|
1
|
Xu Q, Guo H, Wlodawer A, Guo H. The importance of dynamics in substrate-assisted catalysis and specificity. J Am Chem Soc 2007; 128:5994-5. [PMID: 16669642 PMCID: PMC2530918 DOI: 10.1021/ja058831y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The QM/MM MD and free energy simulations show that the dynamics involving a His residue at the P1 site of the substrate may play an important role in substrate-assisted catalysis and specificity for a serine-carboxyl peptidase.
Collapse
Affiliation(s)
- Qin Xu
- Department of Biochemistry and Cellular and Molecular Biology and Center of Excellence for Structural Biology, University of Tennessee, Knoxville, TN 37996
| | - Haobo Guo
- Department of Biochemistry and Cellular and Molecular Biology and Center of Excellence for Structural Biology, University of Tennessee, Knoxville, TN 37996
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology and Center of Excellence for Structural Biology, University of Tennessee, Knoxville, TN 37996
| |
Collapse
|
|
2
|
Bravaya K, Bochenkova A, Grigorenko B, Topol I, Burt S, Nemukhin A. Molecular Modeling the Reaction Mechanism of Serine-Carboxyl Peptidases. J Chem Theory Comput 2006; 2:1168-75. [DOI: 10.1021/ct6000686] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ksenia Bravaya
- Department of Chemistry, M. V. Lomonosov Moscow State University, Moscow 119992, Russian Federation, Advanced Biomedical Computing Center, National Cancer Institute at Frederick, Frederick, Maryland 21702, and Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119997, Russian Federation
| | - Anastasia Bochenkova
- Department of Chemistry, M. V. Lomonosov Moscow State University, Moscow 119992, Russian Federation, Advanced Biomedical Computing Center, National Cancer Institute at Frederick, Frederick, Maryland 21702, and Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119997, Russian Federation
| | - Bella Grigorenko
- Department of Chemistry, M. V. Lomonosov Moscow State University, Moscow 119992, Russian Federation, Advanced Biomedical Computing Center, National Cancer Institute at Frederick, Frederick, Maryland 21702, and Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119997, Russian Federation
| | - Igor Topol
- Department of Chemistry, M. V. Lomonosov Moscow State University, Moscow 119992, Russian Federation, Advanced Biomedical Computing Center, National Cancer Institute at Frederick, Frederick, Maryland 21702, and Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119997, Russian Federation
| | - Stanley Burt
- Department of Chemistry, M. V. Lomonosov Moscow State University, Moscow 119992, Russian Federation, Advanced Biomedical Computing Center, National Cancer Institute at Frederick, Frederick, Maryland 21702, and Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119997, Russian Federation
| | - Alexander Nemukhin
- Department of Chemistry, M. V. Lomonosov Moscow State University, Moscow 119992, Russian Federation, Advanced Biomedical Computing Center, National Cancer Institute at Frederick, Frederick, Maryland 21702, and Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119997, Russian Federation
| |
Collapse
|
|
3
|
Guo H, Wlodawer A, Guo H. A General Acid−Base Mechanism for the Stabilization of a Tetrahedral Adduct in a Serine−Carboxyl Peptidase: A Computational Study. J Am Chem Soc 2005; 127:15662-3. [PMID: 16277482 DOI: 10.1021/ja0520565] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The QM/MM MD and free energy simulations show that serine-carboxyl peptidases (sedolisins) may stabilize the tetrahedral intermediates and tetrahedral adducts primarily through a general acid-base mechanism involving Asp (Asp164 for kumamolisin-As) rather than the oxyanion-hole interactions as in the cases of serine proteases.
Collapse
Affiliation(s)
- Haobo Guo
- Department of Biochemistry and Cellular and Molecular Biology and Center of Excellence for Structural Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | | | | |
Collapse
|