Monday, July 20, 2015 - 11:30am - 12:20pm
Jie Liang (University of Illinois, Chicago)
We discuss how to compute structures, assemblies, and thermodynamic
properties of beta barrel membrane proteins, as well as discovery of
building blocks of this class of protins that might be useful for
design of membrane proteins of desired conductance. Based on a model
of physical interactions, a discrete state space, and an empirical
potential function derived from detailed combinatorial analysis of
protein structures, as well as a model to account for inter-strand
Monday, December 8, 2008 - 9:20am - 10:00am
Robert Baldwin (Stanford University)
Solvation makes major contributions to the energetics of protein folding. In an unfolded protein the free energy of solvating nonpolar side chains is unfavorable while solvating polar peptide groups is favorable. The classical model for the energetics of burying nonpolar side chains through folding is Kauzmann's 1959 proposal to use transfer data for model hydrocarbons from water to an organic solvent.
Wednesday, October 9, 2013 - 11:30am - 12:20pm
Stephen Smale (City University of Hong Kong)
A National Research Council report has called attention to
mathematicians the problem of protein folding. Here we will give a setting
for the problem by putting a geometrical structure on the space of proteins.
A significant question in the understanding of the folding process is this.
Which pairs of positions in a linear string representing the protein will
come into contact in the 3 dimensional structure?
Friday, January 18, 2008 - 9:35am - 10:05am
Using the BlueGene computer at IBM Research we have performed extensive simulations on a mutant construct of lambda repressor. The protein consists of 80 amino acids stuctured as a five helix bundle in the folded state. The mutant was designed in the Gruebele lab at UIUC to exhibit sub-10 microsecond folding times in laser temperature jump experiments. Our simulations employed replica exchange and traditional molecular dynamics at a number of different temperatures.
Friday, January 18, 2008 - 9:00am - 9:30am
Jed Pitera (IBM Research Division)
The replica exchange/parallel tempering method and its variations offer the
hope of
improved sampling for many challenging problems in molecular simulation.
Like all
sampling methods, however, the effectiveness of replica exchange is highly
on the specific physical system being studied. We have carried out large
temperature replica exchange (T-REMD) simulations of peptides and proteins
in explicit solvent
and encountered a number of issues that limit the effectiveness of the
method in sampling
Thursday, January 17, 2008 - 11:25am - 11:55am
Thomas Weikl (Max Planck Institute for Colloids and Interfaces)
Small single-domain proteins often exhibit only a single free-energy
barrier, or transition state, between the denatured and the native state.
The folding kinetics of these proteins is usually explored via mutational
analysis. A central question is which structural information on the
transition state can be derived from the mutational data. To interpret these
data, we have developed models that are based (a) on the substructural
cooperativity of helices and hairpins, and (b) on splitting up
Monday, January 14, 2008 - 9:50am - 10:20am
Ronald Levy (Rutgers, The State University Of New Jersey )
Replica exchange (RE) is a generalized ensemble simulation method for accelerating the exploration of free-energy landscapes which define many challenging problems in computational biophysics, including protein folding and binding. Although replica exchange is a parallel simulation technique whose implementation is relatively straightforward, kinetics and the approach to equilibrium in the replica exchange ensemble are complicated; there is much to learn about how to best employ RE to protein folding and binding problems.
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