Φ-value analysis of a linear, sequential reaction mechanism: Theory and application to ion channel gating

Biophysical Journal

Volumn 89, Issue 6, 2005, Pages 3680-3685

  Zhou, Yu ^a   Pearson, John E ^b   Auerbach, Anthony ^a  

^a UNIVERSITY AT BUFFALO   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHOLINERGIC RECEPTOR; LIGAND;

ARTICLE; CALCULATION; CHANNEL GATING; ENERGY; MATHEMATICAL ANALYSIS; PREDICTION; PROBABILITY; RATE EQUILIBRIUM FREE ENERGY RELATIONSHIP; REACTION ANALYSIS; SIMULATION;

EID: 27744499937     PISSN: 00063495     EISSN: 00063495     Source Type: Journal    
DOI: 10.1529/biophysj.105.067215     Document Type: Article

References (19)

1. Leffler, J. E., and E. Grunwald. 1963. Rates and Equilibria of Organic Reactions. Wiley, New York.
2. Fersht, A. R., R. J. Leatherbarrow, and T. N. C. Wells. 1986. Quantitative analysis of structure-activity relationships in engineered proteins by linear free-energy relationships. Nature. 322:284-286.
3. Jencks, W. P. 1985. A primer for the Bema Hapothle. An empirical approach to the characterization of changing transition state structures. Chem. Rev. 85:511-527.
4. Unwin, N. 2005. Refined structure of the nicotinic acetylcholine receptor at 4 Å resolution. J. Mol. Biol. 346:967-989.
5. Grosman, C., and A. Auerbach. 2000. Asymmetric and independent contribution of the second transmembrane segment 12′ residues to diliganded gating of acetylcholine receptor channels: a single-channel study with choline as the agonist. J. Gen. Physiol. 115:637-651.
6. Maconochie, D. J., G. H. Fletcher, and J. H. Steinbach. 1995. The conductance of the muscle nicotinic receptor channel changes rapidly upon gating. Biophys. J. 68:483-490.
7. Auerbach, A. 2005. Gating of acetylcholine receptor channels: Brownian motion across a broad transition state. Proc. Natl. Acad. Sci. USA. 102:1408-1412.
8. Chakrapani, S., T. D. Bailey, and A. Auerbach. 2004. Gating dynamics of the acetylcholine receptor extracellular domain. J. Gen. Physiol. 123:341-356.
9. Grosman, C., M. Zhou, and A. Auerbach. 2000. Mapping the conformational wave of acetylcholine receptor channel gating. Nature. 403:773-776.
10. Chakrapani, S., and A. Auerbach. 2005. A speed limit for conformational change of an allosteric membrane protein. Proc. Natl. Acad. Sci. USA. 102:87-92.
11. Cleland, W. W. 1975. Partition analysis and the concept of net rate constants as tools in enzyme kinetics. Biochemistry. 14:3220-3224.
12. Ray, W. J., Jr. 1983. Rate-limiting step: a quantitative definition. Application to steady-state enzymic reactions. Biochemistry. 22:4625-4637.
13. Colquhoun, D., and A. G. Hawkes. 1995. Single-Channel Recording. B. Sakman and E. Neher, editors. Plenum Press, New York. 397-482.
14. Hanggi, P., P. Talkner, and M. Borkovec. 1990. Reaction-rate theory: fifty years after Kramers. Rev. Mod. Phys. 62:251-341.
15. Redner, S. 2001. Guide to First-Passage Processes. Cambridge University Press, Cambridge, UK.
16. Chakrapani, S., T. D. Bailey, and A. Auerbach. 2003. The role of loop 5 in acetylcholine receptor channel gating. J. Gen. Physiol. 122:521-539.
17. Grosman, C. 2003. Free-energy landscapes of ion-channel gating are malleable: changes in the number of bound ligands are accompanied by changes in the location of the transition state in acetylcholine receptor channels. Biochemistry. 42:14977-14987.
18. Reference deleted in proof.
19. Mitra, A., T. D. Bailey, and A. L. Auerbach. 2004. Structural dynamics of the M4 transmembrane segment during acetylcholine receptor gating. Structure. 12:1909-1918.