James Ames

James Ames

Position Title

Department of Chemistry, College of Letters and Science

Chemistry Building/ Rm 126

Grad Group Affiliations

  • Biophysics

Specialties / Focus

  • Spectroscopy and Imaging
  • Structural Biology, Membranes and Macromolecular Assembly


1 Li, C. and Ames, J.B. (2007) NMR Assignments of CaBP1, a Calcium Sensor and Regulator of Neuronal Ca2+ Channels. J. Biomol. NMR, 1:77-79. 2 Lusin, J., Vanarotti, M., Li, C., Valiveti, A.and Ames, J.B. (2007) Structural Basis for Ca2+ Sensitive DNA Binding and Dimerization of DREAM, a Calcium Sensor for Pain Control. Biochemistry, in press. 3 Strahl, T., Huttner, I.G., Osawa, M., King, D.S., Thorner, J. and Ames, J.B. (2007) Structural Insights into the Activation of of PtdIns 4-kinase (Pik1) by yeast frequenin. J. Biol. Chem., 282:30949-30959. 4 Stathopulos, P.B., Ames, J.B. and Ikura, M. (2007) Structure of Calcium Binding Proteins and Interactions with Target Proteins. Calcium: a Matter of Life and Death (Edited by Dr. Marek Michalak), Garland Science, New York, NY, vol. 41, pp. 501-512 (Invited review). 5 Ames, J.B. and Ikura, M. (2007) Molecular Structure and Target Recognition of Neuronal Calcium Sensor Proteins. Molecular Anatomy and Physiology of Proteins (Edited by Dr. Vladimir Uversky), Nova Science, New York, NY, Chapter 18, pp. 321-328 (Invited review). 6 Lin, Y., Lusin, J., Ye, D., Dunaway-Mariano, D. and Ames, J.B. (2006) Examination of the Structure, Stability and Catalytic Potential in the Engineered Phosphoryal Carrier Domain of Pyruvate Phosphate Dikinase. Biochemistry, 45:1702-1711. 7 Ikura, M. and Ames, J.B. (2006) Genetic polymorphism and protein conformational plasticity in the calmodulin superfamily: two ways to promote multifunctionality. Proc. Natl. Acad. Sci. USA, 103:1159-1164 (Invited review). 8 Ames, J.B., Wingard, J.N., Lusin, J.D., Levay, K. and Slepak, V.Z. (2006) Structural Basis for Calcium-induced Inhibition of Rhodopsin Kinase by Recoverin. J. Biol. Chem., 281:37237-37245. 9 Stathopulos, P.B., Li, G-Y, Plevin, M.J., Ames, J.B. and Ikura, M. (2006) Stored Ca2+ depletion-induced oligomerization of STIM1 via the EF-SAM region: An initiation mechanism for capacitive Ca2+ entry. J. Biol. Chem., 281: 35855-35862. 10 Wingard, J.N., Chan, J., Bosanac, I., Haeseleer, F., Palczewski, K., Ikura, M. and Ames, J.B. (2005) Structural analysis of Mg2+ and Ca2+ binding to the calcium-binding protein 1 (CaBP1), a neuron-specific regulator of calcium channels. J. Biol. Chem., 280:37461-37470. 11 Ames, J.B., Vyas, V., Lusin, J. and Mariuzza, R. (2005) NMR Structure and ligand recognition of the Natural Killer Cell receptor, 2B4 (CD244): Implications for ligand recognition. Biochemistry, 44:6416-6423. 12 Osawa, M., Dace, A., Tong, K., Valiveti, A., Ikura, M. and Ames, J.B. (2005) Mg2+ and Ca2+ differentially regulate DNA binding and dimerization of DREAM. J. Biol. Chem., 280:18008-18014. 13 Buchanan K, Ames JB, Asfaw SH, Wingard JN, Olson CL, Campana PT, Araujo AP and Engman DM (2005) A flagellum-specific calcium sensor. J Biol Chem, 280: 40104-40111. 14 Hamasaki-Katagiri, N., Molchanova, T. and Ames, J.B. (2004) Fission Yeast Homolog of Neuronal Calcium Sensor-1 (Ncs1p) Regulates Sporulation and Confers Calcium Tolerance. J. Biol. Chem. 279:12744-12754. 15 Zhu, J., Stabler, S.M., Ames, J.B., Baskakov, I., Monteiro, M. (2004) Calcium binding sequences in calmyrin regulates interaction with presenilin-2. Exp. Cell Res., 300:440-454. 16 Valentine, K.G., Mesleh, M.F., Opella, S.J., Ikura, M. and Ames, J.B. (2003) Structure, topology, and dynamics of myristoylated recoverin bound to phospholipid bilayers. Biochemistry, 42:6333-6340. 17 Huttner, I.G., Strahl, T., Osawa, M., King, D.S., Ames, J.B. and Thorner, J. (2003) Molecular interactions of yeast frequenin (Frq1) with the phosphatidylinositol 4-kinase isoform, Pik1. J. Biol. Chem., 278:4862-4874. 18 Ames, J.B., Osawa, M. and Ikura, M. (2002) The role of calcium binding proteins in the control of transcription: structure to function. BioEssays, 24:625-636. (Invited review) 19 Ames J.B. and Ikura M. (2002) Structure and membrane-targeting mechanism of retinal Ca2+-binding proteins, recoverin and GCAP-2. Adv. Exp. Med. Biol., 514:333-48. (Review article) 20 Ames, J.B., Hamasaki, N. and Molchanova, T. (2002) Structure and calcium-binding studies of a recoverin mutant (E85Q) in an allosteric intermediate state. Biochemistry, 18: 5776-5787. 21 Yap, K., Ames, J.B., Swindles, M.B., and Ikura, M. (2002) Vector Geometry Mapping: A Method to Characterize the Conformation of Calcium-binding Proteins. Methods in Molecular Biology (Edited by H.J. Vogel), Humana Press Inc., Totowa, NJ, vol. 173, pp. 317-324. 22 Osawa, M., Tong, K.I., Lilliehook, C., Wasco, W., Buxbaum, J.D., Cheng, H.Y., Penninger, J.M., Ikura, M. and Ames, J.B. (2001) Calcium-regulated DNA binding and oligomerization of the neuronal calcium-sensing protein, Calsenilin/DREAM,/KChIP3. J. Biol. Chem., 276:41005-41013. 23 Ames, J.B. and Ikura, M. (2001) Structure of Recoverin, a Calcium Sensor in Vision. Encyclopedia of Molecular Medicine (Edited by T.E. Creighton), Wiley & Sons Inc., vol. 4, pp. 2745-2747. (Review article) 24 Ames, J.B., Hendricks, K.B., Strahl, T., Huttner, I.G., Hamasaki, N. and Thorner, J. (2000) Structure and Calcium-binding Properties of Frq1, a Novel Calcium Sensor in the Yeast Saccharomyces cerevisiae. Biochemistry, 39:12149-12161. 25 Ames, J.B., Ikura, M., and Stryer. L. (2000) Molecular Structure of Membrane-targeting Calcium Sensors in Vision. Methods in Enzymology, 316:121-132. (Invited review) 26 Palczewski, K., Polans, A.S., Baehr, W., and Ames, J.B. (2000) Calcium-binding Proteins in the Retina: Structure, Function and Etiology of Human Visual Diseases. BioEssays, 22:337-350. (Invited review) 27 Ames, J.B., Dizhoor, A.M., Ikura, M., Palczewski, K., and Stryer, L. (1999) Three-dimensional Structure of Guanylyl Cyclase Activating Protein-2, a Calcium-sensitive Modulator of Photoreceptor Guanylyl Cyclases. J. Biol. Chem. 274:19329-19337. 28 Yap, K.L., Ames, J.B., Swindells, M.B. and Ikura, M. (1999) Diversity of Conformational States and Changes within the EF-hand Protein Superfamily. Proteins: Structure, Function and Genetics, 37:499-507. 29 Baldwin, A. and Ames, J.B. (1998) Core Mutations Promote Ca2+-induced Allosteric Transition in Recoverin. Biochemistry, 37:17408-17419. 30 Tanaka, T., Ames, J.B., Kainosho, M., Stryer, L. and Ikura, M. (1998) Differential Isotope Labeling Strategy for Determining the Structure of Myristoylated Recoverin. J. Biomol. NMR, 11:135-152. 31 Ames, J.B, Ishima, R.I., Tanaka, T., Gordon, J.I., Stryer, L. & Ikura, M. (1997) Molecular Mechanics of Calcium-myristoyl Switches. Nature, 389:198-202. 32 Alattia, J., Ames, J.B., Porumb, T., Tong, K.I., Heng, Y., Ottensmeyer, P., Kay, C.M. and Ikura, M. (1997) Lateral Self-assembly of E-cadherin Operated by Cooperative Calcium Binding. FEBS Letters, 417:405-408. 33 Ames, J.B., Tanaka, T., Stryer, L. & Ikura, M. (1996) Portrait of a Myristoyl Switch Protein. Current Opinion in Structural Biology, 6:432-438. (Invited review) 34 Ames, J.B., Tanaka, T., Ikura, M. & Stryer, L. (1995) Nuclear Magnetic Resonance Evidence for Calcium-induced Extrusion of the Myristoyl Group of Recoverin. J. Biol. Chem., 270, 30909-30913. 35 Tanaka, T., Ames, J.B., Harvey, T.S., Stryer, L. & Ikura, M. (1995) Sequestration of the Membrane-targeting Myristoyl Group of Recoverin in the Calcium-free State. Nature 376, 444-447. 36 Ames, J.B., Porumb, T., Tanaka, T., Ikura, M. & Stryer, L. (1995) Amino-terminal Myristoylation Induces Cooperative Calcium Binding to Recoverin. J. Biol. Chem. 270, 4526-4533. 37 Ames, J.B., Tanaka, T., Stryer, L. & Ikura, M. (1994) Secondary Structure of MyristoylatedRecoverin Determined by Three-dimensional Heteronuclear NMR: Implications for the Calcium-Myristoyl Switch. Biochemistry 33, 10743-10753. 38 Ames, J.B., Raap, J., Lugtenburg, J. & Mathies, R.A. (1992) Resonance Raman Study of Halorhodopsin Photocycle Kinetics, Chromophore Structure, and Chloride-Pumping Mechanism. Biochemistry 31, 12546-12554. 39 Ames, J.B., Ros, M., Raap, J., Lugtenburg, J. & Mathies, R.A. (1992) Time-resolved Ultraviolet Resonance Raman Studies of Protein Structure: Application to Bacteriorhodopsin. Biochemistry 31, 5328-5334. 40 Mathies, R.A., Lin, S.W., Ames, J.B. & Pollard, W.T. (1991) From Femtoseconds to Biology: Mechanism of Bacteriorhodopsin's Light-driven Proton Pump. Annu. Rev. Biophys. Biophys. Chem. 20, 491-518. (Invited review) 41 Ames, J.B., Bolton, S.R., Netto, M.M., and Mathies, R.A. (1990) Ultraviolet Resonance Raman Spectroscopy of Bacteriorhodopsin: Evidence Against Tyrosinate in the Photocycle. J. Am. Chem. Soc. 112, 9007-9009. 42 Ames, J.B. & Mathies, R.A. (1990) The Role of Backreactions and Proton Uptake during the N ? O Transition in Bacteriorhodopsin's Photocycle: A Kinetic Resonance Raman Study. Biochemistry 29, 7181-7190. 43 Ames, J.B., Fodor, S.P.A., Gebhard, R., Raap, J., van den Berg, E.M.M., Lugtenburg, J. & Mathies, R.A. (1989) Bacteriorhodopsin's M412 Intermediate Contains a 13-cis, 14-s-trans,15-anti Retinal Schiff Base Chromophore. Biochemistry 28, 3681-3687. 44 Fodor, S.P.A, Ames, J.B., Gebhard, R., van den Berg, E.M.M., Stoeckenius, W., Lugtenburg, J. & Mathies, R.A. (1988) Chromophore Structure in Bacteriorhodopsin's N Intermediate: Implications for the Proton-pumping Mechanism. Biochemistry 27, 7097-7101.