Van der Waals locks: Loop-n-lock structure of globular proteins

In a globular protein the polypeptide chain returns to itself many times, m aking numerous chain-to-chain contacts. The stability of these contacts is maintained primarily by van der Waals interactions. In this work we isolate d and analysed van der Waals contacts that stabilise spatial structures of nine major folds. We suggest a specific way to identify the tightest contac ts of prime importance for the stability of a given crystallized protein an d introduce the notion of the van der Waals lock. The loops closed by the v an der Waals interactions provide a basically novel view of protein globule organization: the loop-n-lock structure. This opens a new perspective in u nderstanding protein folding as well: the consecutive looping of the polype ptide chain and the locking of the loop ends by tight van der Waals interac tions. (C) 2001 Academic Press.