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James Ames

Research Profile

Chemicals & Drugs

Genes & Molecular Sequences

Amino Acid Sequences

Concepts & Ideas

Procedures

Nuclear Magnetic Resonance, Biomolecular

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Publications

TOP 3
Sunghyuk Lim; Igor V Peshenko; Alexander M Dizhoor; James B Ames
Backbone (1)H, (13)C, and (15)N resonance assignments of guanylyl cyclase activating protein-1, GCAP1.
Xianzhong Xu; David M Engman; Cheryl L Olson; James B Ames
(1)H, (15)N, and (13)C chemical shift assignments of the calflagin Tb24 flagellar calcium binding protein of Trypanosoma brucei.
Xianzhong Xu; David M Engman; Cheryl L Olson; James B Ames
NMR structure of the calflagin Tb24 flagellar calcium binding protein of Trypanosoma brucei.

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All Publications

2013: Sunghyuk Lim; Igor V Peshenko; Alexander M Dizhoor; James B Ames
Backbone (1)H, (13)C, and (15)N resonance assignments of guanylyl cyclase activating protein-1, GCAP1.
Biomolecular NMR assignments 2013;7(1):39-42.
2013: Xianzhong Xu; David M Engman; Cheryl L Olson; James B Ames
(1)H, (15)N, and (13)C chemical shift assignments of the calflagin Tb24 flagellar calcium binding protein of Trypanosoma brucei.
Biomolecular NMR assignments 2013;7(1):9-12.
2012: Xianzhong Xu; David M Engman; Cheryl L Olson; James B Ames
NMR structure of the calflagin Tb24 flagellar calcium binding protein of Trypanosoma brucei.
Protein science : a publication of the Protein Society 2012;21(12):1942-7.
2012: David E Anderson; Charles I Grove; Michelle B Kim; Laura L Lackner; Jared T Moore; Terrence E O'Brien; James B Ames; Nohemy A Sorto; Jared T Shaw
Comparison of small molecule inhibitors of the bacterial cell division protein FtsZ and identification of a reliable cross-species inhibitor.
ACS chemical biology 2012;7(11):1918-28.
2012: Go Sugiarto; James B Ames; Andrew J Fisher; Kam Lau; Yanhong Li; Sunghyuk Lim; Shengmao Mu; Jingyao Qu; Xi Chen
A sialyltransferase mutant with decreased donor hydrolysis and reduced sialidase activities for directly sialylating LewisX.
ACS chemical biology 2012;7(7):1232-40.
2012: Yonghong Zhang; Zhigang Li; David B Sacks; James B Ames
Structural basis for Ca2+-induced activation and dimerization of estrogen receptor α by calmodulin.
The Journal of biological chemistry 2012;287(12):9336-44.
2012: Min-Duk Seo; Peter B Stathopulos; Saroj Velamakanni; James B Ames; Philippa Dale; Mitsuhiko Ikura; Noboru Ishiyama; Samir A Khan; Congmin Li; Ana M Rossi; Colin W Taylor
Structural and functional conservation of key domains in InsP3 and ryanodine receptors.
Nature 2012;483(7387):108-12.
2012: James B Ames; Sunghyuk Lim; Mitsuhiko Ikura
Molecular structure and target recognition of neuronal calcium sensor proteins.
Frontiers in molecular neuroscience 2012;5():10.
2011: Saebomi Park; Congmin Li; James B Ames
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 2011;20(8):1356-66.
2011: Xianzhong Xu; Rieko Ishima; James B Ames
Conformational dynamics of recoverin's Ca2+-myristoyl switch probed by 15N NMR relaxation dispersion and chemical shift analysis.
Proteins 2011;79(6):1910-22.
2011: Sunghyuk Lim; Thomas Strahl; Jeremy Thorner; James B Ames
Structure of a Ca2+-myristoyl switch protein that controls activation of a phosphatidylinositol 4-kinase in fission yeast.
The Journal of biological chemistry 2011;286(14):12565-77.
2011: Congmin Li; Wensheng Pan; Karl H Braunewell; James B Ames
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 2011;286(8):6354-66.
2011: Wei Xu; Xianzhong Xu; Walter S Leal; James B Ames
Extrusion of the C-terminal helix in navel orangeworm moth pheromone-binding protein (AtraPBP1) controls pheromone binding.
Biochemical and biophysical research communications 2011;404(1):335-8.
2011: Yonghong Zhang; Christine A Larsen; H Scott Stadler; James B Ames
Structural basis for sequence specific DNA binding and protein dimerization of HOXA13.
PloS one 2011;6(8):e23069.
2010: Saebomi Park; Congmin Li; James B Ames
1H, 15N, and 13C chemical shift assignments of calcium-binding protein 1 with Ca2+ bound at EF1, EF3 and EF4.
Biomolecular NMR assignments 2010;4(2):159-61.
2010: Yonghong Zhang; Chelsea K Thornburg; H Scott Stadler; James B Ames
Backbone chemical shift assignments of mouse HOXA13 DNA binding domain bound to duplex DNA.
Biomolecular NMR assignments 2010;4(1):97-9.
2010: Xianzhong Xu; Wei Xu; Josep Rayo; Yuko Ishida; Walter S Leal; James B Ames
NMR structure of navel orangeworm moth pheromone-binding protein (AtraPBP1): implications for pH-sensitive pheromone detection.
Biochemistry 2010;49(7):1469-76.
2010: Nobuko Hamasaki-Katagiri; James B Ames
Neuronal calcium sensor-1 (Ncs1p) is up-regulated by calcineurin to promote Ca2+ tolerance in fission yeast.
The Journal of biological chemistry 2010;285(7):4405-14.
2010: Kathleen G Valentine; Ronald W Peterson; Jamil S Saad; Michael F Summers; Xianzhong Xu; James B Ames; A Joshua Wand
Reverse micelle encapsulation of membrane-anchored proteins for solution NMR studies.
Structure (London, England : 1993) 2010;18(1):9-16.
2009: Matthew R Schenauer; John K Meissen; Youjin Seo; James B Ames; Julie A Leary
Heparan sulfate separation, sequencing, and isomeric differentiation: ion mobility spectrometry reveals specific iduronic and glucuronic acid-containing hexasaccharides.
Analytical chemistry 2009;81(24):10179-85.
2009: Yonghong Zhang; Chelsea K Thornburg; H Scott Stadler; James B Ames
(1)H, (15)N, and (13)C chemical shift assignments of mouse HOXA13 DNA binding domain.
Biomolecular NMR assignments 2009;3(2):199-201.
2009: Xianzhong Xu; Wei Xu; Yuko Ishida; Yun Li; Walter S Leal; James B Ames
(1)H, (15)N, and (13)C chemical shift assignments of the mosquito odorant binding protein-1 (CquiOBP1) bound to the mosquito oviposition pheromone.
Biomolecular NMR assignments 2009;3(2):195-7.
2009: Sunghyuk Lim; James B Ames
(1)H, (15)N, and (13)C chemical shift assignments of neuronal calcium sensor-1 homolog from fission yeast.
Biomolecular NMR assignments 2009;3(2):269-71.
2009: Jonel P Saludes; James B Ames; Jacquelyn Gervay-Hague
Synthesis and structural characterization of sialic acid-glutamic acid hybrid foldamers as conformational surrogates of alpha-2,8-linked polysialic acid.
Journal of the American Chemical Society 2009;131(15):5495-505.
2009: Sunghyuk Lim; Igor Peshenko; Alexander Dizhoor; James B Ames
Effects of Ca2+, Mg2+, and myristoylation on guanylyl cyclase activating protein 1 structure and stability.
Biochemistry 2009;48(5):850-62.
2009: Congmin Li; Jenny Chan; Francoise Haeseleer; Katsuhiko Mikoshiba; Krzysztof Palczewski; Mitsuhiko Ikura; James B Ames
Structural insights into Ca2+-dependent regulation of inositol 1,4,5-trisphosphate receptors by CaBP1.
The Journal of biological chemistry 2009;284(4):2472-81.
2009: Walter S Leal; Yuko Ishida; Julien Pelletier; Wei Xu; Josep Rayo; Xianzhong Xu; James B Ames
Olfactory proteins mediating chemical communication in the navel orangeworm moth, Amyelois transitella.
PloS one 2009;4(9):e7235.
2008: Xianzhong Xu; Yun Li; Josep Rayo; Yuko Ishida; Walter Leal; James B Ames
1H, 15N, and 13C Chemical shift assignments of the navel orange worm pheromone-binding protein-1 (Atra-PBP1).
Biomolecular NMR assignments 2008;2(2):105-6.
2008: Jennifer Wingard; Jane E Ladner; Murugendra Vanarotti; Andrew J Fisher; Howard Robinson; Kathryn T Buchanan; David M Engman; James B Ames
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 2008;283(34):23388-96.
2008: Congmin Li; James B Ames
1H, 15N, and 13C chemical shift assignments of calcium-bound calcium-binding protein 1 (CaBP1).
Biomolecular NMR assignments 2008;2(1):61-3.
2008: Jacqueline D Lusin; Murugendra Vanarotti; Congmin Li; Aswani Valiveti; James B Ames
NMR structure of DREAM: Implications for Ca(2+)-dependent DNA binding and protein dimerization.
Biochemistry 2008;47(8):2252-64.
2007: Thomas Strahl; Inken G Huttner; Jacqueline D Lusin; Masanori Osawa; David King; Jeremy Thorner; James B Ames
Structural insights into activation of phosphatidylinositol 4-kinase (Pik1) by yeast frequenin (Frq1).
The Journal of biological chemistry 2007;282(42):30949-59.
2007: Congmin Li; James B Ames
1H, 15N, and 13C chemical shift assignments of calcium-binding protein 1 (CaBP1).
Biomolecular NMR assignments 2007;1(1):77-9.
2006: James B Ames; Konstantin Levay; Jennifer Wingard; Jacqueline D Lusin; Vladlen Z Slepak
Structural basis for calcium-induced inhibition of rhodopsin kinase by recoverin.
The Journal of biological chemistry 2006;281(48):37237-45.
2006: Peter B Stathopulos; Guang-Yao Li; Michael J Plevin; James B Ames; Mitsuhiko Ikura
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 2006;281(47):35855-62.
2006: Ying Lin; Jacqueline D Lusin; Dongmei Ye; Debra Dunaway-Mariano; James B Ames
Examination of the structure, stability, and catalytic potential in the engineered phosphoryl carrier domain of pyruvate phosphate dikinase.
Biochemistry 2006;45(6):1702-11.
2006: Mitsuhiko Ikura; James B Ames
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 2006;103(5):1159-64.
2005: Kathryn T Buchanan; James B Ames; Sofya H Asfaw; Jennifer Wingard; Cheryl L Olson; Patricia T Campana; Ana Paula U Araújo; David M Engman
A flagellum-specific calcium sensor.
The Journal of biological chemistry 2005;280(48):40104-11.
2005: Jennifer Wingard; Jenny Chan; Ivan Bosanac; Francoise Haeseleer; Krzysztof Palczewski; Mitsuhiko Ikura; James B Ames
Structural analysis of Mg2+ and Ca2+ binding to CaBP1, a neuron-specific regulator of calcium channels.
The Journal of biological chemistry 2005;280(45):37461-70.
2005: Masanori Osawa; Alexandra Dace; Kit I Tong; Aswani Valiveti; Mitsuhiko Ikura; James B Ames
Mg2+ and Ca2+ differentially regulate DNA binding and dimerization of DREAM.
The Journal of biological chemistry 2005;280(18):18008-14.
2005: James B Ames; Vinay Vyas; Jacqueline D Lusin; Roy A Mariuzza
NMR structure of the natural killer cell receptor 2B4 (CD244): implications for ligand recognition.
Biochemistry 2005;44(17):6416-23.
2004: Jingsong Zhu; Stacy M Stabler; James B Ames; Ilia Baskakov; Mervyn Monteiro
Calcium binding sequences in calmyrin regulates interaction with presenilin-2.
Experimental cell research 2004;300(2):440-54.
2004: Nobuko Hamasaki-Katagiri; Tatiana Molchanova; Kazuyo Takeda; James B Ames
Fission yeast homolog of neuronal calcium sensor-1 (Ncs1p) regulates sporulation and confers calcium tolerance.
The Journal of biological chemistry 2004;279(13):12744-54.
2003: Kathleen G Valentine; Michael F Mesleh; Stanley J Opella; Mitsuhiko Ikura; James B Ames
Structure, topology, and dynamics of myristoylated recoverin bound to phospholipid bilayers.
Biochemistry 2003;42(21):6333-40.
2003: Inken G Huttner; Thomas Strahl; Masanori Osawa; David S King; James B Ames; Jeremy Thorner
Molecular interactions of yeast frequenin (Frq1) with the phosphatidylinositol 4-kinase isoform, Pik1.
The Journal of biological chemistry 2003;278(7):4862-74.
2002: Mitsuhiko Ikura; Masanori Osawa; James B Ames
The role of calcium-binding proteins in the control of transcription: structure to function.
BioEssays : news and reviews in molecular, cellular and developmental biology 2002;24(7):625-36.
2002: James B Ames; Nobuko Hamasaki; Tatiana Molchanova
Structure and calcium-binding studies of a recoverin mutant (E85Q) in an allosteric intermediate state.
Biochemistry 2002;41(18):5776-87.
2002: James B Ames; Mitsuhiko Ikura
Structure and membrane-targeting mechanism of retinal Ca2+-binding proteins, recoverin and GCAP-2.
Advances in experimental medicine and biology 2002;514():333-48.
2002: Kyoko L Yap; James B Ames; Mark B Swindells; Mitsuhiko Ikura
Vector geometry mapping. A method to characterize the conformation of helix-loop-helix calcium-binding proteins.
Methods in molecular biology (Clifton, N.J.) 2002;173():317-24.
2001: Masanori Osawa; Kit I Tong; Christina Lilliehook; Wilma Wasco; Joseph Buxbaum; H Y Cheng; J M Penninger; Mitsuhiko Ikura; James B Ames
Calcium-regulated DNA binding and oligomerization of the neuronal calcium-sensing protein, calsenilin/DREAM/KChIP3.
The Journal of biological chemistry 2001;276(44):41005-13.
2000: James B Ames; K B Hendricks; Thomas Strahl; Inken G Huttner; N Hamasaki; Jeremy Thorner
Structure and calcium-binding properties of Frq1, a novel calcium sensor in the yeast Saccharomyces cerevisiae.
Biochemistry 2000;39(40):12149-61.
2000: Krzysztof Palczewski; A S Polans; Wolfgang Baehr; James B Ames
Ca(2+)-binding proteins in the retina: structure, function, and the etiology of human visual diseases.
BioEssays : news and reviews in molecular, cellular and developmental biology 2000;22(4):337-50.
2000: James B Ames; Mitsuhiko Ikura; L Stryer
Molecular structure of membrane-targeting calcium sensors in vision: recoverin and guanylate cyclase-activating protein 2.
Methods in enzymology 2000;316():121-32.
1999: Kyoko L Yap; James B Ames; Mark B Swindells; Mitsuhiko Ikura
Diversity of conformational states and changes within the EF-hand protein superfamily.
Proteins 1999;37(3):499-507.
1999: James B Ames; Alexander M Dizhoor; Mitsuhiko Ikura; Krzysztof Palczewski; L Stryer
Three-dimensional structure of guanylyl cyclase activating protein-2, a calcium-sensitive modulator of photoreceptor guanylyl cyclases.
The Journal of biological chemistry 1999;274(27):19329-37.
1998: A N Baldwin; James B Ames
Core mutations that promote the calcium-induced allosteric transition of bovine recoverin.
Biochemistry 1998;37(50):17408-19.
1998: T Tanaka; James B Ames; Masatsune Kainosho; L Stryer; Mitsuhiko Ikura
Differential isotype labeling strategy for determining the structure of myristoylated recoverin by NMR spectroscopy.
Journal of biomolecular NMR 1998;11(2):135-52.
1997: Jean-René Alattia; James B Ames; T Porumb; Kit I Tong; Yew-Meng Heng; P Ottensmeyer; Cyril M Kay; Mitsuhiko Ikura
Lateral self-assembly of E-cadherin directed by cooperative calcium binding.
FEBS letters 1997;417(3):405-8.
1997: James B Ames; R Ishima; T Tanaka; J I Gordon; L Stryer; Mitsuhiko Ikura
Molecular mechanics of calcium-myristoyl switches.
Nature 1997;389(6647):198-202.
1996: James B Ames; T Tanaka; L Stryer; Mitsuhiko Ikura
Portrait of a myristoyl switch protein.
Current opinion in structural biology 1996;6(4):432-8.
1995: James B Ames; T Tanaka; Mitsuhiko Ikura; L Stryer
Nuclear magnetic resonance evidence for Ca(2+)-induced extrusion of the myristoyl group of recoverin.
The Journal of biological chemistry 1995;270(52):30909-13.
1995: T Tanaka; James B Ames; T S Harvey; L Stryer; Mitsuhiko Ikura
Sequestration of the membrane-targeting myristoyl group of recoverin in the calcium-free state.
Nature 1995;376(6539):444-7.
1995: James B Ames; T Porumb; T Tanaka; Mitsuhiko Ikura; L Stryer
Amino-terminal myristoylation induces cooperative calcium binding to recoverin.
The Journal of biological chemistry 1995;270(9):4526-33.
1994: James B Ames; T Tanaka; L Stryer; Mitsuhiko Ikura
Secondary structure of myristoylated recoverin determined by three-dimensional heteronuclear NMR: implications for the calcium-myristoyl switch.
Biochemistry 1994;33(35):10743-53.
1992: James B Ames; J Raap; Johan Lugtenburg; Richard A Mathies
Resonance Raman study of halorhodopsin photocycle kinetics, chromophore structure, and chloride-pumping mechanism.
Biochemistry 1992;31(50):12546-54.
1992: James B Ames; M Ros; J Raap; Johan Lugtenburg; Richard A Mathies
Time-resolved ultraviolet resonance Raman studies of protein structure: application to bacteriorhodopsin.
Biochemistry 1992;31(23):5328-34.
1991: Richard A Mathies; S W Lin; James B Ames; W T Pollard
From femtoseconds to biology: mechanism of bacteriorhodopsin's light-driven proton pump.
Annual review of biophysics and biophysical chemistry 1991;20():491-518.
1990: James B Ames; Richard A Mathies
The role of back-reactions and proton uptake during the N----O transition in bacteriorhodopsin's photocycle: a kinetic resonance Raman study.
Biochemistry 1990;29(31):7181-90.
1989: James B Ames; S P Fodor; R Gebhard; J Raap; E M van den Berg; Johan Lugtenburg; Richard A Mathies
Bacteriorhodopsin's M412 intermediate contains a 13-cis, 14-s-trans, 15-anti-retinal Schiff base chromophore.
Biochemistry 1989;28(9):3681-7.
1988: S P Fodor; James B Ames; R Gebhard; E M van den Berg; W Stoeckenius; Johan Lugtenburg; Richard A Mathies
Chromophore structure in bacteriorhodopsin's N intermediate: implications for the proton-pumping mechanism.
Biochemistry 1988;27(18):7097-101.