Guiding the Search for Native-like Protein Conformations with an Ab-initio Tree-based Exploration

Authors:
Amarda Shehu;Brian Olson
Affiliations:
Department of Computer Science and Department of Bioinformaticsand Computational Biology George Mason University, Fairfax, VA 22030, USA,;Department of Computer Science, George Mason University,Fairfax, VA 22030, USA
Venue:
International Journal of Robotics Research
Year:
2010

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Abstract

In this paper we propose a robotics-inspired method to enhance sampling of native-like conformations when employing only aminoacid sequence information for a protein at hand. Computing such conformations, essential to associating structural and functional information with gene sequences, is challenging due to the high-dimensionality and the rugged energy surface of the protein conformational space. The contribution of this paper is a novel two-layered method to enhance the sampling of geometrically distinct low-energy conformations at a coarse-grained level of detail. The method grows a tree in conformational space reconciling two goals: (i) guiding the tree towards lower energies; and (ii) not oversampling geometrically similar conformations. Discretizations of the energy surface and a low-dimensional projection space are employed to select more often for expansion low-energy conformations in under-explored regions of the conformational space. The tree is expanded with low-energy conformations through a Metropolis Monte Carlo framework that uses a move set of physical fragment configurations. Testing on sequences of eight small-to-medium structurally diverse proteins shows that the method rapidly samples native-like conformations in a few hours on a single CPU. Analysis shows that computed conformations are good candidates for further detailed energetic refinements by larger studies in protein engineering and design.