Linked Life Data

19658542

Source:http://linkedlifedata.com/resource/pubmed/id/19658542

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
6 Pt 1
pubmed:dateCreated
2009-8-7
pubmed:abstractText
A method for reconstructing the potential energy landscape of simple polypeptidic chains is described. We show how to obtain a faithful representation of the energy landscape in terms of a suitable directed graph. Topological and dynamical indicators of the graph are shown to yield an effective estimate of the time scales associated with both folding and equilibration processes. This conclusion is drawn by comparing molecular dynamics simulations at constant temperature with the dynamics on the graph, defined as a temperature-dependent Markov process. The main advantage of the graph representation is that its dynamics can be naturally renormalized by collecting nodes into "hubs" while redefining their connectivity. We show that the dynamical properties at large time scales are preserved by the renormalization procedure. Moreover, we obtain clear indications that the heteropolymers exhibit common topological properties, at variance with the homopolymer, whose peculiar graph structure stems from its spatial homogeneity. In order to distinguish between "fast" and "slow" folders, one has to look at the kinetic properties of the corresponding directed graphs. In particular, we find that the average time needed to the fast folder for reaching its native configuration is two orders of magnitude smaller than its equilibration time while for the bad folder these time scales are comparable.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jun
pubmed:issn
1539-3755
pubmed:author
pubmed:issnType
Print
pubmed:volume
79
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
061925
pubmed:meshHeading
pubmed:year
2009
pubmed:articleTitle
Stochastic dynamics of model proteins on a directed graph.
pubmed:affiliation
Dipartimento di Fisica, Università di Firenze, via Sansone 1, 50019 Sesto Fiorentino, Italy. bongini@fi.infn.it
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't