Algorithm for selection of optimized EPR distance restraints for de novo protein structure determination.

ABSTRACT: A hybrid protein structure determination approach combining sparse Electron Paramagnetic Resonance (EPR) distance restraints and Rosetta de novo protein folding has been previously demonstrated to yield high quality models (Alexander et al. (2008)). However, widespread application of this methodology to proteins of unknown structures is hindered by the lack of a general strategy to place spin label pairs in the primary sequence. In this work, we report the development of an algorithm that optimally selects spin labeling positions for the purpose of distance measurements by EPR. For the α-helical subdomain of T4 lysozyme (T4L), simulated restraints that maximize sequence separation between the two spin labels while simultaneously ensuring pairwise connectivity of secondary structure element

SUBMITTER: Kazmier K 

PROVIDER: S-EPMC3073550 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature