Different Behaviors of ACE Inhibitor Tripeptide Ile-Ile-Pro in Aqueous and DMSO Solutions by All-Atom MD Simulations and 2D-NOESY Spectra

All-atom molecular dynamic simulations and 2D-NOESY spectra were used to study the conformations and hydrogen bonds of ACE inhibitory tripeptide Ile-Ile-Pro(IIP) in aqueous and DMSO solutions. RMSD, Dis, Rg and SASA were adopted to characterize the properties of tripeptide Ile-Ile-Pro in the MD simulations. Interestingly, the tripeptide molecule IIP exhibited different behaviors in aqueous and DMSO solutions. In aqueous solution, IIP was very flexible. The conformation could shift between extended and folded states very quickly. However,in DMSO solution, more folded conformations were observed. The interesting phenomena were proved by 2D-NOESY spectra.     

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.     

Molecular Dynamics Simulations and NMR Experimental Study of Oxidized Glutathione in Aqueous Solution

All-atom molecular simulations and NMR experiments have been used to study the conformations and interactions of oxidized glutathione (GSSG) in aqueous solution. The simulations are characterized by the radius of gyration, intramolecular distance, root-mean-square deviation and solvent-accessible surface area. The variations in these properties show time dependences. Interestingly, the two chains connected by the disulfide linkage in GSSG show different flexibilities in aqueous solution. The conformations of GSSG can convert from ??extended?? to ??folded?? states. Also, the two different kinds of amide hydrogen atoms in cysteine (Cys) and glycin (Gly) show different capabilities in forming N?CH?O hydrogen bonds with water molecules. Temperature-dependent NMR results show agreements with the MD simulations.     

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 Carnosine in Aqueous Solutions by All-Atom Molecular Dynamics Simulations and 2D-NOSEY Spectrum

All-atom molecular simulations and two-dimensional nuclear overhauser effect spectrum have been used to study the conformations of carnosine in aqueous solution. Intramolecular distances, root-mean-square deviation, radius of gyration, and solvent-accessible surface are used to characterize the properties of the carnosine. Carnosine can shift between extended and folded states, but exists mostly in extended state in water. Its preference for extension in pure water has been proven by the 2D nuclear magnetic resonance (NMR) experiment. The NMR experimental results are consistent with the molecular dynamics simulations.     

Adaptive umbrella sampling of the potential energy: modified updating procedure of the umbrella potential and application to peptide folding

Adaptive umbrella sampling of the potential energy is used as a search method to determine the structures and thermodynamics of peptides in solution. It leads to uniform sampling of the potential energy, so as to combine sampling of low-energy conformations that dominate the properties of the system at room temperature with sampling of high-energy conformations that are important for transitions between different minima. A modification of the procedure for updating the umbrella potential is introduced to increase the number of transitions between folded and unfolded conformations. The method does not depend on assumptions about the geometry of the native state. Two peptides with 12 and 13 residues, respectively, are studied using the CHARMM polar-hydrogen energy function and the analytical continuum solvent potential for treatment of solvation. In the original adaptive umbrella sampling simulations of the two peptides, two and six transitions occur between folded and unfolded conformations, respectively, over a simulation time of 10 ns. The modification increases the number of transitions to 6 and 12, respectively, in the same simulation time. The precision of estimates of the average effective energy of the system as a function of temperature and of the contributions to the average effective energy of folded conformations obtained with the adaptive methods is discussed. Received: 11 July 1998 / Accepted: 22 September 1998 / Published online: 17 December 1998     

Carbon-13 NMR spectroscopy of the biological pigments luteoskyrin and rugulosin and some polyhydroxyanthraquinone analogues

The bianthraquinonic biological pigments luteoskyrin and rugulosin and five polyhydroxyanthraquinone derivatives are studied by carbon-13 NMR in DMSO solution. Peak assignment for the fourteen carbon atoms of these compounds is achieved by proton spin decoupling and by investigating the effect of ionisation of the hydroxyl groups upon the carbon chemical shifts. Carbon chemical shifts in the planar hydroxyanthraquinones can be rationalised in terms of conjugation and intramolecular hydrogen bonding. The latter is responsible for the relative acidity of the hydroxyl groups in the analogues, and for the different conformations proposed for luteoskyrin and rugulosin. Tautomeric equilibria occur in DMSO and water–DMSO solutions for the anionic species [LS]^2? and [RG]^2?. This can account for the binding of luteoskyrin and rugulosin to nucleic acids.     

Why 1-NH and 3-NH protons of D-biotin exhibit different activities in aqueous solution

Quantum chemical calculations, combined with the molecular dynamics results, have been employed to explain why the 1- and 3-NH protons of biotin exhibit different activities in aqueous solution. They suggested that the relative proportion of the three different conformations of biotin in the solution was responsible for different activities of the two amide protons of biotin. The relative activity of the two amide protons calculated by theoretical work here is 6, which is in good agreement with the experimental data, which is 5, reinforcing the viewpoint that biotin jumps between the three conformations in aqueous solution and the relative proportion of extended, semifolded, and folded biotin in water is 24:3.6:1. The method for computing the relative activity of the two amide protons of biotin in water here may be used to predict the relative activity in other solutions. The behavior of biotin in aqueous solution may be helpful for better understanding the unusual strong biotin-(strept)avidin binding.     

Protein Conformation and Supercharging with DMSO from Aqueous Solution

The efficacy of dimethyl sulfoxide (DMSO) as a supercharging reagent for protein ions formed by electrospray ionization from aqueous solution and the mechanism for supercharging were investigated. Addition of small amounts of DMSO to aqueous solutions containing hen egg white lysozyme or equine myoglobin results in a lowering of charge, whereas a significant increase in charge occurs at higher concentrations. Results from both near-UV circular dichroism spectroscopy and solution-phase hydrogen/deuterium exchange mass spectrometry indicate that DMSO causes a compaction of the native structure of these proteins at low concentration, but significant unfolding occurs at ~63% and ~43% DMSO for lysozyme and myoglobin, respectively. The DMSO concentrations required to denature these two proteins in bulk solution are ~3–5 times higher than the concentrations required for the onset of supercharging, consistent with a significantly increased concentration of this high boiling point supercharging reagent in the ESI droplet as preferential evaporation of water occurs. DMSO is slightly more basic than m-nitrobenzyl alcohol and sulfolane, two other supercharging reagents, based on calculated proton affinity and gas-phase basicity values both at the B3LYP and MP2 levels of theory, and all three of these supercharging reagents are significantly more basic than water. These results provide additional evidence that the origin of supercharging from aqueous solution is the result of chemical and/or thermal denaturation that occurs in the ESI droplet as the concentration of these supercharging reagents increases, and that proton transfer reactivity does not play a significant role in the charge enhancement observed.     

Structure and conformation of DAB dendrimers in solution via multidimensional NMR techniques.

NOESY-HSQC 3D-NMR and NOESY 2D-NMR techniques have been used on a 750 MHz spectrometer to study the chain conformations of different generation DAB dendrimers (poly[propylene imine] dendrimers) in chloroform and benzene solutions. The high-field multidimensional NMR techniques provided the chemical shift dispersion needed to resolve all of the unique resonances in the dendrimers. By studying the NOE interactions among dendritic chain protons, information about through space interactions between protons on different parts of the dendrimer chain is obtained, which is directly related to the conformation of the dendrimer. These experiments also give further proof of the chemical shift assignments obtained from the HMQC-TOCSY 2D and 3D NMR experiments. The concentration effects on chemical shifts have also been observed, revealing information about the interactions between solvent and different parts of dendrimer molecules. These studies clearly show for DAB dendrimers, that folded chain conformations can occur in nonpolar solvents such as benzene and extended chain conformations are predominant in polar solvents such as chloroform.     

All-atom Molecular Dynamics Simulationsand NMR Spectroscopy Study on Interactions and Structures in N-Glycylglycine Aqueous Solution

All-atom molecular dynamics (MD) simulation and the NMR spectra are used to investi-gate the interactions in N-glycylglycine aqueous solution. Different types of atoms exhibit different capability in forming hydrogen bonds by the radial distribution function analysis. Some typical dominant aggregates are found in different types of hydrogen bonds by the statistical hydrogen-bonding network. Moreover, temperature-dependent NMR are used to compare with the results of the MD simulations. The chemical shifts of the three hydrogen atoms all decrease with the temperature increasing which reveals that the hydrogen bonds are dominant in the glycylglycine aqueous solution. And the NMR results show agreement with the MD simulations. All-atom MD simulations and NMR spectra are successful in revealing the structures and interactions in the N-glycylglycine-water mixtures.     

Effect of pH on the rotational conformations of 1,3‐diamino‐2‐hydroxypropane

The effect of pH on the rotational conformations of 1,3‐diamino‐2‐hydroxypropane in aqueous solution was investigated by proton NMR. Both the observed chemical shifts and coupling constants were used to calculate experimental pK_a values. The observed couplings were correlated with the expected couplings for the various possible staggered conformations to try to determine the pattern of conformations for the diamine and its conjugate acids. The best fits suggested a modest preference for the gauche–gauche conformation, especially at low pH, where the diprotonated hydroxydiamine predominates. In methanol, dimethyl sulfoxide and trichloromethane solutions, it was only possible to evaluate the conformational equilibria of the diamine. Slow proton exchange, which caused uncertainties in both chemical shifts and couplings for the monoprotonated and unprotonated diamine, nullified efforts to determine whether or not hydrogen bonding was important for these species in less polar solvents. Copyright © 2002 John Wiley & Sons, Ltd.     

Solution structure of quinoline- and pyridine-derived oligoamide foldamers

The unambiguous elucidation of a new folded structure in solution may prove to be a very challenging task. The NMR protocols developed for solving the solution structures of alpha-peptides have been applied to aliphatic beta- and gamma-peptides but are not directly applicable to aromatic oligomers. In particular, the string of spin systems in an aromatic sequence cannot be reconstituted solely from correlations between protons. For aromatic oligomers, it is shown that the assignment of a large part of the 13C NMR spectrum through HMBC and HSQC experiments allows to unambiguously assign proton NMR spectra and in turn to interpret NOE correlations. This has been implemented both with quinoline- and pyridine-derived oligoamide foldamers, and should be applicable to a wide range of oligomers including various combinations of monomers. The NOE correlations allow the unambiguous solution structure elucidation of helical conformations of oligoamides derived from pyridine and quinoline monomers showing that, in these series, the solution structures correspond very well to the structures observed in the solid state.     

Understanding interactions between poly(styrene-co-sodium styrene sulfonate) and single-walled carbon nanotubes

Understanding formation mechanisms of hybrids of carbon nanotubes (CNTs) wrapped by polymers and their interactions is critical in modifying solubility of CNTs in aqueous solution and developing new nanotube-based polymer materials. In the present work, we investigate the structural details of poly(styrene-co-sodium styrene sulfonate) (PSS) wrapping around the CNT and the interactions between the PSS chain and the CNT using molecular dynamics (MD) simulations. The fraction of sulfonated groups significantly influences the wrapping conformations of the PSS chain. Due to limited time scale in the MD simulations, two different initial conformations of the chains are introduced to explore the effect of the initial state on the wrapping behavior. When the chains initially wrap around the CNT in a perfect helix manner, more compact pseudo-helical conformations are obtained. For initial straight line arrangement of the chain monomers, the chains adopt looser wrapping conformations. The free-energy analysis and binding interaction of the PSS chain on the CNT surface take a glance on the relationship between the conformational transition of the chain and the energy evolution.     

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.     

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.     

Effect of beta-O-glucosylation on L-Ser and L-Thr diamides: a bias toward alpha-helical conformations

Beta-D-O-glucosylation produces a remarkable effect on the peptide backbone of the model peptides derived from serine and threonine. Consequently, this type of glycosylation is responsible for the experimentally observed shift from extended conformations (model peptides) towards the folded conformations (model glycopeptides). The conclusion has been solidly assessed by a combined NMR/MD protocol. Interestingly, the MD (molecular dynamics) results for the glycopeptides point towards the existence of water-bridging molecules between the sugar and peptide moieties, which could explain the stabilization of the folded conformers in aqueous solution.     

Computational protocols for prediction of solute NMR relative chemical shifts. a case study of L-tryptophan in aqueous solution

In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L-tryptophan in aqueous solution, namely a molecular dynamics simulation and a molecular mechanics conformational search with subsequent geometry re-optimization of the stable conformers using a quantum mechanically based method. These spanning protocols represent standard ways of obtaining a set of conformations on which NMR calculations may be performed. The results stemming from the solute-solvent configurations extracted from the MD simulation at 300 K are found to be inferior to the results stemming from the conformations extracted from the MM conformational search in terms of replicating an experimental reference as well as in achieving the correct sequence of the NMR relative chemical shifts of L-tryptophan in aqueous solution. We find this to be due to missing conformations visited during the molecular dynamics run as well as inaccuracies in geometrical parameters generated from the classical molecular dynamics simulations.     

Characterization of acid-induced protein conformational changes and noncovalent complexes in solution by using coldspray ionization mass spectrometry

Coldspray ionization (CSI) mass spectrometry, a variant of electrospray ionization (ESI) operating at low temperature (20 to −80°C), has been used to characterize protein conformation and noncovalent complexes. A comparison of CSI and ESI was presented for the investigation of the equilibrium acid-induced unfolding of cytochrome c, ubiquitin, myoglobin, and cyclophilin A (CypA) over a wide range of pH values in aqueous solutions. CSI and nanoelectrospray ionization (nanoESI) were also compared in their performance to characterize the conformational changes of cytochrome c and myoglobin. Significant differences were observed, with narrower charged-state distribution and a shift to lower charge state in the CSI mass spectra compared with those in ESI and nanoESI mass spectra. The results suggest that CSI is more prone to preserving folded protein conformations in solution than the ESI and nanoESI methods. Moreover, the CSI-MS data are comparable with those obtained by other established biophysical methods, which are generally acknowledged to be the suitable techniques for monitoring protein conformation in solution. Noncovalent complexes of holomyoglobin and the protein-ligand complex between CypA and cyclosporin A (CsA) were also investigated at a neutral pH using the CSI-MS method. The results of this study suggest the ability of CSI-MS in retaining of protein conformation and noncovalent interactions in solution and probing subtle protein conformational changes. Additionally, the CSI-MS method is capable of analyzing quantitatively equilibrium unfolding transitions of proteins. CSI-MS may become one of the promising techniques for investigating protein conformation and noncovalent protein-ligand interactions in solution.     

Ab initio polypeptide structure prediction

The biological activity of a polypeptide strongly depends on its 3D structure. Ab initio prediction of the native structure from the sequence of amino acids has long motivated the development of an optimum energy model such that interactions present in the native conformation are stronger than those present in nonnative conformations and of algorithms capable of finding the basin of lowest free energy among an astronomically large number of possible conformations. Despite recent progress in our understanding of the factors responsible for both polypeptide stability and formation, computer simulations of polypeptide models are still far from being practical software tools for biologists. In this work, state-of-the-art computer simulations aimed at ab initio structure prediction in aqueous solution are reviewed and their strengths and weaknesses are highlighted. Received: 23 June 1999 / Accepted: 20 September 1999 / Published online: 15 December 1999