Understanding binding affinity: A combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin

Talhout, R., Villa, A., Mark, A. E. and Engberts, J. B. F. N. (2003) Understanding binding affinity: A combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin. Journal of The American Chemical Society, 125 35: 10570-10579. doi:10.1021/ja034676g


Author Talhout, R.
Villa, A.
Mark, A. E.
Engberts, J. B. F. N.
Title Understanding binding affinity: A combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin
Journal name Journal of The American Chemical Society   Check publisher's open access policy
ISSN 0002-7863
Publication date 2003-01-01
Sub-type Article (original research)
DOI 10.1021/ja034676g
Volume 125
Issue 35
Start page 10570
End page 10579
Total pages 10
Place of publication Washington
Publisher Amer Chemical Soc
Language eng
Abstract The binding of a series of p-alkylbenzamidinium chloride inhibitors to the serine proteinase trypsin over a range of temperatures has been studied using isothermal titration (micro)calorimetry and molecular dynamics simulation techniques. The inhibitors have small structural variations at the para position of the benzamidinium ion. They show small differences in relative binding affinity but large compensating differences in enthalpy and entropy. Binding affinity decreases with increased branching at the first carbon but increases with increasing the length of a linear alkyl substituent, suggesting that steric hindrance and hydrophobic interactions play dominant roles in binding. Structural analysis showed that the backbone of the enzyme was unaffected by the change of the para substituent. In addition, binding does not correlate strongly with octanol/water partition data. To further characterize this system, the change in the heat capacity on binding, the change in solvent-accessible surface area on binding, the effect of inhibitor binding on the hydration of the active site, the pK(a) of His57, and interactions within the catalytic triad have been investigated. Although the changes in inhibitor structure are small, it is demonstrated that simple concepts such as steric hindrance, hydrophobicity, and buried surface area are insufficient to explain the binding data. Other factors, such as access to the binding site and the cost of dehydration of the active site, are of equal or greater importance.
Keyword Chemistry, Multidisciplinary
Enthalpy-entropy Compensation
Heat-capacity
Free-energy
Molecular Simulations
Factor Xa
Site
Proteins
Water
Thermodynamics
Energetics
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
School of Chemistry and Molecular Biosciences
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 61 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 62 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Thu, 20 Sep 2007, 04:11:20 EST