亚砜(DMSO)水溶液体系进行分子动力学模拟,计算了四种不同定义下的氢键寿命,并进行了对比阐述,连续性氢键寿命Tc和基于动力学平衡方法下的氢键寿命TR较短,它们忽略了不成功的氢键交换过程,稳定态模型下的氢键寿命TPR能够真实体现氧键转换过程,可作为标度衡量其它量值.间歇性氢键寿命T相对最长,重复统计了氢键成功交换后的恢复概率.随着二甲基亚砜浓度增大,TC、TI、TR和TPR不断增大,分子平动扩散系数在中等浓度达到极小,说明氢键寿命与分子活动性无决定性关联,同类型氢键在不同浓度下的寿命差异表明氢键寿命具有分子环境依赖性;水分子和二甲基亚砜分子氢键个数降低,氢键受激角度扭曲和拉伸概率下降,TC和TR不断接近,氢键交换受体密度降低使氢键交换速率下降,TPR不断增大,氢键寿命与其周围氢键密度密切相关.TI与TPR的比值体现了氢键交换的局域性,其变化趋势与分子平动活动性趋势相同.两种力场下氢键寿命的差异也说明氢键的寿命具有明显的理论模型依赖性.     

尿素/氧化三甲胺混合溶剂影响单壁碳纳米管内部水合性质的分子动力学模拟

尿素是早已被人们认识的蛋白质变性剂,而氧化三甲胺则是最常用的蛋白质结构保护剂。虽然多年来被广泛应用在生物实验中,但是它们是如何在蛋白质结构形成中起作用,特别是氧化三甲胺是如何在高浓度尿素环境中起到抑制尿素蛋白变性作用的分子机制,至今仍然没有得到圆满解答。本文以单壁碳纳米管为模型疏水体系,采用分子动力学模拟研究尿素/氧化三甲胺混合溶液中纳米管内部水合性质,结果表明氧化三甲胺更易与水分子和尿素分子形成较强相互作用从而稳定了水溶液结构,这一结果亦表明了氧化三甲胺可以通过间接机制抵消尿素分子对于碳纳米管内部水合性质的影响。     

醇及脱氧核糖与水分子间三体作用强度的快速准确计算

快速准确预测醇及脱氧核糖分子与水形成的氢键复合物的三体作用强度, 对准确模拟水环境下蛋白质和DNA的结构和功能至关重要. 基于对多体极化作用的理解, 在可极化偶极-偶极作用模型(PBFF)基础上, 将体系中的极性化学键视为化学键偶极, 通过模拟键偶极的极化计算了醇及脱氧核糖与水分子形成的氢键复合物的三体作用能. 通过拟合甲醇与水氢键复合物的三体作用能随分子间距离变化的能量曲线确定了所需的参数. 将模型和所确定的参数应用于计算更多的甲醇、 乙醇及脱氧核糖与水氢键复合物的三体作用能, 检验了模型的准确性和参数的可转移性. 计算结果表明, 可极化偶极-偶极作用模型及所确定的参数能够较好地预测具有不同结构的氢键复合物的三体作用强度, 其精度可与MP2方法的计算精度相当.     

荧光猝灭法和动态光散射法研究1-丙醇和2-丙醇对水溶液中 蛋白质构象的影响

应用荧光猝灭法和动态光散射技术测定牛血清白蛋白(BSA)与荧光素在正丙醇-水和异丙醇-水混合溶剂中的相互作用距离和BSA的流体动力学半径, 研究正丙醇和异丙醇对水溶液中蛋白质构象的影响. 结果显示, 正丙醇-水和异丙醇-水混合溶剂中BSA与荧光素的相互作用距离和BSA的流体动力学半径随着正丙醇和异丙醇浓度的增加而先减小后增大, 表明低浓度的正丙醇和异丙醇有利于蛋白质形成紧密的构象, 而较高浓度的正丙醇和异丙醇则破坏蛋白质的紧密构象. 试验中观察到BSA与荧光素在正丙醇-水混合溶剂中的结合距离大于同浓度的异丙醇-水混合溶剂中的结合距离, 而BSA在前者的流体动力学半径小于后者, 说明无支链的正丙醇分子易于与蛋白质的疏水基团产生较强的疏水相互作用, 而带支链的异丙醇分子的疏水性较弱, 有利于与蛋白质分子的亲水基团相互作用而积聚在蛋白质表面.     

甘油水溶液氢键特性的分子动力学模拟

为了研究低温保护剂溶液的结构和物理化学特性, 以甘油为保护剂, 采用分子动力学方法, 对不同浓度的甘油和水的二元体系进行了模拟. 得到了不同浓度的甘油水溶液在2 ns内的分子动力学运动轨迹, 通过对后1 ns内运动轨迹的分析, 得到了各个原子对的径向分布函数和甘油分子的构型分布. 根据氢键的图形定义, 分析了氢键的结构和动力学特性. 计算了不同浓度下体系中平均每个原子(O和H)和分子(甘油和水)参与氢键个数的百分比分布及其平均值. 同时还计算了所有氢键、水分子之间的氢键以及甘油与水分子之间的氢键的生存周期.     

乳酸脱氢酶—水体系中不冻结水量的测定

许多研究表明,在蛋白质-水体系中由于蛋白质分子和水分子间的相互作用,使蛋白质周围的水的性质和状态发生了变化,其中一部份水分子以氢键与蛋白质分子表面的极性基因相结合,成为不冻结水(在我们的实验条件下,冷却至-40℃仍不冻结的水),而另一部份     

荧光猝灭法和动态光散射法研究尿素-水混合溶剂中牛血清 白蛋白的构象变化

利用荧光猝灭法和动态光散射法测定尿素-水混合溶剂中牛血清白蛋白(BSA)与荧光素的结合距离和BSA的流体动力学半径, 并通过分析BSA和荧光素在BSA-尿素-水和荧光素-尿素-水三元体系以及BSA-荧光素-尿素-水四元体系中荧光光谱的变化, 探讨尿素与蛋白质分子在水溶液中相互作用的机理及其对蛋白质构象的影响. 结果显示, BSA的3个结构域在尿素-水混合溶剂中具有不同的稳定性, 其中结构域III在尿素-水混合溶剂中是不稳定的, 而结构域I和结构域II分别在尿素浓度大于3.0和4.0 mol•L－1的混合溶剂中发生去折叠. 试验发现, BSA结构域II在低于去折叠浓度的尿素-水混合溶剂中形成更为紧密的构象, 这一现象可以归因于尿素与BSA结合引起的“蛋白质粘稠效应”     

Molecular Dynamics Simulation of Diffusion of Vitamin C in Water Solution

Under different temperatures and concentrations, the diffusion of Vitamin C (VC) in water solution was examined by molecular dynamics simulation. The diffusion coefficients were calculated based on the Einstein equation. The influences of temperature, concentration, and simulation time on the diffusion coefficient were discussed. The results showed that at higher temperature and lower concentration the normal diffusions appear relatively late, but the linear range of mean square displacement curves continues longer than that at lower temperature and higher concentration. At the same temperature, the normal diffusion time increases and the diffusion coefficient decreases as the simulation concentration increases. These simulation results are in good agreement with experiments. Analyses of the pair correlation functions of the simulation systems showed that hydrogen bonds are mainly formed between the hydrogen atoms of VC molecules and oxygen atoms of H₂O molecules, rather than between the O atoms of VC molecules and H atoms of H₂O molecules. The diffusion coefficient is higher as the interaction between water molecules and VC molecules is stronger when VC concentration is lower. The water in the model systems affects the diffusion of VC molecules by the short‐range repulsion of O(H₂O)‐O(H₂O) pairs and the non‐bond interaction of H(H₂O)‐H(H₂O) pairs. The short‐range repulsion of O(H₂O)‐O(H₂O) pairs is greater when VC concentration is higher, the diffusion of VC is weaker. The greater the non‐bond interaction of H(H₂O)‐H(H₂O) pairs is, the higher the VC diffusion is. It is expected that this study can provide a theoretical direction for the experiments on the mass transfer of VC in water solution.     

Simulation Study on the Structure and Dynamics of Water in Sodium Tetrafluoroborate/Water

The microstructure, IR spectrum, as well as rotation dynamics of water molecule in sodium tetrafluoroborate （NaBF4）/water mixture at room temperatures were studied with molecular dynamics simulation. Different concentrations of water （6.25%, 25.0%, 50.0%, 75.0%, 90.0%, and 99.6%） in NaBF4/water mixture were simulated to understand the structure and dynamics. It was shown that water molecules tend to be isolated from each other in mixtures with more ions than water molecules in both liquids. With increase of the molar fraction of water in the mixture, the rotation bands and the bending bands of water display red shift whereas the O-H stretch bands show blue shift, and the decay of the reorientation correlation function becomes slower. This suggests that the molecules are hindered and their motions are difficult and slow, due to the hydrogen-bond interactions and the inharmonic interactions between the interor intra-molecular modes.     

Hydrophobic interactions in presence of osmolytes urea and trimethylamine-N-oxide

Molecular dynamics simulations were carried out to study the influences of two naturally occurring osmolytes, urea, and trimethylamine-N-oxide (TMAO) on the hydrophobic interactions between neopentane molecules. In this study, we used two different models of neopentane: One is of single united site (UA) and another contains five-sites. We observe that, these two neopentane models behave differently in pure water as well as solutions containing osmolytes. Presence of urea molecules increases the stability of solvent-separated state for five-site model, whereas osmolytes have negligible effect in regard to clustering of UA model of neopentane. For both models, dehydration of neopentane and preferential solvation of it by urea and TMAO over water molecules are also observed. We also find the collapse of the second-shell of water by urea and water structure enhancement by TMAO. The orientational distributions of water molecules around different layers of neopentane were also calculated and we find that orientation of water molecules near to hydrophobic moiety is anisotropic and osmolytes have negligible effect on it. We also observe osmolyte-induced water-water hydrogen bond life time increase in the hydration shell of neopentane as well as in the subsequent water layers.     

水化Na-蒙脱石和Na/Mg-蒙脱石的分子动力学模拟

利用分子动力学方法(MD)研究了Na-蒙脱石和Na/Mg-蒙脱石层间的补偿阳离子和水分子的结构及扩散性质. 模拟结果表明, 在一定水含量范围内Na-蒙脱石和Na/Mg-蒙脱石表现出不同的膨胀形式, 特别是层间水分子数目在48～72之间时, Na/Mg-蒙脱石的层间距比Na-蒙脱石有较为明显的增大. Na/Mg-蒙脱石两层水化物的层间水分子与Mg2+形成了明显的两层水合壳; 而与Na+只形成了一层平面的水合壳. 在Na/Mg-蒙脱石中, Na+和 Mg2+的扩散方式不同, Na+的扩散范围相对更广, 自扩散系数更大. Na/Mg-蒙脱石比相同水含量下的Na-蒙脱石层间水的自扩散系数小. 由于Mg2+和Na+对层间结构的强烈影响, 从而使有少量Mg2+取代Na+的Na/Mg-蒙脱石与Na-蒙脱石表现出不同的膨胀性质和层间物质的扩散性质.     

Aqueous urea solutions: structure, energetics, and urea aggregation

Urea is ubiquitously used as a protein denaturant. To study the structure and energetics of aqueous urea solutions, we have carried out molecular dynamics simulations for a wide range of urea concentrations and temperatures. The hydrogen bonds between urea and water were found to be significantly weaker than those between water molecules, which drives urea self-aggregation due to the hydrophobic effect. From the reduction of the water exposed urea surface area, urea was found to exhibit an aggregation degree of ca. 20% at concentrations commonly used for protein denaturation. Structurally, three distinct urea pair conformations were identified and their populations were analyzed by translational and orientational pair distribution functions. Furthermore, urea was found to strengthen water structure in terms of hydrogen bond energies and population of solvation shells. Our findings are consistent with a direct interaction between urea and the protein as the main driving force for protein denaturation. As an additional, more indirect effect, urea was found to enhance water structure, which would suggest a weakening of the hydrophobic effect.     

Computational and NMR analyses for the identification of bound water molecules in ribonuclease T1.

A structural characterization of bound water molecules in ribonuclease T1 (RNase T1) was carried out by nuclear magnetic resonance spectroscopy and molecular dynamics simulation. Amide protons of residues Trp59, Leu62, Tyr68 and Phe100 were found to cross-relax with protons of bound waters. Molecular dynamics simulations of the 120 water molecules observed in the free form of the crystal structure indicate that these amide protons donate hydrogen bonds to the less mobile water molecules. Hydrogen-bonded chains of the water molecules that are identified in the simulation study are located in the hairpin-like loop of RNase T1, comprising residues 62 to 76. The temperature factors of the observed water molecules in the crystal structure are very low, indicating that these bound waters are intrinsic components of RNase T1.     

Dynamics of water confined in the interdomain region of a multidomain protein

Molecular dynamics simulations are performed to study the dynamics of interfacial water confined in the interdomain region of a two-domain protein, BphC enzyme. The results show that near the protein surface the water diffusion constant is much smaller and the water-water hydrogen bond lifetime is much longer than that in bulk. The diffusion constant and hydrogen bond lifetime can vary by a factor of as much as 2 in going from the region near the hydrophobic domain surface to the bulk. Water molecules in the first solvation shell persist for a much longer time near local concave sites than near convex sites. Also, the water layer survival correlation time shows that on average water molecules near the extended hydrophilic surfaces have longer residence times than those near hydrophobic surfaces. These results indicate that local surface curvature and hydrophobicity have a significant influence on water dynamics.     

Solvation Dynamics of a Single Water Molecule Probed by Infrared Spectra—Theory Meets Experiment

The dynamics and energetics of water at interfaces or in biological systems plays a fundamental role in all solvation and biological phenomena in aqueous solution. In particular, the migration of water molecules is the first step that controls the overall process in the time domain. Experimentally, the dynamics of individual water molecules is nearly impossible to follow in solution, because signals from molecules in heterogeneous environments overlap. Although molecular dynamics simulations do not have this restriction, there is a lack of experimental data to validate the calculated dynamics. Here, we demonstrate a new strategy, in which the calculated dynamics are verified by measured time‐resolved infrared spectra. The coexistence of fast and slow migrations of water molecules around a CONH peptide linkage is revealed for a model system representative of a hydrate peptide.     

Choline Chloride as a Nano-Crowder Protects HP-36 from Urea-Induced Denaturation: Insights from Solvent Dynamics and Protein-Solvent Interactions

Urea at sufficiently high concentration unfolds the secondary structure of proteins leading to denaturation. In contrast, choline chloride (ChCl) and urea, in 1 : 2 molar ratio, form a deep eutectic mixture, a liquid at room temperature, protecting proteins from denaturation. In order to get a microscopic picture of this phenomenon, we perform extensive all-atom molecular dynamics simulations on a model protein, HP-36. Based on our calculation of Kirkwood-Buff integrals, we analyze the relative accumulation of urea and ChCl around the protein. Additional insights are drawn from the translational and rotational dynamics of solvent molecules and hydrogen bond auto-correlation functions. In the presence of urea, water shows slow subdiffusive dynamics around the protein owing to a strong interaction of water with the backbone atoms. Urea also shows subdiffusive motion. The addition of ChCl further slows down the dynamics of urea, restricting its accumulation around the protein backbone. Adding to this, choline cations in the first solvation shell of the protein show the strongest subdiffusive behavior. In other words, ChCl acts as a nano-crowder by excluding urea from the protein backbone and thereby slowing down the dynamics of water around the protein. This prevents the protein from denaturation and makes it structurally rigid, which is supported by the smaller radius of gyration and root mean square deviation values of HP-36.