ISSN:
0887-3585
Keywords:
free energy perturbation
;
molecular dynamics simulation
;
molecular modeling
;
substrate binding
;
site-specific point mutations
;
ribonuclease T1
;
2-aminopurine
;
Chemistry
;
Biochemistry and Biotechnology
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Medicine
Notes:
We have theoretically and experimentally studied the binding of two different ligands to wild-type ribonuclease T1 (RNT1) and to a mutant of RNT1 with Glu-46 replaced by Gln. The binding of the natural substrate 3′-GMP has been compared with the binding of a fluorescent probe, 2-aminopurine 3′-monophosphate (2AP), and relative free energies of binding of these ligands to the mutant and the wild-type (wt) enzyme have been calculated by free energy perturbation methods. The free energy perturbations predict that the mutant RNT1-Gln-46 binds 2AP better than 3′GMP, in agreement with experiments on dinucleotides. Four free energy perturbations, forming a closed loop, have been performed to allow the detection of systematic errors in the simulation procedure. Because of the larger number of atoms involved, it was necessary to use a much longer simulation time for the change in the protein, i.e., the perturbation from Glu to Gln, than in the perturbation from 3′-GMP to 2AP. Finally the structure of the binding site is analyzed for understanding differences in catalytic speed and binding strength. © 1993 Wiley-Liss, Inc.
Additional Material:
6 Ill.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1002/prot.340170206
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