Ishita Mukerji - Related publications

Wesleyan University, Middletown, CT, United States 
General Biophysics, Molecular Biology
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50 most relevant papers in past 60 days:
Year Citation  Score
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 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 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 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 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 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 Milorey B, Schweitzer-Stenner R, Andrews B, Schwalbe H, Urbanc B. Short peptides as predictors for the structure of polyarginine sequences in disordered proteins. Biophysical Journal. PMID 33453267 DOI: 10.1016/j.bpj.2020.12.026   
2021 Levengood JD, Peterson J, Tolbert BS, Roche J. Thermodynamic stability of hnRNP A1 low complexity domain revealed by high-pressure NMR. Proteins. PMID 33550645 DOI: 10.1002/prot.26058   
2021 Labra-Núñez A, Cofas-Vargas LF, Gutiérrez-Magdaleno G, Gómez-Velasco H, Rodríguez-Hernández A, Rodríguez-Romero A, García-Hernández E. Energetic and structural effects of the Tanford transition on ligand recognition of bovine β-lactoglobulin. Archives of Biochemistry and Biophysics. 699: 108750. PMID 33421379 DOI: 10.1016/   
2021 Labra-Núñez A, Cofas-Vargas LF, Gutiérrez-Magdaleno G, Gómez-Velasco H, Rodríguez-Hernández A, Rodríguez-Romero A, García-Hernández E. Energetic and structural effects of the Tanford transition on ligand recognition of bovine β-lactoglobulin. Archives of Biochemistry and Biophysics. 699: 108750. PMID 33421379 DOI: 10.1016/   
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 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 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 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 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 Yu HS, Modugula K, Ichihara O, Kramschuster K, Keng S, Abel R, Wang L. General Theory of Fragment Linking in Molecular Design: Why Fragment Linking Rarely Succeeds and How to Improve Outcomes. Journal of Chemical Theory and Computation. 17: 450-462. PMID 33372778 DOI: 10.1021/acs.jctc.0c01004   
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 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 Mahmoudinobar F, Nilsson BL, Dias CL. Effects of Ions and Small Compounds on the Structure of Aβ Monomers. The Journal of Physical Chemistry. B. 125: 1085-1097. PMID 33481611 DOI: 10.1021/acs.jpcb.0c09617   
2021 Wilt HM, Yu P, Tan K, Wang YX, Stagno JR. Tying the knot in the tetrahydrofolate (THF) riboswitch: a molecular basis for gene regulation. Journal of Structural Biology. 107703. PMID 33571639 DOI: 10.1016/j.jsb.2021.107703   
2021 Hervø-Hansen S, Højgaard C, Johansson KE, Wang Y, Wahni K, Young D, Messens J, Teilum K, Lindorff-Larsen K, Winther JR. Charge Interactions in a Highly Charge-Depleted Protein. Journal of the American Chemical Society. PMID 33529004 DOI: 10.1021/jacs.0c10789   
2021 Xia Y, Xia CQ, Pan X, Shen HB. GraphBind: protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues. Nucleic Acids Research. PMID 33577689 DOI: 10.1093/nar/gkab044   
2021 Paiz EA, Lewis KA, Whitten ST. Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins. Molecules (Basel, Switzerland). 26. PMID 33530506 DOI: 10.3390/molecules26030634   
2021 Makley LN, Johnson OT, Ghanakota P, Rauch JN, Osborn D, Wu TS, Cierpicki T, Carlson HA, Gestwicki JE. Chemical validation of a druggable site on Hsp27/HSPB1 using in silico solvent mapping and biophysical methods. Bioorganic & Medicinal Chemistry. 34: 115990. PMID 33549906 DOI: 10.1016/j.bmc.2020.115990   
2021 Millan CR, Francis M, Kumar Khandelwal N, Thompson VF, Thaker TM, Tomasiak TM. A conserved motif in intracellular loop 1 stabilizestheoutward-facing conformation of TmrAB. Journal of Molecular Biology. 166834. PMID 33524413 DOI: 10.1016/j.jmb.2021.166834   
2021 Saha S, Bhattacharjee S, Chowdhury J. Exploring the binding interactions of janus green blue with serum albumins from spectroscopic and calorimetric studies aided by calculations. Journal of Biomolecular Structure & Dynamics. 1-17. PMID 33410370 DOI: 10.1080/07391102.2020.1870156   
2021 Liu Y, Parks FC, Sheetz EG, Chen CH, Flood AH. Polarity-Tolerant Chloride Binding in Foldamer Capsules by Programmed Solvent-Exclusion. Journal of the American Chemical Society. PMID 33596052 DOI: 10.1021/jacs.0c12562   
2021 Raich L, Meier K, Günther J, Christ CD, Noé F, Olsson S. Discovery of a hidden transient state in all bromodomain families. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33468647 DOI: 10.1073/pnas.2017427118   
2021 Ham D, Ahn D, Ashim J, Cho Y, Kim HR, Yu W, Chung KY. Conformational switch that induces GDP release from Gi. Journal of Structural Biology. 107694. PMID 33418033 DOI: 10.1016/j.jsb.2020.107694   
2021 Megalathan A, Wijesinghe KM, Ranson L, Dhakal S. Single-Molecule Analysis of Nanocircle-Embedded I-Motifs under Crowding. The Journal of Physical Chemistry. B. PMID 33629846 DOI: 10.1021/acs.jpcb.0c09640   
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 de Vries RMJM, Meijer FA, Doveston RG, Leijten-van de Gevel IA, Brunsveld L. Cooperativity between the orthosteric and allosteric ligand binding sites of RORγt. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33536342 DOI: 10.1073/pnas.2021287118   
2021 Tsai WC, Aleem AM, Whittington C, Cortopassi WA, Kalyanaraman C, Baroz A, Iavarone AT, Skrzypczak-Jankun E, Jacobson MP, Offenbacher AR, Holman T. Mutagenesis, Hydrogen-Deuterium Exchange, and Molecular Docking Investigations Establish the Dimeric Interface of Human Platelet-Type 12-Lipoxygenase. Biochemistry. PMID 33635645 DOI: 10.1021/acs.biochem.1c00053   
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 Xu X, Gagné D, Aramini JM, Gardner KH. Volume and Compressibility Differences Between Protein Conformations Revealed by High-Pressure NMR. Biophysical Journal. PMID 33524371 DOI: 10.1016/j.bpj.2020.12.034   
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 Kim CS, Brown AM, Grove TZ, Etzkorn FA. Designed Leucine-Rich Repeat Proteins Bind Two Muramyl Dipeptide Ligands. Protein Science : a Publication of the Protein Society. PMID 33512005 DOI: 10.1002/pro.4031   
2021 Monsen RC, Chakravarthy S, Dean WL, Chaires JB, Trent JO. The solution structures of higher-order human telomere G-quadruplex multimers. Nucleic Acids Research. PMID 33469644 DOI: 10.1093/nar/gkaa1285   
2021 Mohd-Kipli F, Claridge JK, Habjanič J, Jiang A, Schnell JR. Conformational triggers associated with influenza matrix protein 1 polymerization. The Journal of Biological Chemistry. 100316. PMID 33516724 DOI: 10.1016/j.jbc.2021.100316   
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 Diaz DB, Appavoo SD, Bogdanchikova AF, Lebedev Y, McTiernan TJ, Dos Passos Gomes G, Yudin AK. Illuminating the dark conformational space of macrocycles using dominant rotors. Nature Chemistry. PMID 33589789 DOI: 10.1038/s41557-020-00620-y   
2021 Valles GJ, Ashton NW, Jaiswal N, Woodgate R, Bezsonova I. Nuclear magnetic resonance spectral data of the USP7 TRAF and UBL1-2 domains in complex with DNA polymerase ι peptides. Data in Brief. 34: 106680. PMID 33437851 DOI: 10.1016/j.dib.2020.106680   
2021 Quesada Moreno MM, Pinacho P, Perez C, Sekutor M, Schreiner PR, Schnell M. Do docking sites persist upon fluorination? The diadamantyl ether-aromatics challenge for rotational spectroscopy and theory. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 33512017 DOI: 10.1002/chem.202100078   
2021 Birkedal V, Aznauryan M, Noer SL, Pedersen CW, Mergny JL, Teulade-Fichou MP. Ligand binding to dynamically populated G-quadruplex DNA. Chembiochem : a European Journal of Chemical Biology. PMID 33450114 DOI: 10.1002/cbic.202000792   
2021 Spencer SEF, Rodger A. Bayesian inference assessment of protein secondary structure analysis using circular dichroism data - how much structural information is contained in protein circular dichroism spectra? Analytical Methods : Advancing Methods and Applications. PMID 33393941 DOI: 10.1039/d0ay01645d   
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 Vugmeyster L. Recent developments in deuterium solid-state NMR for the detection of slow motions in proteins. Solid State Nuclear Magnetic Resonance. 111: 101710. PMID 33450712 DOI: 10.1016/j.ssnmr.2020.101710   
2021 Lin MH, Cho CC, Chiu YC, Chien CY, Huang YP, Chang CF, Hsu CH. Elucidating the tunability of binding behavior for the MERS-CoV macro domain with NAD metabolites. Communications Biology. 4: 123. PMID 33504944 DOI: 10.1038/s42003-020-01633-6   
2021 Ansari S, Ray A, Ali MF, Bano S, Jairajpuri MA. Contrasting conformational dynamics of β-sheet A and helix F with implications in neuroserpin inhibition and aggregation. International Journal of Biological Macromolecules. PMID 33516851 DOI: 10.1016/j.ijbiomac.2021.01.171   
2021 Siu HW, Heck B, Kovermann M, Hauser K. Template-assisted design of monomeric polyQ models to unravel the unique role of glutamine side chains in disease-related aggregation. Chemical Science. 12: 412-426. PMID 33552461 DOI: 10.1039/d0sc05299j