Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: The Folding Thermodynamics and Kinetics of Crambin Using an All-Atom
  Monte Carlo Simulation   We present a novel Monte Carlo simulation of protein folding, in which all
heavy atoms are represented as interacting hard spheres. This model includes
all degrees of freedom relevant to folding - all sidechain and backbone
torsions - and uses a Go potential. In this study, we focus on the 46 residue
alpha-beta protein crambin and two of its structural components, the helix and
helix hairpin. For a wide range of temperatures, we have recorded multiple
folding events of these three structures from random coils to native
conformations that differ by less than 1 A dRMS from their crystal structure
coordinates. The thermodynamics and kinetic mechanism of the helix-coil
transition obtained from our simulation shows excellent agreement with
currently available experimental and molecular dynamics data. Based on insights
obtained from folding its smaller structural components, a possible folding
mechanism for crambin is proposed. We observe that the folding occurs via a
cooperative, first order-like process, and that many folding pathways to the
native state exist. One particular sequence of events constitutes a
``fast-folding'' pathway where kinetic traps are avoided. At very low
temperatures, a kinetic trap arising from the incorrect packing of sidechains
was observed. These results demonstrate that folding to the native state can be
observed in a reasonable amount of time on desktop computers even when an
all-atom representation is used, provided the energetics sufficiently stabilize
the native state.

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The categories of this paper are: hep-ex
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The categories of this paper are: solv-int
37
The categories of this paper are: supr-con
2
The categories of this paper are: math
5
The categories of this paper are: gr-qc
6
The categories of this paper are: astro-ph
29
The categories of this paper are: funct-an
0
The categories of this paper are: hep-ph
22
The categories of this paper are: chao-dyn
35
The categories of this paper are: mtrl-th
30
The categories of this paper are: q-alg
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The categories of this paper are: nlin
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The categories of this paper are: stat
21
The categories of this paper are: adap-org
15
The categories of this paper are: nucl-ex
34
The categories of this paper are: chem-ph