Berlin 2008 – scientific programme
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BP: Fachverband Biologische Physik
BP 26: Posters II
BP 26.3: Poster
Thursday, February 28, 2008, 17:00–19:30, Poster A
Effective Connectivity profile: A Structural Representation that Evidences the Relationship between Protein Structures and Sequences — Ugo Bastolla1, Angel R. Ortiz1, Markus Porto2, and •Florian Teichert2 — 1Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6-8, 64289 Darmstadt, Germany — 2Centro de Biología Molecular “Severo Ochoa”, (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain
We recently defined the vectorial Effective Connectivity profile (EC) to describe protein structures [1] which is highly correlated with the average hydrophobicity profile (HP) of simulated proteins with stable native structure. We showed analytically that the optimally stable HP belongs to a family of profiles that we call the Generalized Effective Connectivity family (GEC), of which the EC is a distinctive member, as well as the previously defined revised PE profile [2]. This mathematical relationship unveils the close relationship between different vectorial representations derived from structural and from sequence data, as we could demonstrate. Finally, we show that structurally similar proteins have similar EC profiles, a property that we exploit to perform protein structure alignments [3].
[1] U. Bastolla, A.R. Ortíz, M. Porto, and F. Teichert, (submitted).
[2] F. Teichert and M. Porto, Eur. Phys. J. B 54, 131-136 (2006).
[3] F. Teichert, U. Bastolla, and M. Porto, BMC Bioinformatics 8, 425 (2007).