Abstract of talk by Srinivasan and Rose

Max Vasquez maxv at ISERVER.PDL.COM
Tue May 9 14:42:44 EST 1995

Below, without editorial comment (and I hope *no* typos), an abstract that
may be of interest.

"How do proteins avoid getting stuck in the wrong conformation during
folding" by R. Srinivasan and G.D. Rose Johns Hopkins University, School of

The central verity of protein folding is the existence of a unique native
conformation, which comprises residues distant in sequence but close in
space, with a closed-packed core, enriched in hydrophobic residues.  How
does the protein screen conformations effectively and select the native one
reliably on a biological time-scale, without getting stuck in non-native
energy minima along the pathway to the native state? This search process is
spontaneous and effective for the protein, but vexing for the protein
folder. Based on a hierarchic organizing principle, we have developed a
simple algorithm called LINUS that can fold a protein from its amino acid
sequence alone.  LINUS is an acronym for Local Independent Nucleated Units
of Structure.  The algorithms ascends the folding hierarchy in discrete
stages, with concomitant accretion of structure at each step.  The chain is
represented by idealized geometry, and favorable conformations are selected
using a highly simplified energy function.  The algorithm has been applied
to a diverse test set of X-ray elucidated proteins, with results that
accurately, though imprecisely, predict the overall fold in each case.

** This will be presented at the ASBMB meeting May 21-25 in San Francisco,

Max Vasquez, PhD
Protein Design Labs, Inc.
2375 Garcia Ave.
Mountain View, CA 94043
(415) 903-3744
(415) 903-3730 (FAX)
Internet:  maxv at pdl.com
           micifos at ix.netcom.com

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