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Stochastic reconstruction of protein structures from effective connectivity profiles.

Wolff K, Vendruscolo M, Porto M - PMC Biophys (2008)

Bottom Line: Structure information thus enters the folding dynamics via the effective connectivity, but the interaction is not restricted to pairs of amino acids that form native contacts, resulting in a free energy landscape which does not rely on the assumption of minimal frustration.Moreover, effective connectivity vectors can be predicted more readily from the amino acid sequence of proteins than the corresponding contact maps, thus suggesting that the stochastic protocol presented here could be effectively combined with other current methods for predicting native structures.PACS codes: 87.14.Ee.

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Affiliation: Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstrasse 6, 64289 Darmstadt, Germany. porto@fkp.tu-darmstadt.de.

ABSTRACT
We discuss a stochastic approach for reconstructing the native structures of proteins from the knowledge of the "effective connectivity", which is a one-dimensional structural profile constructed as a linear combination of the eigenvectors of the contact map of the target structure. The structural profile is used to bias a search of the conformational space towards the target structure in a Monte Carlo scheme operating on a Calpha-chain of uniform, finite thickness. Structure information thus enters the folding dynamics via the effective connectivity, but the interaction is not restricted to pairs of amino acids that form native contacts, resulting in a free energy landscape which does not rely on the assumption of minimal frustration. Moreover, effective connectivity vectors can be predicted more readily from the amino acid sequence of proteins than the corresponding contact maps, thus suggesting that the stochastic protocol presented here could be effectively combined with other current methods for predicting native structures. PACS codes: 87.14.Ee.

No MeSH data available.


Distribution of contact overlap. Distribution of full contact overlaps, i.e. not restricted to cooperative contacts, for the cases of successful reconstructions discussed in this work.
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Figure 5: Distribution of contact overlap. Distribution of full contact overlaps, i.e. not restricted to cooperative contacts, for the cases of successful reconstructions discussed in this work.

Mentions: Here Qt is the set of contacts in the target and Qc the contacts in the present structure. This corresponds to a contact overlap qfull to the full (unrestricted) contact map of 74% to 100% for the various proteins (see Fig. 5). This percentage of recovered native contacts can be enough to allow reconstruction to good resolution [26].


Stochastic reconstruction of protein structures from effective connectivity profiles.

Wolff K, Vendruscolo M, Porto M - PMC Biophys (2008)

Distribution of contact overlap. Distribution of full contact overlaps, i.e. not restricted to cooperative contacts, for the cases of successful reconstructions discussed in this work.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2666633&req=5

Figure 5: Distribution of contact overlap. Distribution of full contact overlaps, i.e. not restricted to cooperative contacts, for the cases of successful reconstructions discussed in this work.
Mentions: Here Qt is the set of contacts in the target and Qc the contacts in the present structure. This corresponds to a contact overlap qfull to the full (unrestricted) contact map of 74% to 100% for the various proteins (see Fig. 5). This percentage of recovered native contacts can be enough to allow reconstruction to good resolution [26].

Bottom Line: Structure information thus enters the folding dynamics via the effective connectivity, but the interaction is not restricted to pairs of amino acids that form native contacts, resulting in a free energy landscape which does not rely on the assumption of minimal frustration.Moreover, effective connectivity vectors can be predicted more readily from the amino acid sequence of proteins than the corresponding contact maps, thus suggesting that the stochastic protocol presented here could be effectively combined with other current methods for predicting native structures.PACS codes: 87.14.Ee.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstrasse 6, 64289 Darmstadt, Germany. porto@fkp.tu-darmstadt.de.

ABSTRACT
We discuss a stochastic approach for reconstructing the native structures of proteins from the knowledge of the "effective connectivity", which is a one-dimensional structural profile constructed as a linear combination of the eigenvectors of the contact map of the target structure. The structural profile is used to bias a search of the conformational space towards the target structure in a Monte Carlo scheme operating on a Calpha-chain of uniform, finite thickness. Structure information thus enters the folding dynamics via the effective connectivity, but the interaction is not restricted to pairs of amino acids that form native contacts, resulting in a free energy landscape which does not rely on the assumption of minimal frustration. Moreover, effective connectivity vectors can be predicted more readily from the amino acid sequence of proteins than the corresponding contact maps, thus suggesting that the stochastic protocol presented here could be effectively combined with other current methods for predicting native structures. PACS codes: 87.14.Ee.

No MeSH data available.