Kimberly J. Zanotti, Ph.D. - Related publications

2011 Carnegie Mellon University, Pittsburgh, PA 
Biochemistry, Analytical Chemistry, Molecular Biology
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Teng FY, Jiang ZZ, Huang LY, Guo M, Chen F, Hou XM, Xi XG, Xu Y. A Toolbox for Site-Specific Labeling of RecQ Helicase With a Single Fluorophore Used in the Single-Molecule Assay. Frontiers in Molecular Biosciences. 7: 586450. PMID 33102530 DOI: 10.3389/fmolb.2020.586450   
2020 Gray MD, Deore PS, Chung AJ, Van Riesen AJ, Manderville RA, Prabhakar PS, Wetmore SD. Lighting Up the Thrombin-Binding Aptamer G-Quadruplex with an Internal Cyanine-Indole-Quinolinium Nucleobase Surrogate. Direct Fluorescent Intensity Readout for Thrombin Binding without Topology Switching. Bioconjugate Chemistry. PMID 33156614 DOI: 10.1021/acs.bioconjchem.0c00530   
2020 Hossain MJ, Rashid MA, Sultan MZ. Transition Metal Chelation Augments the Half-life of Secnidazole: Molecular Docking and Fluorescence Spectroscopic Approaches. Drug Research. PMID 33098081 DOI: 10.1055/a-1252-2322   
2020 Sindhikara D, Wagner M, Gkeka P, Güssregen S, Tiwari G, Hessler G, Yapici E, Li Z, Evers A. Automated Design of Macrocycles for Therapeutic Applications: From Small Molecules to Peptides and Proteins. Journal of Medicinal Chemistry. PMID 33017535 DOI: 10.1021/acs.jmedchem.0c01500   
2020 Kohlberger M, Wildner S, Regl C, Huber CG, Gadermaier G. Rituximab-specific DNA aptamers are able to selectively recognize heat-treated antibodies. Plos One. 15: e0241560. PMID 33151990 DOI: 10.1371/journal.pone.0241560   
2020 Lucas JE, Kortemme T. New computational protein design methods for de novo small molecule binding sites. Plos Computational Biology. 16: e1008178. PMID 33017412 DOI: 10.1371/journal.pcbi.1008178   
2020 Mukhopadhyay S. The Dynamism of Intrinsically Disordered Proteins: Binding-Induced Folding, Amyloid Formation, and Phase Separation. The Journal of Physical Chemistry. B. PMID 33108190 DOI: 10.1021/acs.jpcb.0c07598   
2020 Neira JL, Rizzuti B, Jiménez-Alesanco A, Abián O, Velázquez-Campoy A, Iovanna JL. The Paralogue of the Intrinsically Disordered Nuclear Protein 1 Has a Nuclear Localization Sequence that Binds to Human Importin α3. International Journal of Molecular Sciences. 21. PMID 33050086 DOI: 10.3390/ijms21197428   
2020 Bozovic O, Zanobini C, Gulzar A, Jankovic B, Buhrke D, Post M, Wolf S, Stock G, Hamm P. Real-time observation of ligand-induced allosteric transitions in a PDZ domain. Proceedings of the National Academy of Sciences of the United States of America. PMID 33020277 DOI: 10.1073/pnas.2012999117   
2020 Heller GT, Aprile FA, Michaels TCT, Limbocker R, Perni M, Ruggeri FS, Mannini B, Löhr T, Bonomi M, Camilloni C, De Simone A, Felli IC, Pierattelli R, Knowles TPJ, Dobson CM, et al. Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer's disease. Science Advances. 6. PMID 33148639 DOI: 10.1126/sciadv.abb5924   
2020 Zhang S, Gan R, Zhao L, Sun Q, Xiang H, Xiang X, Zhao G, Li H. Unveiling the interaction mechanism of alogliptin benzoate with human serum albumin: Insights from spectroscopy, microcalorimetry, and molecular docking and molecular dynamics analyses. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 246: 119040. PMID 33068900 DOI: 10.1016/j.saa.2020.119040   
2020 Kumar S, Akabayov SR, Kessler N, Cohen LS, Solanki J, Naider F, Kay LE, Anglister J. The methyl C-edited/C-filtered transferred NOE for studying protein interactions with short linear motifs. Journal of Biomolecular Nmr. PMID 32997264 DOI: 10.1007/s10858-020-00340-y   
2020 Scull NW, Lucius AL. Kinetic Analysis of AAA+ Translocases by Combined Fluorescence and Anisotropy Methods. Biophysical Journal. 119: 1335-1350. PMID 32997959 DOI: 10.1016/j.bpj.2020.08.018   
2020 Stainer S, Reisetbauer S, Ahiable JEA, Ebner L, Zhu R, Reindl D, Körmöczi GF, Ebner A. Single molecule distribution of RhD binding epitopes on ultraflat erythrocyte ghosts. Nanoscale. PMID 33118583 DOI: 10.1039/d0nr04393a   
2020 Yan Z, Wang J. Funneled energy landscape unifies principles of protein binding and evolution. Proceedings of the National Academy of Sciences of the United States of America. PMID 33067388 DOI: 10.1073/pnas.2013822117   
2020 Paprocki J, Biener G, Stoneman M, Raicu V. In-Cell Detection of Conformational Substates of a G Protein-Coupled Receptor Quaternary Structure: Modulation of Substate Probability by Cognate Ligand Binding. The Journal of Physical Chemistry. B. PMID 33119987 DOI: 10.1021/acs.jpcb.0c06081   
2020 Walkowiak JJ, Ballauff M, Zimmermann R, Freudenberg U, Werner C. Thermodynamic Analysis of the Interaction of Heparin with Lysozyme. Biomacromolecules. PMID 32662630 DOI: 10.1021/acs.biomac.0c00780   
2020 Chowdhury SM, Hossain MN, Rafe MR. design and evaluation of novel 5-fluorouracil analogues as potential anticancer agents. Heliyon. 6: e04978. PMID 33033767 DOI: 10.1016/j.heliyon.2020.e04978   
2020 Bolcato G, Bissaro M, Sturlese M, Moro S. Comparing Fragment Binding PosesPrediction Using HSP90 as a Key Study: When Bound Water Makes the Difference. Molecules (Basel, Switzerland). 25. PMID 33053878 DOI: 10.3390/molecules25204651   
2020 Agarwal S, Smith M, De La Rosa I, Verba KA, Swartz P, Segura-Totten M, Mattos C. Development of a structure-analysis pipeline using multiple-solvent crystal structures of barrier-to-autointegration factor. Acta Crystallographica. Section D, Structural Biology. 76: 1001-1014. PMID 33021502 DOI: 10.1107/S2059798320011341   
2020 Forouzesh N, Onufriev AV. MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor. Biorxiv : the Preprint Server For Biology. PMID 32869029 DOI: 10.1101/2020.08.25.267625   
2020 Karlsson E, Paissoni C, Erkelens AM, Tehranizadeh ZA, Sorgenfrei FA, Andersson E, Ye W, Camilloni C, Jemth P. Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. The Journal of Biological Chemistry. PMID 33067355 DOI: 10.1074/jbc.RA120.015645   
2020 Reddy CN, Manzar N, Ateeq B, Sankararamakrishnan R. Computational Design of BH3-Mimetic Peptide Inhibitors That Can Bind Specifically to Mcl-1 or Bcl-X: Role of Non-Hot Spot Residues. Biochemistry. PMID 33146015 DOI: 10.1021/acs.biochem.0c00661   
2020 Wang X, Kleerekoper Q, Revtovich AV, Kang D, Kirienko NV. Identification and validation of a novel anti-virulent that binds to pyoverdine and inhibits its function. Virulence. 11: 1293-1309. PMID 32962519 DOI: 10.1080/21505594.2020.1819144   
2020 Wang X, Unarta IC, Cheung PP, Huang X. Elucidating molecular mechanisms of functional conformational changes of proteins via Markov state models. Current Opinion in Structural Biology. 67: 69-77. PMID 33126140 DOI: 10.1016/   
2020 Fujino Y, Miyagawa T, Torii M, Inoue M, Fujii Y, Okanishi H, Kanai Y, Masui R. Structural changes induced by ligand-binding drastically increase the thermostability of the Ser/Thr protein kinase TpkD from Thermus thermophilus HB8. Febs Letters. PMID 33159808 DOI: 10.1002/1873-3468.13996   
2020 Shityakov S, Fischer A, Su KP, Hussein AA, Dandekar T, Broscheit J. Novel Approach for Characterizing Propofol Binding Affinities to Serum Albumins from Different Species. Acs Omega. 5: 25543-25551. PMID 33073080 DOI: 10.1021/acsomega.0c01295   
2020 Guichard G, Cussol L, Mauran L, Buratto J, Belorusova AY, Neuville M, Osz J, Fribourg S, Fremaux J, Dolain C, Goudreau S, Rochel N. Structural basis for α-helix mimicry and inhibition of protein-protein interactions with oligourea foldamers. Angewandte Chemie (International Ed. in English). PMID 32935897 DOI: 10.1002/anie.202008992   
2020 Liu J, Chen WM, Shao YH, Liu YP, Tu ZC. Improved antitumor activity and IgE/IgG-binding ability of α-Lactalbumin/β-lactoglobulin induced by ultrasonication prior to binding with oleic acid. Journal of Food Biochemistry. e13502. PMID 33025647 DOI: 10.1111/jfbc.13502   
2020 Mohammad T, Mathur Y, Hassan MI. InstaDock: A single-click graphical user interface for molecular docking-based virtual high-throughput screening. Briefings in Bioinformatics. PMID 33105480 DOI: 10.1093/bib/bbaa279   
2020 Olotu FA, Omolabi KF, Soliman MES. Leaving no stone unturned: Allosteric targeting of SARS-CoV-2 spike protein at putative druggable sites disrupts human angiotensin-converting enzyme interactions at the receptor binding domain. Informatics in Medicine Unlocked. 21: 100451. PMID 33083517 DOI: 10.1016/j.imu.2020.100451   
2020 Chen T, Pham H, Mohamadi A, Miller LW. Single-Chain Lanthanide Luminescence Biosensors for Cell-Based Imaging and Screening of Protein-Protein Interactions. Iscience. 23: 101533. PMID 33083762 DOI: 10.1016/j.isci.2020.101533   
2020 Silva SRB, de Lima Neto JX, Fuzo CA, Fulco UL, Vieira DS. A quantum biochemistry investigation of the protein-protein interactions for the description of allosteric modulation on biomass-degrading chimera. Physical Chemistry Chemical Physics : Pccp. PMID 33164009 DOI: 10.1039/d0cp04415f   
2020 Neira JL, Rizzuti B, Jiménez-Alesanco A, Palomino-Schätzlein M, Abián O, Velázquez-Campoy A, Iovanna JL. A Phosphorylation-Induced Switch in the Nuclear Localization Sequence of the Intrinsically Disordered NUPR1 Hampers Binding to Importin. Biomolecules. 10. PMID 32933064 DOI: 10.3390/biom10091313   
2020 Szabó G, Pénzes K, Torner B, Fagyas M, Tarr T, Soltész P, Kis G, Antal M, Kappelmayer J. Distinct and overlapping effects of β-glycoprotein I conformational variants in ligand interactions and functional assays. Journal of Immunological Methods. 112877. PMID 33031793 DOI: 10.1016/j.jim.2020.112877   
2020 Romero JA, Nawrocka EK, Shchukina A, Blanco FJ, Diercks T, Kazimierczuk K. Non-Stationary Complementary Non-Uniform Sampling (NOSCO NUS) for Fast Acquisition of Serial 2D NMR Titration Data. Angewandte Chemie (International Ed. in English). PMID 32852098 DOI: 10.1002/anie.202009479   
2020 Danielsen MB, Christensen NJ, Jørgensen PT, Jensen KJ, Wengel J, Lou C. Polyamine-functionalized 2'-amino-LNA in oligonucleotides: Facile synthesis of novel monomers and high affinity binding towards ssDNA and dsDNA. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 33073896 DOI: 10.1002/chem.202004495   
2020 Sonar P, Bellucci L, Mossa A, Heidarsson PO, Kragelund BB, Cecconi C. Effects of Ligand Binding on the Energy Landscape of Acyl-CoA-Binding Protein. Biophysical Journal. PMID 33080224 DOI: 10.1016/j.bpj.2020.09.016   
2020 Ou X, Xue B, Lao Y, Wutthinitikornkit Y, Tian R, Zou A, Yang L, Wang W, Cao Y, Li J. Structure and sequence features of mussel adhesive protein lead to its salt-tolerant adhesion ability. Science Advances. 6. PMID 32978166 DOI: 10.1126/sciadv.abb7620   
2020 Nakamura A, Ishiwata D, Visootsat A, Uchiyama T, Mizutani K, Kaneko S, Murata T, Igarashi K, Iino R. Domain architecture divergence leads to functional divergence in binding and catalytic domains of bacterial and fungal cellobiohydrolases. The Journal of Biological Chemistry. 295: 14606-14617. PMID 32816991 DOI: 10.1074/jbc.RA120.014792   
2020 Lin W, Li Y, Min J, Liu J, Yang L, Lee RE, Chen T. Development of BODIPY FL Thalidomide As a High-Affinity Fluorescent Probe for Cereblon in a Time-Resolved Fluorescence Resonance Energy Transfer Assay. Bioconjugate Chemistry. PMID 33070611 DOI: 10.1021/acs.bioconjchem.0c00507   
2020 Bessas NC, da Silva LA, Comar Júnior M, de Lima RG. Interaction of nitrosyl ruthenium complexes, [Ru (NH.NHq-R)(tpy)NO] with human serum albumin: a spectroscopic and computational investigation. Luminescence : the Journal of Biological and Chemical Luminescence. PMID 32986923 DOI: 10.1002/bio.3955   
2020 Dominguez-Martin MA, Hammel M, Gupta S, Lechno-Yossef S, Sutter M, Rosenberg DJ, Chen Y, Petzold CJ, Ralston CY, Polívka T, Kerfeld CA. Structural analysis of a new carotenoid-binding protein: the C-terminal domain homolog of the OCP. Scientific Reports. 10: 15564. PMID 32968135 DOI: 10.1038/s41598-020-72383-y   
2020 Jade DD, Pandey R, Kumar R, Gupta D. Ligand-based pharmacophore modeling of TNF-α to design novel inhibitors using virtual screening and molecular dynamics. Journal of Biomolecular Structure & Dynamics. 1-17. PMID 33034255 DOI: 10.1080/07391102.2020.1831962   
2020 Wang Y, Liu Y, Yang Q, Mao X, Chai WM, Peng Y. Study on the interaction between 4-(1H-indol-3-yl)-2-(p-tolyl)quinazoline-3-oxide and human serum albumin. Bioorganic & Medicinal Chemistry. 28: 115720. PMID 33065445 DOI: 10.1016/j.bmc.2020.115720   
2020 Shi Y, Sang P, Yin G, Gao R, Liang X, Brzozowski R, Odom T, Eswara P, Zheng Y, Li X, Cai J. Aggregation-Induced Emissive and Circularly Polarized Homogeneous Sulfono-γ-AApeptide Foldamers. Advanced Optical Materials. 8. PMID 33072491 DOI: 10.1002/adom.201902122   
2020 Patel K, Walport LJ, Walshe JL, Solomon PD, Low JKK, Tran DH, Mouradian KS, Silva APG, Wilkinson-White L, Norman A, Franck C, Matthews JM, Guss JM, Payne RJ, Passioura T, et al. Cyclic peptides can engage a single binding pocket through highly divergent modes. Proceedings of the National Academy of Sciences of the United States of America. PMID 33046654 DOI: 10.1073/pnas.2003086117   
2020 Ahamad S, Kanipakam H, Birla S, Ali MS, Gupta D. Screening Malaria-box compounds to identify potential inhibitors against SARS-CoV-2 M, using molecular docking and dynamics simulation studies. European Journal of Pharmacology. 173664. PMID 33131721 DOI: 10.1016/j.ejphar.2020.173664   
2020 Jespers W, Verdon G, Azuaje J, Majellaro M, Keränen H, García-Mera X, Congreve M, Deflorian F, de Graaf C, Zhukov A, Doré AS, Mason JS, Åqvist J, Cooke RM, Sotelo E, et al. X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A Adenosine Receptor Antagonists. Angewandte Chemie (International Ed. in English). PMID 32542862 DOI: 10.1002/anie.202003788   
2020 Santoro AM, D'Urso A, Cunsolo A, Milardi D, Purrello R, Sbardella D, Tundo GR, Diana D, Fattorusso R, Dato AD, Paladino A, Persico M, Coletta M, Fattorusso C. Cooperative Binding of the Cationic Porphyrin Tris-T4 Enhances Catalytic Activity of 20S Proteasome Unveiling a Complex Distribution of Functional States. International Journal of Molecular Sciences. 21. PMID 33003385 DOI: 10.3390/ijms21197190