Publications of M.R.Gunner and group

Calculation & Experiment

Computation (Continuum electrostatic and MCCE analysis of proteins)

• Song, Y., Michonova-Alexova, E., and Gunner, M. R. (2006) Calculated proton uptake on anaerobic reduction of cytochrome c oxidase: Is the reaction electroneutral?, Biochemistry 45, 7959-7975.pdf
  
  
• Song, Y., Mao, J., and Gunner, M. R. (2006) Electrostatic environment of hemes in proteins: pKas of hydroxyl ligands, Biochemistry 45, 7949-7958.pdf
  
  
• Kim, J., Mao, J., Gunner, M.R. (2005) Are acidic and basic groups in buried proteins predicted to be ionized? J.Mol. Biol. 348: 1283-1298. pdf
  
  
• Zhu, Z., Gunner, M.R. (2005) Energetics of Quinone-Dependent Electron and Proton Transfers in Rhodobacter sphaeroides Photosynthetic Reaction Centers. Biochemistry 44: 82-96. pdf
  
  
• Gunner, M.R., Zhu, Z. (2004) Protons forge new paths. Structure 12: 518-519.
  
  
• Hauser, K., Mao, J. Gunner, M.R. (2004) pH dependence of heme electrochemistry in cytochromes investigated by multiconformation continuum electrostatic calculations. Biopolymers. 2004 74:51-4
  
  
• Mao J., Hauser K., Gunner M.R. (2003) Multi-conformation continuum electrostatic analysis of heme electrochemistry in cytochromes with different structures. Biochemistry 42: 829-40. pdf
  
  
• Song Y., Gunner (M.R. 2003) Calculation of Proton Transfers in Bacteriorhodopsin bR and M Intermediates. Biochemistry 42: 9875-88.pdf
  
  
• Georgescu R.E., Alexov E.G., Gunner M.R.(2002). Combining conformational flexibility and continuum electrostatics for calculating pKa's in proteins. Biophys J. 83, 1731-1748.pdf
  
  
• Alexov, E., Miksovska, J., Baciou, L. Schiffer, M., Hanson, D. K., Sebban, P., and Gunner, M. R.(2000) Modeling the effects of mutations within the QB pocket in reaction center proteins. Biochemistry; 39(20); 5940-5952.MEDLINE. pdf
  
  
• Gunner, M. R., Saleh, M., Cross, E., ud-Doula, A., and Wise, M.. (2000) Backbone dipoles generate positive potentials in all proteins. Origins and implications of the effect. Biophys. J ;78(3):1126-1144 MEDLINE pdf
  
  
• Gunner, M.R. and Alexov, E.. (2000) A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins. Biochim and Biophys. Acta. 1458, 63-87. MEDLINE pdf
  
  
• Alexov, E. and Gunner, M.R. (1999) Calculating protein and proton motions coupled to electron transfer: The electron transfer from QA- to QB in photosynthetic reaction centers from Rb. sphaeroides. Biochemistry. 38, 8253-8270 MEDLINE .pdf
  
  
• Gunner, M. R., Alexov, E., Torres, E. and Lipovaca, S. (1997). The importance of the protein in controlling the electrochemistry of heme metalloproteins: methods of calculation and analysis. JBIC 2: 126-134.
  
  
• Alexov, E. and Gunner, M.R. (1997) Incorporating protein conformational flexibility into pH- titration calculations: Results on T4 Lysozyme. Biophys. J. 74, 2075-2093. MEDLINE
  
  
• van Beek, J. Callender, R. and Gunner, M.R. (1997) Geometry and electrostatic interactions account for the extreme stereospecificity in the reaction catalyzed by lactate dehydrogenase. Biophysical J. 619-626 MEDLINE
  
  
• Gunner, M. R., Nicholls, A. and Honig, B. (1996) Electrostatic potentials in Rhodopseudomonas viridis reaction center : Implications for the driving force and directionality of electron transfer. J. Phys. Chem. 100, 4277-4291.pdf
  
  
• Lancaster, C. R. D., Michel, H., Honig, B. and Gunner, M. R. (1996) The coupling of light-induced electron transfer and proton uptake: Electrostatic calculations on the photosynthetic reaction center of Rhodopseudomonas viridis. Biophys. J. 70, 2469-2492.MEDLINE.
  
  
• Yang, A.-S., M. R. Gunner, R. Sampogna, K. Sharp and B. Honig.(1993) On the calculation of pKa's in proteins. Proteins 15, 252-265. MEDLINE
  
  
• Tiede, D. M., A.-C. Vashishta and M. R. Gunner.(1993) Electron transfer kinetics and electrostatic properties of the Rhodobacter sphaeroides reaction center and soluble c-cytochromes. Biochemistry 32, 4515-4531 MEDLINE .
  

Experimental
(Quinone dependent electron transfer in bacterial photosynthetic reaction centers)

• Xu Q, Baciou L, Sebban P, Gunner MR. (2002) Exploring the energy landscape for QA- to QB electron transfer in bacterial photosynthetic reaction centers: effect of substrate position and tail length on the conformational gating step.Biochemistry. 41,10021-10025.pdf
  
  
• Xu, Q. and Gunner, M.R. (2002) Exploring the Energy Profile of the QA- to QB Electron Transfer Reaction in Bacterial Photosynthetic Reaction Centers: pH Dependence of the Conformational Gating Step. Biochemistry 41, 2694-701.pdf
  
  
• Xu, Q. and Gunner, M.R. (2001) Trapping conformational intermediate states in the reaction center protein from photosynthetic bacteria. Biochemistry 40, 3232-3241.pdf
  
  
• Xu, Q. and Gunner, M.R. (2000) Temperature dependence of the free energy, enthalpy and entropy of P+QA- charge recombination in photosynthetic reaction centers. J.Phys. Chem. 104(33); 8035-8043.pdf
  
  
• Li, J., Takahashi, E. and Gunner, M.R. (2000) -deltaG°AB and pH Dependence on the Electron Transfer from P+QA~QB to P+QAQB- in Rhodobacter sphaeroides Reaction Centers. Biochemistry,39(25); 7445-7454 MEDLINE .pdf
  
  
• Li, J., Coleman, W. J., Youvan, D. C. and Gunner, M. R. (2000) Characterization of a symmetrized mutant RC with 42 residues from the QA site replacing residues in the QB site. Photosynthesis Res. 64, 41-52.
  
  
• Edens, G.L, Gunner, M.R., Xu, Q. and Mauzerall, D. (2000) The enthaply and entropy of reaction for formation of P+QA- from excited reaction centers of Rhodobacter sphaeroides J. Am. Chem. Soc. 122, 1479-1485.pdf
  
  
• Li, J., Gilroy, D. Tiede, D.M. , and, Gunner, M.R. (1998) Electron transfer from P+QA-QB to P+QAQB- and associated processes in Rhodobacter sphaeroides in R-26 reaction centers. Biochemistry 37, 2818-2829 MEDLINE .pdf
  
  
• Morris, A. L., Synder, S. W., Zhang, Y., Thurnauer, M. C., Dutton, P. L., Robertson, D. E. and Gunner, M. R. (1995). An electron spin polarization model applied to sequential electron transfer in iron-containing photosynthetic bacterial reaction centers. J. Phys. Chem. 99, 3854-3866.
  
  
• Mauzerall, D.C., Gunner, M.R., Zhang, J.W. (1995) The volume contraction of photoexcitation of the reaction center from R. sphaeroides R-26: an internal probe of dielectrics. Biophys. J. 68, 275-280. MEDLINE .
  
  
• Warncke, K., Gunner, M. R., Braun, B. S., Yu, C. A. and Dutton, P. L. (1994). Effect of hydrocarbon substituent structure on the interaction of quinone with the Qa and Qb sites in reaction center protein from Rhodobacter sphaeroides R-26. Biochemistry 33, 7830-7841. MEDLINE