James Benjamin Ames - Publications

Affiliations: 
1998-2006 University of Maryland, College Park, College Park, MD 
 2006- University of California, Davis, Davis, CA 
Area:
Molecular Biology, Biochemistry
Website:
https://chemistry.ucdavis.edu/people/james-ames

55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Peshenko IV, Yu Q, Lim S, Cudia D, Dizhoor AM, Ames JB. Retinal degeneration 3 (RD3) protein, a retinal guanylyl cyclase regulator, forms a monomeric and elongated four helix bundle. The Journal of Biological Chemistry. PMID 30559291 DOI: 10.1074/jbc.RA118.006106  1
2018 Lim S, Roseman G, Peshenko I, Manchala G, Cudia D, Dizhoor AM, Millhauser G, Ames JB. Retinal guanylyl cyclase activating protein 1 forms a functional dimer. Plos One. 13: e0193947. PMID 29513743 DOI: 10.1371/journal.pone.0193947  1
2018 Lim S, Cudia D, Yu Q, Peshenko I, Dizhoor AM, Ames JB. Chemical shift assignments of retinal degeneration 3 protein (RD3). Biomolecular Nmr Assignments. 12: 167-170. PMID 29327102 DOI: 10.1007/s12104-018-9802-y  1
2016 Li C, Lim S, Braunewell KH, Ames JB. Structure and Calcium Binding Properties of a Neuronal Calcium-Myristoyl Switch Protein, Visinin-Like Protein 3. Plos One. 11: e0165921. PMID 27820860 DOI: 10.1371/journal.pone.0165921  1
2016 Lim S, Peshenko IV, Olshevskaya EV, Dizhoor AM, Ames JB. Structure of Guanylyl Cyclase Activator Protein 1 (GCAP1) Mutant V77E in a Ca2+-free/Mg2+-bound Activator State. The Journal of Biological Chemistry. 291: 4429-41. PMID 26703466 DOI: 10.1074/jbc.M115.696161  1
2014 Park S, Li C, Haeseleer F, Palczewski K, Ames JB. Structural insights into activation of the retinal L-type Ca²⁺ channel (Cav1.4) by Ca²⁺-binding protein 4 (CaBP4). The Journal of Biological Chemistry. 289: 31262-73. PMID 25258313 DOI: 10.1074/jbc.M114.604439  1
2014 Lim S, Dizhoor AM, Ames JB. Structural diversity of neuronal calcium sensor proteins and insights for activation of retinal guanylyl cyclase by GCAP1. Frontiers in Molecular Neuroscience. 7: 19. PMID 24672427 DOI: 10.3389/fnmol.2014.00019  1
2014 Peshenko IV, Olshevskaya EV, Lim S, Ames JB, Dizhoor AM. Identification of target binding site in photoreceptor guanylyl cyclase-activating protein 1 (GCAP1). The Journal of Biological Chemistry. 289: 10140-54. PMID 24567338 DOI: 10.1074/jbc.M113.540716  1
2014 Park S, Li C, Ames JB. ¹H, ¹⁵N, and ¹³C chemical shift assignments of murine calcium-binding protein 4. Biomolecular Nmr Assignments. 8: 361-4. PMID 23925854 DOI: 10.1007/s12104-013-9517-z  1
2014 Li C, Ames JB. ¹H, ¹³C, and ¹⁵N chemical shift assignments of neuronal calcium sensor protein, hippocalcin. Biomolecular Nmr Assignments. 8: 63-6. PMID 23250791 DOI: 10.1007/s12104-012-9453-3  1
2013 Lim S, Peshenko IV, Dizhoor AM, Ames JB. Structural insights for activation of retinal guanylate cyclase by GCAP1. Plos One. 8: e81822. PMID 24236217 DOI: 10.1371/journal.pone.0081822  1
2013 Myers WK, Xu X, Li C, Lagerstedt JO, Budamagunta MS, Voss JC, Britt RD, Ames JB. Double electron-electron resonance probes Ca²⁺-induced conformational changes and dimerization of recoverin. Biochemistry. 52: 5800-8. PMID 23906368 DOI: 10.1021/bi400538w  1
2013 Li C, Enomoto M, Rossi AM, Seo MD, Rahman T, Stathopulos PB, Taylor CW, Ikura M, Ames JB. CaBP1, a neuronal Ca2+ sensor protein, inhibits inositol trisphosphate receptors by clamping intersubunit interactions. Proceedings of the National Academy of Sciences of the United States of America. 110: 8507-12. PMID 23650371 DOI: 10.1073/pnas.1220847110  1
2013 Lim S, Peshenko IV, Dizhoor AM, Ames JB. Backbone (1)H, (13)C, and (15)N resonance assignments of guanylyl cyclase activating protein-1, GCAP1. Biomolecular Nmr Assignments. 7: 39-42. PMID 22392341 DOI: 10.1007/s12104-012-9373-2  1
2012 Peshenko IV, Olshevskaya EV, Lim S, Ames JB, Dizhoor AM. Calcium-myristoyl Tug is a new mechanism for intramolecular tuning of calcium sensitivity and target enzyme interaction for guanylyl cyclase-activating protein 1: dynamic connection between N-fatty acyl group and EF-hand controls calcium sensitivity. The Journal of Biological Chemistry. 287: 13972-84. PMID 22383530 DOI: 10.1074/jbc.M112.341883  1
2012 Ames JB, Lim S, Ikura M. Molecular structure and target recognition of neuronal calcium sensor proteins. Frontiers in Molecular Neuroscience. 5: 10. PMID 22363261 DOI: 10.3389/fnmol.2012.00010  1
2012 Seo MD, Velamakanni S, Ishiyama N, Stathopulos PB, Rossi AM, Khan SA, Dale P, Li C, Ames JB, Ikura M, Taylor CW. Structural and functional conservation of key domains in InsP3 and ryanodine receptors. Nature. 483: 108-12. PMID 22286060 DOI: 10.1038/nature10751  1
2011 Park S, Li C, Ames JB. Nuclear magnetic resonance structure of calcium-binding protein 1 in a Ca(2+) -bound closed state: implications for target recognition. Protein Science : a Publication of the Protein Society. 20: 1356-66. PMID 21608059 DOI: 10.1002/pro.662  1
2011 Xu X, Ishima R, Ames JB. Conformational dynamics of recoverin's Ca2+-myristoyl switch probed by 15N NMR relaxation dispersion and chemical shift analysis. Proteins. 79: 1910-22. PMID 21465563 DOI: 10.1002/prot.23014  1
2011 Li C, Pan W, Braunewell KH, Ames JB. Structural analysis of Mg2+ and Ca2+ binding, myristoylation, and dimerization of the neuronal calcium sensor and visinin-like protein 1 (VILIP-1). The Journal of Biological Chemistry. 286: 6354-66. PMID 21169352 DOI: 10.1074/jbc.M110.173724  1
2010 Park S, Li C, Ames JB. 1H, 15N, and 13C chemical shift assignments of calcium-binding protein 1 with Ca2+ bound at EF1, EF3 and EF4. Biomolecular Nmr Assignments. 4: 159-61. PMID 20503119 DOI: 10.1007/s12104-010-9235-8  1
2009 Li C, Chan J, Haeseleer F, Mikoshiba K, Palczewski K, Ikura M, Ames JB. Structural insights into Ca2+-dependent regulation of inositol 1,4,5-trisphosphate receptors by CaBP1. The Journal of Biological Chemistry. 284: 2472-81. PMID 19008222 DOI: 10.1074/jbc.M806513200  1
2008 Li C, Ames JB. 1H, 15N, and 13C chemical shift assignments of calcium-bound calcium-binding protein 1 (CaBP1). Biomolecular Nmr Assignments. 2: 61-3. PMID 19636926 DOI: 10.1007/s12104-008-9085-9  1
2008 Wingard JN, Ladner J, Vanarotti M, Fisher AJ, Robinson H, Buchanan KT, Engman DM, Ames JB. Structural insights into membrane targeting by the flagellar calcium-binding protein (FCaBP), a myristoylated and palmitoylated calcium sensor in Trypanosoma cruzi. The Journal of Biological Chemistry. 283: 23388-96. PMID 18559337 DOI: 10.1074/jbc.M803178200  1
2008 Lusin JD, Vanarotti M, Li C, Valiveti A, Ames JB. NMR structure of DREAM: Implications for Ca(2+)-dependent DNA binding and protein dimerization. Biochemistry. 47: 2252-64. PMID 18201103 DOI: 10.1021/bi7017267  1
2007 Li C, Ames JB. 1H, 15N, and 13C chemical shift assignments of calcium-binding protein 1 (CaBP1). Biomolecular Nmr Assignments. 1: 77-9. PMID 19636832 DOI: 10.1007/s12104-007-9019-y  1
2007 Strahl T, Huttner IG, Lusin JD, Osawa M, King D, Thorner J, Ames JB. Structural insights into activation of phosphatidylinositol 4-kinase (Pik1) by yeast frequenin (Frq1). The Journal of Biological Chemistry. 282: 30949-59. PMID 17720810 DOI: 10.1074/jbc.M705499200  1
2006 Ames JB, Levay K, Wingard JN, Lusin JD, Slepak VZ. Structural basis for calcium-induced inhibition of rhodopsin kinase by recoverin. The Journal of Biological Chemistry. 281: 37237-45. PMID 17020884 DOI: 10.1074/jbc.M606913200  1
2006 Stathopulos PB, Li GY, Plevin MJ, Ames JB, Ikura M. Stored Ca2+ depletion-induced oligomerization of stromal interaction molecule 1 (STIM1) via the EF-SAM region: An initiation mechanism for capacitive Ca2+ entry. The Journal of Biological Chemistry. 281: 35855-62. PMID 17020874 DOI: 10.1074/jbc.M608247200  1
2006 Lin Y, Lusin JD, Ye D, Dunaway-Mariano D, Ames JB. Examination of the structure, stability, and catalytic potential in the engineered phosphoryl carrier domain of pyruvate phosphate dikinase. Biochemistry. 45: 1702-11. PMID 16460017 DOI: 10.1021/bi051816l  1
2006 Ikura M, Ames JB. Genetic polymorphism and protein conformational plasticity in the calmodulin superfamily: two ways to promote multifunctionality. Proceedings of the National Academy of Sciences of the United States of America. 103: 1159-64. PMID 16432210 DOI: 10.1073/pnas.0508640103  1
2005 Wingard JN, Chan J, Bosanac I, Haeseleer F, Palczewski K, Ikura M, Ames JB. Structural analysis of Mg2+ and Ca2+ binding to CaBP1, a neuron-specific regulator of calcium channels. The Journal of Biological Chemistry. 280: 37461-70. PMID 16147998 DOI: 10.1074/jbc.M508541200  1
2005 Ames JB, Vyas V, Lusin JD, Mariuzza R. NMR structure of the natural killer cell receptor 2B4 (CD244): implications for ligand recognition. Biochemistry. 44: 6416-23. PMID 15850375 DOI: 10.1021/bi050139s  1
2005 Osawa M, Dace A, Tong KI, Valiveti A, Ikura M, Ames JB. Mg2+ and Ca2+ differentially regulate DNA binding and dimerization of DREAM. The Journal of Biological Chemistry. 280: 18008-14. PMID 15746104 DOI: 10.1074/jbc.M500338200  1
2003 Valentine KG, Mesleh MF, Opella SJ, Ikura M, Ames JB. Structure, topology, and dynamics of myristoylated recoverin bound to phospholipid bilayers. Biochemistry. 42: 6333-40. PMID 12767213 DOI: 10.1021/bi0206816  1
2003 Huttner IG, Strahl T, Osawa M, King DS, Ames JB, Thorner J. Molecular interactions of yeast frequenin (Frq1) with the phosphatidylinositol 4-kinase isoform, Pik1. The Journal of Biological Chemistry. 278: 4862-74. PMID 12477731 DOI: 10.1074/jbc.M207920200  1
2002 Ames JB, Ikura M. Structure and membrane-targeting mechanism of retinal Ca2+-binding proteins, recoverin and GCAP-2. Advances in Experimental Medicine and Biology. 514: 333-48. PMID 12596931  1
2002 Ikura M, Osawa M, Ames JB. The role of calcium-binding proteins in the control of transcription: structure to function. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 24: 625-36. PMID 12111723 DOI: 10.1002/bies.10105  1
2002 Yap KL, Ames JB, Swindells MB, Ikura M. Vector geometry mapping. A method to characterize the conformation of helix-loop-helix calcium-binding proteins. Methods in Molecular Biology (Clifton, N.J.). 173: 317-24. PMID 11859772 DOI: 10.1385/1-59259-184-1:317  1
2001 Osawa M, Tong KI, Lilliehook C, Wasco W, Buxbaum JD, Cheng HY, Penninger JM, Ikura M, Ames JB. Calcium-regulated DNA binding and oligomerization of the neuronal calcium-sensing protein, calsenilin/DREAM/KChIP3. The Journal of Biological Chemistry. 276: 41005-13. PMID 11535596 DOI: 10.1074/jbc.M105842200  1
2000 Ames JB, Ikura M, Stryer L. Molecular structure of membrane-targeting calcium sensors in vision: recoverin and guanylate cyclase-activating protein 2. Methods in Enzymology. 316: 121-32. PMID 10800672  1
1999 Ames JB, Dizhoor AM, Ikura M, Palczewski K, Stryer L. Three-dimensional structure of guanylyl cyclase activating protein-2, a calcium-sensitive modulator of photoreceptor guanylyl cyclases. The Journal of Biological Chemistry. 274: 19329-37. PMID 10383444 DOI: 10.1074/jbc.274.27.19329  1
1998 Tanaka T, Ames JB, Kainosho M, Stryer L, Ikura M. Differential isotype labeling strategy for determining the structure of myristoylated recoverin by NMR spectroscopy. Journal of Biomolecular Nmr. 11: 135-52. PMID 9679292  1
1997 Ames JB, Ishima R, Tanaka T, Gordon JI, Stryer L, Ikura M. Molecular mechanics of calcium-myristoyl switches. Nature. 389: 198-202. PMID 9296500 DOI: 10.1038/38310  1
1996 Ames JB, Tanaka T, Stryer L, Ikura M. Portrait of a myristoyl switch protein. Current Opinion in Structural Biology. 6: 432-8. PMID 8794166 DOI: 10.1016/S0959-440X(96)80106-0  1
1995 Ames JB, Tanaka T, Ikura M, Stryer L. Nuclear magnetic resonance evidence for Ca(2+)-induced extrusion of the myristoyl group of recoverin. The Journal of Biological Chemistry. 270: 30909-13. PMID 8537345  1
1995 Ames JB, Porumb T, Tanaka T, Ikura M, Stryer L. Amino-terminal myristoylation induces cooperative calcium binding to recoverin. The Journal of Biological Chemistry. 270: 4526-33. PMID 7876221 DOI: 10.1074/jbc.270.9.4526  1
1995 Tanaka T, Ames JB, Harvey TS, Stryer L, Ikura M. Sequestration of the membrane-targeting myristoyl group of recoverin in the calcium-free state. Nature. 376: 444-7. PMID 7630423 DOI: 10.1038/376444a0  1
1994 Ames JB, Tanaka T, Stryer L, Ikura M. Secondary structure of myristoylated recoverin determined by three-dimensional heteronuclear NMR: implications for the calcium-myristoyl switch. Biochemistry. 33: 10743-53. PMID 8075075  1
1992 Ames JB, Ros M, Raap J, Lugtenburg J, Mathies RA. Time-resolved ultraviolet resonance Raman studies of protein structure: application to bacteriorhodopsin. Biochemistry. 31: 5328-34. PMID 1606157  1
1992 Ames JB, Raap J, Lugtenburg J, Mathies RA. Resonance Raman study of halorhodopsin photocycle kinetics, chromophore structure, and chloride-pumping mechanism. Biochemistry. 31: 12546-54. PMID 1472492  1
1991 Mathies RA, Lin SW, Ames JB, Pollard WT. From femtoseconds to biology: mechanism of bacteriorhodopsin's light-driven proton pump. Annual Review of Biophysics and Biophysical Chemistry. 20: 491-518. PMID 1867724 DOI: 10.1146/annurev.bb.20.060191.002423  1
1990 Ames JB, Mathies RA. The role of back-reactions and proton uptake during the N----O transition in bacteriorhodopsin's photocycle: a kinetic resonance Raman study. Biochemistry. 29: 7181-90. PMID 2169875  1
1989 Ames JB, Fodor SP, Gebhard R, Raap J, van den Berg EM, Lugtenburg J, Mathies RA. Bacteriorhodopsin's M412 intermediate contains a 13-cis, 14-s-trans, 15-anti-retinal Schiff base chromophore. Biochemistry. 28: 3681-7. PMID 2751988  1
1988 Fodor SP, Ames JB, Gebhard R, van den Berg EM, Stoeckenius W, Lugtenburg J, Mathies RA. Chromophore structure in bacteriorhodopsin's N intermediate: implications for the proton-pumping mechanism. Biochemistry. 27: 7097-101. PMID 2848578  1
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