Characterization of heteropolymer collapse
Ø. Skjaeveland - K. Sneppen
NORDITA, Blegdamsvej 17, DK-2100 Copenhagen
Ø, Denemark
sneppen@nbivms.nbi.dk
Received 28 October 1999
Abstract
This paper proposes a method to enumerate and characterize the
multidimensional rearrangement that a heteropolymer collapse
represents. We follow the collapse using Langevin dynamics, and
analyze folding pathways by measuring how matches to the final
state develop, when viewed from each monomer in the polymer. The
method is illustrated by following one specific heteropolymer,
which was selected to have repeatable dynamical access to its final
state. For this heteropolymer we found a nucleation event that
precedes the correctly folded state.
PACS
45.50.-j Dynamics and kinematics of a particle and a system
of particles - 87.14.Ee Proteins - 87.15.-v Biomolecules:
structure and physical properties
Copyright EDP Sciences, Società Italiana di Fisica, Springer-Verlag
