Chu-Young Kim, Ph.D. - Related publications

Affiliations: 
2001 University of Pennsylvania, Philadelphia, PA, United States 
Area:
structure-mechanism of hydrolytic metalloenzymes
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Han JT, Zhu Y, Pan DB, Xue HX, Wang S, Peng Y, Liu H, He YX, Yao X. Discovery of pentapeptide-inhibitor hits targeting FKBP51 by combining computational modeling and X-ray crystallography. Computational and Structural Biotechnology Journal. 19: 4079-4091. PMID 34401048 DOI: 10.1016/j.csbj.2021.07.015   
2021 Pao PJ, Hsu MF, Chiang MH, Chen CT, Lee CC, Wang AH. Structural basis of an epitope tagging system derived from Haloarcula marismortui bacteriorhodopsin I D94N and its monoclonal antibody GD-26. The Febs Journal. PMID 34499806 DOI: 10.1111/febs.16184   
2021 Fritz ZR, Schloss RS, Yarmush ML, Williams LJ. HSymM-Guided Engineering of the Immunodominant p53 Transactivation Domain Putative Peptide Antigen for Improved Binding to its Anti-p53 Monoclonal Antibody. Bioorganic & Medicinal Chemistry Letters. 128341. PMID 34454062 DOI: 10.1016/j.bmcl.2021.128341   
2021 Jedhe GS, Arora PS. Hydrogen bond surrogate helices as minimal mimics of protein α-helices. Methods in Enzymology. 656: 1-25. PMID 34325784 DOI: 10.1016/bs.mie.2021.04.007   
2021 Hymel D, Tsuji K, Grant RA, Chingle RM, Kunciw DL, Yaffe MB, Burke TR. Design and synthesis of a new orthogonally protected glutamic acid analog and its use in the preparation of high affinity polo-like kinase 1 polo-box domain - binding peptide macrocycles. Organic & Biomolecular Chemistry. PMID 34346472 DOI: 10.1039/d1ob01120k   
2021 Parker JL, Deme JC, Wu Z, Kuteyi G, Huo J, Owens RJ, Biggin PC, Lea SM, Newstead S. Cryo-EM structure of PepT2 reveals structural basis for proton-coupled peptide and prodrug transport in mammals. Science Advances. 7. PMID 34433568 DOI: 10.1126/sciadv.abh3355   
2021 Sanches K, Wai DCC, Norton RS. Conformational dynamics in peptide toxins: Implications for receptor interactions and molecular design. Toxicon : Official Journal of the International Society On Toxinology. 201: 127-140. PMID 34454969 DOI: 10.1016/j.toxicon.2021.08.020   
2021 Rathman BM, Rowe JL, Del Valle JR. Synthesis and conformation of backbone N-aminated peptides. Methods in Enzymology. 656: 271-294. PMID 34325790 DOI: 10.1016/bs.mie.2021.04.013   
2021 Gómez-González J, Bouzada D, Pérez-Márquez LA, Sciortino G, Maréchal JD, Vázquez López M, Vázquez ME. Stereoselective Self-Assembly of DNA Binding Helicates Directed by the Viral β-Annulus Trimeric Peptide Motif. Bioconjugate Chemistry. PMID 34320309 DOI: 10.1021/acs.bioconjchem.1c00312   
2021 Unarta IC, Xu J, Shang Y, Cheung CHP, Zhu R, Chen X, Cao S, Cheung PP, Bierer D, Zhang M, Huang X, Li X. Entropy of stapled peptide inhibitors in free state is the major contributor to the improvement of binding affinity with the GK domain. Rsc Chemical Biology. 2: 1274-1284. PMID 34458841 DOI: 10.1039/d1cb00087j   
2021 Dhusia K, Su Z, Wu Y. A structural-based machine learning method to classify binding affinities between TCR and peptide-MHC complexes. Molecular Immunology. 139: 76-86. PMID 34455212 DOI: 10.1016/j.molimm.2021.07.020   
2021 Guryanov I, Korzhikov-Vlakh V, Bhattacharya M, Biondi B, Masiero G, Formaggio F, Tennikova T, Urtti A. Conformationally Constrained Peptides with High Affinity to the Vascular Endothelial Growth Factor. Journal of Medicinal Chemistry. PMID 34269584 DOI: 10.1021/acs.jmedchem.1c00219   
2021 Guryanov I, Korzhikov-Vlakh V, Bhattacharya M, Biondi B, Masiero G, Formaggio F, Tennikova T, Urtti A. Conformationally Constrained Peptides with High Affinity to the Vascular Endothelial Growth Factor. Journal of Medicinal Chemistry. PMID 34269584 DOI: 10.1021/acs.jmedchem.1c00219   
2021 Zhang D, Wu H, Zhao J. Computational design and experimental substantiation of conformationally constrained peptides from the complex interfaces of transcriptional enhanced associate domains with their cofactors in gastric cancer. Computational Biology and Chemistry. 94: 107569. PMID 34500324 DOI: 10.1016/j.compbiolchem.2021.107569   
2021 Ascencio-Ibáñez JT, Bobay BG. Conserved Structural Motif Identified in Peptides That Bind to Geminivirus Replication Protein Rep. Biochemistry. PMID 34464102 DOI: 10.1021/acs.biochem.1c00408   
2021 Brandt AAML, Rodrigues-da-Silva RN, Lima-Junior JC, Alves CR, de Souza-Silva F. Combining Well-Tempered Metadynamics Simulation and SPR Assays to Characterize the Binding Mechanism of the Universal T-Lymphocyte Tetanus Toxin Epitope TT830-843. Biomed Research International. 2021: 5568980. PMID 34285916 DOI: 10.1155/2021/5568980   
2021 Butrón D, Zamora-Carreras H, Devesa I, Treviño MA, Abian O, Velázquez-Campoy A, Bonache MÁ, Lagartera L, Martín-Martínez M, González-Rodríguez S, Baamonde A, Fernández-Carvajal A, Ferrer-Montiel A, Jiménez MÁ, González-Muñiz R. DD04107-Derived neuronal exocytosis inhibitor peptides: Evidences for synaptotagmin-1 as a putative target. Bioorganic Chemistry. 115: 105231. PMID 34388485 DOI: 10.1016/j.bioorg.2021.105231   
2021 Sadremomtaz A, Al-Dahmani ZM, Ruiz-Moreno AJ, Monti A, Wang C, Azad T, Bell JC, Doti N, Velasco-Velázquez MA, de Jong D, de Jonge J, Smit J, Dömling A, van Goor H, Groves MR. Synthetic Peptides That Antagonize the Angiotensin-Converting Enzyme-2 (ACE-2) Interaction with SARS-CoV-2 Receptor Binding Spike Protein. Journal of Medicinal Chemistry. PMID 34328726 DOI: 10.1021/acs.jmedchem.1c00477   
2021 Liu Y, Shao X, Wang T, Wang X, Li N, Zhao Y, Xia W, Sun L. [Structure prediction and biological activity analysis of dybowskin-1ST antimicrobial peptide in Rana dybowskii]. Sheng Wu Gong Cheng Xue Bao = Chinese Journal of Biotechnology. 37: 2890-2902. PMID 34472306 DOI: 10.13345/j.cjb.200564   
2021 Abraham ET, Oecal S, Mörgelin M, Schmid PWN, Buchner J, Baumann U, Gebauer JM. Collagen's primary structure determines collagen:HSP47 complex stoichiometry. The Journal of Biological Chemistry. 101169. PMID 34487762 DOI: 10.1016/j.jbc.2021.101169   
2021 Macpherson A, Birtley JR, Broadbridge RJ, Brady K, Schulze MED, Tang Y, Joyce C, Saunders K, Bogle G, Horton J, Kelm S, Taylor RD, Franklin RJ, Selby MD, Laabei M, et al. The Chemical Synthesis of Knob Domain Antibody Fragments. Acs Chemical Biology. PMID 34406751 DOI: 10.1021/acschembio.1c00472   
2021 Munhoz VHO, Ferreira CS, Nunes LO, Santos TL, Aisenbrey C, Adão R, de Carvalho Alcântara AF, de Magalhães MTQ, Piló-Veloso D, Resende JM, Bechinger B, Verly RM. Epimers l- and d-Phenylseptin: How the relative stereochemistry affects the peptide-membrane interactions. Biochimica Et Biophysica Acta. Biomembranes. 1863: 183708. PMID 34310911 DOI: 10.1016/j.bbamem.2021.183708   
2021 Lopez-Silva TL, Schneider JP. From structure to application: Progress and opportunities in peptide materials development. Current Opinion in Chemical Biology. 64: 131-144. PMID 34329941 DOI: 10.1016/j.cbpa.2021.06.006   
2021 Saranya V, Shankar R, Gatasheh MK, Zehra S. Impact of Au metal clusters on the structural and inhibitory mechanism of Aβ peptide: A theoretical approach. Environmental Research. 204: 111920. PMID 34464618 DOI: 10.1016/j.envres.2021.111920   
2021 Bourbiaux K, Legrand B, Verdié P, Mallart S, Manette G, Minoletti C, Stepp JD, Prigent P, Le Bail JC, Gauzy-Lazo L, Duclos O, Martinez J, Amblard M. Potent Lys Patch-Containing Stapled Peptides Targeting PCSK9. Journal of Medicinal Chemistry. PMID 34266235 DOI: 10.1021/acs.jmedchem.0c02051   
2021 Metz A, Wollenhaupt J, Glöckner S, Messini N, Huber S, Barthel T, Merabet A, Gerber HD, Heine A, Klebe G, Weiss MS. Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking. Acta Crystallographica. Section D, Structural Biology. 77: 1168-1182. PMID 34473087 DOI: 10.1107/S2059798321008196   
2021 Si W, Yang H, Wu G, Zhang Y, Sha J. Velocity control of protein translocation through a nanopore by tuning the fraction of benzenoid residues. Nanoscale. PMID 34498657 DOI: 10.1039/d1nr04492c   
2021 Mayerthaler F, Feldberg AL, Alfermann J, Sun X, Steinchen W, Yang H, Mootz HD. Intermediary conformations linked to the directionality of the aminoacylation pathway of nonribosomal peptide synthetases. Rsc Chemical Biology. 2: 843-854. PMID 34458813 DOI: 10.1039/d0cb00220h   
2021 Ayyamperumal S, Dj D, Tallapaneni V, Mohan S, S B, Selvaraj J, Joghee NM, Mjn C. Molecular docking analysis of α-Topoisomerase II with δ-Carboline derivatives as potential anticancer agents. Bioinformation. 17: 249-265. PMID 34393444 DOI: 10.6026/97320630017249   
2021 Faragó Z, Mirzahosseini A, Horváth D, Pálla T, Horváth P, Perczel A, Noszál B. Solution Structure and Acid-Base Properties of Reduced α-Conotoxin MI. Chemistry & Biodiversity. e2100464. PMID 34467647 DOI: 10.1002/cbdv.202100464   
2021 El Bakri Y, Anouar EH, Ahmad S, Nassar AA, Taha ML, Mague JT, El Ghayati L, Essassi EM. Synthesis and Identification of Novel Potential Molecules Against COVID-19 Main Protease Through Structure-Guided Virtual Screening Approach. Applied Biochemistry and Biotechnology. PMID 34324152 DOI: 10.1007/s12010-021-03615-8   
2021 Toyama Y, Harkness RW, Kay LE. Dissecting the role of interprotomer cooperativity in the activation of oligomeric high-temperature requirement A2 protein. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34446566 DOI: 10.1073/pnas.2111257118   
2021 Sharma G, Braga CB, Chen KE, Jia X, Ramanujam V, Collins BM, Rittner R, Mobli M. Structural basis for the binding of the cancer targeting scorpion toxin, ClTx, to the vascular endothelia growth factor receptor neuropilin-1. Current Research in Structural Biology. 3: 179-186. PMID 34401749 DOI: 10.1016/j.crstbi.2021.07.003   
2021 Lee H, Kim H, Lee SY. Self-Assembling Peptidic Bolaamphiphiles for Biomimetic Applications. Acs Biomaterials Science & Engineering. PMID 34309378 DOI: 10.1021/acsbiomaterials.1c00576   
2021 Lee H, Kim H, Lee SY. Self-Assembling Peptidic Bolaamphiphiles for Biomimetic Applications. Acs Biomaterials Science & Engineering. PMID 34309378 DOI: 10.1021/acsbiomaterials.1c00576   
2021 Uday RVS, Misra R, Harika A, Dolui S, Saha A, Pal U, Ravichandiran V, Maiti NC. Dabrafenib, idelalisib and nintedanib act as significant allosteric modulator for dengue NS3 protease. Plos One. 16: e0257206. PMID 34506566 DOI: 10.1371/journal.pone.0257206   
2021 Abdollahi K, Condict L, Hung A, Kasapis S. Binding parameters and molecular dynamics of β-lactoglobulin-vanillic acid complexation as a function of pH - part B: Neutral pH. Food Chemistry. 367: 130655. PMID 34371277 DOI: 10.1016/j.foodchem.2021.130655   
2021 Egbert M, Ghani U, Ashizawa R, Kotelnikov S, Nguyen T, Desta I, Hashemi N, Padhorny D, Kozakov D, Vajda S. Assessing the binding properties of CASP14 targets and models. Proteins. PMID 34368994 DOI: 10.1002/prot.26209   
2021 Wang W, Liu Q, Liu Q, Hendrickson WA. Conformational equilibria in allosteric control of Hsp70 chaperones. Molecular Cell. PMID 34453889 DOI: 10.1016/j.molcel.2021.07.039   
2021 Herlan CN, Sonnefeld A, Gloge T, Brückel J, Schlee LC, Muhle-Goll C, Nieger M, Bräse S. Macrocyclic Tetramers-Structural Investigation of Peptide-Peptoid Hybrids. Molecules (Basel, Switzerland). 26. PMID 34361700 DOI: 10.3390/molecules26154548   
2021 González-Castro R, Gómez-Lim MA, Plisson F. Cysteine-Rich Peptides: Hyperstable Scaffolds for Protein Engineering. Chembiochem : a European Journal of Chemical Biology. 22: 961-973. PMID 33095969 DOI: 10.1002/cbic.202000634   
2021 Guo M, Rosbottom I, Zhou L, Yong CW, Zhou L, Yin Q, Todorov IT, Errington E, Heng JYY. Triglycine (GGG) Adopts a Polyproline II (pPII) Conformation in Its Hydrated Crystal Form: Revealing the Role of Water in Peptide Crystallization. The Journal of Physical Chemistry Letters. 8416-8422. PMID 34436909 DOI: 10.1021/acs.jpclett.1c01622   
2021 Werner N, Werten S, Hoppen J, Palm GJ, Göttfert M, Hinrichs W. The Induction Mechanism of the Flavonoid-Responsive Regulator FrrA. The Febs Journal. PMID 34314575 DOI: 10.1111/febs.16141   
2021 Gupta A, Vijayan V, Pant P, Kaur P, Singh TP, Sharma P, Sharma S. Structure prediction and discovery of inhibitors against phosphopantothenoyl cysteine synthetase of . Journal of Biomolecular Structure & Dynamics. 1-13. PMID 34348086 DOI: 10.1080/07391102.2021.1958699   
2021 Xiao T, Sun L, Zhang M, Li Z, Haura EB, Schonbrunn E, Ji H. Synthesis and Structural Characterization of a Monocarboxylic Inhibitor for GRB2 SH2 Domain. Bioorganic & Medicinal Chemistry Letters. 128354. PMID 34506932 DOI: 10.1016/j.bmcl.2021.128354   
2021 Honisch C, Ragazzi E, Hussain R, Brazier J, Siligardi G, Ruzza P. Interaction of a Short Peptide with G-Quadruplex-Forming Sequences: An SRCD and CD Study. Pharmaceutics. 13. PMID 34452065 DOI: 10.3390/pharmaceutics13081104   
2021 Talapati SR, Goyal M, Nataraj V, Pothuganti M, Sreevidya MR, Gore S, Ramachandra M, Antony T, More SS, Rao NK. Structural and binding studies of Cyclin dependent kinase 2 with NU6140 inhibitor. Chemical Biology & Drug Design. PMID 34423559 DOI: 10.1111/cbdd.13941   
2021 Qin X, Chen H, Tu L, Ma Y, Liu N, Zhang H, Li D, Riedl B, Bierer D, Yin F, Li Z. Potent Inhibition of HIF1α and p300 Interaction by a Constrained Peptide Derived from CITED2. Journal of Medicinal Chemistry. PMID 34472840 DOI: 10.1021/acs.jmedchem.1c01043   
2021 Tanaka M, Kato T, Oda M. Conformational changes of α-helical peptides with different hydrophobic residues induced by metal-ion binding. Biophysical Chemistry. 277: 106661. PMID 34388679 DOI: 10.1016/j.bpc.2021.106661   
2021 Ukey S, Choudhury C, Sharma P. Identification of unique subtype-specific interaction features in Class II zinc-dependent HDAC subtype binding pockets: A computational study. Journal of Biosciences. 46. PMID 34323221