2gjf
From Proteopedia
OCA (Talk | contribs)
(New page: 200px<br /><applet load="2gjf" size="350" color="white" frame="true" align="right" spinBox="true" caption="2gjf" /> '''NMR structure of the computationally designe...)
Next diff →
Revision as of 18:01, 29 January 2008
|
NMR structure of the computationally designed procarboxypeptidase-A (1AYE) domain
Overview
Recent efforts to design de novo or redesign the sequence and structure of, proteins using computational techniques have met with significant success., Most, if not all, of these computational methodologies attempt to model, atomic-level interactions, and hence high-resolution structural, characterization of the designed proteins is critical for evaluating the, atomic-level accuracy of the underlying design force-fields. We previously, used our computational protein design protocol RosettaDesign to completely, redesign the sequence of the activation domain of human, procarboxypeptidase A2. With 68% of the wild-type sequence changed, the, designed protein, AYEdesign, is over 10 kcal/mol more stable than the, wild-type protein. Here, we describe the high-resolution crystal structure, and solution NMR structure of AYEdesign, which show that the, experimentally determined backbone and side-chains conformations are, effectively superimposable with the computational model at atomic, resolution. To isolate the origins of the remarkable stabilization, we, have designed and characterized a new series of procarboxypeptidase, mutants that gain significant thermodynamic stability with a minimal, number of mutations; one mutant gains more than 5 kcal/mol of stability, over the wild-type protein with only four amino acid changes. We explore, the relationship between force-field smoothing and conformational sampling, by comparing the experimentally determined free energies of the overall, design and these focused subsets of mutations to those predicted using, modified force-fields, and both fixed and flexible backbone sampling, protocols.
About this Structure
2GJF is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
High-resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human Procarboxypeptidase by Computational Protein Design., Dantas G, Corrent C, Reichow SL, Havranek JJ, Eletr ZM, Isern NG, Kuhlman B, Varani G, Merritt EA, Baker D, J Mol Biol. 2007 Mar 2;366(4):1209-21. Epub 2006 Dec 2. PMID:17196978 [[Category: ]]
Page seeded by OCA on Tue Jan 29 20:01:07 2008
