Exploration of the relationship between topology and designability of conformations

dc.contributor.author Leelananda, Sumudu
dc.contributor.author Towfic, Fadi
dc.contributor.author Jernigan, Robert
dc.contributor.author Kloczkowski, Andrzej
dc.contributor.department Biochemistry, Biophysics and Molecular Biology, Roy J. Carver Department of
dc.contributor.department Computer Science
dc.contributor.department Biochemistry, Biophysics and Molecular Biology
dc.date 2018-02-19T01:02:18.000
dc.date.accessioned 2020-06-29T23:46:00Z
dc.date.available 2020-06-29T23:46:00Z
dc.date.copyright Sat Jan 01 00:00:00 UTC 2011
dc.date.issued 2011-01-01
dc.description.abstract <p>Protein structures are evolutionarily more conserved than sequences, and sequences with very low sequence identity frequently share the same fold. This leads to the concept of protein <em>designability</em>. Some folds are more designable and lots of sequences can assume that fold. Elucidating the relationship between protein sequence and the three-dimensional (3D) structure that the sequence folds into is an important problem in computational structural biology. Lattice models have been utilized in numerous studies to model protein folds and predict the designability of certain folds. In this study, all possible compact conformations within a set of two-dimensional and 3D lattice spaces are explored. Complementary interaction graphs are then generated for each conformation and are described using a set of graph features. The full HP sequence space for each lattice model is generated and contact energies are calculated by threading each sequence onto all the possible conformations. Unique conformation giving minimum energy is identified for each sequence and the number of sequences folding to each conformation (designability) is obtained. Machine learning algorithms are used to predict the designability of each conformation. We find that the highly designable structures can be distinguished from other non-designable conformations based on certain graphical geometric features of the interactions. This finding confirms the fact that the topology of a conformation is an important determinant of the extent of its designability and suggests that the interactions themselves are important for determining the designability.</p>
dc.description.comments <p>This article is published as Leelananda, Sumudu P., Fadi Towfic, Robert L. Jernigan, and Andrzej Kloczkowski. "Exploration of the relationship between topology and designability of conformations." The Journal of chemical physics 134, 235101 (2011). doi: <a href="https://doi.org/10.1063/1.3596947">10.1063/1.3596947</a>. Posted with permission.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/bbmb_ag_pubs/150/
dc.identifier.articleid 1158
dc.identifier.contextkey 10977877
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath bbmb_ag_pubs/150
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/10611
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/bbmb_ag_pubs/150/2011_Jernigan_ExplorationRelationship.pdf|||Fri Jan 14 20:34:19 UTC 2022
dc.source.uri 10.1063/1.3596947
dc.subject.disciplines Biochemistry
dc.subject.disciplines Bioinformatics
dc.subject.disciplines Biophysics
dc.subject.disciplines Molecular Biology
dc.subject.disciplines Structural Biology
dc.title Exploration of the relationship between topology and designability of conformations
dc.type article
dc.type.genre article
dspace.entity.type Publication
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