Different Behaviors of Glutathione in Aqueous and DMSO Solutions: Molecular Dynamics Simulation and NMR Experimental Study

An all-atom molecular simulation and NMR experiments have been carried out to investigate the interactions and conformations of glutathione (GSH) in aqueous and DMSO solutions. The simulations started, from different initial conformations, are characterized by intramolecular distance, radius of gyration, root-mean-square deviation, and solvent-accessible surface. Interestingly, different behaviors are found in the two different solutions. GSH is highly flexible in an aqueous solution with transitions to the extended, semifolded, and folded states. However, once GSH reaches the folded state in DMSO, it remains there and becomes difficult to break down. The NMR results show agreement with the MD simulations. The water molecule is small. It is also a good proton donor and a good proton acceptor. Water molecules can easily break down the “folded” conformation. In DMSO solution, the stronger hydrogen bonds and the hydrophobic interactions are more important, which can make the GSH in the folded state stable. Variations in the distribution of conformations and the hydrogen-bonding network may play an important role in its function under physiological conditions.     

Studies on the Conformations and Hydrogen Bonding of ACE Inhibitory Tripeptide VEF by All-atom Molecular Dynamics Simulations and Molecular Docking

Molecular dynamic simulations and molecular docking are performed to study the conformations and hydrogen bonding interactions of ACE inhibitory tripeptide VEF. Intramolecular distance, radius of gyration, solvent-accessible surface, and root-mean-square deviations are used to characterize the properties of VEF in aqueous solution. The VEF molecule is highly flexible in water and conformations can shift between the extended and folded states. The VEF molecule exists in extended state mostly in aqueous solution and the conformations bonded with ACE are also the extended ones. The findings indicate that MD simulations have a good agreement with the molecular docking analysis.     

Conformations of Oxidized Glutathione in Aqueous Urea Solution by All-Atom Molecular Dynamic Simulations and 2D-NOESY Spectrum

All-atom molecular simulations and two-dimensional nuclear overhauser effect spectra have been used to study the conformations and interactions of oxidized glutathione (GSSG) in aqueous urea solution. The simulations were characterized by intramolecular distance, radius of gyration, solvent-accessible surface area, and root-mean-square deviation. Interestingly, the two chains connected by the GSSG disulfide linkage exhibited different flexibilities in the aqueous urea solution. GSSG can convert from “extended” to “folded” states in the simulations. Its preferred conformation in aqueous urea solutions is “extended”, which was confirmed by the 2D nuclear magnetic resonance (NMR) experiment. The two different types of amide hydrogen atoms in cysteine and glycine also showed different capacities to form N–H?O hydrogen bonds. The results were confirmed by temperature-dependent NMR experiment.     

The IR Absorption Spectra of Aqueous Solutions of Dimethylsulfoxide over the Frequency Range 50–300 cm−1 and the Mobility of Water Molecules

The IR absorption spectra of aqueous solutions of dimethylsulfoxide (DMSO) with concentrations from 100% H₂O to 100% DMSO were recorded over the frequency range 50–500 cm^?1. The absorption spectra were described using the theoretical scheme of hindered rotators. A model was developed according to which orientation relaxation in solution was related to separate rotations of H₂O and DMSO molecules through fixed small and (or) large angles in a unified network of H-bonds consisting of several subsystems ordered to various degrees. The calculated absorption spectra were in agreement with the experimental data in the far IR region. Elementary motions of molecules were found to slow down in the passage from pure dimethylsulfoxide to its aqueous solutions. The special features of the hydrophilic and hydrophobic hydration of DMSO polar and nonpolar groups were considered.     

Solvent effects and hydration of a tripeptide in sodium halide aqueous solutions: an in silico study

In this work we are trying to gain insight into the mechanisms of ion-protein interactions in aqueous media at the molecular scale through fully atomistic molecular dynamics simulations. We present a systematic molecular simulation study of interactions of sodium and halide ions with a trialanine peptide in aqueous sodium halide solutions with different salts concentrations (0.20, 0.50, 1.0 and 2.0 M). Each simulation covers more than fifty nanoseconds to ensure the convergence of the results and to enable a proper determination of the tripeptide-ion interactions through the potentials of mean force. Changes in ion densities in the vicinity of different peptide groups are analysed and implications for the tripeptide conformations are discussed.     

Synthesis of guanidinium-derived receptor libraries and screening for selective peptide receptors in water

A library of "tweezer" receptors, incorporating a guanidinium "head group" and two peptide derived side arms has been prepared on the solid-phase using an orthogonally protected guanidinium scaffold 12. The library was screened with various tripeptide derivatives in an aqueous solvent system. A tweezer receptor 25 for the side chain protected tripeptide 19 was identified from the screening experiments. Receptor 25 was resynthesised and solution binding studies were carried out, which revealed that 25 binds to tripeptide 19 with K(a)=8.2 x 10(4) +/- 2.5 x 10(4) (15 % DMSO/H(2)O, pH 8.75) and with appreciable selectivity over the tripeptide enantiomer 22 and the side chain deprotected tripeptide 20.     

The effect of hydrogen bonding on oligoleucine structure in water: A molecular dynamics simulation study

Molecular dynamics simulations were conducted in order to improve our understanding of the forces that determine polyleucine chains conformations and govern polyleucine self-assembly in aqueous solutions. Simulations of 10 repeat unit oligoleucine in aqueous solution were performed using the optimized potential for liquid simulations (OPLS) - all atom force field using the canonical ensemble for a minimum of 1.3 ns. These simulations provided information on conformations, chain collapse and intermolecular aggregation. Simulations indicate that single isotactic oligoleucine chains in dilute solution assume tightly packed, regular hairpin conformations while atactic oligoleucine assumes a much less regular and less compact structure. The regular, compact collapsed isotactic chain exhibited a greater degree of intramolecular hydrogen bonding and an increased level of hydrophobic t-butyl functional group aggregation compared to the atactic chain. This occurs at the expense of reduced leucine-water hydrogen bonding.     

N2,O2水溶液光谱的分子动力学模拟

用分子动力学模拟方法研究了N2和O2水溶液的光谱性质．给出了能描述分子内部运动的溶质－溶剂相互作用势．对溶质和溶剂原子的速度自相关函数（VACF）作了计算．讨论了所得VACF的性质并计算了其谱密度．溶质分子振动谱出现的红移，与液态N2，O2的Raman实验结果相吻合．模拟得出的转动谱表明了溶剂分子对溶质转动运动的阻滞，模拟结果也表明VACF计算对溶液和液体光谱的研究十分有效．     

Spectroscopic and computational studies of aqueous ethylene glycol solution surfaces

The combination of Monte Carlo, ab initio, and DFT computational studies of ethylene glycol (EG) and EG-water hydrogen-bonding complexes indicate that experimental vibrational spectra of EG and EG-water solution surfaces have contributions from numerous conformations of both EG and EG-water. The computed spectra, derived from harmonic vibrational frequency calculations and a theoretical Boltzmann distribution, show similarity to the experimental surface vibrational spectra of EG taken by broad-bandwidth sum frequency generation (SFG) spectroscopy. This similarity suggests that, at the EG and aqueous EG surfaces, there are numerous coexisting conformations of stable EG and EG-water complexes. A blue shift of the CH2 symmetric stretch peak in the SFG spectra was observed with an increase in the water concentration. This change indicates that EG behaves as a hydrogen-bond acceptor when solvated by additional water molecules. This also suggests that, in aqueous solutions of EG, EG-EG aggregates are unlikely to exist. The experimental blue shift is consistent with the results from the computational studies.     

癸胺盐酸盐分子构象的拉曼光谱

用拉曼光谱考察了物态变化、水溶液浓度、温度和稀土离子等对癸胺盐酸盐分子构象的影响。结果表明固态标题化合物分子以有序的全反式链构象存在,在大于临界胶束浓度的水溶液中分子以无序的旁式链构象存在;增加浓度、升高温度和添加稀土离子都使得链的扭曲和无序程度增加。     

Fluorescence study of the state of tryptophane in aqueous dimethylsulfoxide

The fluorescence spectra of tryptophane were measured in a wide range of concentrations of aqueous dimethylsulfoxide (DMSO) solutions. In solutions with different compositions, tryptophane is surrounded by water molecules alone. This result is in agreement with the known fact of microseparation of aqueous DMSO solutions. Evidently, in a water-DMSO system, the tryptophane molecules are built into water microregions, in which they have a pure aqueous environment and are thus isolated from the nonelectrolyte present in the solution. Based on the experimental data, we determined induced relaxation time of water molecules forming the nearest environment of excited tryptophane (0.59 ns for aqueous tryptophane). Translated fromZhurnal Strukturnoi Khimii, Vol. 38, No. 1, pp. 98–103, January–February, 1997.     

Structure of butanol and hexanol at aqueous, ammonium bisulfate, and sulfuric acid solution surfaces investigated by vibrational sum frequency generation spectroscopy

The organization of 1-butanol and 1-hexanol at the air-liquid interface of aqueous, aqueous ammonium bisulfate, and sulfuric acid solutions was investigated using vibrational broad bandwidth sum frequency generation spectroscopy. There is spectroscopic evidence supporting the formation of centrosymmetric structures at the surface of pure butanol and pure hexanol. At aqueous, ammonium bisulfate, and at most sulfuric acid solution surfaces, butanol molecules organize in all-trans conformations. This suggests that butanol self-aggregates. The spectrum for the 0.052 M butanol in 59.5 wt % sulfuric acid solution is different from the other butanol solution spectra, that is, the surface butanol molecules are observed to possess a significant number of gauche defects. Relative to surface butanol, surface hexanol chains are more disordered at the surface of their respective solutions. Statistically, an increase in the number of gauche defects is expected for hexanol relative to butanol, a six carbon chain vs a four carbon chain. Yet, self-aggregation of hexanol at its aqueous solution surfaces is not ruled out because the methylene spectral contribution is relatively small. The surface spectra for butanol and hexanol also show evidence for salting out from the ammonium bisulfate solutions.     

Synthesis and conformational studies of novel cyclic peptides constrained into a 3 10 helical structure by a heterochiral D-pro-L-pro dipeptide template

An acyclic tripeptide based on a heterochiral D-pro-L-pro template shows a propensity to exist as a 3(10) helical conformation and can be cyclized, via ring-closing metathesis, to the corresponding cyclic tetrapeptides without disrupting the helical conformations in CDCl(3) as well as in DMSO-d(6) solutions. The detailed conformational studies were carried out by using NMR spectroscopy, X-ray crystallography, molecular dynamic simulations, and circular dichroism spectroscopy.     

Studies on the Structures and Hydrogen-bonding Interactions in Aqueous Glycine Solutions Using All-atom Molecular Dynamics Simulations and NMR Spectroscopy

All-atom molecular dynamics （MD） simulations and chemical shifts were used to study interactions and structures in the glycine-water system. Radial distribution functions and the hydrogen-bond network were applied in MD simulations. Aggregates in the aqueous glycine solution could be classified into different regions by analysis of the hydrogen-bonding network. Temperature-dependent NMR spectra and the viscosity of glycine in aqueous solutions were measured to compare with the results of MD simulations. The variation tendencies of the hydrogen atom chemical shifts and viscosity with concentration of glycine agree with the statistical results of hydrogen bonds in the MD simulations.     

二甲基亚砜及一些含氮稠环化合物与DNA的作用

A method for studying the effect of some organic compounds, which are neither soluble in water nor to be made into soluble salts in water, on DNA has been investigated by a series of experiments. The solubility experiments have shown that dimethyl sulphoxide (DMSO) and its aqueous solution are excellent solvents for the hydrophobic multicycles compounds with nitrogen atoms. The data of UV (298 K), CD (298 K), ~(31)P-NMR (323 K) spectra and molar enthalpy changes (298 K) for the effect of DMSO on DNA have not shown that DMSO has an effect on DNA when the pH of solution is equal to 7.0 and its concentration is less than 0.15 mol·L~(-1). This has further proved it is safe when DMSO is used as a carrier of medicinal compounds and enters into human bodies. Under the fixed experimental conditions, no differences were found out from the results of viscous tests (298 K) and UV spectra (298 K) for the effect of harmine hydrochloride on DNA in the presence and absence of DMSO even if the concentration of DMSO reached 0.5 mol·L~(-1). It has indicated that the existence of DMSO in aqueous solutions doesn't disturb the effect of compounds on DNA. The data of UV (298 K), CD(298 K), ~(31)P-NMR (323 K) spectra and molar enthalpy changes (298 K) for the effect of some multicycles compounds with nitrogen atoms on DNA in aqueous solutions of DMSO have also given a clear explanation to the intercalation bindings of these organic compounds to DNA, and a method to study the effect of these compounds on DNA can be developed from these experiments. By analying all the data for the effect of the above compounds on DNA, both the mechanism of interaction between the compounds and DNA and the relationship between the rule of intercalation binding of a series of compounds with same multicycles structures to DNA and their microstructures have been discussed. Since the two multicycles compounds with nitrogen atoms including harmine have high bioactivity, the further experiments inside animal bodies and clinical trial on patients as anticancer drugs should be carried out.     

Dependency of ligand free energy landscapes on charge parameters and solvent models

We performed replica-exchange molecular dynamics (REMD) simulations of six ligands to examine the dependency of their free energy landscapes on charge parameters and solvent models. Six different charge parameter sets for each ligand were first generated by RESP and AM1-BCC methods using three different conformations independently. RESP charges showed some conformational dependency. On the other hand, AM1-BCC charges did not show conformational dependency and well reproduced the overall trend of RESP charges. The free energy landscapes obtained from the REMD simulations of ligands in vacuum, Generalized-Born (GB), and TIP3P solutions were then analyzed. We found that even small charge differences can produce qualitatively different landscapes in vacuum condition, but the differences tend to be much smaller under GB and TIP3P conditions. The simulations in the GB model well reproduced the landscapes in the TIP3P model using only a fraction of the computational cost. The protein-bound ligand conformations were rarely the global minimum states, but similar conformations were found to exist in aqueous solution without proteins in regions close to the global minimum, local minimum or intermediate states.     

Fragmentation-based QM/MM simulations: length dependence of chain dynamics and hydrogen bonding of polyethylene oxide and polyethylene in aqueous solutions

Molecular fragmentation quantum mechanics (QM) calculations have been combined with molecular mechanics (MM) to construct the fragmentation QM/MM method for simulations of dilute solutions of macromolecules. We adopt the electrostatics embedding QM/MM model, where the low-cost generalized energy-based fragmentation calculations are employed for the QM part. Conformation energy calculations, geometry optimizations, and Born-Oppenheimer molecular dynamics simulations of poly(ethylene oxide), PEO(n) (n = 6-20), and polyethylene, PE(n) ( n = 9-30), in aqueous solution have been performed within the framework of both fragmentation and conventional QM/MM methods. The intermolecular hydrogen bonding and chain configurations obtained from the fragmentation QM/MM simulations are consistent with the conventional QM/MM method. The length dependence of chain conformations and dynamics of PEO and PE oligomers in aqueous solutions is also investigated through the fragmentation QM/MM molecular dynamics simulations.     

Molecular dynamics simulation of the A-DNA to B-DNA transition in aqueous RbCl solution

Unrestrained molecular dynamics (MD) simulations have been carried out to characterize the stability of DNA conformations and the dynamics of A-DNA→B-DNA conformational transitions in aqueous RbCl solutions. The PARM99 force field in the AMBER8 package was used to investigate the effect of RbCl concentration on the dynamics of the A→B conformational transition in the DNA duplex d(CGCGAATTCGCG)2 . Canonical Aand B-form DNA were assumed for the initial conformation and the final conformation had a length per complete turn that matched the canonical B-DNA. The DNA structure was monitored for 3.0 ns and the distances between the C5′ atoms were obtained from the simulations. It was found that all of the double stranded DNA strands of A-DNA converged to the structure of B-form DNA within 1.0 ns during the unrestrained MD simulations. In addition, increasing the RbCl concentration in aqueous solution hindered the A→B conformational transition and the transition in aqueous RbCl solution was faster than that in aqueous NaCl solution for the same electrolyte strength. The effects of the types and concentrations of counterions on the dynamics of the A→B conformational transition can be understood in terms of the variation in water activity and the number of accumulated counterions in the major grooves of A-DNA. The rubidium ion distributions around both fixed A-DNA and B-DNA were obtained using the restrained MD simulations to help explain the effect of RbCl concentration on the dynamics of the A→B conformational transition.