Ron Elber

Elber, Ron
Professor of Chemistry and Biochemistry
W.A. "Tex" Moncrief Chair in Computational Life Sciences and Biology

E-mail: ron@ices.utexas.edu

Website: http://research.cm.utexas.edu/relber/

Main Office: ACE 4.422
Phone: 2325415

Alternate Office: ACE 4.422
Phone: 232-5415

Mailing Address:
1 University Station
ICES
Austin, Texas 78712
Research Summary:
   Two thrusts in computational biology are considered in the laboratory of Ron Elber in the Institute of Computational Engineering and Sciences (ICES): (i) The study of the dynamics and function of proteins and RNA, and (ii) The evolutionary processes that led to the set of biological molecules that we see today. We are particularly interested in atomically detailed descriptions of bio-molecular processes at time scales relevant to biology. The high sensitivity of these molecules to mutations and changes in the environment strongly suggests that atomically detailed modeling is desirable. Examples for studies of type (i) include allosteric transitions of proteins (microseconds), conversion of chemical to mechanical energy (milliseconds), ligand binding and protein-RNA interactions (milliseconds to seconds). There is a time scale gap between computations and experimental measurements that may exceed fifteen orders of magnitude in time. These observations are not accessible to straightforward modeling. A major thrust of the Center is therefore the development and application of novel techniques to bridge the temporal gap and coarse-grain calculations of time. The second thrust in Elber's laboratory is on molecular evolution. Proteins (and RNA) undergo mutations and adjustments of their function during the process of evolution. As such, they provide useful fingerprints of past, present, and perhaps also future adaptation. We study the implication of molecular stability on evolution. For example, proteins that are more stable are found to evolve faster. The laboratory develops a network picture of protein evolution within and between folds which is useful as a core model for molecular evolution. In other bioinformatic applications we focus on determining protein structures and on protein-protein interactions. The models are studied on a high-performance computing platform. A new supercomputer with 1,600 computing cores is installed in Texas Advance Computing Center (TACC) for the use of Elber's laboratory.
 
Research Images:

The network of sequence flow between protein structures - The network of sequence flow between protein structures. The network predicts which protein folds are connected by a single amino acid change, e.g. a single change in the protein myoglobin may convert the overall fold to that of lysozyme. Leonid Meyerguz, Jon Kleinberg, and Ron Elber, The network of sequence flow between protein structures PNAS 2007 104: 11627-11632

Ligand diffusion out of the protein matrix of myoglobin - The escape of a diatomic ligand (carbon monoxide - yellow) from the heme pocket (red) of the protein matrix of myoglobin. The backbone of the protein is a green ribbon, and the side chains are in white stick. One of 200 straightforward molecular dynamics trajectories sampled this rare event. The simulation was carried out in a box of water for 2 nanoseconds. For clarity the water molecules were removed from the image and only a single structure of the protein is shown. The progress of the ligand as a function of time is illustrated by following the carbon monoxide molecule each 10 picoseconds. Joint work of Ron Elber and Quentin Gibson.

 
Publications:
The dynamics of water evaporation from partially solvated cytochrome c in the gas phase (2007) Phys Chem Chem Phys 9, 4690-4697.
Extending molecular dynamics timescales with milestoning: Example of complex kinetics in a solvated peptide (2007) J Chem Phys 126, 145104.
A milestoning study of the kinetics of an allosteric transition: Atomically detailed simulations of deoxy Scapharca hemoglobin (2007) Biophys J 92, 85-87.
The network of sequence flow between protein structures (2007) Proc Natl Acad Sci U S A 104, 11627-11632.

 
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