Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Site Tools

  • AAAS
  • Subscribe
  • Feedback

Site Search

Search Advanced

Science 12 June 1987:
Vol. 236. no. 4807, pp. 1460 - 1463
DOI: 10.1126/science.3589666
Prev | Table of Contents | Next

Articles

Science, Vol 236, Issue 4807, 1460-1463
Copyright © 1987 by American Association for the Advancement of Science

articles

Computer simulations of the diffusion of a substrate to an active site of an enzyme

K Sharp, R Fine, and B Honig

Computer simulations of the diffusion of a substrate to an enzyme active site were performed. They included the detailed shape of the protein and an accurate description of its electrostatic potential. Application of the method to the diffusion of the superoxide anion to the protein superoxide dismutase revealed that the electric field of the enzyme enhances the association rate of the anion by a factor of 30 or more. Calculated changes in the association rate as a function of ionic strength and amino acid modification paralleled the observed behavior. Design principles of superoxide dismutase are considered with respect to insights provided by the simulations. A possible means of enhancing the enzyme turnover rate through site-directed mutagenesis is proposed.


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Dissection of the high rate constant for the binding of a ribotoxin to the ribosome.
S. Qin and H.-X. Zhou (2009)
PNAS 106, 6974-6979
   Abstract »    Full Text »    PDF »
1,3-Propanediol Dehydrogenase from Klebsiella pneumoniae: Decameric Quaternary Structure and Possible Subunit Cooperativity.
D. Marcal, A. T. Rego, M. A. Carrondo, and F. J. Enguita (2009)
J. Bacteriol. 191, 1143-1151
   Abstract »    Full Text »    PDF »
Conduction through the Inward Rectifier Potassium Channel, Kir2.1, Is Increased by Negatively Charged Extracellular Residues.
N. D'Avanzo, H. C. Cho, I. Tolokh, R. Pekhletski, I. Tolokh, C. Gray, S. Goldman, and P. H. Backx (2005)
J. Gen. Physiol. 125, 493-503
   Abstract »    Full Text »    PDF »
Convergent evolution sheds light on the anti-beta -elimination mechanism common to family 1 and 10 polysaccharide lyases.
S. J. Charnock, I. E. Brown, J. P. Turkenburg, G. W. Black, and G. J. Davies (2002)
PNAS 99, 12067-12072
   Abstract »    Full Text »    PDF »
Improving macromolecular electrostatics calculations.
J. E. Nielsen, K. V. Andersen, B. Honig, R. W. W. Hooft, G. Klebe, G. Vriend, and R. C. Wade (1999)
Protein Eng. Des. Sel. 12, 657-662
   Abstract »    Full Text »    PDF »
A structural snapshot of an intermediate on the streptavidin-biotin dissociation pathway.
S. Freitag, V. Chu, J. E. Penzotti, L. A. Klumb, R. To, D. Hyre, I. Le Trong, T. P. Lybrand, R. E. Stenkamp, and P. S. Stayton (1999)
PNAS 96, 8384-8389
   Abstract »    Full Text »    PDF »
Design of fast enzymes by optimizing interaction potential in active site.
H.-X. Zhou, K.-Y. Wong, and M. Vijayakumar (1997)
PNAS 94, 12372-12377
   Abstract »    Full Text »    PDF »
Classical electrostatics in biology and chemistry.
B Honig and A Nicholls (1995)
Science 268, 1144-1149
   Abstract »    PDF »
Mutant potassium channels with altered binding of charybdotoxin, a pore-blocking peptide inhibitor.
R MacKinnon and C Miller (1989)
Science 245, 1382-1385
   Abstract »    PDF »
Brownian dynamics of cytochrome c and cytochrome c peroxidase association.
S. Northrup, J. Boles, and J. Reynolds (1988)
Science 241, 67-70
   Abstract »    PDF »
Computer-aided molecular design.
J. McCammon (1987)
Science 238, 486-491
   Abstract »    PDF »
Structural Plasticity of an Invariant Hydrophobic Triad in the Switch Regions of Rab GTPases Is a Determinant of Effector Recognition.
E. Merithew, S. Hatherly, J. J. Dumas, D. C. Lawe, R. Heller-Harrison, and D. G. Lambright (2001)
J. Biol. Chem. 276, 13982-13988
   Abstract »    Full Text »    PDF »


To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)