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Functional Domain Motions and Processivity in Bacterial Hyaluronate Lyase

A Molecular Dynamics Study

by Harshad Joshi

e-Book PDF
Institution: Max Planck Institute for Biophysical Chemistry
Advisor(s): Prof. Dr. Bert L. de Groot
Degree: Ph.D. in Computational Biophysics
Year: 2007
Volume: 175 pages
ISBN-10: 1599423200
ISBN-13: 9781599423203


Processive enzymes are a special class of enzymes which presumably remain attached to their polymeric substrates between multiple rounds of catalysis. Due to this property, the substrate slides along the enzyme and reduces the time for the random diffusional enzyme-substrate encounters thereby increasing the efficiency of these enzymes manifold. Although structural information from many processive enzymes is available, the atomistic details of particularly the substrate sliding process, which is an inherently dynamic process, remain largely unknown. We take first steps to understand the sliding process by investigating a prototypic processive enzyme: Streptococcus Pneumoniae Hyaluronate lyase, a bacterial enzyme that degrades the polysaccharide substrate hyaluronan. Here we have investigated the flexibility of the enzyme as observed from essential dynamics simulations and its relation to the enzyme-substrate interactions by employing several free and enforced molecular dynamics simulations (on sub-microsecond timescale). This way we have identified a coupling between domain motions of the enzyme and the processivity or the sliding phase of the substrate. In the putative mechanism for the substrate translocation phase we observed an energy barrier along the processive direction and it is speculated that this may arise because of the reorientation of the sugar inside the cleft of the protein. This view was supported from the Force probe molecular dynamics simulations and umbrella sampling simulations that were employed to obtain a preliminary free energy profile underlying the mechanism. The observed free energy barrier is low enough to be easily crossed by thermal fluctuations, renderring essential slow collective domain rearrangements as likely rate-limiting factor for the processive cycle. The collective conformational motions of the protein along with particular interactions of individual amino acids may be involved in this translocation phase. Experimental validation along with further computational studies will be useful to understand this complex mechanism.

About The Author

Harshad Joshi received his Ph.D. in computational biophysics from the Max Planck Institute for Biophysical Chemistry, Germany, in 2007. His thesis on Functional Domain Motions and Processivity in Bacterial Hyaluronate Lyase, and a Postdoc in forced unfolding of proteins at University of Cincinnati provide him experience in the functional motions and dynamics of biomolecules. He has extensive experience with popular biomolecular simulation packages, and modern hardware architectures used in the simulations such as GPUs. His interest lies in understanding biomolecular interactions with the aid of various computational techniques.