Local densities orthogonal to beta-sheet amide planes: patterns of packing in globular proteins.
We have investigated the efficiency of packing by calculating intramolecular packing density above and below peptide planes of internal beta-pleated sheet residues in five globular proteins. The orientation of interest was chosen to allow study of regions that are approximately perpendicular to the faces of beta-pleated sheets. In these locations, nonbonded van der Waals packing interactions predominate over hydrogen bonding and solvent interactions. We observed considerable variability in packing densities within these regions, confirming that the interior packing of a protein does not result in uniform occupation of the available space. Patterns of fluctuation in packing density suggest that the regular backbone-to-backbone network of hydrogen bonds is not likely to be interrupted to maximize van der Waals interactions. However, high-density packing tends to occur toward the ends of beta-structure strands where hydrogen bonds are more likely to involve nonpolar side-chain groups or solvent molecules. These features result in internal protein folding with a central low-density core surrounded by a higher-density subsurface shell, consistent with our previous calculations regarding overall protein packing density.
Beardsley
D S
DS
Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06510, USA.
Kauzmann
W J
WJ
D000577:Amides; D002268:Carboxypeptidases / Q000737:chemistry; D043422:Carboxypeptidases A; D002918:Chymotrypsin / Q000737:chemistry; D004798:Enzymes / Q000737:chemistry*; D006860:Hydrogen Bonding; D008961:Models, Structural; D009113:Muramidase / Q000737:chemistry; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012260:Ribonucleases / Q000737:chemistry; D012984:Software; D013381:Subtilisins / Q000737:chemistry
D000577:Amides; D004798:Enzymes; D012260:Ribonucleases; D009113:Muramidase; D002268:Carboxypeptidases; D043422:Carboxypeptidases A; D013381:Subtilisins; D002918:Chymotrypsin