BIOPHYSICAL THEORY AND MODELING |
Molecular dynamics simulation of WSK-3, a computationally-designed, water-soluble variant of the integral membrane protein KcsA
Jonathan Bronson 1, One-Sun Lee 1 and Jeffery G Saven 1*
1 University of Pennsylvania
* To whom correspondence should be addressed. E-mail: saven{at}sas.upenn.edu.
Submitted on June 17, 2005
Revised on July 20, 2005
Accepted on 21 October 2005
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Abstract |
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Poor solubility and low expression levels often make membrane proteins difficult to study. An alternative to the use of detergents to solubilize these aggregation-prone proteins is the partial redesign of the sequence so as to confer water solubility. Recently, computationally assisted membrane protein solubilization (CAMPS) has been reported, where exposed hydrophobic residues on a protein's surface are computationally redesigned. Herein, the structure and fluctuations of a designed, water-soluble variant of KcsA (WSK-3), were studied using molecular dynamics simulations. The root mean square deviation of the protein from its starting structure, where the backbone coordinates are those of KcsA, was 1.8 Å. The structure of salt bridges involved in structural specificity and solubility were examined. The preferred configuration of ions and water in the selectivity filter of WSK-3 was consistent with the reported preferences for KcsA. The structure of the selectivity filter is maintained, which is consistent with WSK-3 having an affinity for agitoxin2 comparable to that of wild-type KcsA. In contrast to KcsA, the central cavity's side chains were observed to reorient, allowing water diffusion through the side of the cavity wall. These simulations provide an atomistic analysis of the CAMPS strategy and its implications for further investigations of membrane proteins.
Key Words:
KcsA, computational design, membrane protein, molecular simulation, protein design, solubilization
