Kunio Miki - Related publications

Affiliations: 
Chemistry-Graduate School of Science Kyoto University, Kyōto-shi, Kyōto-fu, Japan 
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Gao B, Ji R, Li Z, Su X, Li H, Sun Y, Ji C, Gan J, Li J. Structural analysis and functional study of phosphofructokinase B (PfkB) from Mycobacterium marinum. Biochemical and Biophysical Research Communications. 579: 129-135. PMID 34597996 DOI: 10.1016/j.bbrc.2021.09.051   
2021 Zweckstetter M. NMR hawk-eyed view of AlphaFold2 structures. Protein Science : a Publication of the Protein Society. PMID 34469019 DOI: 10.1002/pro.4175   
2021 Jia Z, Liu C, Chen Y, Jiang H, Wang Z, Yao J, Yang J, Zhu J, Zhang B, Yuchi Z. Crystal structures of the SARS-CoV-2 nucleocapsid protein C-terminal domain and development of nucleocapsid-targeting nanobodies. The Febs Journal. PMID 34665939 DOI: 10.1111/febs.16239   
2021 Sheikh AY, Mattei A, Miglani Bhardwaj R, Hong RS, Abraham NS, Schneider-Rauber G, Engstrom KM, Diwan M, Henry RF, Gao Y, Juarez V, Jordan E, DeGoey DA, Hutchins CW. Implications of the Conformationally Flexible, Macrocyclic Structure of the First-Generation, Direct-Acting Anti-Viral Paritaprevir on Its Solid Form Complexity and Chameleonic Behavior. Journal of the American Chemical Society. PMID 34637297 DOI: 10.1021/jacs.1c06837   
2021 Blundell TL. The first resolution revolution in protein structure analysis: X-ray diffraction of polypeptide conformations and globular protein folds in 1950s and 1960s. Progress in Biophysics and Molecular Biology. PMID 34520786 DOI: 10.1016/j.pbiomolbio.2021.09.002   
2021 Tanramluk D*, Pakotiprapha D, Phoochaijaroen S, Chantravisut P, Thampradid S, Vanichtanankul J, Narupiyakul L, Akavipat R, Yuvaniyama J. MANORAA: A machine learning platform to guide protein-ligand design by anchors and influential distances. Structure. PMID 34614393 DOI: 10.1016/j.str.2021.09.004   
2021 Maben Z, Arya R, Georgiadis D, Stratikos E, Stern LJ. Conformational dynamics linked to domain closure and substrate binding explain the ERAP1 allosteric regulation mechanism. Nature Communications. 12: 5302. PMID 34489420 DOI: 10.1038/s41467-021-25564-w   
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 Wong SWK, Liu Z. Conformational variability of loops in the SARS-CoV-2 spike protein. Proteins. PMID 34661307 DOI: 10.1002/prot.26266   
2021 Liu W, Chen J, Jin L, Liu ZY, Lu M, Jiang G, Yang Q, Quan C, Nam KH, Xu Y. Functional and structural analysis of catabolite control protein C that responds to citrate. Scientific Reports. 11: 20285. PMID 34645869 DOI: 10.1038/s41598-021-99552-x   
2021 Li S, Hsieh KY, Su SC, Pintilie GD, Zhang K, Chang CI. Molecular basis for ATPase-powered substrate translocation by the Lon AAA+ protease. The Journal of Biological Chemistry. 101239. PMID 34563541 DOI: 10.1016/j.jbc.2021.101239   
2021 Sato Y, Matsugami A, Watanabe S, Hayashi F, Arai M, Kigawa T, Nishimura C. Changes in dynamic and static structures of the HIV-1 p24 capsid protein N-domain caused by amino-acid substitution are associated with its viral viability. Protein Science : a Publication of the Protein Society. PMID 34523753 DOI: 10.1002/pro.4184   
2021 Asthana P, Singh D, Pedersen JS, Hynönen MJ, Sulu R, Murthy AV, Laitaoja M, Jänis J, Riley LW, Venkatesan R. Structural insights into the substrate-binding proteins Mce1A and Mce4A from . Iucrj. 8: 757-774. PMID 34584737 DOI: 10.1107/S2052252521006199   
2021 Feng N, Feng H, Wang S, Punekar AS, Ladenstein R, Wang DC, Zhang Q, Ding J, Liu W. Structures of heat shock factor trimers bound to DNA. Iscience. 24: 102951. PMID 34458700 DOI: 10.1016/j.isci.2021.102951   
2021 Grahame DAS, Dupuis JH, Bryksa BC, Tanaka T, Yada RY. Improving the alkaline stability of pepsin through rational protein design using renin, an alkaline-stable aspartic protease, as a structural and functional reference. Enzyme and Microbial Technology. 150: 109871. PMID 34489030 DOI: 10.1016/j.enzmictec.2021.109871   
2021 Bandera AM, Bartho J, Lammens K, Drexler DJ, Kleinschwärzer J, Hopfner KP, Witte G. BusR senses bipartite DNA binding motifs by a unique molecular ruler architecture. Nucleic Acids Research. PMID 34432045 DOI: 10.1093/nar/gkab736   
2021 Evangelista W, Knapp J, Zandarashvili L, Esadze A, White MA, Gribenko AV, Lee JC. Signal Transmission in Cyclic AMP Receptor Protein for Survival in Extreme Acidic Conditions. Biochemistry. PMID 34605636 DOI: 10.1021/acs.biochem.1c00388   
2021 Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. Critical Assessment of Methods of Protein Structure Prediction (CASP) - Round XIV. Proteins. PMID 34533838 DOI: 10.1002/prot.26237   
2021 Mikkelsen MD, Cao HTT, Roret T, Rhein-Knudsen N, Holck J, Tran VTT, Nguyen TT, Tran VHN, Lezyk MJ, Muschiol J, Pham TD, Czjzek M, Meyer AS. A novel thermostable prokaryotic fucoidan active sulfatase PsFucS1 with an unusual quaternary hexameric structure. Scientific Reports. 11: 19523. PMID 34593864 DOI: 10.1038/s41598-021-98588-3   
2021 Tušar L, Usenik A, Turk B, Turk D. Mechanisms Applied by Protein Inhibitors to Inhibit Cysteine Proteases. International Journal of Molecular Sciences. 22. PMID 33498210 DOI: 10.3390/ijms22030997   
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 Nakamura T, Yokaichiya T, Fedorov DG. Quantum-Mechanical Structure Optimization of Protein Crystals and Analysis of Interactions in Periodic Systems. The Journal of Physical Chemistry Letters. 8757-8762. PMID 34478310 DOI: 10.1021/acs.jpclett.1c02510   
2021 Pinkston J, Jo J, Olsen KJ, Comer D, Glaittli CA, Loria JP, Johnson SJ, Hengge AC. Significant Loop Motions in the SsoPTP Protein Tyrosine Phosphatase Allow for Dual General Acid Functionality. Biochemistry. PMID 34496202 DOI: 10.1021/acs.biochem.1c00365   
2021 Alvarado SK, Miller MD, Bhardwaj M, Thorson JS, Van Lanen SG, Phillips GN. Structural characterization of DynU16, a START/Bet v1-like protein involved in dynemicin biosynthesis. Acta Crystallographica. Section F, Structural Biology Communications. 77: 328-333. PMID 34605436 DOI: 10.1107/S2053230X21008943   
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 Hwang J, Park SH, Lee CW, Do H, Shin SC, Kim HW, Lee SG, Park HH, Kwon S, Lee JH. Crystal structure of a MarR family protein from the psychrophilic bacterium sp. TG-14 in complex with a lipid-like molecule. Iucrj. 8: 842-852. PMID 34584745 DOI: 10.1107/S2052252521005704   
2021 Sun Z, Gu M, Li Q, Liu X, Liu B, Zhang J, Huang S, Ni C. Performance of a CsI(Tl) scintillation screen with a dual-periodic structure based on an oxidized silicon micropore array template in X-ray imaging. Optics Express. 29: 23752-23763. PMID 34614634 DOI: 10.1364/OE.428145   
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 Quadir F, Roy RS, Soltanikazemi E, Cheng J. DeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling. Frontiers in Molecular Biosciences. 8: 716973. PMID 34497831 DOI: 10.3389/fmolb.2021.716973   
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 Duan J, Xu P, Cheng X, Mao C, Croll T, He X, Shi J, Luan X, Yin W, You E, Liu Q, Zhang S, Jiang H, Zhang Y, Jiang Y, et al. Structures of full-length glycoprotein hormone receptor signalling complexes. Nature. PMID 34552239 DOI: 10.1038/s41586-021-03924-2   
2021 Cudia D, Roseman GP, Assafa TE, Shahu MK, Scholten A, Menke-Sell SK, Yamada H, Koch KW, Milhauser G, Ames JB. NMR and EPR-DEER Structure of a Dimeric Guanylate Cyclase Activator Protein-5 from Zebrafish Photoreceptors. Biochemistry. 60: 3058-3070. PMID 34609135 DOI: 10.1021/acs.biochem.1c00612   
2021 Busto-Moner L, Feng CJ, Antoszewski A, Tokmakoff A, Dinner AR. Structural Ensemble of the Insulin Monomer. Biochemistry. PMID 34637307 DOI: 10.1021/acs.biochem.1c00583   
2021 Malliavin TE. Tandem domain structure determination based on a systematic enumeration of conformations. Scientific Reports. 11: 16925. PMID 34413388 DOI: 10.1038/s41598-021-96370-z   
2021 Schwarz M, Eno RFM, Freitag-Pohl S, Coxon CR, Straker HE, Wortley DJ, Hughes DJ, Mitchell G, Moore J, Cummins I, Onkokesung N, Brazier-Hicks M, Edwards R, Pohl E, Steel PG. Flavonoid-based inhibitors of the Phi-class glutathione transferase from black-grass to combat multiple herbicide resistance. Organic & Biomolecular Chemistry. PMID 34643629 DOI: 10.1039/d1ob01802g   
2021 Huang S, Mei H, Lu L, Kuang Z, Heng Y, Xu L, Liang X, Qiu M, Pan X. Conformational transitions of caspase-6 in substrate-induced activation process explored by perturbation-response scanning combined with targeted molecular dynamics. Computational and Structural Biotechnology Journal. 19: 4156-4164. PMID 34527189 DOI: 10.1016/j.csbj.2021.07.017   
2021 Fowler NJ, Sljoka A, Williamson MP. The accuracy of NMR protein structures in the Protein Data Bank. Structure (London, England : 1993). PMID 34331857 DOI: 10.1016/j.str.2021.07.001   
2021 Schormann N, Purushotham S, Mieher JL, Patel M, Wu H, Deivanayagam C. Structural and functional analysis of the C-terminal region of Streptococcus gordonii SspB. Acta Crystallographica. Section D, Structural Biology. 77: 1206-1215. PMID 34473090 DOI: 10.1107/S2059798321008135   
2021 Škerlová J, Berndtsson J, Nolte H, Ott M, Stenmark P. Structure of the native pyruvate dehydrogenase complex reveals the mechanism of substrate insertion. Nature Communications. 12: 5277. PMID 34489474 DOI: 10.1038/s41467-021-25570-y   
2021 Murray BW, Rogers E, Zhai D, Deng W, Chen X, Sprengeler PA, Zhang X, Graber A, Reich SH, Stopatschinskaja S, Solomon B, Besse B, Drilon A. Molecular Characteristics of Repotrectinib That Enable Potent Inhibition of TRK Fusion Proteins and Resistant Mutations. Molecular Cancer Therapeutics. PMID 34625502 DOI: 10.1158/1535-7163.MCT-21-0632   
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 Li J, Hou C, Ma X, Guo S, Zhang H, Shi L, Liao C, Zheng B, Ye L, Yang L, He X. Entropy-Enthalpy Compensations Fold Proteins in Precise Ways. International Journal of Molecular Sciences. 22. PMID 34502559 DOI: 10.3390/ijms22179653   
2021 Fernández-Quintero ML, Kroell KB, Bacher LM, Loeffler JR, Quoika PK, Georges G, Bujotzek A, Kettenberger H, Liedl KR. Germline-Dependent Antibody Paratope States and Pairing Specific V-V Interface Dynamics. Frontiers in Immunology. 12: 675655. PMID 34447370 DOI: 10.3389/fimmu.2021.675655   
2021 Chen Y, Liu Y, Fang X. The new evidence of China's economic downturn: From structural bonus to structural imbalance. Plos One. 16: e0257456. PMID 34555078 DOI: 10.1371/journal.pone.0257456   
2021 Gu W, Luo Z, Vonrhein C, Jia X, Ve T, Nanson JD, Kobe B. Crystal structure determination of the armadillo repeat domain of Drosophila SARM1 using MIRAS phasing. Acta Crystallographica. Section F, Structural Biology Communications. 77: 364-373. PMID 34605441 DOI: 10.1107/S2053230X21006786   
2021 Anchal, Kaushik V, Goel M. Distribution of Peptidyl-Prolyl Isomerase (PPIase) in the Archaea. Frontiers in Microbiology. 12: 751049. PMID 34691003 DOI: 10.3389/fmicb.2021.751049   
2021 Bergmann J, Oksanen E, Ryde U. Combining crystallography with quantum mechanics. Current Opinion in Structural Biology. 72: 18-26. PMID 34392061 DOI: 10.1016/j.sbi.2021.07.002   
2021 Xu Q, Sun N, Xiao Q, Huang CY, Xu M, Zhang W, Li L, Wang Q, Olieric V, Wang W, He J, Sun B. The crystal structure of MreC provides insights into polymer formation. Febs Open Bio. PMID 34510818 DOI: 10.1002/2211-5463.13296   
2021 Skolnick J, Gao M, Zhou H, Singh S. AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function. Journal of Chemical Information and Modeling. PMID 34586808 DOI: 10.1021/acs.jcim.1c01114   
2021 Kumar A, Chakraborty D, Mugnai ML, Straub JE, Thirumalai D. Sequence Determines the Switch in the Fibril Forming Regions in the Low-Complexity FUS Protein and Its Variants. The Journal of Physical Chemistry Letters. 9026-9032. PMID 34516126 DOI: 10.1021/acs.jpclett.1c02310