Anisha Shakya - Related publications

Affiliations: 
2016 Chemistry University of Michigan, Ann Arbor, Ann Arbor, MI 
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Kim J, Mandal R, Hilty C. 2D NMR spectroscopy of refolding RNase Sa using polarization transfer from hyperpolarized water. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 326: 106942. PMID 33713971 DOI: 10.1016/j.jmr.2021.106942   
2021 Khamari L, Pramanik U, Shekhar S, Mohanakumar S, Mukherjee S. Thermal Reversibility and Structural Stability in Lysozyme Induced by Epirubicin Hydrochloride. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 33703900 DOI: 10.1021/acs.langmuir.1c00179   
2021 Fernandes DD, Neale C, Gomes GW, Li Y, Malik A, Pandey A, Orazietti AP, Wang X, Ye L, Scott Prosser R, Gradinaru CC. Ligand modulation of the conformational dynamics of the A adenosine receptor revealed by single-molecule fluorescence. Scientific Reports. 11: 5910. PMID 33723285 DOI: 10.1038/s41598-021-84069-0   
2021 Fernandes DD, Neale C, Gomes GW, Li Y, Malik A, Pandey A, Orazietti AP, Wang X, Ye L, Scott Prosser R, Gradinaru CC. Ligand modulation of the conformational dynamics of the A adenosine receptor revealed by single-molecule fluorescence. Scientific Reports. 11: 5910. PMID 33723285 DOI: 10.1038/s41598-021-84069-0   
2021 Liu B, Shi H, Al-Hashimi HM. Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids. Current Opinion in Structural Biology. 70: 16-25. PMID 33836446 DOI: 10.1016/j.sbi.2021.02.007   
2021 Krishnan VV, Bentley T, Xiong A, Maitra K. Conformational Ensembles by NMR and MD Simulations in Model Heptapeptides with Select Tri-Peptide Motifs. International Journal of Molecular Sciences. 22. PMID 33573010 DOI: 10.3390/ijms22031364   
2021 Sikkema HR, Poolman B. In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy. Scientific Reports. 11: 5756. PMID 33707507 DOI: 10.1038/s41598-021-85003-0   
2021 Lu W, Wang S, Liu R, Guan Y, Zhang Y. Human serum albumin-imprinted polymers with high capacity and selectivity for abundant protein depletion. Acta Biomaterialia. PMID 33722786 DOI: 10.1016/j.actbio.2021.03.010   
2021 Sanders JC, Holmstrom ED. Integrating single-molecule FRET and biomolecular simulations to study diverse interactions between nucleic acids and proteins. Essays in Biochemistry. PMID 33600559 DOI: 10.1042/EBC20200022   
2021 Pinto SMV, Tasinato N, Barone V, Zanetti-Polzi L, Daidone I. A computational insight into the relationship between side chain IR line shapes and local environment in fibril-like structures. The Journal of Chemical Physics. 154: 084105. PMID 33639764 DOI: 10.1063/5.0038913   
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 Josephs TM, Belousoff MJ, Liang YL, Piper SJ, Cao J, Garama DJ, Leach K, Gregory KJ, Christopoulos A, Hay DL, Danev R, Wootten D, Sexton PM. Structure and dynamics of the CGRP receptor in apo and peptide-bound forms. Science (New York, N.Y.). PMID 33602864 DOI: 10.1126/science.abf7258   
2021 Mundlapati VR, Imani Z, Goldsztejn G, Gloaguen E, Brenner V, Le Barbu-Debus K, Zehnacker-Rentien A, Baltaze JP, Robin S, Mons M, Aitken DJ. A theoretical and experimental case study of the hydrogen bonding predilection of S-methylcysteine. Amino Acids. PMID 33743071 DOI: 10.1007/s00726-021-02967-z   
2021 Dias D'Andréa É, Sebastian Retel J, Diehl A, Schmieder P, Oschkinat H, Ricardo Pires J. NMR structure and dynamics of Q4DY78, a conserved kinetoplasid-specific protein from Trypanosoma cruzi. Journal of Structural Biology. 107715. PMID 33705979 DOI: 10.1016/j.jsb.2021.107715   
2021 Hays JM, Boland E, Kasson PM. Inference of Joint Conformational Distributions from Separately Acquired Experimental Measurements. The Journal of Physical Chemistry Letters. 12: 1606-1611. PMID 33596657 DOI: 10.1021/acs.jpclett.0c03623   
2021 Kaplan AR, Olson R, Alexandrescu AT. Protein Yoga: Conformational Versatility of the Hemolysin II C-terminal Domain Detailed by NMR Structures for Multiple States. Protein Science : a Publication of the Protein Society. PMID 33733504 DOI: 10.1002/pro.4066   
2021 Niu C, Du Y, Kaltashov IA. Towards better understanding of the heparin role in NETosis: feasibility of using native mass spectrometry to monitor interactions of neutrophil elastase with heparin oligomers. International Journal of Mass Spectrometry. 463. PMID 33692650 DOI: 10.1016/j.ijms.2021.116550   
2021 Fogarty CA, Fadda E. Oligomannose -Glycans 3D Architecture and Its Response to the FcγRIIIa Structural Landscape. The Journal of Physical Chemistry. B. PMID 33661628 DOI: 10.1021/acs.jpcb.1c00304   
2021 Lindsay RJ, Mansbach RA, Gnanakaran S, Shen T. Effects of pH on an IDP conformational ensemble explored by molecular dynamics simulation. Biophysical Chemistry. 271: 106552. PMID 33581430 DOI: 10.1016/j.bpc.2021.106552   
2021 Staheli CF, Barney J, Clark TR, Bowles M, Jeppesen B, Oblinsky DG, Steffensen MB, Dean JC. Spectroscopic and Photophysical Investigation of Model Dipyrroles Common to Bilins: Exploring Natural Design for Steering Torsion to Divergent Functions. Frontiers in Chemistry. 9: 628852. PMID 33681146 DOI: 10.3389/fchem.2021.628852   
2021 Barnes CA, Starich MR, Tjandra N, Mishra P. Simultaneous measurement of H-R's for rapid acquisition of backbone and sidechain paramagnetic relaxation enhancements (PREs) in proteins. Journal of Biomolecular Nmr. PMID 33625630 DOI: 10.1007/s10858-021-00359-9   
2021 Guseva S, Perez LM, Camacho-Zarco A, Bessa LM, Salvi N, Malki A, Maurin D, Blackledge M. H, C and N Backbone chemical shift assignments of the n-terminal and central intrinsically disordered domains of SARS-CoV-2 nucleoprotein. Biomolecular Nmr Assignments. PMID 33730325 DOI: 10.1007/s12104-021-10014-x   
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 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 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   
2021 Dey S, Misra R, Saseendran A, Pahan S, Gopi H. Metal Coordinated Supramolecular Polymers from the Minimalistic Hybrid Peptide Foldamers. Angewandte Chemie (International Ed. in English). PMID 33543831 DOI: 10.1002/anie.202015838   
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 Ravikumar A, de Brevern AG, Srinivasan N. Conformational Strain Indicated by Ramachandran Angles for the Protein Backbone Is Only Weakly Related to the Flexibility. The Journal of Physical Chemistry. B. PMID 33666418 DOI: 10.1021/acs.jpcb.1c00168   
2021 Dawson WM, Lang EJM, Rhys GG, Shelley KL, Williams C, Brady RL, Crump MP, Mulholland AJ, Woolfson DN. Structural resolution of switchable states of a de novo peptide assembly. Nature Communications. 12: 1530. PMID 33750792 DOI: 10.1038/s41467-021-21851-8   
2021 LeVatte M, Lipfert M, Roy D, Kovalenko A, Wishart DS. Cloning and high-level expression of monomeric human superoxide dismutase 1 (SOD1) and its interaction with pyrimidine analogs. Plos One. 16: e0247684. PMID 33635895 DOI: 10.1371/journal.pone.0247684   
2021 Gianni S, Freiberger MI, Jemth P, Ferreiro DU, Wolynes PG, Fuxreiter M. Fuzziness and Frustration in the Energy Landscape of Protein Folding, Function, and Assembly. Accounts of Chemical Research. PMID 33550810 DOI: 10.1021/acs.accounts.0c00813   
2021 Nasreen K, Parray ZA, Shamsi A, Ahmad F, Ahmed A, Malik A, Lakhrm NA, Hassan MI, Islam A. Crowding Milleu stabilizes apo-myoglobin against chemical-induced denaturation: Dominance of hardcore repulsions in the heme devoid protein. International Journal of Biological Macromolecules. PMID 33744250 DOI: 10.1016/j.ijbiomac.2021.03.089   
2021 Nasreen K, Parray ZA, Shamsi A, Ahmad F, Ahmed A, Malik A, Lakhrm NA, Hassan MI, Islam A. Crowding Milleu stabilizes apo-myoglobin against chemical-induced denaturation: Dominance of hardcore repulsions in the heme devoid protein. International Journal of Biological Macromolecules. PMID 33744250 DOI: 10.1016/j.ijbiomac.2021.03.089   
2021 Bhatia S, Krishnamoorthy G, Udgaonkar JB. Resolving Site-Specific Heterogeneity of the Unfolded State under Folding Conditions. The Journal of Physical Chemistry Letters. 3295-3302. PMID 33764778 DOI: 10.1021/acs.jpclett.1c00098   
2021 Zou J, Xiao S, Simmerling C, Raleigh DP. Quantitative Analysis of Protein Unfolded State Energetics: Experimental and Computational Studies Demonstrate That Non-Native Side-Chain Interactions Stabilize Local Native Backbone Structure. The Journal of Physical Chemistry. B. PMID 33779182 DOI: 10.1021/acs.jpcb.0c08922   
2021 Khan FI, Song H, Hassan F, Tian J, Tang L, Lai D, Juan F. Impact of amino acid substitutions on the behavior of a photoactivatable near infrared fluorescent protein PAiRFP1. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 253: 119572. PMID 33631627 DOI: 10.1016/j.saa.2021.119572   
2021 Varner TA, Mohamed-Raseek N, Miller AF. Assignments of F NMR resonances and exploration of dynamics in a long-chain flavodoxin. Archives of Biochemistry and Biophysics. 108839. PMID 33727041 DOI: 10.1016/j.abb.2021.108839   
2021 Luo H, Li H, Liu Y, Yang L, Xiao Q, Huang S. Investigation on conformational variation and activity of trypsin affected by black phosphorus quantum dots via multi-spectroscopy and molecular modeling. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 256: 119746. PMID 33819763 DOI: 10.1016/j.saa.2021.119746   
2021 Sagar A, Jeffries CM, Petoukhov MV, Svergun DI, Bernadó P. Comment on the Optimal Parameters to Derive Intrinsically Disordered Protein Conformational Ensembles from Small-Angle X-ray Scattering Data Using the Ensemble Optimization Method. Journal of Chemical Theory and Computation. PMID 33725442 DOI: 10.1021/acs.jctc.1c00014   
2021 Roche R, Bhattacharya S, Bhattacharya D. Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins. Plos Computational Biology. 17: e1008753. PMID 33621244 DOI: 10.1371/journal.pcbi.1008753   
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 Wang L, Cao C, Zuo S. Protein secondary structure assignment using pc-polyline and convolutional neural network. Proteins. PMID 33780034 DOI: 10.1002/prot.26079   
2021 Monzon AM, Bonato P, Necci M, Tosatto SCE, Piovesan D. FLIPPER: Predicting and Characterizing Linear Interacting Peptides in the Protein Data Bank. Journal of Molecular Biology. 433: 166900. PMID 33647288 DOI: 10.1016/j.jmb.2021.166900   
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 Casillo A, Fabozzi A, Russo Krauss I, Parrilli E, Biggs CI, Gibson MI, Lanzetta R, Appavou MS, Radulescu A, Tutino ML, Paduano L, Corsaro MM. Physicochemical Approach to Understanding the Structure, Conformation, and Activity of Mannan Polysaccharides. Biomacromolecules. PMID 33729771 DOI: 10.1021/acs.biomac.0c01659   
2021 Choi YK, Cao Y, Frank M, Woo H, Park SJ, Yeom MS, Croll TI, Seok C, Im W. Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane. Journal of Chemical Theory and Computation. PMID 33689337 DOI: 10.1021/acs.jctc.0c01144   
2021 Badasyan A, Valant M, Grdadolnik J, Uversky VN. The Finite Size Effects and Two-State Paradigm of Protein Folding. International Journal of Molecular Sciences. 22. PMID 33671738 DOI: 10.3390/ijms22042184   
2021 Kisiela DI, Magala P, Interlandi G, Carlucci LA, Ramos A, Tchesnokova V, Basanta B, Yarov-Yarovoy V, Avagyan H, Hovhannisyan A, Thomas WE, Stenkamp RE, Klevit RE, Sokurenko EV. Toggle switch residues control allosteric transitions in bacterial adhesins by participating in a concerted repacking of the protein core. Plos Pathogens. 17: e1009440. PMID 33826682 DOI: 10.1371/journal.ppat.1009440   
2021 Zhan T, Cui S, Liu X, Zhang C, Huang YM, Zhuang S. Enhanced Disrupting Effect of Benzophenone-1 Chlorination Byproducts to the Androgen Receptor: Cell-Based Assays and Gaussian Accelerated Molecular Dynamics Simulations. Chemical Research in Toxicology. PMID 33684284 DOI: 10.1021/acs.chemrestox.1c00023   
2021 Young VC, Artigas P. Displacement of the Na/K pump's transmembrane domains demonstrates conserved conformational changes in P-type 2 ATPases. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33597302 DOI: 10.1073/pnas.2019317118