Kim, Soo-Kyung

Article from CaltechAUTHORS

• Hernández, Pedro M. and Arango, Carlos A., el al. (2026) The atomistic Mechanism Underlying Regulation of the GPA1 G Protein Signaling Pathway Mediated by Abscisic Acid (ABA) Phytohormone Binding to the GCR1 Plant G Protein Coupled Receptor; Journal of Chemical Information and Modeling; Vol. 66; No. 7; 4075-4084; PMCID PMC13080986; 10.1021/acs.jcim.5c02308
• Yang, Xuyu and Lee, Joo-Youn, el al. (2025) Predicted molecules followed by experimental validation for protecting human neurons from oxidative stress–induced cytotoxicity; Proceedings of the National Academy of Sciences; Vol. 122; No. 45; e2505359122; PMCID PMC12625973; 10.1073/pnas.2505359122
• Yang, Moon Young and Kim, Soo-Kyung, el al. (2025) Metabotropic GABAB Receptor Activation Induced by G Protein Coupling; Journal of the American Chemical Society; Vol. 147; No. 2; 1911 - 1919; 10.1021/jacs.4c14672
• Yang, Moon Young and Duy Mac, Khuong, el al. (2024) Agonist activation to open the Gα subunit of the GPCR–G protein precoupled complex defines functional agonist activation of TAS2R5; Proceedings of the National Academy of Sciences; Vol. 121; No. 48; e2409987121; 10.1073/pnas.2409987121
• Yang, Xuyu and Lee, Joo-Youn, el al. (2024) Experimental Validation of the Neurotrophic Factor-α1 Binding Site on the Serotonin Receptor 1E (HTR1E) Responsible for β-Arrestin Activation and Subsequent Neuroprotection; ACS Omega; Vol. 9; No. 39; 40749–40758; 10.1021/acsomega.4c05367
• Li, Bo and Yang, Moon Young, el al. (2024) The G Protein-First Mechanism for Activation of the Class B Glucagon-like Peptide 1 Receptor Coupled to N-Terminal Domain-Mediated Conformational Progression; Journal of the American Chemical Society; Vol. 146; No. 38; 26251–26260; 10.1021/jacs.4c08128
• Kim, Soo-Kyung and Guthrie, Brian, el al. (2024) Ligand-Dependent and G Protein-Dependent Properties for the Sweet Taste Heterodimer, TAS1R2/1R3; Journal of Physical Chemistry B; Vol. 128; No. 37; 8927–8932; 10.1021/acs.jpcb.4c04610
• Kim, Soo-Kyung and Suebka, Sartanee, el al. (2024) Methotrexate Inhibits the Binding of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Receptor Binding Domain to the Host-Cell Angiotensin-Converting Enzyme-2 (ACE-2) Receptor; ACS Pharmacology & Translational Science; Vol. 7; No. 2; 348-362; PMCID PMC10863433; 10.1021/acsptsci.3c00197
• Vo, Amy-Doan P. and Kim, Soo-Kyung, el al. (2023) Fully activated structure of the sterol-bound Smoothened GPCR-Gi protein complex; Proceedings of the National Academy of Sciences; Vol. 120; No. 49; e2300919120; PMCID PMC10710022; 10.1073/pnas.2300919120
• Ko, Bongki and Jang, Yongsoo, el al. (2023) Discovery of 3-Phenyl Indazole-Based Novel Chemokine-like Receptor 1 Antagonists for the Treatment of Psoriasis; Journal of Medicinal Chemistry; Vol. 66; No. 21; 14564-14582; 10.1021/acs.jmedchem.3c01011
• Li, Bo and Maruszko, Krystyna, el al. (2023) Structure and Molecular Mechanism of Signaling for the Glucagon-like Peptide-1 Receptor Bound to Gs Protein and Exendin-P5 Biased Agonist; Journal of the American Chemical Society; Vol. 145; No. 37; 20422-20431; PMCID PMC10777869; 10.1021/jacs.3c05996
• Mafi, Amirhossein and Kim, Soo-Kyung, el al. (2023) The dynamics of agonist-β₂-adrenergic receptor activation induced by binding of GDP-bound Gs protein; Nature Chemistry; 10.1038/s41557-023-01238-6
• Nag, Arundhati and Mafi, Amirhossein, el al. (2023) Stereochemical engineering yields a multifunctional peptide macrocycle inhibitor of Akt2 by fine-tuning macrocycle-cell membrane interactions; Communications Chemistry; Vol. 6; Art. No. 95; PMCID PMC10195864; 10.1038/s42004-023-00890-w
• Tokmakova, Alina and Kim, Donghwa, el al. (2023) Predicted structure and cell signaling of TAS2R14 reveal receptor hyper-flexibility for detecting diverse bitter tastes; iScience; Vol. 26; No. 4; Art. No. 106422; PMCID PMC10121769; 10.1016/j.isci.2023.106422
• Jung, Jae-Hoon and Jang, In Hee, el al. (2023) Discovery and Binding Mechanism of Pyrazoloisoquinoline-Based Novel β-Arrestin Inverse Agonists of the Kappa-Opioid Receptor; Journal of Medicinal Chemistry; Vol. 66; No. 7; 5154-5170; 10.1021/acs.jmedchem.3c00064
• Hernández, Pedro M. and Arango, Carlos A., el al. (2023) Predicted Three-Dimensional Structure of the GCR1 Putative GPCR in Arabidopsis thaliana and Its Binding to Abscisic Acid and Gibberellin A1; Journal of Agricultural and Food Chemistry; Vol. 71; No. 14; 5770-5782; 10.1021/acs.jafc.2c06846
• Wang, Xudong and Neale, Chris, el al. (2023) Intermediate-state-trapped mutants pinpoint G protein-coupled receptor conformational allostery; Nature Communications; Vol. 14; 1325; PMCID PMC10006191; 10.1038/s41467-023-36971-6
• Sharma, Vinay Kumar and Yang, Xuyu, el al. (2023) Correction to: Novel interaction between neurotrophic factor-α1/carboxypeptidase E and serotonin receptor, 5-HTR1E, protects human neurons against oxidative/neuroexcitotoxic stress via β-arrestin/ERK signaling; Cellular and Molecular Life Sciences; Vol. 80; No. 3; Art. No. 65; PMCID PMC9941249; 10.1007/s00018-023-04711-0
• Yang, Moon Young and Kim, Soo-Kyung, el al. (2022) G protein coupling and activation of the metabotropic GABA₈ heterodimer; Nature Communications; Vol. 13; Art. No. 4612; PMCID PMC9360005; 10.1038/s41467-022-32213-3
• Mafi, Amirhossein and Kim, Soo-Kyung, el al. (2022) The mechanism for ligand activation of the GPCR–G protein complex; Proceedings of the National Academy of Sciences of the United States of America; Vol. 119; No. 18; e2110085119; PMCID PMC9170043; 10.1073/pnas.2110085119
• Wen, Xin and Wang, Sen, el al. (2022) Complete inhibition of a polyol nucleation by a micromolar biopolymer additive; Cell Reports Physical Science; Vol. 3; No. 2; Art. No. 100723; PMCID PMC8903182; 10.1016/j.xcrp.2021.100723
• Sharma, Vinay Kumar and Yang, Xuyu, el al. (2022) Novel interaction between neurotrophic factor-α1/carboxypeptidase E and serotonin receptor, 5-HTR1E, protects human neurons against oxidative/neuroexcitotoxic stress via β-arrestin/ERK signaling; Cellular and Molecular Life Sciences; Vol. 79; Art. No. 24; PMCID PMC8732845; 10.1007/s00018-021-04021-3
• Jang, Jaewan and Kim, Soo-Kyung, el al. (2021) Synergic Effects in the Activation of the Sweet Receptor GPCR Heterodimer for Various Sweeteners Predicted Using Molecular Metadynamics Simulations; Journal of Agricultural and Food Chemistry; Vol. 69; No. 41; 12250-12261; 10.1021/acs.jafc.1c03779
• Mafi, Amirhossein and Kim, Soo-Kyung, el al. (2021) Predicted Structure of Fully Activated Tas1R3/1R3′ Homodimer Bound to G Protein and Natural Sugars: Structural Insights into G Protein Activation by a Class C Sweet Taste Homodimer with Natural Sugars; Journal of the American Chemical Society; Vol. 143; No. 40; 16824-16838; 10.1021/jacs.1c08839
• Yang, Moon Young and Kim, Soo-Kyung, el al. (2021) Structures and Agonist Binding Sites of Bitter Taste Receptor TAS2R5 Complexed with Gi Protein and Validated against Experiment; Journal of Physical Chemistry Letters; Vol. 12; No. 38; 9293-9300; PMCID PMC8650975; 10.1021/acs.jpclett.1c02162
• Mafi, Amirhossein and Kim, Soo-Kyung, el al. (2021) The G protein-first activation mechanism of opioid receptors by Gi protein and agonists; QRB Discovery; Vol. 2; No. 2021; e9; PMCID PMC10392629; 10.1017/qrd.2021.7
• Yang, Moon Young and Mafi, Amirhossein, el al. (2021) Predicted structure of fully activated human bitter taste receptor TAS2R4 complexed with G protein and agonists; QRB Discovery; Vol. 2; E3; PMCID PMC10392674; 10.1017/qrd.2021.1
• Mafi, Amirhossein and Purohit, Rahul, el al. (2021) Hedgehog proteins create a dynamic cholesterol interface; PLoS ONE; Vol. 16; No. 2; Art. No. e0246814; 10.1371/journal.pone.0246814
• Mafi, Amirhossein and Kim, Soo-Kyung, el al. (2020) Mechanism of β-arrestin recruitment by the μ-opioid G protein-coupled receptor; Proceedings of the National Academy of Sciences of the United States of America; Vol. 117; No. 28; 16346-16355; PMCID PMC7368253; 10.1073/pnas.1918264117
• Sharma, Vinay Kumar and Xuyu, Yang, el al. (2020) Extracellular interaction between Neurotrophic factor-α1 and HTR1E serotonin receptor promotes cell survival; FASEB Journal; Vol. 34; No. S1; 1-1; 10.1096/fasebj.2020.34.s1.01952
• Mafi, Amirhossein and Kim, Soo-Kyung, el al. (2020) The atomistic level structure for the activated human κ-opioid receptor bound to the full Gi protein and the MP1104 agonist; Proceedings of the National Academy of Sciences of the United States of America; Vol. 117; No. 11; 5836-5843; PMCID PMC7084096; 10.1073/pnas.1910006117
• Jeong, Pyeonghwa and Kim, Soo-Kyung, el al. (2019) Discovery of Novel Biased Opioid Receptor Ligands through Structure-Based Pharmacophore Virtual Screening and Experiment; ChemMedChem; Vol. 14; No. 20; 1783-1794; 10.1002/cmdc.201900418
• Shankar, Vishnu and Goddard, William A., III, el al. (2018) The Predicted 3D Structure of Human DP Prostaglandin G Protein-Coupled Receptor Bound to CPI Antagonist; Journal of Chemical Theory and Computation; Vol. 14; No. 3; 1624-1642; 10.1021/acs.jctc.7b00842
• Kim, Soo-Kyung and Chen, Yalu, el al. (2017) Activation mechanism of the G protein-coupled sweet receptor heterodimer with sweeteners and allosteric agonists; Proceedings of the National Academy of Sciences of the United States of America; Vol. 114; No. 10; 2568-2573; PMCID PMC5347580; 10.1073/pnas.1700001114
• Wen, Xin and Wang, Sen, el al. (2016) Antifreeze proteins govern the precipitation of trehalose in a freezing-avoiding insect at low temperature; Proceedings of the National Academy of Sciences of the United States of America; Vol. 113; No. 24; 6683-6688; PMCID PMC4914155; 10.1073/pnas.1601519113
• Kim, Jeong-hyun and Kim, Soo-Kyung, el al. (2016) Homology modeling and molecular docking studies of Drosophila and Aedes sex peptide receptors; Journal of Molecular Graphics and Modelling; Vol. 66; 115-122; 10.1016/j.jmgm.2016.03.014
• de March, Claire and Kim, Soo-Kyung, el al. (2015) G Protein-Coupled Odorant Receptors: from sequence to structure; Protein Science; Vol. 24; No. 9; 1543-1548; PMCID PMC4570547; 10.1002/pro.2717
• Li, Quanjie and Kim, Soo-Kyung, el al. (2015) Predicted Structures for Kappa Opioid G‑Protein Coupled Receptor Bound to Selective Agonists; Journal of Chemical Information and Modeling; Vol. 55; No. 3; 614-627; 10.1021/ci500523z
• Viano, Marilyne and Kim, Soo-Kyung, el al. (2015) Deciphering the odorant binding protein - olfactory receptor interactions; Chemical Senses; Vol. 40; No. 3; 242; 10.1093/chemse/bju073
• Kim, Soo-Kyung and Goddard, William A., III (2014) Predicted 3D structures of olfactory receptors with details of odorant binding to OR1G1; Journal of Computer-Aided Molecular Design; Vol. 28; No. 12; 1175-1190; 10.1007/s10822-014-9793-4
• Rios, Alejandra and Liu, Fan, el al. (2014) Probing the binding of antifreeze proteins to trehalose crystals; Abstracts of Papers of the American Chemical Society; Vol. 248; 81-BIOL
• Charlier, Landry and Topin, Jérémie, el al. (2012) How broadly tuned olfactory receptors equally recognize their agonists. Human OR1G1 as a test case; Cellular and Molecular Life Sciences; Vol. 69; No. 24; 4205-4213; PMCID PMC11115053; 10.1007/s00018-012-1116-0
• Kim, Soo-Kyung and Fristrup, Peter, el al. (2011) Structure-Based Prediction of Subtype Selectivity of Histamine H_3 Receptor Selective Antagonists in Clinical Trials; Journal of Chemical Information and Modeling; Vol. 51; No. 12; 3262-3274; PMCID PMC3246544; 10.1021/ci200435b
• Abrol, Ravinder and Kim, Soo-Kyung, el al. (2011) Characterizing and predicting the functional and conformational diversity of seven-transmembrane proteins; Methods; Vol. 55; No. 4; 405-414; PMCID PMC3286597; 10.1016/j.ymeth.2011.12.005
• Kim, Soo-Kyung and Riley, Lindsay, el al. (2011) Predicted structures of agonist and antagonist bound complexes of adenosine A_3 receptor; Proteins; Vol. 79; No. 6; 1878-1897; PMCID PMC3092833; 10.1002/prot.23012
• Kim, Soo-Kyung and Li, Youyong, el al. (2011) Predicted Structures and Dynamics for Agonists and Antagonists Bound to Serotonin 5-HT2B and 5-HT2C Receptors; Journal of Chemical Information and Modeling; Vol. 51; No. 2; 420-433; PMCID PMC3070210; 10.1021/ci100375b
• Kim, Soo-Kyung and Li, Youyong, el al. (2010) Prediction of the Three-Dimensional Structure for the Rat Urotensin II Receptor, and Comparison of the Antagonist Binding Sites and Binding Selectivity between Human and Rat Receptors from Atomistic Simulations; ChemMedChem; Vol. 5; No. 9; 1594-1608; PMCID PMC3517062; 10.1002/cmdc.201000175
• Goddard, William A., III and Kim, Soo-Kyung, el al. (2010) Predicted 3D structures for adenosine receptors bound to ligands: Comparison to the crystal structure; Journal of Structural Biology; Vol. 170; No. 1; 10-20; 10.1016/j.jsb.2010.01.001
• Rubin, D. and Hony, S., el al. (2009) A spatially resolved study of photoelectric heating and [C II] cooling in the LMC; Astronomy and Astrophysics; Vol. 494; No. 2; 647-661; 10.1051/0004-6361:200810968
• Kim, Soo-Kyung and Jacobson, Kenneth A. (2007) Three-Dimensional Quantitative Structure−Activity Relationship of Nucleosides Acting at the A_3 Adenosine Receptor: Analysis of Binding and Relative Efficacy; Journal of Chemical Information and Modeling; Vol. 47; No. 3; 1225-1233; 10.1021/ci600501z
• Scarselli, Marco and Li, Bo, el al. (2007) Multiple Residues in the Second Extracellular Loop Are Critical for M3 Muscarinic Acetylcholine Receptor Activation; Journal of Biological Chemistry; Vol. 282; No. 10; 7385-7396; 10.1074/jbc.M610394200