Ubiquitin carboxyl-terminal hydrolase L1 (UCH-L1) is a neuron-specific deubiquitinating enzyme. Single amino acid changes (S18Y and I93M) within UCH-L1 are associated with decreased and increased risk of Parkinson's disease (PD), respectively. However, the molecular mechanism of pathogenesis in UCH-L1-associated PD remains to be elucidated. In this study, we performed molecular dynamics simulations of UCH-L1 variants. The simulation results show that I93M UCH-L1 is less stable than S18Y UCH-L1. In particular, the H7 and H8 alpha-helices in I93M UCH-L1 are partially denatured. Information regarding the aberrant UCH-L1 structures provides new insight into UCH-L1-associated PD. (C) 2012 Elsevier B.V. All rights reserved.