Abstract
Lactate Dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of NADH and NAD+. Due to the widespread presence in a variety of organisms, LDH has been served as a general model for studying the catalytic mechanism of enzymes. Extensive IR spectroscopic studies by Callender et al. have revealed complex conformational sub-states for different substrate binding to LDH in mesophilic and thermophilic organisms. To facilitate the elucidation of the underling mechanism of LDH enzyme reaction, molecular dynamics simulation approaches were applied to study the conformational dynamics of mesophilic LDH in complex with substrate or its mimics. The functionally important motions were characterized by conformational sampling. To determine the relationship between protein stability, flexibility, and catalytic activity, thermophilic LDH enzyme will be further investigated. The energy landscape within the Michaelis complex will be explored. The computational study in connection with the experimental findings will shed new light on the mechanism of enzyme dynamics and function.
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