Biomedical subjects

Léo Degrève

Publications and source records attributed to Léo Degrève.

3 recordsLinked to original sources

PubMed2005

Correlation of temperature induced conformation change with optimum catalytic activity in the recombinant G/11 xylanase A from Bacillus subtilis strain 168 (1A1).

The 1.7A resolution crystal structure of recombinant family G/11 beta-1,4-xylanase (rXynA) from Bacillus subtilis 1A1 shows a jellyroll fold in which two curved beta-sheets form the active-site and substrate-binding cleft. The onset of thermal denaturation of rXynA occurs at 328 K, in excellent agreement with the optimum catalytic temperature. Molecular dynamics simulations at temperatures of 298-328 K demonstrate that below the optimum temperature the thumb loop and palm domain adopt a closed conformation. However, at 328 K these two domains separate facilitating substrate access to the active-site pocket, thereby accounting for the optimum catalytic temperature of the rXynA.

Bacillus subtilis↗

PubMed2004

LMProt: an efficient algorithm for Monte Carlo sampling of protein conformational space.

A new and efficient Monte Carlo algorithm for sampling protein configurations in the continuous space is presented; the efficiency of this algorithm, named Local Moves for Proteins (LMProt), was compared to other alternative algorithms. For this purpose, we used an intrachain interaction energy function that is proportional to the root mean square deviation (rmsd) with respect to alpha-carbons from native structures of real proteins. For phantom chains, the LMProt method is approximately 10(4) and 20 times faster than the algorithms Thrashing (no local moves) and Sevenfold Way (local moves), respectively. Additionally, the LMProt was tested for real chains (excluded-volume all-atoms model); proteins 5NLL (138 residues) and 1BFF (129 residues) were used to determine the folding success xi as a function of the number eta of residues involved in the chain movements, and as a function of the maximum amplitude of atomic displacement delta r(max). Our results indicate that multiple local moves associated with relative chain flexibility, controlled by appropriate adjustments for eta and delta r(max), are essential for configurational search efficiency.

Algorithms↗

PubMed2002

Liquid correlation across the walls in a slit pore: effect on the wetting and drying transition.

The liquid structure next to the walls of a slit pore, immersed in a model simple liquid, is studied through a liquid theory and grand canonical Monte Carlo simulations. A liquid correlation across slit walls, of finite width, is found. This correlation modifies the structure and capillary partial wetting and drying transitions of the nonhomogeneous fluid, when close to its liquid-vapor coexistence curve.

Journal Article↗