Journal
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
Volume 28, Issue 2, Pages 143-157Publisher
ADENINE PRESS
DOI: 10.1080/073911010010524953
Keywords
Molecular dynamics; Proteinase K; Essential dynamics; Dynamic pockets; Induced fit; Large concerted motion
Categories
Funding
- National Natural Science Foundation of China [30860011]
- Yunnan University [KL070002]
- [2006C008M]
- [2007C163M]
- [07Z10756]
- [2007PY-22]
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Because of the significant industrial, agricultural and Notechnological importance of serine protease proteinase K, it has been extensively investigated using experimental approaches such as X-ray crystallography, site-directed mutagenesis and kinetic measurement. However, detailed aspects of enzymatic mechanism such as substrate binding, release and relevant regulation remain unstudied. Molecular dynamics (MD) simulations of the proteinase K alone and in complex with the peptide substrate AAPA were performed to investigate the effect of substrate binding on the dynamics/molecular motions of proteinase K. The results indicate that during simulations the substrate-complexed proteinase K adopt a more compact and stable conformation than the substrate-free form. Further essential dynamics (El)) analysis reveals that the major internal motions are confined within a subspace of very small dimension. Upon substrate binding, the overall flexibility of the protease is reduced; and the noticeable displacements are observed not only in substrate-binding regions hut also in regions opposite the substrate-binding groove/pockets. The dynamic pockets caused by the large concerted motions are proposed to be linked to the substrate recognition, binding, orientation and product release; and the significant displacements in regions opposite the binding groove/pockets are considered to play a role in modulating the dynamics of enzyme-substrate interaction. Our simulation results complement the biochemical and structural studies, highlighting the dynamic mechanism of the functional properties of proteinase K.
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