Hydrogen bond network analysis reveals the pathway for the proton transfer in the E-channel of T. thermophilus Complex I. Khaniya U, Gupta C, Cai X, Mao J, Kaur D, Zhang Y, Singharoy A, Gunner MR, Biochim Biophys Acta Bioenerg. 2020;1861(10):148240.

Identifying the proton loading site cluster in the ba3 cytochrome c oxidase that loads and traps protons. Cai X, Son CY, Mao J, Kaur D, Zhang Y, Khaniya U, Cui Q, Gunner MR. Biochim Biophys Acta Bioenerg. 2020;1861(10):148239.

Standard state free energies, not pKas, are ideal for describing small molecule protonation and tautomeric states. Gunner MR, Murakami T, Rustenburg AS, Işık M, Chodera JD. J Comput Aided Mol Des. 2020;34(5):561-573.

Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I. Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov L, Chipot C, Singharoy A,  J Am Chem Soc. 2020;142(20):9220-9230.

Identification of a Na+-Binding Site near the Oxygen-Evolving Complex of Spinach Photosystem II.Wang J, Perez-Cruet JM, Huang HL, Reiss K, Gisriel CJ, Banerjee G, Kaur D, Ghosh I, Dziarski A, Gunner MR, Batista VS, Brudving GW, Biochemistry. 2020;59(30):2823-2831.

Photosystem II oxygen-evolving complex photoassembly displays an inverse H/D solvent isotope effect under chloride-limiting conditions. Vinyard DJ, Badshah SL, Riggio MR, Kaur D, Fanguy AR, Gunner MR. Proc Natl Acad Sci U S A. 2019;116(38):18917-18922.

Thermodynamics of the S2-to-S3 state transition of the oxygen-evolving complex of photosystem II. Amin M, Kaur D, Yang KR, Wang J, Mohamed Z, Brudvig GW, Gunner MR, Batista V, Phys Chem Chem Phys. 2019; 21(37)

Tracing the Pathways of Waters and Protons in Photosystem II and Cytochrome c Oxidase.Kaur, D.; Cai, X.; Khaniya, U.; Zhang, Y.; Mao, J.; Mandal, M.; Gunner, M.R. Inorganics, 20197, 14.

Relative stability of the S2 isomers of the oxygen evolving complex of photosystem II. Kaur D, Szejgis W, Mao J, Amin M, Reiss KM, Askerka M, Cai X, Khaniya U, Zhang Y, Brudvig GW, Batista VS, Gunner MR. Photosynth. Res., 2019, 4, 2.

Network analysis of a proposed exit pathway for protons to the P-side of cytochrome c oxidase.Cai X, Haider K, Lu J, Radic S, Son CY, Cui Q, Gunner MR. Biochim. Biophys. Acta Bioenerg., 2018, 1859, 997–1005.

Characterization of ammonia binding to the second coordination shell of the oxygen-evolving complex of photosystem II. Mandal M, Askerka M, Banerjee G, Amin M, Brudvig GW, Batista VS, Gunner MR. Dalton Trans., 2017, 46, 16089-16095

X-ray Free Electron Laser Radiation Damage through the S-State Cycle of the Oxygen-Evolving Complex of Photosystem II. Amin M, Askerka M, Batista VS, Brudvig GW, Gunner MR. J. Phys. Chem. B. , 2017, 121, 9382-9388.

Two Cl ions and a Glu Compete for a helix cage in the CLC proton/Cl-Antiporter.  Chenal C and Gunner MR. Biophys. J. , 2017, 113, 1025-1036.

L-2-hydroxyglutarate production arises from non-canonical enzyme function at acidic pH. Intlekofer A, Wang B, Liu H., Shah H., Carmona-Fontaine C., Rustenburg A.S., Salah S., Gunner M.R., Chodera, J.D., Cross, J.R., and Thompson, C.B. Nat. Chem. Biol., 2017, 13(5),4 94-500.

The design features cells use to build their transmembrane proton gradient. Gunner, M.R. and Koder, R. Phys. Biol. , 2017,1 4(1),013001.

Unraveling the mechanism of proton translocation in the extracellular half-channel of bacteriorhodopsin. Ge X, Gunner MR. Proteins, 2016, 84, 639-54.

Continuum electrostatics approaches to calculating pKas and Ems in proteins.  Gunner MR, Baker NA. Methods Enzymol, 2016, 578, 1-20.

Proton-coupled electron transfer during the S-state transitions of the oxygen-evolving complex of photosystem II. Muhamed Amin, Serguei Vassiliev, Leslie Vogt, Gary W. Brudvig, Doug Bruceand, M. R. Gunner J. Phys. Chem. B., 2015, 119, 7366-7377.

Halorhodopsin pumps Cl- and bacteriorhodopsin pumps protons by a common mechanism that uses conserved electrostatic interactions. Song Y, Gunner MR. Proc. Natl. Acad. Sci., 2014, 10, 1073

Characterizing the proton loading site in cytochrome c oxidase.Lu, J, Gunner, MR. Proc. Natl. Acad. Sci., 2014, 111(34).

Changing hydration level in an internal cavity modulates the proton affinity of a key glutamate in cytochrome c oxidase. Goyal P, Lu J, Yang S, Gunner MR, Cui Q. Proc. Natl. Acad. Sci., 2013, 110: 18, 886-91.  

Electrostatic effects on proton-coupled electron transfer in oxomanganes complexes inspired by the oxygen-evolving complex of photosystem II Muhamed Amin, Leslie Vogt, Serguei Vassiliev, Ivan Rivalta, Muneeb Sultan, Doug Bruce, Gary W. Brudvig, Victor S. Batista, and M. R. Gunner J. Phys. Chem. B., 2013, 117:6217-26.

Molecular mechanisms for generating transmembrane proton gradients. (2013) MR Gunner, Muhamed Amin, Xuyu Zhu, Jianxun Lu. Biochim. Biophys. Acta, 2013, 827:892-913.

Affinity and function of non-native quinones at the Q­B site of bacterial photosynthetic reaction centers. Xinyu Zhang and M. R. Gunner, Photosynth. Res., 2014, 120(1-2):181-96.

The pKa cooperative: a collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins. Nielsen, J.E., Gunner, M.R. and Garcia-Moreno E. B, 2011, Proteins 79, 3249-3259. 

MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease. Gunner, M.R. Zhu, X., and Klein, M.C. Proteins, 2011 79, 3306-3319.

Slow dissociation of a charge ligand: Analysis of the primary quinone Q­A sit of photosynthetic bacterial reaction centers.Madeo, J., Mihajlovic, M., Lazaridis, T. and Gunner, M.R.   J. Am. Chem. Soc., 2011, 133, 17,375-17.

Efficiency of photosynthesis in a Chl d-utilizing cyanobacterium is comparable to or higher than that in a Chl a-utilizing oxygenic species.Mielke, S.P., Kiang, N.Y., Blankenship, R.E., Gunner, M.R., and Mauzerall, D. Biochim. Biophys. Acta, 2011,807(9):1231-6.

Structural-functional role of chloride in Photosystem II. , Rivalta, I., Amin, M., Luber, S., Vassilev, S., Pokhrel, R. Umena, Y., Kawakami, K., Shen, J.R., Kamiya, N., Bruce, D., Brudvig, G.W., Gunner, M.R., and Batista, V.S. Biochemistry, 2011, 50, 6312-6315. 

Comparing photosynthetic and photovoltaic efficiencies and recognizing the potential for improvement. Blankenship, R.E. Tiede, D.M., Barber, J. Brudvig, G.W., Fleming, G. Ghiradi, M. Gunner, M.R., Junge, W., Kramer, D.M., Melis, A., Moore, T. A., Moser, C.C., Nocera, D.G., Nozik, A.J., Ort, D.R., Parson, W.W., Prince, R.C. and Sayre, R.T Science, 2011 ,332, 805-809.

The measured and calculated affinity of methyl and methoxy substituted benzoquinones for the QA site of bacterial reaction centers, Zheng, Z., Dutton, P.L. and Gunner, M.R. Proteins, 2010,78, 2638-2354.

Multiconformation Continuum Electrostatics Analysis of Heme a Redox Reactions in the Rb. sphaeroides Cytochrome c oxidase S44D Mutant, Zhang, J and Gunner, M.R.,Biochemistry, 2010, 49, 8043-8052.

Using Multiconformation Continuum Electrostatics to Compare Chloride Binding Motifs in α-Amylase Human Serum Albumin, and Omp32, Song, Y. and Gunner, MR, J. Mol. Biol., 2009, 387: 840-856.

Microscopic pKa Analysis of Glu286 in Cytochrome c Oxidase (Rhodobacter sphaeroides): Toward a Calibrated Molecular Model, Ghosh, N., Prat-Resina, X., Gunner, M. R., and Cui, Q Biochemistry, 2009, 48: 2468-2485.

MCCE2: Improving Protein pKa Calculations with Extensive Side Chain Rotamer Sampling. Song, Y. Mao, J, and Gunner, MR.,  J. Comp. Chem. ,2009 30, 2231-2247.

Modification of quinone electrochemistry by the proteins in the biological electron transfer chains: examples from photosynthetic reaction centers.Gunner, M.R. Zhu, Z. and Madeo, J. J Bioenerg. Biomembr., 2008, 40: 509-519.  doi: 10.1007/s10863-008-9179-1

Computational analysis of photosynthetic systems. Gunner, M.R. Photosynth. Res, 2008,97, 1-3.

Analysis of the electrochemistry of hemes with Ems spanning 800 mV.  , Zheng, Z and Gunner, M.R. Proteins, 2009, 75: 719-34.

Ligand preference and orientation in b- and c-type heme-binding proteins. Fufezan, C., Zhang, J. and Gunner, M.R., Proteins, 2008, 73: 690-704.

.Factors influencing the energetics of electron and proton transfer in proteins.  What we can learn from calculations.Gunner, M.R., Mao, J., Yifan Song, Y. and Kim, J.,  Biochim. Biophys. Acta , 2006, 1757: 942-968.

Electrostatic environment of hemes in proteins: pKas of hydroxyl ligands, Song, Y., Mao, J. and Gunner, M.R., Biochemistry, 2006,45: 7959-7975.

Calculated proton uptake on anaerobic reduction of cytochrome c oxidase: Is the reaction electroneutral?Song, Y., Michonova-Alexova, E. and Gunner, M.R, Biochemistry, 2006 45: 7949-7958.

Modeling Binding Kinetics at the QA Site in Bacterial Reaction Centers. Madeo, J. and Gunner, M.R, Biochemistry, 2005, 44:994- 1004.

Are acidic and basic groups in buried proteins predicted to be ionized? Kim J, Mao J, Gunner MR. J. Mol. Biol, 2005, 348: 1283-1298.

The energetics of quinone dependent electron and proton transfers in Rhodobacter sphaeroides photosynthetic reaction centers.  Zhu, Z and Gunner M.R. Biochemistry, 2004 44:82-96.

pH dependence of heme electrochemistry in cytochromes investigated by multiconformation continuum electrostatic calculations.Hauser K, Mao, J. Gunner, MR, 2004, Biopolymers 74: 51-4

Protons forge new paths. Gunner, M.R. and Zhu, Z ., Structure, 2004, 12: 518-9.

Calculation of proton transfers in bacteriorhodopsin bR and M intermediates. Song Y., Mao, J., Gunner M.R. , Biochemistry, 2003 42: 9875-88.

Multi-conformation continuum electrostatic analysis of heme electrochemistry in cytochromes with different structures. Mao J., Hauser K., Gunner M.R. , Biochemistry, 2003,42: 829-40.

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. Xu Q., Baciou L., Sebban P., Gunner M.R. , Biochemistry, 2002, 41:10021-5.

Exploring the energy profile of the QA to QB electron transfer reaction in bacterial photosynthetic reaction centers:  pH dependence of the conformational gating step. Xu Q., Gunner M.R, Biochemistry, 2002, 41:2694-701.

Combining conformational flexibility and continuum electrostatics for calculating pKa‘s in proteins. Georgescu R.E., Alexov E.G., Gunner M.R. J. Biophys, 2002, 83:1731-48.

Trapping conformational intermediate states in the reaction center protein from photosynthetic bacteria. Xu Q., Gunner M.R. Biochemistry, 2001, 40:3232-41.

Temperature dependence of the free energy, enthalpy and entropy of P+QA charge recombination in photosynthetic reaction centers. Xu Q., Gunner M.R., J.Phys.Chem. B. , 2000, 104:8035-43.  

-∆G°AB and pH dependence on the electron transfer from P+QAQB to P+QAQB in Rhodobacter sphaeroides reaction centers. Li J., Takahashi E., Gunner M.R. . , Biochemistry, 2000, 39:7445-54.

Characterization of a symmetrized mutant RC with 42 residues from the QA site replacing residues in the QB  site. Li J., Coleman W.J., Youvan D.C., Gunner M.R., Photosyn. Res., 2000, 64:41-52.

A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins. Gunner M.R., Alexov E., Biochim. Biophys. Acta., 2000, 1458:63-87.

Backbone dipoles generate positive potentials in all proteins.  Origins and implications of the effect., Gunner M.R., Saleh M., Cross E., ud-Doula A., Wise M. . Biophys. J., 2000, 78:1126-44.  

The enthalpy and entropy of reaction for formation of P+QA from excited reaction centers of Rhodobacter sphaeroides. Edens G.J., Gunner M.R., Xu Q., Mauzerall D. J., Am. Chem. Soc., 2000, 122:1479-85.

Modeling the effects of mutations on the free energy of the first electron transfer from QA to QB in photosynthetic reaction centers., Alexov E., Miksovska J., Baciou L., Schiffer M., Hanson D., Sebban P., Gunner M.R. , Biochemistry, 2000, 39:5940-52.

Calculated protein and proton motions coupled to electron transfer: The electron transfer from QA to QB in bacterial photosynthetic RCs. Alexov E., Gunner M. , Biochemistry, 1999, 38:8253-70.

Kinetic phases in the electron transfer from P+QAQB to P+QAQB and the associated processes in Rhodobacter sphaeroides R-26 reaction centers., Li J., Gilroy D., Tiede D.M., Gunner M.R., Biochemistry, 1998, 37:2818-29.

The contribution of electrostatic and van der Waals interactions to the stereospecificity of the reaction catalyzed by lactate dehydrogenase. van Beek J., Callender R., Gunner M.R. . Biophys. J. ,1997, 72:619-26.

The importance of the protein in controlling the electrochemistry of heme metalloproteins: Methods of calculation and analysis. Gunner M.R., Alexov E., Torres E., Lipovaca S. J. Biol. Inorg. Chem., 1997, 2:126-34

Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties. Alexov E.G., Gunner M.R., Biophys. J. ,1997, 72:2075-93.

Calculated coupling of electron and proton transfer in the photosynthetic reaction center of Rhodopseudomonas viridis., Lancaster C.R.D., Michel H., Honig B., Gunner M.R. Biophys. J., 1996, 70:2469-92.

Electrostatic potentials in Rhodopseudomonas viridis reaction center: Implications for the driving force and directionality of electron transfer. Gunner M.R., Nicholls A., Honig B. ., J. Phys. Chem., 1996, 100:4277-91

Electron spin polarization model applied to sequential electron transfer in iron-containing photosynthetic bacterial reaction centers with different quinones as QA. Morris A.L., Synder S.W., Zhang Y., Thurnauer M.C., Dutton P.L., Robertson D.E., Gunner M.R. J. Phys. Chem., 1995, 99:3854-66.

Volume contraction on photoexcitation of the reaction from Rhodobacter sphaeroides R-26: Internal probe of dielectrics. Mauzerall D.C., Gunner M.R., Zhang J.W. Biophys. J., 1995, 68:275-80.

Influence of hydrocarbon tail structure on quinone binding and electron-transfer performance at the QA and QB sites of the photosynthetic reaction center protein. Warncke K., Gunner M.R., Braun B.S., Gu L., Yu C., Bruce J.M., Dutton P.L. Biochemistry, 1994. 33:7830-41.

On the calculation of pKa‘s in proteins. Yang A.-S., Gunner M.R., Sampogna R., Sharp K., Honig B, Proteins, 1993, 15:252-65.

Electron transfer kinetics and electrostatic properties of the Rhodobacter sphaeroides reaction center and soluble c-cytochromes.Tiede D.M., Vashishta A.-C., Gunner M.R. Biochemistry, 1993, 32:4515-31.

Electrostatic control of midpoint potentials in the cytochrome subunit of the Rhodopseudomonas viridis reaction center. Gunner M.R., Honig B. ., Proc. Natl. Acad. Sci. USA, 1991 88:9151-5.

The reaction center protein from purple bacteria: Structure and function. , Gunner M.R. Current Topics in Bioenergetics, 1991, 16:319-67.

Temperature and -∆G° dependence of the electron transfer from BPh to QA in reaction center protein from Rhodobacter sphaeroides with different quinones as QA. Gunner M.R., Dutton P.L., J. Am. Chem. Soc., 1989, 111:3400-12.

Radical-pair energetics and decay mechanisms in reaction center containing anthraquinones or benzoquinones in place of ubiquinone.Woodbury N.W., Parson W.W., Gunner M.R., Prince R.C., Dutton P.L., Biochim. Biophys., 1986, Acta. 851:6-22.

Kinetic studies on the reaction center protein from Rhodopseudomonas sphaeroides:  The temperature and free energy dependence of electron transfer between various quinones in the QA site and the oxidized bacteriochlorophyll dimer. Gunner M.R., Robertson D.E., Dutton P.L., J. Phys. Chem., 1986., 90:3783-95.

Picosecond kinetics: Absorption studies of an iron porphyrin and bacteriopheophytin using a streak camera. Liang Y., Nagus D.K., Hochstrasser R.M., Gunner M.R., Dutton P.L. ,Chem. Phys. Lett. , 1981, 84:236-40.