Folding Events in Small Proteins: Gas-phase Versus Solvated Systems
Poster Number
41
Format
Poster Presentation
Abstract/Artist Statement
The folding of large proteins can be examined in part through the simulation of smaller proteins or peptide using molecular dynamics (MD) simulations. The data generated in atomistic simulations is able to give a fine-grained picture of the dynamics of such systems, assuming that the force field used is representative of the real systems. A common problem with such simulations, however, is an inability to sample large-enough portions of the folding landscape of the protein. Replica exchange molecular dynamics (REX-MD) simulation is effective in solving this problem. Copies (replicas) of the molecule of interest are simultaneously simulated at a range of temperatures, allowing a more complete sampling of the folding landscape. We use REX-MD in order to compare folding in gas phase and solvated peptides and find that the processes are fundamentally different, both in lifetime and scope. These data provide insight in the how forces of solvation affect and drive protein folding, and provide understanding in the nature of systems of small proteins in both the gas phase and under more natural conditions..
Location
DeRosa University Center, Ballroom B
Start Date
1-5-2010 1:00 PM
End Date
1-5-2010 3:00 PM
Folding Events in Small Proteins: Gas-phase Versus Solvated Systems
DeRosa University Center, Ballroom B
The folding of large proteins can be examined in part through the simulation of smaller proteins or peptide using molecular dynamics (MD) simulations. The data generated in atomistic simulations is able to give a fine-grained picture of the dynamics of such systems, assuming that the force field used is representative of the real systems. A common problem with such simulations, however, is an inability to sample large-enough portions of the folding landscape of the protein. Replica exchange molecular dynamics (REX-MD) simulation is effective in solving this problem. Copies (replicas) of the molecule of interest are simultaneously simulated at a range of temperatures, allowing a more complete sampling of the folding landscape. We use REX-MD in order to compare folding in gas phase and solvated peptides and find that the processes are fundamentally different, both in lifetime and scope. These data provide insight in the how forces of solvation affect and drive protein folding, and provide understanding in the nature of systems of small proteins in both the gas phase and under more natural conditions..