Biomedical subjects

Xuhui Huang

Publications and source records attributed to Xuhui Huang.

6 recordsLinked to original sources

PubMed2006

Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent.

A hydrophobic aided replica exchange method (HAREM) is introduced to accelerate the simulation of all-atom protein folding in explicit solvent. This method is based on exaggerating the hydrophobic effect of various protein amino acids in water by attenuating the protein-water attractive interactions (mimicking the Chaperon effect) while leaving other interactions among protein atoms and water molecules unchanged. The method is applied to a small representative protein, the alpha-helix 3K(I), and it is found that the HAREM method successfully folds the protein within 4 ns, while the regular replica exchange method does not fold the same protein within 5 ns, even with many more replicas.

Algorithms↗

PubMed2006

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.

Computer Simulation↗

PubMed2005

Why is the partial molar volume of CO2 so small when dissolved in a room temperature ionic liquid? Structure and dynamics of CO2 dissolved in [Bmim+] [PF6(-)].

When supercritical CO2 is dissolved in an ionic liquid, its partial molar volume is much smaller than that observed in most other solvents. In this article we explore in atomistic detail and explain in an intuitive way the peculiar volumetric behavior experimentally observed when supercritical CO2 is dissolved in 1-butyl-3-methylimidazolium hexafluorophosphate ([Bmim+] [PF6(-)]). We also provide physical insight into the structure and dynamics occurring across the boundary of the CO2 ionic liquid interface. We find that the liquid structure of [Bmim+] [PF6(-)] in the presence of CO2 is nearly identical to that in the neat ionic liquid (IL) even at fairly large mole fractions of CO2. Our simulations indicate, in agreement with experiments, that partial miscibilities of one fluid into the other are very unsymmetrical, CO2 being highly soluble in the ionic liquid phase while the ionic liquid is highly insoluble in the CO2 phase. We interpret our results in terms of the size and shape of spontaneously forming cavities in the ionic liquid phase, and we propose that CO2 occupies extremely well-defined locations in the IL. Even though our accurate prediction of cavity sizes in the neat IL indicates that these cavities are small compared with the van der Waals radius of a single carbon or oxygen atom, CO2 appears to occupy a space that was for the most part a priori "empty".

Journal Article↗

PubMed2005

Observation of a dewetting transition in the collapse of the melittin tetramer.

Marked hydration changes occur during the self-assembly of the melittin protein tetramer in water. Hydrophobicity induces a drying transition in the gap between simple sufficiently large (more than 1 nm(2)) strongly hydrophobic surfaces as they approach each other, resulting in the subsequent collapse of the system, as well as a depletion of water next to single surfaces. Here we investigate whether the hydrophobic induced collapse of multidomain proteins or the formation of protein oligimers exhibits a similar drying transition. We performed computer simulations to study the collapse of the tetramer of melittin in water, and observed a marked water drying transition inside a nanoscale channel of the tetramer (with a channel size of up to two or three water-molecule diameters). This transition, although occurring on a microscopic length scale, is analogous to a first-order phase transition from liquid to vapour. We find that this drying is very sensitive to single mutations of the three isoleucines to less hydrophobic residues and that such mutations in the right locations can switch the channel from being dry to being wet. Thus, quite subtle changes in hydrophobic surface topology can profoundly influence the drying transition. We show that, even in the presence of the polar protein backbone, sufficiently hydrophobic protein surfaces can induce a liquid-vapour transition providing an enormous driving force towards further collapse. This behaviour was unexpected because of the absence of drying in the collapse of the multidomain protein 2,3-dihydroxybiphenyl dioxygenase (BphC).

Dioxygenases↗

PubMed2005

Drying and hydrophobic collapse of paraffin plates.

We perform molecular dynamics simulations of the hydrophobic collapse of two paraffin plates to examine how the collapse is mediated by realistic paraffin-water attractive van der Waals forces. We explore several aspects of the drying transition between the plates, including the critical separation for drying and the critical size of the vapor bubble required for the nucleation of the drying event. We also investigate the kinetics of hydrophobic collapse and find that the hydrophobic collapse occurs in about 100 ps. We compare these results with the simulations with the plate-water van der Waals attractions turned off and with recent results on the hydrophobic collapse of multidomain proteins. Last, we discuss the relationship among the dewetting transition critical distance, van der Waals potential well depth, and water contact angle on solute surface using a simple macroscopic theory.

Chemistry, Physical↗

PubMed2004

Hydrophobic collapse in multidomain protein folding.

We performed molecular dynamics simulations of the collapse of a two-domain protein, the BphC enzyme, into a globular structure to examine how water molecules mediate hydrophobic collapse of proteins. In the interdomain region, liquid water persists with a density 10 to 15% lower than in the bulk, even at small domain separations. Water depletion and hydrophobic collapse occur on a nanosecond time scale, which is two orders of magnitude slower than that found in the collapse of idealized paraffin-like plates. When the electrostatic protein-water forces are turned off, a dewetting transition occurs in the interdomain region and the collapse speeds up by more than an order of magnitude. When attractive van der Waals forces are turned off as well, the dewetting in the interdomain region is more profound, and the collapse is even faster.

Computer Simulation↗