The entropic cost of protein-protein association: A case study on acetylcholinesterase binding to fasciculin-2

Biophysical Journal

Volumn 89, Issue 4, 2005, Pages

  Minh, David D L ^a   Bui, Jennifer M ^a   Chang, Chia En ^a   Jain, Tushar ^a   Swanson, Jessica M J ^a   McCammon, J Andrew ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYLCHOLINESTERASE; FASCICULIN; FASCICULIN 2; UNCLASSIFIED DRUG;

ANALYSIS; ARTICLE; ATOM; ATOMIC MOTION; CRYSTAL; ENTROPY; ENTROPY LOSS; ENZYME BINDING; EXTERNAL ENTROPY; HISTOGRAM; MOLECULAR DYNAMICS; MOTION; PROBABILITY; PROTEIN PROTEIN INTERACTION; QUASIHARMONIC ANALYSIS; ROTATION; ROTATIONAL ENTROPY; SIMULATION; TRANSLATIONAL ENTROPY;

EID: 25844507555     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.069336     Document Type: Article

References (11)

1. Gilson, M. K., J. A. Given, B. L. Bush, and J. A. McCammon. 1997. The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys. J. 72:1047-1069.
2. Finkelstein, A. V., and J. Janin. 1989. The price of lost freedom: entropy of bimolecular complex formation. Protein Eng. 3:1-3.
3. Carlsson, J., and J. Aqvist. 2005. Absolute and relative entropies from computer simulation with applications to ligand binding. J. Phys. Chem. B. 109:6448-6456.
4. Luo, H., and K. Sharp. 2002. On the calculation of absolute macromolecular binding free energies. Proc. Natl. Acad. Sci. USA. 99:10399-10404.
5. Swanson, J. M., R. H. Henchman, and J. A. McCammon. 2004. Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys. J. 86:67-74.
6. Tai, K., T. Shen, R. H. Henchman, Y. Bourne, P. Marchot, and J. A. McCammon. 2002. Mechanism of acetylcholinesterase inhibition by fasciculin: a 5-ns molecular dynamics simulation. J. Am. Chem. Soc. 124:6153-6161.
7. Bui, J. M., K. Tai, and J. A. McCammon. 2004. Acetylcholinesterase: enhanced fluctuations and alternative routes to the active site in the complex with fasciculin-2. J. Am. Chem. Soc. 126:7198-7205.
8. McQuarrie, D. A. 1975. Statistical Mechanics. Harper & Row, New York.
9. Karplus, M., and J. Kushick. 1981. Method for estimating the configurational entropy of macromolecules. Macromolecules. 14:325-332.
10. Chang, C. E., W. Chen, and M. K. Gilson. 2005. Evaluating the accuracy of the quasiharmonic approximation. J. Chem. Theory Comput. In press.
11. Dunitz, I. 1994. The entropic cost of bound water in crystals and biomolecules. Science. 264:670.