Yubo Fan

Effects of Urea, Tetramethyl Urea, and Trimethylamine N-Oxide on Aqueous Solution Structure and Solvation of Protein Backbones: A Molecular Dynamics Simulation Study

The effects of urea, tetramethyl urea (TMU), and trimethylamine N-oxide (TMAO) on the structure and dynamics of aqueous solutions are studied using molecular dynamics simulations. It was found that urea has little effects on the water-water hydrogen-bond length and angle distributions except that it induces a slight collapse of the second shell in the hydrogen-bonding network. TMU and TMAO both strengthen the individual hydrogen bonds and significantly slow the orientational relaxation of water, but have opposite effects on the second shell structure of the hydrogen-bonding network: TMU distorts while TMAO enhances the tetrahedral water structure. Furthermore, TMAO significantly weakens the interactions between the amide carbonyl group and the water molecules, while TMU and urea both strengthen these interactions, with the effect of urea being much less significant than that of TMU. These conclusions are supported by molecular dynamics simulations of three different systems: a model amide compound CH(3)-NH-CO-CH(3) (NMA), and two polypeptides, GB1 and ELP. Consistent with earlier studies, we also found that urea interacts strongly with the carbonyl group through direct hydrogen bonding. The simulations for the denaturation of the polypeptide GB1 in urea solutions showed that the breaking of its native hydrogen bonds follows a step-by-step process and each step is strongly coupled to the formation of water-carbonyl hydrogen bonds, and to a less extent to the urea-carbonyl hydrogen-bond formation. Our simulation results reveal the potential importance of the indirect effects of cosolvents in protein denaturation or structure protection, particularly through modifying of the water-amide interactions.

On the Structure of Water at the Aqueous/Air Interface

Vibrational sum frequency spectroscopy (VSFS) and molecular dynamics (MD) simulations were used in concert to investigate the molecular structure and hydrogen bonding of the air/water interface. MD simulations were performed with a variety of water models. The results indicated that only the upper most two layers of water molecules are ordered in this system. There is a strong preference to have the top layer arranged such that the OH moiety points upward into the air. This orientational preference arises from two factors that involve the maximization of the number of hydrogen bonds formed and the minimization of partial charge that is exposed. Specifically, the lone pairs from oxygen are less likely to face into the air compared with the OH moiety because this would expose more partial charge and, therefore, be unfavorable on enthalpic grounds. The two-layer interfacial water structure model implies that there should be four distinct types of OH stretches for this system. Namely, one directs upward and another points downward in each layer. Interestingly, VSFS experiments revealed the presence of four OH stretch region peaks at 3117, 3222, 3448, and 3696 cm(-1). The phases of the 3117 and 3696 cm(-1) resonances carried a positive sign, which indicates that these features arise from OH groups with protons facing upward toward the air. The other two resonances emanate from OH groups with protons facing downward toward the bulk aqueous solution. On the basis of this, we assign the 3117 cm(-1) peak to the OH moiety from a water molecule in the second layer, which is hydrogen bonded upward toward the top layer. On the other hand, the peak at 3222 cm(-1) should arise from water molecules in the top layer with the OH moiety facing downward to hydrogen bond to the second layer. The 3448 cm(-1) peak arises from hydrogen bonding between water molecules in the second layer and the more disordered water molecules of the bulk liquid. Finally, the peak at 3696 cm(-1) is assigned to the free OH moiety pointing upward in the top layer.

Differences of cations and anions: their hydration, surface adsorption, and impact on water dynamics.

The higher tendency for anions to accumulate at the salt aqueous solution/air interface than that of cations has been observed experimentally and theoretically, suggesting that the size and polarizability of the ions play essential roles in this effect. Here, we investigate the influence of the nonsymmetrical positive-vs-negative charge distribution in water molecules to the hydration and surface/bulk partition of the solvated positively and negatively charged particles by using molecular dynamics simulations with hypothetical ions to validate our theoretical models. The results indicate that positive and negative charges (called cations and anions, respectively, although they may not really exist in experiments) with all other properties identical are hydrated differently and that the anions are more likely to populate at the surface. The simulation on a combination series of cations and anions in aqueous solution shows significant variations on water dynamics, likely due to the specific cooperativity between oppositely charged ions.

From protein denaturant to protectant: Comparative molecular dynamics study of alcohol/protein interactions

It is well known that alcohols can have strong effects on protein structures. For example, monohydric methanol and ethanol normally denature, whereas polyhydric glycol and glycerol protect, protein structures. In a recent combined theoretical and NMR experimental study, we showed that molecular dynamics simulations can be effectively used to understand the molecular mechanism of methanol denaturing protein. In this study, we used molecular dynamics simulations to investigate how alcohols with varied hydrophobicity and different numbers of hydrophilic groups (hydroxyl groups) exert effects on the structure of the model polypeptide, BBA5. First, we showed that methanol and trifluoroethanol (TFE) but not glycol or glycerol disrupt hydrophobic interactions. The latter two alcohols instead protect the assembly of the α- and β-domains of the polypeptide. Second, all four alcohols were shown to generally increase the stability of secondary structures, as revealed by the increased number of backbone hydrogen bonds formed in alcohol/water solutions compared to that in pure water, although individual hydrogen bonds can be weakened by certain alcohols, such as TFE. The two monohydric alcohols, methanol and TFE, display apparently different sequence-dependence in affecting the backbone hydrogen bond stability: methanol tends to enhance the stability of backbone hydrogen bonds of which the carbonyl groups are from polar residues, whereas TFE tends to stabilize those involving non-polar residues. These results demonstrated that subtle differences in the solution environment could have distinct consequences on protein structures.

Thermodynamics and kinetics simulations of multi-time-scale processes for complex systems

We discuss in this review paper the recent development of enhanced sampling methods for searching in energy and configuration space, as well as that for the reactive transition paths. These methods allow accelerated calculations of thermodynamics and kinetics. We summarize in this review the theoretical background and numerical implementation of a variety of methods. Examples of applications are given for each method.

A Combined Theoretical and Experimental Study of the Ammonia Tunnel in Carbamoyl Phosphate Synthetase

The transfer of ammonia in carbamoyl phosphate synthetase (CPS) was investigated by molecular dynamics simulations and experimental characterization of mutations within the ammonia tunnel. In CPS, ammonia is derived from the hydrolysis of glutamine and this intermediate must travel approximately 45 A from the site of formation in the small subunit to the site of utilization in the large subunit. In this investigation, the migration of ammonia was analyzed from the exit of the small subunit through the large subunit where it ultimately reacts with the carboxy phosphate intermediate. Potential of mean force calculations along the transfer pathway for ammonia indicate a relatively low free-energy barrier for the translocation of ammonia. The highest barrier of 7.2 kcal/mol is found at a narrow turning gate surrounded by the side chains of Cys-232, Ala-251, and Ala-314 in the large subunit. The environment of the ammonia tunnel from the exit of the small subunit to the turning gate in the tunnel is filled with clusters of water molecules and the ammonia is able to travel through this area easily. After ammonia passes through the turning gate, it enters a hydrophobic passage. A hydrogen bond then forms between the ammonia and Thr-249, which facilitates the delivery to a more hydrophilic environment near the active site for the reaction with the carboxy phosphate intermediate. The transport process from the turning gate to the end of the tunnel is favored by an overall downhill free-energy potential and no free-energy barrier higher than 3 kcal/mol. A conformational change of the turning gate, caused by formation of the carboxy phosphate intermediate, is consistent with a mechanism in which the reaction between ATP and bicarbonate triggers the transport of ammonia and consequently accelerates the rate of glutamine hydrolysis in the small subunit. A blockage in the turning gate passageway was introduced by the triple mutant C232V/A251V/A314V. This mutant is unable to synthesize carbamoyl phosphate using glutamine as a nitrogen source.

Structural Determinants for the Stereoselective Hydrolysis of Chiral Substrates by Phosphotriesterase

Wild-type phosphotriesterase (PTE) preferentially hydrolyzes the R(P) enantiomers of the nerve agents sarin (GB) and cyclosarin (GF) and their chromophoric analogues. The active site of PTE can be subdivided into three binding pockets that have been denoted as the small, large, and leaving group pockets based on high-resolution crystal structures. The sizes and shapes of these pockets dictate the substrate specificity and stereoselectivity for catalysis. Mutants of PTE that exhibit substantial changes in substrate specificity and the ability to differentiate between chiral substrates have been prepared. For example, the G60A mutant is stereoselective for the hydrolysis of the R(P) enantiomer of the chromophoric analogues of sarin and cyclosarin, whereas the H254G/H257W/L303T (GWT) mutant reverses the stereoselectivity for the enantiomers of these two compounds. Molecular dynamics simulations and high-resolution X-ray structures identified the correlations between structural changes in the active site and the experimentally determined kinetic parameters for substrate hydrolysis. New high-resolution structures were determined for the H257Y/L303T (YT), I106G/F132G/H257Y (GGY), and H254Q/H257F (QF) mutants of PTE. Molecular dynamics calculations were conducted using the S(P) and R(P) enantiomers of the analogues for sarin and cyclosarin for the wild-type PTE and the G60A, YT, GGY, QF, and GWT mutants. The experimental stereoselectivity correlated nicely with the difference in the computed angle of attack for the nucleophilic hydroxide relative to the phenolic leaving group of the substrate.

Carbamate Transport in Carbamoyl Phosphate Synthetase: A Theoretical and Experimental Investigation

The transport of carbamate through the large subunit of carbamoyl phosphate synthetase (CPS) from Escherichia coli was investigated by molecular dynamics and site-directed mutagenesis. Carbamate, the product of the reaction involving ATP, bicarbonate, and ammonia, must be delivered from the site of formation to the site of utilization by traveling nearly 40 A within the enzyme. Potentials of mean force (PMF) calculations along the entire tunnel for the translocation of carbamate indicate that the tunnel is composed of three continuous water pockets and two narrow connecting parts, near Ala-23 and Gly-575. The two narrow parts render two free energy barriers of 6.7 and 8.4 kcal/mol, respectively. Three water pockets were filled with about 21, 9, and 9 waters, respectively, and the corresponding relative free energies of carbamate residing in these free energy minima are 5.8, 0, and 1.6 kcal/mol, respectively. The release of phosphate into solution at the site for the formation of carbamate allows the side chain of Arg-306 to rotate toward Glu-25, Glu-383, and Glu-604. This rotation is virtually prohibited by a barrier of at least 23 kcal/mol when phosphate remains bound. This conformational change not only opens the entrance of the tunnel but also shields the charge-charge repulsion from the three glutamate residues when carbamate passes through the tunnel. Two mutants, A23F and G575F, were designed to block the migration of carbamate through the narrowest parts of the carbamate tunnel. The mutants retained only 1.7% and 3.8% of the catalytic activity for the synthesis of carbamoyl phosphate relative to the wild type CPS, respectively.

Counterion Effects on the Denaturing Activity of Guanidinium Cation to Protein.

The denaturation of a three-α-helix bundle, the B domain of protein A, by guanidinium is studied by molecular dynamics simulations. The simulation results showed that in GdmCl solution, guanidinium cations accumulate around the protein surface, whereas chloride anions are expelled from the protein. In contrast, in GdmSCN solution, both cations and anions accumulate around the protein surface and the degree of Gdm(+) accumulation is higher than that in GdmCl, suggesting the cooperativity between the cations and anions in preferential binding. Moreover, the accumulation of guanidinium around the protein surface is not uniform, and it prefers to populate near residues with negatively charged or planar side chains. On the other hand, guanidinium participates in direct hydrogen bonding with backbone carbonyl groups. Meanwhile, guanidinium also promotes the hydrogen bonding of water to a backbone carbonyl group by changing the hydrogen bonding network within solvent. Therefore, the attack from both water and guanidinium breaks backbone hydrogen bonds and results in the destruction of secondary structures of the protein. The stronger accumulation of guanidinium and more hydrogen bonding from guanidinium in GdmSCN leads to the increase of its denaturing efficiency compared to GdmCl. In the latter solution, the ion pairing between Cl(-) and guanidinium limits the approach of guanidinium to protein and the hydrogen bonding between guanidinium and protein, and the main denaturing contributor is the hydrogen bonding from water.

Long-range effects of confinement on water structure.

Molecular dynamics simulations were performed for water confined between two extended hydrophobic surfaces, which were represented by either planar surfaces or, more realistically, linear alkane monolayers, separated up to hundreds of angstroms. These simulations show that the confinement significantly affects the structure and density distribution of water, as well as the hydration of the confining surfaces. The results are largely independent of model surfaces used. At large separation distances (up to 800 A) between the confining hydrophobic surfaces, it was found that the water distribution is inhomogeneous: the water density is high near the surfaces and low in the middle of the water slab. Using a simple free energy density functional approach, these features seen from simulations were reproduced when a nonlocal free energy density term was introduced. The confinement was also found to have a noticeable effect on the hydrogen bond network of water. For water confined between two hydrophobic plates separated at distances in the range of 100-800 A, the tetrahedrality parameter q was found to be more liquid-like near the surface (distribution shifts toward random arrangements) and more ice-like in the middle (distribution shifts toward more perfectly tetrahedral bonding). These rather long-range effects are expected to vanish at even longer distances, which shall be simulated in the future with the state of the art computational resources. On the other hand, confinement was found to have little effects on water orientational relaxation dynamics.