研究领域

Biochemistry

In the broadest sense, our research objectives are to understand how proteins function in biological systems. Our interests range from understanding how energy is converted in photosynthetic systems to how changes in proteins can cause certain diseases. We use a variety of biochemical and biophysical approaches to examine each problem, with an emphasis on relating the functional properties to the structure. Therefore, one major aspect of our research is the determination of the three-dimensional structures of proteins by x-ray crystallography. One major focus is the photosynthetic process, the conversion of light energy into chemical energy that involves a variety of pigment-protein complexes. Our research goal is to develop models for the transfer of electrons and energy in these complexes, in particular to understand how these processes changed as primitive bacteria evolved into cyanobacteria and plants. To achieve this goal, we create bacterial complexes with a new Mn cofactor that resembles the site of water oxidation in cyanobacteria and plants. The influence of proteins on medical problems is also studied in our laboratory. The major leading genetic cause of childhood deaths is SMA, spinal muscular atrophy, in which neurological systems fail to properly develop. The cause of this disease is a change in the protein SMN, for survival of motor neurons. To determine the molecular reasons for why changes in the SMN protein give rise to SMA, we are investigating the three-dimensional structures of the SMN protein found in both healthy and SMA patients.

近期论文

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"Interface for light-driven electron transfer by photosynthetic complexes across block copolymer membranes," L. Kuang, T. L. Olson, S. Lin, M. Flores, Y. Jiang, W. Zheng, J. C. Williams, J. P. Allen, H. Liang , J. Phys. Chem. Lett. 5 787-791 (2014) "Influence of protein interactions on oxidation/reduction midpoint potentials of cofactors in natural and de novo metalloproteins," T. L. Olson, J. C. Williams, and J. P. Allen , Biochim. Biophys. Acta 1827 914-922 (2013) "The role of four conserved basic amino acids in a ferredoxin-dependent cyanobacterial nitrate reductase," A. P. Srivastava, M. Hirasawa, M. Bhalla, J.-S. Chung. J. P. Allen, M. K. Johnson, J. N. Tripathy, L. M. Rubio, B. Vaccaro, S. Subramanian, E. Flores, A. Herrero, M. Zabet-Moghaddam, K. Stitle, and D. B. Knaff , Biochemistry 52 4343-4353 (2013) "pH dependent structural conformations of B-phycoerythrin from Porphyridium cruentum," A. Camara-Artigas, M. Andujar-Sanchez, E. Ortiz-Salmeron, J. Bacarizo, C. Mesa-Valle, C. Cuadri, J. M. Martin-Garcia, T. M. Sobcuk, J. Ibanez and J. P. Allen , FEBS J. 279 3680–3691 (2012) "Light-driven oxygen production from superoxide by Mn-binding bacterial reaction centers," J. P. Allen, T. L. Olson, P. Oyala, W.-J. Lee, A. Tufts, and J. C. Williams , Proc. Natl. Acad. Sci. USA 109 2314-2318 (2012) "Reinterpretation of the electron density at the site of the eighth bacteriochlorophyll in the FMO protein from Pelodictyon phaeum," D. Tronrud and J. P. Allen , Photosynthesis Research 112 71-74 (2012) "pH dependent structural conformations of B-phycoerythrin from Porphyridium cruentum," A. Camara-Artigas, M. Andujar-Sanchez, E. Ortiz-Salmeron, J. Bacarizo, C. Mesa-Valle, C. Cuadri, J. M. Martin-Garcia, T. M. Sobcuk, J. Ibanez and J. P. Allen , FEBS Journal 279 3680-3691 (2012) "Carotenoid excited state properties in photosynthetic purple bacterial reaction centers: Effects of the protein environment," J. Pan, S. Lin, J. P. Allen, J. C. Williams, H. A. Frank, and N. W. Woodbury , J. Phys. Chem. B 115 7058-7068 (2011) "Thin film voltammetry of wild type and mutant reaction center proteins from photosynthetic bacteria," Y. Zhang, A. M. LaFountain, N. Magdaong, M. Fuciman, J. P. Allen, H. A. Frank, and J. F. Rusling , J. Phys. Chem. B 115 3226-3232 (2011) "The evolutionary pathway from anoxygenic to oxygenic photosynthesis examined by comparison of the properties of photosystem II and bacterial reaction centers," J. P. Allen and J. C. Williams , Photosynthesis Research 107 59-69 (2011) "Light-induced conformational changes in photosynthetic reaction centers: Redox regulated proton pathway near the dimer," S. S. Deshmukh, J. C. Williams, J. P. Allen, and L. Kalman , Biochemistry 50 3321-3331 (2011) "Light-induced conformational changes in photosynthetic reaction centers: Impact of detergents and lipids on the electronic structure of the primary electron donor," S. S. Deshmukh, J. C. Williams, J. P. Allen, and L. Kalman , Biochemistry 50 5249-5262 (2011) "Energetics for oxidation of a bound manganese cofactor in modified bacterial reaction centers," L. Kalman, G. Uyeda, J. C. Williams, and J. P. Allen , Biochemistry 50 3310-3320 (2011) "Light-induced conformational changes in photosynthetic reaction centers: Dielectric relaxation in the vicinity of the dimer," S. S. Deshmukh, J. C. Williams, J. P. Allen, and L. Kalman , Biochemistry 50 340-348 (2011) "The three dimensional structure of the FMO protein from Pelodictyon phaeum and the implications for energy transfer," C. R. Larson, C. Seng, L. Lauman, H. J. Matthies, J. Wen, R. E. Blankenship, and J. P. Allen , Photosynthesis Research 107 139-150 (2011) "Understanding the polymorphic behaviour of a mutant of the alpha-spectrin SH3 domain by means of two 1.1 A resolution structures," A. Camara-Artigas, J. A. Gavira, S. Casares, J. M. Garcia-Ruiz, F. Conejero-Lara, J. P. Allen and J. Martinez , Acta Crystallogr. D 67 189-196 (2011) "Electronic structure of Fe3+ at a metal binding site introduced in modified bacterial reaction centers ," L. Kalman, M. Flores, J. C. Williams, and J. P. Allen , Appl. Magn. Res. 37 27-37 (2010) "Enzymatic properties of the ferredoxin-dependent nitrite reductase from Chlamydomonas reinhardtii. Evidence for hydroxylamine as a late intermediate in ammonia production," M. Hirasawa, J. N. Tripathy, F. Sommer, R. Somasundaram, J. S. Chung, M. Nestander, M. Kruthiventi, M. Zabet-Moghaddam, M. K. Johnson, S. Merchant, J. P. Allen and D. B. Knaff , Photosynthesis Research 103 67-77 (2010) "The influence of hydrogen bonds on the electronic structure of light harvesting complexes from purple bacteria ," G. Uyeda, J. C. Williams, M. Roman, T. A. Mattioli, and J. P. Allen , Biochemistry 49 1146-1159 (2010) "Implications of unusual ligand binding in a synthetic class of de novo proteins," C. R. Simmons, C. L. Magee, D. A. Smith, L. Lauman, J. C. Chaput and J. P. Allen , Biochemistry 49 8689-8699 (2010) "Effect of anions on the binding and oxidation of divalent manganese and iron in modified bacterial reaction centers ," K. Tang, J. C. Williams, J. P. Allen, and L. Kalman , Biophysical J. 96 3295-3304 (2009) "Electron transfer in Rhodobacter sphaeroides reaction centers assembled with zinc bacteriochlorophylls ," S. Lin, P. R. Jaschke, H. Wang, M. Paddock, A. Tufts, J. P. Allen, F. I. Rosell, G. A. Mauk, N. W. Woodbury, and J. T. Beatty , Proc. Natl. Acad. Sci. USA 106 8537-8542 (2009) "Structures of proteins and cofactors: X-ray crystallography," J. P. Allen, C. Seng, and C. Larson , Photosynthesis Research 102 231-240 (2009) "A synthetic protein selected for ligand binding affinity mediates ATP hydrolysis ," C. R. Simmons, J. M. Stomel, M. D. McConnell, D. A. Smith, M. D. Smith, J. L. Watkins, J. P. Allen, and J. C. Chaput , ACS Chem. Biol. 4 649-658 (2009) "Unusual temperature dependence of photosynthetic electron transfer due to protein dynamics," H. Wang, S. Lin, E. Katilius, C. Laser, J. P. Allen, J. C. Williams, N. W. Woodbury , J. Phys. Chem. B 113 818-824 (2009) "EPR, ENDOR and Special TRIPLE measurements of P+ in wild type and modified reaction centers from Rb. sphaeroides," J. P. Allen, J. M. Cordova, C. C. Jolley, T. A. Murray, J. W. Schneider, N. W. Woodbury, J. C. Williams, J. Niklas, G. Klihm, M. Reus, and W. Lubitz , Photosynthesis Research 99 1-10 (2009) "The interaction of spinach nitrite reductase with ferredoxin: a site-directed mutation study," M. Hirasawa, J. N. Tripathy, R. Somasundaram, M. K. Johnson, M. Bhalla, J. P. Allen, and D. B. Knaff , Molecular Plant 3 407-415 (2009) "X-ray crystallography of photosynthetic proteins, in Biophysical techniques in photosynthesis," P. Fromme and J. P. Allen , Advances in Photosynthesis and Respiration, Springer Publishers 97-124 (2008) "Comparison of bacterial reaction centers and photosystem II," L. Kalman, J. C. Williams, and J. P. Allen , Photosynthesis Research 98 643-655 (2008) "Protein dynamics control the kinetics of initial electron transfer in photosynthesis," H. Wang, S. Lin, J. P. Allen, J. C. Williams, and N. Woodbury , Science 316 747-750 (2007)