Publications

For a full list of publications visit: Pubmed

1. Yu Q, Lim S, Rockwell NC, Martin SS, Clark Lagarias J, Ames JB. 1H, 15N, and 13C 
chemical shift assignments of cyanobacteriochrome NpR6012g4 in the red-absorbing 
dark state. Biomolecular NMR assignments. 2016; 10(1):139-42. NIHMSID:
NIHMS731734 PubMed [journal] PMID: 26482922, PMCID: PMC4789077

2. Turner M, Anderson DE, Rajan S, Hell JW, Ames JB. Chemical shift assignments of
the C-terminal EF-hand domain of α-actinin-1. Biomolecular NMR assignments. 2016;
10(1):219-22. NIHMSID: NIHMS759275 PubMed [journal] PMID: 26861220, PMCID:
PMC4789133

3. Turner M, Zhang Y, Carlson HL, Stadler HS, Ames JB. Chemical shift assignments of
mouse HOXD13 DNA binding domain bound to duplex DNA. Biomolecular NMR
assignments. 2015; 9(2):267-70. NIHMSID: NIHMS648256 PubMed [journal] PMID:
25491407, PMCID: PMC4465062

4. Rockwell NC, Martin SS, Lim S, Lagarias JC, Ames JB. Characterization of
Red/Green Cyanobacteriochrome NpR6012g4 by Solution Nuclear Magnetic Resonance
Spectroscopy: A Protonated Bilin Ring System in Both Photostates. Biochemistry.
2015; 54(16):2581-600. PubMed [journal] PMID: 25843271

5. Nepomuceno GM, Chan KM, Huynh V, Martin KS, Moore JT, O'Brien TE, Pollo LA,
Sarabia FJ, Tadeus C, Yao Z, Anderson DE, Ames JB, Shaw JT. Synthesis and
Evaluation of Quinazolines as Inhibitors of the Bacterial Cell Division Protein
FtsZ. ACS medicinal chemistry letters. 2015; 6(3):308-12. PubMed [journal] PMID: 
25815151, PMCID: PMC4360151

6. 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. 2014; 289(45):31262-73. PubMed
[journal] PMID: 25258313, PMCID: PMC4223327

7. Lim S, Rockwell NC, Martin SS, Lagarias JC, Ames JB. ¹H, ¹⁵N, and ¹³C chemical
shift assignments of cyanobacteriochrome NpF2164g3 in the photoproduct state.
Biomolecular NMR assignments. 2014; 8(2):259-62. NIHMSID: NIHMS490632 PubMed
[journal] PMID: 23749453, PMCID: PMC3808498

8. Park S, Li C, Ames JB. ¹H, ¹⁵N, and ¹³C chemical shift assignments of murine
calcium-binding protein 4. Biomolecular NMR assignments. 2014; 8(2):361-4.
NIHMSID: NIHMS513846 PubMed [journal] PMID: 23925854, PMCID: PMC3877709

9. Zhang Y, Matt L, Patriarchi T, Malik ZA, Chowdhury D, Park DK, Renieri A, Ames
JB, Hell JW. Capping of the N-terminus of PSD-95 by calmodulin triggers its
postsynaptic release. The EMBO journal. 2014; 33(12):1341-53. PubMed [journal]
PMID: 24705785, PMCID: PMC4194123

10. Lim S, Rockwell NC, Martin SS, Dallas JL, Lagarias JC, Ames JB. Photoconversion
changes bilin chromophore conjugation and protein secondary structure in the
violet/orange cyanobacteriochrome NpF2164g3' [corrected]. Photochemical &
photobiological sciences : Official journal of the European Photochemistry
Association and the European Society for Photobiology. 2014; 13(6):951-62.
NIHMSID: NIHMS588768 PubMed [journal] PMID: 24745038, PMCID: PMC4062569

11. 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. 2014; 289(14):10140-54. PubMed [journal] PMID:
24567338, PMCID: PMC3974984

12. Li C, Ames JB. ¹H, ¹³C, and ¹⁵N chemical shift assignments of neuronal calcium
sensor protein, hippocalcin. Biomolecular NMR assignments. 2014; 8(1):63-6.
NIHMSID: NIHMS430307 PubMed [journal] PMID: 23250791, PMCID: PMC3625700

13. 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. 2014; 7:19. PubMed [journal] PMID: 24672427,
PMCID: PMC3956117

14. 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. 2013; 52(34):5800-8. NIHMSID:
NIHMS516506 PubMed [journal] PMID: 23906368, PMCID: PMC3784611

15. 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. 2013; 110(21):8507-12.
PubMed [journal] PMID: 23650371, PMCID: PMC3666712

16. 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. 2013; 7(1):39-42. NIHMSID: NIHMS601698 PubMed
[journal] PMID: 22392341, PMCID: PMC4080920

17. Lim S, Peshenko IV, Dizhoor AM, Ames JB. Structural insights for activation of
retinal guanylate cyclase by GCAP1. PloS one. 2013; 8(11):e81822. PubMed
[journal] PMID: 24236217, PMCID: PMC3827477

18. Xu X, Olson CL, Engman DM, Ames JB. 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. PubMed [journal] PMID: 23011904, PMCID:
PMC3575923

19. Anderson DE, Kim MB, Moore JT, O'Brien TE, Sorto NA, Grove CI, Lackner LL, Ames
JB, Shaw JT. 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. NIHMSID: NIHMS407513 PubMed [journal] 
PMID: 22958099, PMCID: PMC3514448

20. Kim MB, O'Brien TE, Moore JT, Anderson DE, Foss MH, Weibel DL, Ames JB, Shaw JT. 
The Synthesis and Antimicrobial Activity of Heterocyclic Derivatives of Totarol. 
ACS medicinal chemistry letters. 2012; 3(10):818-822. NIHMSID: NIHMS407501 PubMed
[journal] PMID: 23119123, PMCID: PMC3483140

21. Ames JB, Lim S. Molecular structure and target recognition of neuronal calcium
sensor proteins. Biochimica et biophysica acta. 2012; 1820(8):1205-13. NIHMSID:
NIHMS331535 PubMed [journal] PMID: 22020049, PMCID: PMC3266469

22. Sugiarto G, Lau K, Qu J, Li Y, Lim S, Mu S, Ames JB, Fisher AJ, Chen X. A
sialyltransferase mutant with decreased donor hydrolysis and reduced sialidase
activities for directly sialylating LewisX. ACS chemical biology. 2012;
7(7):1232-40. NIHMSID: NIHMS377686 PubMed [journal] PMID: 22583967, PMCID:
PMC3521065

23. 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. 2012; 287(17):13972-84. PubMed [journal] PMID: 22383530,
PMCID: PMC3340203

24. Zhang Y, Li Z, Sacks DB, Ames JB. Structural basis for Ca2+-induced activation
and dimerization of estrogen receptor α by calmodulin. The Journal of biological 
chemistry. 2012; 287(12):9336-44. PubMed [journal] PMID: 22275375, PMCID:
PMC3308758

25. 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. 2012; 483(7387):108-12.
NIHMSID: UKMS40158 PubMed [journal] PMID: 22286060, PMCID: PMC3378505

26. 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. 2011; 20(8):1356-66.
PubMed [journal] PMID: 21608059, PMCID: PMC3189521

27. 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. 2011; 79(6):1910-22. NIHMSID: NIHMS274078 PubMed [journal] PMID:
21465563, PMCID: PMC3092842

28. Lim S, Strahl T, Thorner J, Ames JB. 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. PubMed [journal] PMID:
21288895, PMCID: PMC3069458

29. 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. 2011;
286(8):6354-66. PubMed [journal] PMID: 21169352, PMCID: PMC3057812

30. Xu W, Xu X, Leal WS, Ames JB. 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. NIHMSID:
NIHMS262017 PubMed [journal] PMID: 21130734, PMCID: PMC3019287

31. Wang CK, Simon A, Jessen CM, Oliveira CL, Mack L, Braunewell KH, Ames JB,
Pedersen JS, Hofmann A. Divalent cations and redox conditions regulate the
molecular structure and function of visinin-like protein-1. PloS one. 2011;
6(11):e26793. PubMed [journal] PMID: 22073194, PMCID: PMC3206844

32. Mao Y, Xu X, Xu W, Ishida Y, Leal WS, Ames JB, Clardy J. Crystal and solution
structures of an odorant-binding protein from the southern house mosquito
complexed with an oviposition pheromone. Proceedings of the National Academy of
Sciences of the United States of America. 2010; 107(44):19102-7. PubMed [journal]
PMID: 20956299, PMCID: PMC2973904

33. 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. 2010; 4(2):159-61. PubMed [journal] PMID: 20503119, PMCID:
PMC2947014

34. Kohler AC, Gae DD, Richley MA, Stoll S, Gunn A, Lim S, Martin SS, Doukov TI,
Britt RD, Ames JB, Lagarias JC, Fisher AJ. Structural basis for hydration
dynamics in radical stabilization of bilin reductase mutants. Biochemistry. 2010;
49(29):6206-18. NIHMSID: NIHMS219109 PubMed [journal] PMID: 20557110, PMCID:
PMC2914091

35. Zhang Y, Thornburg CK, Stadler HS, Ames JB. Backbone chemical shift assignments
of mouse HOXA13 DNA binding domain bound to duplex DNA. Biomolecular NMR
assignments. 2010; 4(1):97-9. PubMed [journal] PMID: 20232265, PMCID: PMC2862170

36. Xu X, Xu W, Rayo J, Ishida Y, Leal WS, Ames JB. NMR structure of navel orangeworm
moth pheromone-binding protein (AtraPBP1): implications for pH-sensitive
pheromone detection. Biochemistry. 2010; 49(7):1469-76. NIHMSID: NIHMS173959
PubMed [journal] PMID: 20088570, PMCID: PMC2822879

37. Neuronal calcium sensor-1 (Ncs1p) is up-regulated by calcineurin to promote Ca2+ 
tolerance in fission yeast
Katagiri-Hamasaki N, Ames JB.
The Journal of biological chemistry. 2010 February 12; 285(7):4405.
My Bibliography [journal] 

38. Hamasaki-Katagiri N, Ames JB. 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. PubMed [journal] PMID: 20018864,
PMCID: PMC2836045

39. Valentine KG, Peterson RW, Saad JS, Summers MF, Xu X, Ames JB, Wand AJ. Reverse
micelle encapsulation of membrane-anchored proteins for solution NMR studies.
Structure (London, England : 1993). 2010; 18(1):9-16. NIHMSID: NIHMS166055 PubMed
[journal] PMID: 20152148, PMCID: PMC2876244

40. Schenauer MR, Meissen JK, Seo Y, Ames JB, Leary JA. 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. NIHMSID: NIHMS161069 PubMed [journal] PMID:
19925012, PMCID: PMC2810830

41. Zhang Y, Thornburg CK, Stadler HS, Ames JB. (1)H, (15)N, and (13)C chemical shift
assignments of mouse HOXA13 DNA binding domain. Biomolecular NMR assignments.
2009; 3(2):199-201. PubMed [journal] PMID: 19888690, PMCID: PMC2772948

42. Xu X, Xu W, Ishida Y, Li Y, Leal WS, Ames JB. (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. PubMed [journal] PMID: 19888689, PMCID: PMC2772962

43. Lim S, Ames JB. (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. PubMed [journal] PMID: 19851889, PMCID: PMC2772964

44. Leal WS, Ishida Y, Pelletier J, Xu W, Rayo J, Xu X, Ames JB. Olfactory proteins
mediating chemical communication in the navel orangeworm moth, Amyelois
transitella. PloS one. 2009; 4(9):e7235. PubMed [journal] PMID: 19789654, PMCID: 
PMC2749207

45. Lim S, Peshenko I, Dizhoor A, Ames JB. Effects of Ca2+, Mg2+, and myristoylation 
on guanylyl cyclase activating protein 1 structure and stability. Biochemistry.
2009; 48(5):850-62. NIHMSID: NIHMS91590 PubMed [journal] PMID: 19143494, PMCID:
PMC2637916

46. 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.
2009; 284(4):2472-81. PubMed [journal] PMID: 19008222, PMCID: PMC2629100