Article
Free energy calculations on binding and catalysis by alpha-lytic protease: the role of substrate size in the P1 pocket.
Proteins - 1 Jan 1991
Caldwell J W, Agard D A, Kollman P A
Abstract excerpt
We present free energy calculations using molecular dynamics on different substrates of alpha-lytic protease in the gas phase, in solution, while forming a noncovalent Michaelis complex with the enzyme, and in a tetrahedral structure representing a transition state/intermediate for acylation by the enzyme. Various P1 substrates were studied, with P1 = Gly, Ala, Val, and Leu. In qualitative agreement with...
Topics
- Amino Acid Sequence
- Catalysis
- Hydrogen Bonding
- Molecular Sequence Data
- Mutation
- Protein Binding
- Protein Conformation
- Serine Endopeptidases
- Stereoisomerism
- Substrate Specificity
- Thermodynamics