Enhanced crystal packing due to solvent reorganization through reductive methylation of lysine residues in oxidoreductase from Streptococcus pneumoniae.
Protein crystallization is in part driven by the changes in the entropy of the system, but opinions differ as to whether the solute (protein) or solvent (water) molecules make more of a contribution to the overall entropic change. Methylation of lysine residues in proteins has been used to enhance protein crystallization. We investigated using molecular dynamics simulations with explicit solvent molecules, the behavior of several native proteins and their methylated counterparts chosen from an earlier large-scale study. Methylated lysines are capable of making a variety of interactions including H-bonds with protein residues and solvent. We demonstrate that methylation on the lysine slightly increases its side chain conformational entropy by about 3.5 J mol(-1) K(-1). Analysis of the radial and spatial distributions of the water molecules around the methylated lysine surface in oxidoreductase from Streptococcus pneumoniae revealed a larger sphere of water molecules with low entropy, as compared with solvent associated with unmethylated lysine. If methylated lysine were to make interactions at the protein-protein interface, the low-entropy water molecules associated with methylated lysines would be released, resulting in a gain of entropy. We show that this gain more than compensates for the loss of protein entropy. Therefore, we propose that lysine methylation favors the formation of crystals through solvent entropic gain.
Fan
Yao
Y
Biosciences Division, Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL 60439, USA.
Joachimiak
Andrzej
A
D003460:Crystallization; D019277:Entropy; D006860:Hydrogen Bonding; D008239:Lysine / Q000737:chemistry*; D008745:Methylation; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D010088:Oxidoreductases / Q000737:chemistry*; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry*; D013296:Streptococcus pneumoniae / Q000201:enzymology*; D013816:Thermodynamics
D012997:Solvents; D010088:Oxidoreductases; D008239:Lysine