Masayo Kotaka, Ph.D. - Related publications

Physiology The University of Hong Kong, San Francisco, Hong Kong Island, Hong Kong 
Protein Structural Studies
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Bae JE, Kim IJ, Xu Y, Nam KH. Structural Flexibility of Peripheral Loops and Extended C-terminal Domain of Short Length Substrate Binding Protein from Rhodothermus marinus. The Protein Journal. PMID 33651244 DOI: 10.1007/s10930-021-09970-z   
2021 Buchholz I, McDonnell T, Nestler P, Tharad S, Kulke M, Radziszewska A, Ripoll VM, Schmidt F, Hammer E, Toca-Herrera JL, Rahman A, Delcea M. Specific domain V reduction of beta-2-glycoprotein I induces protein flexibility and alters pathogenic antibody binding. Scientific Reports. 11: 4542. PMID 33633190 DOI: 10.1038/s41598-021-84021-2   
2021 Huang Y, Jin F, Funato Y, Xu Z, Zhu W, Wang J, Sun M, Zhao Y, Yu Y, Miki H, Hattori M. Structural basis for the Mg recognition and regulation of the CorC Mg transporter. Science Advances. 7. PMID 33568487 DOI: 10.1126/sciadv.abe6140   
2021 Dietrich MH, Chan LJ, Adair A, Keremane S, Pymm P, Lo AW, Cao YC, Tham WH. Nanobody generation and structural characterization of Plasmodium falciparum 6-cysteine protein Pf12p. The Biochemical Journal. PMID 33480416 DOI: 10.1042/BCJ20200415   
2021 Kato M, Tu BP, McKnight SL. Redox-mediated regulation of low complexity domain self-association. Current Opinion in Genetics & Development. 67: 111-118. PMID 33454579 DOI: 10.1016/j.gde.2020.12.006   
2021 Mori T, Jung J, Kobayashi C, Dokainish HM, Re S, Sugita Y. Elucidation of Interactions Regulating Conformational Stability and Dynamics of SARS-CoV-2 S-Protein. Biophysical Journal. PMID 33484712 DOI: 10.1016/j.bpj.2021.01.012   
2021 Dang TKL, Nguyen T, Habeck M, Gültas M, Waack S. A graph-based algorithm for detecting rigid domains in protein structures. Bmc Bioinformatics. 22: 66. PMID 33579190 DOI: 10.1186/s12859-021-03966-3   
2021 Ching WY, Adhikari P, Jawad B, Podgornik R. Ultra-large-scale quantum chemical computation of bio-molecular systems: the case of Spike protein of SARS-CoV-2 virus. Computational and Structural Biotechnology Journal. PMID 33623641 DOI: 10.1016/j.csbj.2021.02.004   
2021 Sharma A, Kumari S, Goel M. Uncovering the structure-function aspects of an archaeal CsaA protein. Biochimica Et Biophysica Acta. Proteins and Proteomics. 140615. PMID 33561579 DOI: 10.1016/j.bbapap.2021.140615   
2021 Elgamoudi BA, Andrianova EP, Shewell LK, Day CJ, King RM, Taha, Rahman H, Hartley-Tassell LE, Zhulin IB, Korolik V. The chemoreceptor Tlp10 has a bimodal ligand-binding domain and specificity for multiple classes of chemoeffectors. Science Signaling. 14. PMID 33402336 DOI: 10.1126/scisignal.abc8521   
2021 Tőke O, Koprivanacz K, Radnai L, Merő B, Juhász T, Liliom K, Buday L. Solution NMR Structure of the SH3 Domain of Human Caskin1 Validates the Lack of a Typical Peptide Binding Groove and Supports a Role in Lipid Mediator Binding. Cells. 10. PMID 33467043 DOI: 10.3390/cells10010173   
2021 Gupta D, Tiwari P, Haque MA, Sachdeva E, Hassan MI, Ethayathulla AS, Kaur P. Structural insights into the transient closed conformation and pH dependent ATPase activity of S.Typhi GyraseB N- terminal domain. Archives of Biochemistry and Biophysics. 108786. PMID 33548211 DOI: 10.1016/   
2021 Aiyer S, Swapna GVT, Ma LC, Liu G, Hao J, Chalmers G, Jacobs BC, Montelione GT, Roth MJ. A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins. Structure (London, England : 1993). PMID 33592170 DOI: 10.1016/j.str.2021.01.010   
2021 Kolodny R, Nepomnyachiy S, Tawfik DS, Ben-Tal N. Bridging themes: short protein segments found in different architectures. Molecular Biology and Evolution. PMID 33502503 DOI: 10.1093/molbev/msab017   
2021 Ajadi MB, Soremekun OS, Elrashedy AA, Olotu FA, Kumalo HM, Soliman MES. Probing Protein-Protein Interactions and Druggable Site Identification: Mechanistic Binding Events between Ubiquitin and Zinc Finger with UFM1-Specific Peptidase Domain Protein (ZUFSP). Combinatorial Chemistry & High Throughput Screening. PMID 33538664 DOI: 10.2174/1386207324666210203175142   
2021 Preethi D, Anishetty S, Gautam P. Molecular dynamics study of in silico mutations in the auto-inhibitory loop of human endothelial nitric oxide synthase FMN sub-domain. Journal of Molecular Modeling. 27: 63. PMID 33527205 DOI: 10.1007/s00894-020-04643-7   
2021 Smith RD, Carlson HA. Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics. Journal of Chemical Information and Modeling. PMID 33599485 DOI: 10.1021/acs.jcim.0c01002   
2021 Wang X, Ma Q. Wzb of Vibrio vulnificus represents a new group of low molecular weight protein tyrosine phosphatases with a unique insertion in the W-loop. The Journal of Biological Chemistry. 100280. PMID 33450227 DOI: 10.1016/j.jbc.2021.100280   
2021 Fry MY, Saladi SM, Clemons WM. The STI1-domain is a flexible alpha-helical fold with a hydrophobic groove. Protein Science : a Publication of the Protein Society. PMID 33620121 DOI: 10.1002/pro.4049   
2021 Salvi N, Bessa LM, Guseva S, Camacho-Zarco A, Maurin D, Perez LM, Malki A, Hengesbach M, Korn SM, Schlundt A, Schwalbe H, Blackledge M. H, C and N backbone chemical shift assignments of SARS-CoV-2 nsp3a. Biomolecular Nmr Assignments. PMID 33475934 DOI: 10.1007/s12104-020-10001-8   
2021 Xu X, Zhang D, Zhou B, Zhen X, Ouyang S. Structural and biochemical analyses of the tetrameric cell binding domain of Lys170 from enterococcal phage F170/08. European Biophysics Journal : Ebj. PMID 33609147 DOI: 10.1007/s00249-021-01511-x   
2021 Stuffle EC, Johnson MS, Watts KJ. PAS domains in bacterial signal transduction. Current Opinion in Microbiology. 61: 8-15. PMID 33647528 DOI: 10.1016/j.mib.2021.01.004   
2021 Ortega-Alarcon D, Claveria-Gimeno R, Vega S, Jorge-Torres OC, Esteller M, Abian O, Velazquez-Campoy A. Influence of the disordered domain structure of MeCP2 on its structural stability and dsDNA interaction. International Journal of Biological Macromolecules. 175: 58-66. PMID 33548325 DOI: 10.1016/j.ijbiomac.2021.01.206   
2021 Thompson EJ, Paul A, Iavarone AT, Klinman JP. Identification of Thermal Conduits That Link the Protein-Water Interface to the Active Site Loop and Catalytic Base in Enolase. Journal of the American Chemical Society. PMID 33395523 DOI: 10.1021/jacs.0c09423   
2021 Qin W, Yu F, Zhou H, Li P, Zhou F, Li HJ, He CX, Xing L, Zhou X, Zhao D, Li PQ, Jin X, Wang QS, He JH, Cao HL. Complex crystal structure determination and anti-non-small-cell lung cancer activity of the Hsp90 inhibitor Debio0932. Acta Crystallographica. Section D, Structural Biology. 77: 86-97. PMID 33404528 DOI: 10.1107/S2059798320014990   
2021 He J, Han Z, Farooq QUA, Li C. Study on functional sites in human multidrug resistance protein 1 (hMRP1). Proteins. PMID 33469960 DOI: 10.1002/prot.26049   
2021 Li Y, Bedi RK, Wiedmer L, Sun X, Huang D, Caflisch A. Atomistic and Thermodynamic Analysis of N6-Methyladenosine (mA) Recognition by the Reader Domain of YTHDC1. Journal of Chemical Theory and Computation. PMID 33472367 DOI: 10.1021/acs.jctc.0c01136   
2021 Bedford JT, Poutsma J, Diawara N, Greene LH. The nature of persistent interactions in two model β-grasp proteins reveals the advantage of symmetry in stability. Journal of Computational Chemistry. PMID 33534913 DOI: 10.1002/jcc.26477   
2021 Hubbard PA, Xia C, Shen AL, Kim JP. Structural and kinetic investigations of the carboxy terminus of NADPH cytochrome P450 oxidoreductase. Archives of Biochemistry and Biophysics. 108792. PMID 33556357 DOI: 10.1016/   
2021 Zhang Y, Greer RA, Song Y, Praveen H, Song Y. In silico identification of available drugs targeting cell surface BiP to disrupt SARS-CoV-2 binding and replication: Drug repurposing approach. European Journal of Pharmaceutical Sciences : Official Journal of the European Federation For Pharmaceutical Sciences. 105771. PMID 33617948 DOI: 10.1016/j.ejps.2021.105771   
2021 Knight KM, Ghosh S, Campbell SL, Lefevre TJ, Olsen RHJ, Smrcka AV, Valentin NH, Yin G, Vaidehi N, Dohlman HG. A universal allosteric mechanism for G protein activation. Molecular Cell. PMID 33636126 DOI: 10.1016/j.molcel.2021.02.002   
2021 Rostøl JT, Xie W, Kuryavyi V, Maguin P, Kao K, Froom R, Patel DJ, Marraffini LA. The Card1 nuclease provides defence during type-III CRISPR immunity. Nature. PMID 33461211 DOI: 10.1038/s41586-021-03206-x   
2021 Lin KF, Fry MY, Saladi SM, Clemons WM. Molecular basis of tail-anchored integral membrane protein recognition by the cochaperone Sgt2. The Journal of Biological Chemistry. 100441. PMID 33610544 DOI: 10.1016/j.jbc.2021.100441   
2021 Chaoprasid P, Lukat P, Mühlen S, Heidler T, Gazdag EM, Dong S, Bi W, Rüter C, Kirchenwitz M, Steffen A, Jänsch L, Stradal TEB, Dersch P, Blankenfeldt W. Crystal structure of bacterial cytotoxic necrotizing factor CNF reveals molecular building blocks for intoxication. The Embo Journal. e105202. PMID 33410511 DOI: 10.15252/embj.2020105202   
2021 Ping YQ, Mao C, Xiao P, Zhao RJ, Jiang Y, Yang Z, An WT, Shen DD, Yang F, Zhang H, Qu C, Shen Q, Tian C, Li ZJ, Li S, et al. Structures of the glucocorticoid-bound adhesion receptor GPR97-G complex. Nature. PMID 33408414 DOI: 10.1038/s41586-020-03083-w   
2021 Feng W, Nguyen H, Shen D, Deng H, Jiang Z, Podolnikova N, Ugarova T, Wang X. Structural Characterization of the Interaction between the αI-Domain of the Integrin Mac-1 (αβ) and the Cytokine Pleiotrophin. Biochemistry. PMID 33427449 DOI: 10.1021/acs.biochem.0c00700   
2021 Romero-Tamayo S, Laplaza R, Velazquez-Campoy A, Villanueva R, Medina M, Ferreira P. W196 and the -Hairpin Motif Modulate the Redox Switch of Conformation and the Biomolecular Interaction Network of the Apoptosis-Inducing Factor. Oxidative Medicine and Cellular Longevity. 2021: 6673661. PMID 33510840 DOI: 10.1155/2021/6673661   
2021 Mondal B, Nagesh J, Reddy G. Double Domain Swapping in Human γC and γD Crystallin Drives Early Stages of Aggregation. The Journal of Physical Chemistry. B. PMID 33566611 DOI: 10.1021/acs.jpcb.0c07833   
2021 Lai HTT, Giorgetti A, Rossetti G, Nguyen TT, Carloni P, Kranjc A. The Interplay of Cholesterol and Ligand Binding in TSPO from Classical Molecular Dynamics Simulations. Molecules (Basel, Switzerland). 26. PMID 33652554 DOI: 10.3390/molecules26051250   
2021 Gupta M, Venkatramani R, Ainavarapu SRK. Role of Ligand Binding Site in Modulating the Mechanical Stability of Proteins with β-Grasp Fold. The Journal of Physical Chemistry. B. PMID 33492970 DOI: 10.1021/acs.jpcb.0c08085   
2021 Bhatia S, Krishnamoorthy G, Udgaonkar JB. Mapping Distinct Sequences of Structure Formation Differentiating Multiple Folding Pathways of a Small Protein. Journal of the American Chemical Society. PMID 33430589 DOI: 10.1021/jacs.0c11097   
2021 Pastor M, Czapinska H, Helbrecht I, Krakowska K, Lutz T, Xu SY, Bochtler M. Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA. Nucleic Acids Research. PMID 33450012 DOI: 10.1093/nar/gkaa1218   
2021 Jurásek M, Kumar J, Paclíková P, Kumari A, Tripsianes K, Bryja V, Vácha R. Phosphorylation-induced changes in the PDZ domain of Dishevelled 3. Scientific Reports. 11: 1484. PMID 33452274 DOI: 10.1038/s41598-020-79398-5   
2021 Feinberg H, Jégouzo SAF, Lasanajak Y, Smith DF, Drickamer K, Weis WI, Taylor ME. Structural analysis of carbohydrate binding by the macrophage mannose receptor CD206. The Journal of Biological Chemistry. 100368. PMID 33545173 DOI: 10.1016/j.jbc.2021.100368   
2021 Deshpande S, Altermann E, Sarojini V, Lott JS, Lee TV. Structural characterization of a PCP-R di-domain from an archaeal non-ribosomal peptide synthetase reveals novel inter-domain interactions. The Journal of Biological Chemistry. 100432. PMID 33610550 DOI: 10.1016/j.jbc.2021.100432   
2021 Liauw BW, Afsari HS, Vafabakhsh R. Conformational rearrangement during activation of a metabotropic glutamate receptor. Nature Chemical Biology. PMID 33398167 DOI: 10.1038/s41589-020-00702-5   
2021 Naudin EA, McEwen AG, Tan SK, Poussin-Courmontagne P, Schmitt JL, Birck C, DeGrado WF, Torbeev V. Acyl Transfer Catalytic Activity in De Novo Designed Protein with N-Terminus of α-Helix As Oxyanion-Binding Site. Journal of the American Chemical Society. PMID 33635059 DOI: 10.1021/jacs.0c10053   
2021 Fujimoto Z, Hong LTT, Kishine N, Suzuki N, Kimura K. Tetramer formation of Bacillus subtilis YabJ protein that belongs to YjgF/YER057c/UK114 family. Bioscience, Biotechnology, and Biochemistry. PMID 33590041 DOI: 10.1093/bbb/zbaa037   
2021 Escalante DE, Ferguson DM. Structural modeling and analysis of the SARS-CoV-2 cell entry inhibitor camostat bound to the trypsin-like protease TMPRSS2. Medicinal Chemistry Research : An International Journal For Rapid Communications On Design and Mechanisms of Action of Biologically Active Agents. 1-11. PMID 33564221 DOI: 10.1007/s00044-021-02708-7   
2021 Sundaram R, Manohar K, Patel SK, Acharya N, Vasudevan D. Structural analyses of PCNA from the fungal pathogen Candida albicans identify three regions with species-specific conformations. Febs Letters. PMID 33544878 DOI: 10.1002/1873-3468.14055