Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Identifying critical residues in protein folding: Insights from
  phi-value and Pfold analysis   We apply a simulational proxy of the phi-value analysis and perform extensive
mutagenesis experiments to identify the nucleating residues in the folding
reactions of two small lattice Go polymers with different native geometries.
These results are compared with those obtained from an accurate analysis based
on the reaction coordinate folding probability Pfold, and on structural
clustering methods. For both protein models, the transition state ensemble is
rather heterogeneous and splits-up into structurally different populations. For
the more complex geometry the identified subpopulations are actually
structurally disjoint. For the less complex native geometry we found a broad
transition state with microscopic heterogeneity. For both geometries, the
identification of the folding nucleus via the Pfold analysis agrees with the
identification of the folding nucleus carried out with the phi-value analysis.
For the most complex geometry, however, the apllied methodologies give more
consistent results than for the more local geometry. The study of the
transition state' structure reveals that the nucleus residues are not
necessarily fully native in the transition state. Indeed, it is only for the
more complex geometry that two of the five critical residues show a
considerably high probability of having all its native bonds formed in the
transition state. Therefore, one concludes that in general the phi-value
correlates with the acceleration/deceleration of folding induced by mutation,
rather than with the degree of nativeness of the transition state, and that the
traditional interpretation of phi-values may provide a more realistic picture
of the structure of the transition state only for more complex native
geometries.

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The categories of this paper are: supr-con
31
The categories of this paper are: ao-sci
8
The categories of this paper are: hep-ex
29
The categories of this paper are: funct-an
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The categories of this paper are: q-fin
16
The categories of this paper are: stat
20
The categories of this paper are: acc-phys
7
The categories of this paper are: hep-th
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The categories of this paper are: econ
34
The categories of this paper are: chem-ph
12
The categories of this paper are: nucl-th
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The categories of this paper are: mtrl-th
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The categories of this paper are: adap-org
6
The categories of this paper are: astro-ph
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The categories of this paper are: chao-dyn
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The categories of this paper are: quant-ph