Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution
- A. Radzicka, R. Wolfenden
- Chemistry
- 8 March 1988
To obtain an indication of the tendencies of amino acids to leave water and enter a truly nonpolar condensed phase, distribution coefficients between dilute solution in water and dilute solution in…
The depth of chemical time and the power of enzymes as catalysts.
- R. Wolfenden, M. Snider
- Chemistry, BiologyAccounts of Chemical Research
- 10 October 2001
Thermodynamic comparisons between spontaneous and enzyme-catalyzed reactions, coupled with structural information, suggest that in addition to electrostatic and H-bonding interactions, the liberation of water molecules from an enzyme's active site into bulk solvent sometimes plays a prominent role in determining the relative binding affinities of the altered substrate in the ground state and transition state.
The ribosome as an entropy trap.
- Annette Sievers, M. Beringer, M. Rodnina, R. Wolfenden
- Chemistry, BiologyProceedings of the National Academy of Sciences…
- 25 May 2004
The results are consistent with the view that the ribosome enhances the rate of peptide bond formation mainly by positioning the substrates and/or water exclusion within the active site, rather than by conventional chemical catalysis.
A proficient enzyme.
- A. Radzicka, R. Wolfenden
- ChemistryScience
- 6 January 1995
Values of the known range of spontaneous rate constants for reactions that are also susceptible to catalysis by enzymes are extended to more than 14 orders of magnitude, in contrast to previous work.
Affinities of amino acid side chains for solvent water.
- R. Wolfenden, L. Andersson, P. Cullis, C. C. Southgate
- ChemistryBiochemistry
- 17 February 1981
Equilibria of distribution of amino acid side chains, between their dilute aqueous solutions and the vapor phase at 25 degrees C, have been determined by dynamic vapor pressure measurements, and hydration potentials are more closely correlated with the relative tendencies of the various amino acids to appear at the surface of globular proteins than had been evident from earlier distribution studies on the free amino acids.
Cytidine deaminase. The 2.3 A crystal structure of an enzyme: transition-state analog complex.
- L. Betts, S. Xiang, S. Short, R. Wolfenden, C. Carter
- Chemistry, BiologyJournal of Molecular Biology
- 13 January 1994
The differences in zinc ligands, ligand-binding stereochemistry, and tertiary structures of CDA and ADA strongly suggest that the common features of transition state stabilization arose by convergent evolution.
Rates of Uncatalyzed Peptide Bond Hydrolysis in Neutral Solution and the Transition State Affinities of Proteases
- A. Radzicka, R. Wolfenden
- Biology, Chemistry
- 3 July 1996
To assess the relative proficiencies of enzymes that catalyze the hydrolysis of internal and C-terminal peptide bonds, the rates of the corresponding nonenzymatic reactions were examined at elevated…
Experimental Measures of Amino Acid Hydrophobicity and the Topology of Transmembrane and Globular Proteins
- R. Wolfenden
- BiologyThe Journal of General Physiology
- 1 May 2007
The noncovalent binding interactions of biological molecules involve the stripping away of solvent water from regions of contact between the binding partners. Accordingly, the net strength of their…
Anatomy of a proficient enzyme: the structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog.
- B. Miller, A. Hassell, R. Wolfenden, M. Milburn, S. Short
- Chemistry, BiologyProceedings of the National Academy of Sciences…
- 29 February 2000
Interactions between the enzyme and the phosphoribosyl group anchor the pyrimidine within the active site, helping to explain the phosphorus group's remarkably large contribution to catalysis despite its distance from the site of decarboxylation.
Water, protein folding, and the genetic code.
- R. Wolfenden, P. Cullis, C. C. Southgate
- BiologyScience
- 2 November 1979
The absolute affinities of amino acid side chains for solvent water closely match their relative distributions between the surface and the interior of native proteins and are associated with a…
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