Computational Simulation of the Docking of Prochlorothrix Hollandica Plastocyanin to Potosystem I: Modeling the Electron Transfer Complex

Overview

Journal Biophys J

Publisher Cell Press

Specialty Biophysics

Date 2002 May 23

PMID 12023253

Citations 2

Authors

Eugene Myshkin

Neocles B Leontis

George S Bullerjahn

Affiliations

Soon will be listed here.

Abstract

We have used several docking algorithms (GRAMM, FTDOCK, DOT, AUTODOCK) to examine protein-protein interactions between plastocyanin (Pc)/photosystem I (PSI) in the electron transfer reaction. Because of the large size and complexity of this system, it is faster and easier to use computer simulations than conduct x-ray crystallography or nuclear magnetic resonance experiments. The main criterion for complex selection was the distance between the copper ion of Pc and the P700 chlorophyll special pair. Additionally, the unique tyrosine residue (Tyr(12)) of the hydrophobic docking surface of Prochlorothrix hollandica Pc yields a specific interaction with the lumenal surface of PSI, thus providing the second constraint for the complex. The structure that corresponded best to our criteria was obtained by the GRAMM algorithm. In this structure, the solvent-exposed histidine that coordinates copper in Pc is at the van der Waals distance from the pair of stacked tryptophans that separate the chlorophylls from the solvent, yielding the shortest possible metal-to-metal distance. The unique tyrosine on the surface of the Prochlorothrix Pc hydrophobic patch also participates in a hydrogen bond with the conserved Asn(633) of the PSI PsaB polypeptide (numbering from the Synechococcus elongatus crystal structure). Free energy calculations for complex formation with wild-type Pc, as well as the hydrophobic patch Tyr(12)Gly and Pro(14)Leu Pc mutants, were carried out using a molecular mechanics Poisson-Boltzman, surface area approach (MM/PBSA). The results are in reasonable agreement with our experimental studies, suggesting that the obtained structure can serve as an adequate model for P. hollandica Pc-PSI complex that can be extended for the study of other cyanobacterial Pc/PSI reaction pairs.

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References

Navarro J, Myshkin E, De la Rosa M, Bullerjahn G, Hervas M . The unique proline of the Prochlorothrix hollandica plastocyanin hydrophobic patch impairs electron transfer to photosystem I. J Biol Chem. 2001; 276(40):37501-5. DOI: 10.1074/jbc.M105367200. View

Wang J, Morin P, Wang W, Kollman P . Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. J Am Chem Soc. 2001; 123(22):5221-30. DOI: 10.1021/ja003834q. View

De Rienzo F, Gabdoulline R, Menziani M, De Benedetti P, Wade R . Electrostatic analysis and Brownian dynamics simulation of the association of plastocyanin and cytochrome f. Biophys J. 2001; 81(6):3090-104. PMC: 1301771. DOI: 10.1016/S0006-3495(01)75947-4. View

Sommer F, Drepper F, Hippler M . The luminal helix l of PsaB is essential for recognition of plastocyanin or cytochrome c6 and fast electron transfer to photosystem I in Chlamydomonas reinhardtii. J Biol Chem. 2001; 277(8):6573-81. DOI: 10.1074/jbc.M110633200. View

Northrup S, Boles J, Reynolds J . Brownian dynamics of cytochrome c and cytochrome c peroxidase association. Science. 1988; 241(4861):67-70. DOI: 10.1126/science.2838904. View

Gilson M, Honig B . Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins. 1988; 4(1):7-18. DOI: 10.1002/prot.340040104. View

Goodsell D, Olson A . Automated docking of substrates to proteins by simulated annealing. Proteins. 1990; 8(3):195-202. DOI: 10.1002/prot.340080302. View

Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem A, Aflalo C, Vakser I . Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci U S A. 1992; 89(6):2195-9. PMC: 48623. DOI: 10.1073/pnas.89.6.2195. View

Zhou H . Brownian dynamics study of the influences of electrostatic interaction and diffusion on protein-protein association kinetics. Biophys J. 1993; 64(6):1711-26. PMC: 1262506. DOI: 10.1016/S0006-3495(93)81543-1. View

10.

Haehnel W, Jansen T, Gause K, Klosgen R, Stahl B, Michl D . Electron transfer from plastocyanin to photosystem I. EMBO J. 1994; 13(5):1028-38. PMC: 394910. DOI: 10.1002/j.1460-2075.1994.tb06351.x. View

11.

Koehl P, Delarue M . Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J Mol Biol. 1994; 239(2):249-75. DOI: 10.1006/jmbi.1994.1366. View

12.

. Proceedings of the 8th European Bioenergetics Conference. Valencia, Spain, 12-17 September 1994. Biochim Biophys Acta. 1994; 1187(2):99-276. View

13.

Thompson J, Higgins D, Gibson T . CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994; 22(22):4673-80. PMC: 308517. DOI: 10.1093/nar/22.22.4673. View

14.

Vakser I, Aflalo C . Hydrophobic docking: a proposed enhancement to molecular recognition techniques. Proteins. 1994; 20(4):320-9. DOI: 10.1002/prot.340200405. View

15.

Jones S, Thornton J . Protein-protein interactions: a review of protein dimer structures. Prog Biophys Mol Biol. 1995; 63(1):31-65. DOI: 10.1016/0079-6107(94)00008-w. View

16.

Honig B, Nicholls A . Classical electrostatics in biology and chemistry. Science. 1995; 268(5214):1144-9. DOI: 10.1126/science.7761829. View

17.

Hervas M, Navarro J, Diaz A, Bottin H, De la Rosa M . Laser-flash kinetic analysis of the fast electron transfer from plastocyanin and cytochrome c6 to photosystem I. Experimental evidence on the evolution of the reaction mechanism. Biochemistry. 1995; 34(36):11321-6. DOI: 10.1021/bi00036a004. View

18.

Vakser I . Protein docking for low-resolution structures. Protein Eng. 1995; 8(4):371-7. DOI: 10.1093/protein/8.4.371. View

19.

Jones S, Thornton J . Principles of protein-protein interactions. Proc Natl Acad Sci U S A. 1996; 93(1):13-20. PMC: 40170. DOI: 10.1073/pnas.93.1.13. View

20.

Vakser I . Long-distance potentials: an approach to the multiple-minima problem in ligand-receptor interaction. Protein Eng. 1996; 9(1):37-41. DOI: 10.1093/protein/9.1.37. View