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Literature DB >> 21116528

Serine protease acylation proceeds with a subtle re-orientation of the histidine ring at the tetrahedral intermediate.

Abstract

The acylation mechanism of a prototypical serine protease trypsin and its complete free energy reaction profile have been determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella sampling.

Entities: Chemical Disease Gene Species

Mesh：

Substances：
Histidine
Trypsin

Year: 2010 PMID： 21116528 PMCID： PMC3213857 DOI： 10.1039/c0cc04112b

Source DB: PubMed Journal: Chem Commun (Camb) ISSN： 1359-7345 Impact factor: 6.222

36 in total

Review 1. How do serine proteases really work?

Authors: A Warshel; G Naray-Szabo; F Sussman; J K Hwang
Journal: Biochemistry Date: 1989-05-02 Impact factor: 3.162

Review 2. "Strong" hydrogen bonds in chemistry and biology.

Authors: C L Perrin; J B Nielson
Journal: Annu Rev Phys Chem Date: 1997 Impact factor: 12.703

3. Highly dissociative and concerted mechanism for the nicotinamide cleavage reaction in Sir2Tm enzyme suggested by ab initio QM/MM molecular dynamics simulations.

Authors: Po Hu; Shenglong Wang; Yingkai Zhang
Journal: J Am Chem Soc Date: 2008-12-10 Impact factor: 15.419

Review 4. Short strong hydrogen bonds: can they explain enzymic catalysis?

Authors: J P Guthrie
Journal: Chem Biol Date: 1996-03

5. Role of a buried acid group in the mechanism of action of chymotrypsin.

Authors: D M Blow; J J Birktoft; B S Hartley
Journal: Nature Date: 1969-01-25 Impact factor: 49.962

6. On low-barrier hydrogen bonds and enzyme catalysis.

Authors: A Warshel; A Papazyan; P A Kollman
Journal: Science Date: 1995-07-07 Impact factor: 47.728

7. Catalytic reaction mechanism of acetylcholinesterase determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations.

Authors: Yanzi Zhou; Shenglong Wang; Yingkai Zhang
Journal: J Phys Chem B Date: 2010-07-08 Impact factor: 2.991

8. Fractionation factors and activation energies for exchange of the low barrier hydrogen bonding proton in peptidyl trifluoromethyl ketone complexes of chymotrypsin.

Authors: J Lin; W M Westler; W W Cleland; J L Markley; P A Frey
Journal: Proc Natl Acad Sci U S A Date: 1998-12-08 Impact factor: 11.205

9. Active site cysteine is protonated in the PAD4 Michaelis complex: evidence from Born-Oppenheimer ab initio QM/MM molecular dynamics simulations.

Authors: Zhihong Ke; Yanzi Zhou; Po Hu; Shenglong Wang; Daiqian Xie; Yingkai Zhang
Journal: J Phys Chem B Date: 2009-09-24 Impact factor: 2.991

Review 10. Serine peptidases: classification, structure and function.

Authors: M J Page; E Di Cera
Journal: Cell Mol Life Sci Date: 2008-04 Impact factor: 9.261

11 in total

1. Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions.

Authors: Y Zhou; S Wang; Y Li; Y Zhang
Journal: Methods Enzymol Date: 2016-06-23 Impact factor: 1.600

2. Insights into the phosphoryl transfer mechanism of cyclin-dependent protein kinases from ab initio QM/MM free-energy studies.

Authors: Gregory K Smith; Zhihong Ke; Hua Guo; Alvan C Hengge
Journal: J Phys Chem B Date: 2011-11-03 Impact factor: 2.991

10. Kinetic Studies of the Effect of pH on the Trypsin-Catalyzed Hydrolysis of N-α-benzyloxycarbonyl-l-lysine-p-nitroanilide: Mechanism of Trypsin Catalysis.

Authors: J Paul G Malthouse
Journal: ACS Omega Date: 2020-03-03

Serine protease acylation proceeds with a subtle re-orientation of the histidine ring at the tetrahedral intermediate.

Review 1. How do serine proteases really work?

Review 2. "Strong" hydrogen bonds in chemistry and biology.

3. Highly dissociative and concerted mechanism for the nicotinamide cleavage reaction in Sir2Tm enzyme suggested by ab initio QM/MM molecular dynamics simulations.

Review 4. Short strong hydrogen bonds: can they explain enzymic catalysis?

5. Role of a buried acid group in the mechanism of action of chymotrypsin.

6. On low-barrier hydrogen bonds and enzyme catalysis.

7. Catalytic reaction mechanism of acetylcholinesterase determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations.

8. Fractionation factors and activation energies for exchange of the low barrier hydrogen bonding proton in peptidyl trifluoromethyl ketone complexes of chymotrypsin.

9. Active site cysteine is protonated in the PAD4 Michaelis complex: evidence from Born-Oppenheimer ab initio QM/MM molecular dynamics simulations.

Review 10. Serine peptidases: classification, structure and function.

1. Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions.

2. Insights into the phosphoryl transfer mechanism of cyclin-dependent protein kinases from ab initio QM/MM free-energy studies.

3. Sirtuin Deacetylation Mechanism and Catalytic Role of the Dynamic Cofactor Binding Loop.

4. Amide Rotation Hindrance Predicts Proteolytic Resistance of Cystine-Knot Peptides.

5. Aging mechanism of soman inhibited acetylcholinesterase.

6. Revelation of a catalytic calcium-binding site elucidates unusual metal dependence of a human apyrase.

7. How is acetylcholinesterase phosphonylated by soman? An ab initio QM/MM molecular dynamics study.

8. Mechanistic insights into a classic wonder drug--aspirin.

9. Quantum mechanical modeling: a tool for the understanding of enzyme reactions.

10. Kinetic Studies of the Effect of pH on the Trypsin-Catalyzed Hydrolysis of N-α-benzyloxycarbonyl-l-lysine-p-nitroanilide: Mechanism of Trypsin Catalysis.