Title

Folding Events in Small Proteins: Where, when, how often?

Poster Number

42

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 investigate the folding processes of small peptides, both in detail (where the peptide folds or unfolds along its length; how the folding proceeds), and statistically (folding efficiencies and populations). These data provide insight towards understanding the overall folding processes in larger proteins.

Location

DeRosa University Center, Ballroom B

Start Date

1-5-2010 1:00 PM

End Date

1-5-2010 3:00 PM

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May 1st, 1:00 PM May 1st, 3:00 PM

Folding Events in Small Proteins: Where, when, how often?

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 investigate the folding processes of small peptides, both in detail (where the peptide folds or unfolds along its length; how the folding proceeds), and statistically (folding efficiencies and populations). These data provide insight towards understanding the overall folding processes in larger proteins.