- 1:24 PM

Insights into a Model Peptide System - a Polarizable Force Field Molecular Simulation Study

Di Wu and Teresa Head-Gordon. Department of Bioengineering, University of California, Berkeley and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720

Proteins fold in vivo in aqueous environments. How the aqueous environment assists the folding process has been studied for a long time. It is well known that the solvent contributions derive from two counterpart forces namely the hydrophobic and the hydrophilic interactions. However the quantitative description of these interactions is limited either by the insufficient sampling of the large biological system or by the inaccurate representation of the empirical force field.

We present the study of a simplified amino acid model system N-acetyl-leucine-methylamide (NALMA), which has both the hydrophobic and the hydrophilic regions well-characterized for the study. The folding process can be mimicked by the self-assembly of these blocked amino acids with increasing concentration representing the different stages. Such calculations are more simplified and the sampling becomes more efficient while the information pertaining to the protein folding process is remained. We have used the AMOEBA force field developed by the Ponder group for our model peptide study. We prefer to use this polarizable force field because it has shown the improved calculations for the bulk water properties and it adapts well to the environmental changes which is very important in studying the heterogeneous environment like in a protein system. Our NALMA simulation shows that the transport property calculated by AMOEBA yields much better values than those calculated by a non-polarizable force field both compared with the experimental results. It also provides the more accurate structure descriptions of the NALMA molecule surrounded by water. We find that NALMA-water system has a well-defined structure near the hydrophilic region, where we clearly see the second hydration shell surrounding the carbonyl oxygen and the amide hydrogen. While in the vicinity of the hydrophobic region, the network of peptide-water molecules is less structured. Indeed, by calculating the diffusion coefficient, we find that water molecules diffuse much faster near the hydrophobic region than near the hydrophilic region. This expedites the movement of the hydrophobic residues and increases the probability of the hydrophobic collapse in a self-assembly process. These features are more pronounced with the increased concentration of the solution. The structure study also confirms the finding of the hydrated shell near the hydrophobic residue. This requires overcoming the dehydration barrier at the late stage in the folding process, which may play an important role in protein folding mechanisms. By studying such a system, we hope to gain molecular insights into the detailed structural and dynamic descriptions of the driving forces that accelerate protein folding in the aqueous environment.