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Choel Kim Lab

Publications

Master
Content

Peer reviewed publications:

Spraggon G, Kim C, Nguyen-Huu X, Yee MC, Yanofsky C, Mills SE. The structures of anthranilate synthase of Serratia marcescens crystallized in the presence of (i) its substrates, chorismate and glutamine, and a product, glutamate, and (ii) its end-product inhibitor, L-tryptophan. Proc Natl Acad Sci U S A. 2001;98(11):6021-6. doi: 10.1073/pnas.111150298. PubMed PMID: 11371633; PMCID: 33415.

Kim C, Xuong NH, Edwards S, Madhusudan, Yee MC, Spraggon G, Mills SE. The crystal structure of anthranilate phosphoribosyltransferase from the enterobacterium Pectobacterium carotovorum. FEBS Lett. 2002;523(1-3):239-46. PubMed PMID: 12123839.

Deng W, Parbhu-Patel A, Meyer DJ, Baker DA. The role of two novel regulatory sites in the activation of the cGMP-dependent protein kinase from Plasmodium falciparum. Biochem J. 2003;374(Pt 2):559-65. doi: 10.1042/BJ20030474. PubMed PMID: 12817987; PMCID: PMC1223622.

Kim C, Xuong NH, Taylor SS. Crystal structure of a complex between the catalytic and regulatory (RIalpha) subunits of PKA. Science. 2005;307(5710):690-6. doi: 10.1126/science.1104607. PubMed PMID: 15692043.

Taylor SS, Kim C, Vigil D, Haste NM, Yang J, Wu J, Anand GS. Dynamics of signaling by PKA. Biochim Biophys Acta. 2005;1754(1-2):25-37. doi: 10.1016/j.bbapap.2005.08.024. PubMed PMID: 16214430.

Gullingsrud J, Kim C, Taylor SS, McCammon JA. Dynamic binding of PKA regulatory subunit RI alpha. Structure. 2006;14(1):141-9. doi: 10.1016/j.str.2005.09.019. PubMed PMID: 16407073.

Kim C, Vigil D, Anand G, Taylor SS. Structure and dynamics of PKA signaling proteins. Eur J Cell Biol. 2006;85(7):651-4. doi: 10.1016/j.ejcb.2006.02.004. PubMed PMID: 16647784.

Kinderman FS, Kim C, von Daake S, Ma Y, Pham BQ, Spraggon G, Xuong NH, Jennings PA, Taylor SS. A dynamic mechanism for AKAP binding to RII isoforms of cAMP-dependent protein kinase. Mol Cell. 2006;24(3):397-408. doi: 10.1016/j.molcel.2006.09.015. PubMed PMID: 17081990; PMCID: 1855097.

Kim C, Cheng CY, Saldanha SA, Taylor SS. PKA-I holoenzyme structure reveals a mechanism for cAMP-dependent activation. Cell. 2007;130(6):1032-43. doi: 10.1016/j.cell.2007.07.018. PubMed PMID: 17889648.

Brown SH, Wu J, Kim C, Alberto K, Taylor SS. Novel isoform-specific interfaces revealed by PKA RIIbeta holoenzyme structures. J Mol Biol. 2009;393(5):1070-82. doi: 10.1016/j.jmb.2009.09.014. PubMed PMID: 19748511; PMCID: PMC3435109.

Thompson EE, Kornev AP, Kannan N, Kim C, Ten Eyck LF, Taylor SS. Comparative surface geometry of the protein kinase family. Protein Sci. 2009;18(10):2016-26. doi: 10.1002/pro.209. PubMed PMID: 19610074; PMCID: 2786965.

Casteel DE, Smith-Nguyen EV, Sankaran B, Roh SH, Pilz RB, Kim C. A crystal structure of the cyclic GMP-dependent protein kinase I{beta} dimerization/docking domain reveals molecular details of isoform-specific anchoring. J Biol Chem. 2010;285(43):32684-8. doi: 10.1074/jbc.C110.161430. PubMed PMID: 20826808; PMCID: 2963381.

Sarma GN, Kinderman FS, Kim C, von Daake S, Chen L, Wang BC, Taylor SS. Structure of D-AKAP2:PKA RI complex: insights into AKAP specificity and selectivity. Structure. 2010;18(2):155-66. doi: 10.1016/j.str.2009.12.012. PubMed PMID: 20159461; PMCID: 3090270.

Badireddy S, Yunfeng G, Ritchie M, Akamine P, Wu J, Kim CW, Taylor SS, Qingsong L, Swaminathan K, Anand GS. Cyclic AMP analog blocks kinase activation by stabilizing inactive conformation: conformational selection highlights a new concept in allosteric inhibitor design. Mol Cell Proteomics. 2011;10(3):M110 004390. doi: 10.1074/mcp.M110.004390. PubMed PMID: 21081668; PMCID: 3047156.

Boettcher AJ, Wu J, Kim C, Yang J, Bruystens J, Cheung N, Pennypacker JK, Blumenthal DA, Kornev AP, Taylor SS. Realizing the allosteric potential of the tetrameric protein kinase A RIalpha holoenzyme. Structure. 2011;19(2):265-76. doi: 10.1016/j.str.2010.12.005. PubMed PMID: 21300294; PMCID: 3097484.

Kim JJ, Casteel DE, Huang G, Kwon TH, Ren RK, Zwart P, Headd JJ, Brown NG, Chow DC, Palzkill T, Kim C. Co-crystal structures of PKG Ibeta (92-227) with cGMP and cAMP reveal the molecular details of cyclic-nucleotide binding. PLoS One. 2011;6(4):e18413. Epub 2011/04/29. doi: 10.1371/journal.pone.0018413. PubMed PMID: 21526164; PMCID: 3080414.

Kryshtafovych A, Moult J, Bartual SG, Bazan JF, Berman H, Casteel DE, Christodoulou E, Everett JK, Hausmann J, Heidebrecht T, Hills T, Hui R, Hunt JF, Seetharaman J, Joachimiak A, Kennedy MA, Kim C, Lingel A, Michalska K, Montelione GT, Otero JM, Perrakis A, Pizarro JC, van Raaij MJ, Ramelot TA, Rousseau F, Tong L, Wernimont AK, Young J, Schwede T. Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. Proteins. 2011;79 Suppl 10:6-20. doi: 10.1002/prot.23196. PubMed PMID: 22020785; PMCID: 3692002.

Lee JH, Li S, Liu T, Hsu S, Kim C, Woods VL, Jr., Casteel DE. The amino terminus of cGMP-dependent protein kinase Ibeta increases the dynamics of the protein's cGMP-binding pockets. Int J Mass Spectrom. 2011;302(1-3):44-52. doi: 10.1016/j.ijms.2010.07.021. PubMed PMID: 21643460; PMCID: 3107041.

Baeza-Raja B, Li P, Le Moan N, Sachs BD, Schachtrup C, Davalos D, Vagena E, Bridges D, Kim C, Saltiel AR, Olefsky JM, Akassoglou K. p75 neurotrophin receptor regulates glucose homeostasis and insulin sensitivity. Proc Natl Acad Sci U S A. 2012;109(15):5838-43. doi: 10.1073/pnas.1103638109. PubMed PMID: 22460790; PMCID: 3326459.

Grimster NP, Stump B, Fotsing JR, Weide T, Talley TT, Yamauchi JG, Nemecz A, Kim C, Ho KY, Sharpless KB, Taylor P, Fokin VV. Generation of candidate ligands for nicotinic acetylcholine receptors via in situ click chemistry with a soluble acetylcholine binding protein template. J Am Chem Soc. 2012;134(15):6732-40. doi: 10.1021/ja3001858. PubMed PMID: 22394239; PMCID: 3618991.

Guo DC, Regalado E, Casteel DE, Santos-Cortez RL, Gong L, Kim JJ, Dyack S, Horne SG, Chang G, Jondeau G, Boileau C, Coselli JS, Li Z, Leal SM, Shendure J, Rieder MJ, Bamshad MJ, Nickerson DA, Gen TACRC, National Heart L, Blood Institute Grand Opportunity Exome Sequencing P, Kim C, Milewicz DM. Recurrent gain-of-function mutation in PRKG1 causes thoracic aortic aneurysms and acute aortic dissections. American journal of human genetics. 2013;93(2):398-404. doi: 10.1016/j.ajhg.2013.06.019. PubMed PMID: 23910461; PMCID: 3738837.

Campeau PM, Kasperaviciute D, Lu JT, Burrage LC, Kim C, Hori M, Powell BR, Stewart F, Felix TM, van den Ende J, Wisniewska M, Kayserili H, Rump P, Nampoothiri S, Aftimos S, Mey A, Nair LD, Begleiter ML, De Bie I, Meenakshi G, Murray ML, Repetto GM, Golabi M, Blair E, Male A, Giuliano F, Kariminejad A, Newman WG, Bhaskar SS, Dickerson JE, Kerr B, Banka S, Giltay JC, Wieczorek D, Tostevin A, Wiszniewska J, Cheung SW, Hennekam RC, Gibbs RA, Lee BH, Sisodiya SM. The genetic basis of DOORS syndrome: an exome-sequencing study. Lancet Neurol. 2014;13(1):44-58. doi: 10.1016/S1474-4422(13)70265-5. PubMed PMID: 24291220; PMCID: 3895324.

Du D, Wang Z, James NR, Voss JE, Klimont E, Ohene-Agyei T, Venter H, Chiu W, Luisi BF. Structure of the AcrAB-TolC multidrug efflux pump. Nature. 2014;509(7501):512-5. doi: 10.1038/nature13205. PubMed PMID: 24747401; PMCID: PMC4361902.

Huang GY, Gerlits OO, Blakeley MP, Sankaran B, Kovalevsky AY, Kim C. Neutron diffraction reveals hydrogen bonds critical for cGMP-selective activation: insights for cGMP-dependent protein kinase agonist design. Biochemistry. 2014;53(43):6725-7. doi: 10.1021/bi501012v. PubMed PMID: 25271401; PMCID: 4222537.

Huang GY, Kim JJ, Reger AS, Lorenz R, Moon EW, Zhao C, Casteel DE, Bertinetti D, Vanschouwen B, Selvaratnam R, Pflugrath JW, Sankaran B, Melacini G, Herberg FW, Kim C. Structural basis for cyclic-nucleotide selectivity and cGMP-selective activation of PKG I. Structure. 2014;22(1):116-24. doi: 10.1016/j.str.2013.09.021. PubMed PMID: 24239458; PMCID: 4019043.

Lu Z, Baquero MT, Yang H, Yang M, Reger AS, Kim C, Levine DA, Clarke CH, Liao WS, Bast RC, Jr. DIRAS3 regulates the autophagosome initiation complex in dormant ovarian cancer cells. Autophagy. 2014;10(6):1071-92. doi: 10.4161/auto.28577. PubMed PMID: 24879154; PMCID: PMC4091169.

Reger AS, Yang MP, Koide-Yoshida S, Guo E, Mehta S, Yuasa K, Liu A, Casteel DE, Kim C. Crystal structure of the cGMP-dependent protein kinase II leucine zipper and Rab11b protein complex reveals molecular details of G-kinase-specific interactions. J Biol Chem. 2014;289(37):25393-403. doi: 10.1074/jbc.M114.575894. PubMed PMID: 25070890; PMCID: 4162144.

Wang Z, Hryc CF, Bammes B, Afonine PV, Jakana J, Chen DH, Liu X, Baker ML, Kao C, Ludtke SJ, Schmid MF, Adams PD, Chiu W. An atomic model of brome mosaic virus using direct electron detection and real-space optimization. Nat Commun. 2014;5:4808. doi: 10.1038/ncomms5808. PubMed PMID: 25185801; PMCID: PMC4155512.

Kim J.J., G.Y. H, R. R, A. K, D.C. C, Kim C. Protocol for Expression and Purification of Cyclic Nucleotide–Free Protein in Escherichia coli. Cyclic Nucleotide Signaling. 2015;13:191-8.

Kim JJ, Flueck C, Franz E, Sanabria-Figueroa E, Thompson E, Lorenz R, Bertinetti D, Baker DA, Herberg FW, Kim C. Crystal Structures of the Carboxyl cGMP Binding Domain of the Plasmodium falciparum cGMP-dependent Protein Kinase Reveal a Novel Capping Triad Crucial for Merozoite Egress. PLoS pathogens. 2015;11(2):e1004639. doi: 10.1371/journal.ppat.1004639. PubMed PMID: 25646845.

Knight JM, Mak G, Shaw J, Porter P, McDermott C, Roberts L, You R, Yuan X, Millien VO, Qian Y, Song LZ, Frazier V, Kim C, Kim JJ, Bond RA, Milner JD, Zhang Y, Mandal PK, Luong A, Kheradmand F, McMurray JS, Corry DB. Long-Acting Beta Agonists Enhance Allergic Airway Disease. PLoS One. 2015;10(11):e0142212. doi: 10.1371/journal.pone.0142212. PubMed PMID: 26605551; PMCID: PMC4659681.

Nakamura T, Ranek MJ, Lee DI, Shalkey Hahn V, Kim C, Eaton P, Kass DA. Prevention of PKG1alpha oxidation augments cardioprotection in the stressed heart. J Clin Invest. 2015. doi: 10.1172/JCI80275. PubMed PMID: 25938783.

Qin L, Reger AS, Guo E, Yang MP, Zwart P, Casteel DE, Kim C. Structures of cGMP-Dependent Protein Kinase (PKG) Ialpha Leucine Zippers Reveal an Interchain Disulfide Bond Important for Dimer Stability. Biochemistry. 2015;54(29):4419-22. doi: 10.1021/acs.biochem.5b00572. PubMed PMID: 26132214; PMCID: PMC4838416.

VanSchouwen B, Selvaratnam R, Giri R, Lorenz R, Herberg FW, Kim C, Melacini G. Mechanism of cAMP Partial Agonism in Protein Kinase G (PKG). J Biol Chem. 2015. doi: 10.1074/jbc.M115.685305. PubMed PMID: 26370085.

Campbell JC, Kim JJ, Li KY, Huang GY, Reger AS, Matsuda S, Sankaran B, Link TM, Yuasa K, Ladbury JE, Casteel DE, Kim C. Structural Basis of Cyclic Nucleotide Selectivity in cGMP-dependent Protein Kinase II. J Biol Chem. 2016;291(11):5623-33. doi: 10.1074/jbc.M115.691303. PubMed PMID: 26769964; PMCID: PMC4786703.

Campbell JC, Tischer A, Machha V, Moon-Tasson L, Sankaran B, Kim C, Auton M. Data on the purification and crystallization of the loss-of-function von Willebrand disease variant (p.Gly1324Ser) of the von Willebrand factor A1 domain. Data Brief. 2016;7:1700-6. doi: 10.1016/j.dib.2016.05.004. PubMed PMID: 27761512; PMCID: PMC5063811.

Cho KJ, Casteel DE, Prakash P, Tan L, van der Hoeven D, Salim AA, Kim C, Capon RJ, Lacey E, Cunha SR, Gorfe AA, Hancock JF. AMPK and Endothelial Nitric Oxide Synthase Signaling Regulates K-Ras Plasma Membrane Interactions via Cyclic GMP-Dependent Protein Kinase 2. Mol Cell Biol. 2016;36(24):3086-99. doi: 10.1128/MCB.00365-16. PubMed PMID: 27697864; PMCID: PMC5126295.

Kim JJ, Lorenz R, Arold ST, Reger AS, Sankaran B, Casteel DE, Herberg FW, Kim C. Crystal Structure of PKG I:cGMP Complex Reveals a cGMP-Mediated Dimeric Interface that Facilitates cGMP-Induced Activation. Structure. 2016. doi: 10.1016/j.str.2016.03.009. PubMed PMID: 27066748.

Tischer A, Campbell JC, Machha VR, Moon-Tasson L, Benson LM, Sankaran B, Kim C, Auton M. Mutational Constraints on Local Unfolding Inhibit the Rheological Adaptation of von Willebrand Factor. J Biol Chem. 2016;291(8):3848-59. doi: 10.1074/jbc.M115.703850. PubMed PMID: 26677223; PMCID: PMC4759165.

Campbell JC, Henning P, Franz E, Sankaran B, Herberg FW, Kim C. Structural Basis of Analog Specificity in PKG I and II. ACS Chem Biol. 2017. doi: 10.1021/acschembio.7b00369. PubMed PMID: 28793191.

Campbell JC, VanSchouwen B, Lorenz R, Sankaran B, Herberg FW, Melacini G, Kim C. Crystal structure of cGMP-dependent protein kinase Ibeta cyclic nucleotide-binding-B domain : Rp-cGMPS complex reveals an apo-like, inactive conformation. FEBS Lett. 2017;591(1):221-30. doi: 10.1002/1873-3468.12505. PubMed PMID: 27914169.

He D, Lorenz R, Kim C, Herberg FW, Lim CJ. Switching cyclic nucleotide-selective activation of PKA holoenzyme reveals distinct roles of tandem CNB domains. ACS Chem Biol. 2017. doi: 10.1021/acschembio.7b00732. PubMed PMID: 29111666.

Lee CS, Fu H, Baratang N, Rousseau J, Kumra H, Sutton VR, Niceta M, Ciolfi A, Yamamoto G, Bertola D, Marcelis CL, Lugtenberg D, Bartuli A, Kim C, Hoover-Fong J, Sobreira N, Pauli R, Bacino C, Krakow D, Parboosingh J, Yap P, Kariminejad A, McDonald MT, Aracena MI, Lausch E, Unger S, Superti-Furga A, Lu JT, Baylor-Hopkins Center for Mendelian G, Cohn DH, Tartaglia M, Lee BH, Reinhardt DP, Campeau PM. Mutations in Fibronectin Cause a Subtype of Spondylometaphyseal Dysplasia with "Corner Fractures". American journal of human genetics. 2017;101(5):815-23. doi: 10.1016/j.ajhg.2017.09.019. PubMed PMID: 29100092.

Lorenz R, Moon EW, Kim JJ, Schmidt SH, Sankaran B, Pavlidis IV, Kim C, Herberg FW. Mutations of PKA cyclic nucleotide-binding domains reveal novel aspects of cyclic nucleotide selectivity. Biochem J. 2017;474(14):2389-403. doi: 10.1042/BCJ20160969. PubMed PMID: 28583991.

Gerlits OO, Campbell JC, Blakeley MP, Kim C, Kovalevsky AY. Neutron crystallography detects differences in protein dynamics: Structure of PKG II cyclic nucleotide binding domain in complex with an activator. Biochemistry. 2018. doi: 10.1021/acs.biochem.8b00010. PubMed PMID: 29517905.

Qin L, Sankaran B, Aminzai S, Casteel D, Kim C. Structural basis for selective inhibition of human PKG Ialpha by the balanol-like compound N46. J Biol Chem. 2018. doi: 10.1074/jbc.RA118.002427. PubMed PMID: 29769318.

Non-peer reviewed/book chapter:

JJ Kim, GY Huang, R Rieger, A Koller, D Chow, C Kim(2015). “A Protocol for Expression and Purification of Cyclic Nucleotide–Free Protein in Escherichia coli.” Cyclic Nucleotide Signaling: CRC Press: 191-202.