Sharmistha Sinha - Related publications

Institute of Nano Science and Technology, Mohali, India 
Biophysical Chemistry
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Chen S, Gong X, Tan H, Liu Y, He L, Ouyang J. Study of the noncovalent interactions between phenolic acid and lysozyme by cold spray ionization mass spectrometry (CSI-MS), multi-spectroscopic and molecular docking approaches. Talanta. 211: 120762. PMID 32070628 DOI: 10.1016/j.talanta.2020.120762   
2020 Di Natale C, La Manna S, Avitabile C, Florio D, Morelli G, Netti PA, Marasco D. Engineered β-hairpin scaffolds from human prion protein regions: Structural and functional investigations of aggregates. Bioorganic Chemistry. 96: 103594. PMID 31991323 DOI: 10.1016/j.bioorg.2020.103594   
2020 Zhong S, Huang K, Luo S, Dong S, Duan L. Improving the performance of the MM/PBSA and MM/GBSA methods in recognizing the native structure of the Bcl-2 family using the interaction entropy method. Physical Chemistry Chemical Physics : Pccp. PMID 32043094 DOI: 10.1039/c9cp06459a   
2020 Rangubpit W, Sompornpisut P, Pandey R. Structure and dynamics of aquaporin-1. Vitamins and Hormones. 112: 29-46. PMID 32061346 DOI: 10.1016/bs.vh.2019.09.001   
2020 Sladek V, Harada R, Shigeta Y. Protein Dynamics and the Folding Degree. Journal of Chemical Information and Modeling. PMID 32090564 DOI: 10.1021/acs.jcim.9b00942   
2020 Konar M, Sahoo H. Tyrosine mediated conformational change in bone morphogenetic protein - 2: Biophysical implications of protein - Phytoestrogen interaction. International Journal of Biological Macromolecules. PMID 32061704 DOI: 10.1016/j.ijbiomac.2020.02.113   
2020 Bansal R, Haque A, Hassan I, Ethayathulla AS, Kaur P. Structural and conformational behavior of MurE ligase from Salmonella enterica serovar Typhi at different temperature and pH conditions. International Journal of Biological Macromolecules. PMID 32018007 DOI: 10.1016/j.ijbiomac.2020.01.306   
2020 Nguyen LH, Tran TT, Truong LTN, Mai HH, Nguyen TT. Overcharging of zinc ion in the structure of zinc-finger protein is needed for DNA binding stability. Biochemistry. PMID 32043865 DOI: 10.1021/acs.biochem.9b01055   
2020 Purslow JA, Khatiwada B, Bayro MJ, Venditti V. NMR Methods for Structural Characterization of Protein-Protein Complexes. Frontiers in Molecular Biosciences. 7: 9. PMID 32047754 DOI: 10.3389/fmolb.2020.00009   
2020 Zhao B, Payne WG, Sai J, Lu Z, Olejniczak ET, Fesik SW. Structural Elucidation of Peptide Binding to KLHL-12, a Substrate Specific Adapter Protein in a Cul3-Ring E3 Ligase Complex. Biochemistry. PMID 32032490 DOI: 10.1021/acs.biochem.9b01073   
2020 Longo LM, Petrović D, Kamerlin SCL, Tawfik DS. Short and simple sequences favored the emergence of N-helix phospho-ligand binding sites in the first enzymes. Proceedings of the National Academy of Sciences of the United States of America. PMID 32079722 DOI: 10.1073/pnas.1911742117   
2020 Gill M, McCully ME. Molecular dynamics simulations suggest stabilizing mutations in a de novo designed α/β protein. Protein Engineering, Design & Selection : Peds. PMID 32086513 DOI: 10.1093/protein/gzaa005   
2020 Guéret SM, Thavam S, Carbajo RJ, Potowski M, Larsson N, Dahl G, Dells Eacute N A, Grossmann TN, Plowright AT, Valeur E, Lemurell M, Waldmann H. Macrocyclic Modalities Combining Peptide Epitopes and Natural Product Fragments. Journal of the American Chemical Society. PMID 32058716 DOI: 10.1021/jacs.0c00269   
2020 Alderson TR, Ying J, Bax A, Benesch JLP, Baldwin AJ. Conditional disorder in small heat-shock proteins. Journal of Molecular Biology. PMID 32081587 DOI: 10.1016/j.jmb.2020.02.003   
2020 Wu Y, Lou L, Xie ZR. A Pilot Study of All-Computational Drug Design Protocol-From Structure Prediction to Interaction Analysis. Frontiers in Chemistry. 8: 81. PMID 32117898 DOI: 10.3389/fchem.2020.00081   
2020 Myrhammar A, Rosik D, Eriksson Karlström A. Photo-controlled reversible binding between the protein A-derived Z domain and immunoglobulin G. Bioconjugate Chemistry. PMID 32027501 DOI: 10.1021/acs.bioconjchem.9b00786   
2020 Kim H, Kim JG, Muniyappan S, Kim TW, Lee SJ, Ihee H. Effect of Occluded Ligand Migration on the Kinetics and Structural Dynamics of Homodimeric Hemoglobin. The Journal of Physical Chemistry. B. PMID 32027135 DOI: 10.1021/acs.jpcb.9b11749   
2020 Láng A, Jákli I, Enyedi KN, Mező G, Menyhárd DK, Perczel A. Off-pathway 3D-structure provides protection against spontaneous Asn/Asp isomerization: shielding proteins Achilles heel. Quarterly Reviews of Biophysics. 53: e2. PMID 32000865 DOI: 10.1017/S003358351900009X   
2020 Ghosh C, Jana B. Inter-Subunit Assisted Folding of DNA Binding Domains in Dimeric Catabolite Activator Protein. The Journal of Physical Chemistry. B. PMID 31999927 DOI: 10.1021/acs.jpcb.9b10941   
2020 Makarov AA, Iacob RE, Pirrone GF, Rodriguez-Granillo A, Joyce L, Mangion I, Moore JC, Sherer EC, Engen JR. Combination of HDX-MS and in silico modeling to study enzymatic reactivity and stereo-selectivity at different solvent conditions. Journal of Pharmaceutical and Biomedical Analysis. 182: 113141. PMID 32036298 DOI: 10.1016/j.jpba.2020.113141   
2020 Jin Z, Wang Y, Yu XF, Tan QQ, Liang SS, Li T, Zhang H, Shaw PC, Wang J, Hu C. Structure-based virtual screening of influenza virus RNA polymerase inhibitors from natural compounds: Molecular dynamics simulation and MM-GBSA calculation. Computational Biology and Chemistry. 85: 107241. PMID 32120300 DOI: 10.1016/j.compbiolchem.2020.107241   
2020 Neira JL, Ortore MG, Florencio FJ, Muro-Pastor MI, Rizzuti B. Dynamics of the intrinsically disordered inhibitor IF7 of glutamine synthetase in isolation and in complex with its partner. Archives of Biochemistry and Biophysics. 108303. PMID 32074499 DOI: 10.1016/   
2020 Kalabova D, Filandr F, Alblova M, Petrvalska O, Horvath M, Man P, Obsil T, Obsilova V. 14-3-3 protein binding blocks the dimerization interface of caspase-2. The Febs Journal. PMID 31961068 DOI: 10.1111/febs.15215   
2020 Anighoro A. Underappreciated Chemical Interactions in Protein-Ligand Complexes. Methods in Molecular Biology (Clifton, N.J.). 2114: 75-86. PMID 32016887 DOI: 10.1007/978-1-0716-0282-9_5   
2020 Ernst P, Zosel F, Reichen C, Nettels D, Schuler B, Plückthun A. Structure-guided design of a peptide lock for modular peptide binders. Acs Chemical Biology. PMID 31985201 DOI: 10.1021/acschembio.9b00928   
2020 Fei X, Bell TA, Jenni S, Stinson BM, Baker TA, Harrison SC, Sauer RT. Structures of the ATP-fueled ClpXP proteolytic machine bound to protein substrate. Elife. 9. PMID 32108573 DOI: 10.7554/eLife.52774   
2020 Islam SM, Havranek B, Ibnat Z, Roy PN. New Insights into the Role of Hydrogen Bonding in Furanoside Binding to Protein. The Journal of Physical Chemistry. B. PMID 32075374 DOI: 10.1021/acs.jpcb.9b11924   
2020 Glöckner S, Ngo K, Sager CP, Hüfner-Wulsdorf T, Heine A, Klebe G. Conformational changes in alkyl chains determine the thermodynamic and kinetic binding profiles of Carbonic Anhydrase inhibitors. Acs Chemical Biology. PMID 32027480 DOI: 10.1021/acschembio.9b00895   
2020 Idress M, Milne BF, Thompson GS, Trembleau L, Jaspars M, Houssen WE. Structure-Based Design, Synthesis and Bioactivity of a New Anti-TNFα Cyclopeptide. Molecules (Basel, Switzerland). 25. PMID 32093030 DOI: 10.3390/molecules25040922   
2020 Kelly CM, Manukian S, Kim E, Gage MJ. Differences in stability and calcium sensitivity of the Ig Domains in Titin's N2A Region. Protein Science : a Publication of the Protein Society. PMID 32112607 DOI: 10.1002/pro.3848   
2020 Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chemical Reviews. PMID 32101406 DOI: 10.1021/acs.chemrev.9b00636   
2020 Chakravarty D, McElfresh GW, Kundrotas PJ, Vakser IA. How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking. Proteins. PMID 31994759 DOI: 10.1002/prot.25875   
2020 McMahon CM, Isabella CR, Windsor IW, Kosma P, Raines RT, Kiessling LL. Stereoelectronic Effects Impact Glycan Recognition. Journal of the American Chemical Society. PMID 31930911 DOI: 10.1021/jacs.9b11699   
2020 García-Recio A, Navarro G, Franco R, Olivella M, Guixà-González R, Cordomí A. DIMERBOW: exploring possible GPCR dimer interfaces. Bioinformatics (Oxford, England). PMID 32096817 DOI: 10.1093/bioinformatics/btaa117   
2020 Li X, Lee KH, Shorkey S, Chen J, Chen M. Different Anomeric Sugar Bound States of MBP Resolved by a Cytolysin A Nanopore Tweezer. Acs Nano. PMID 31995359 DOI: 10.1021/acsnano.9b07385   
2020 Katigbak J, Li H, Rooklin DW, Zhang Y. AlphaSpace 2.0: Representing Concave Biomolecular Surfaces using Beta-Clusters. Journal of Chemical Information and Modeling. PMID 31995373 DOI: 10.1021/acs.jcim.9b00652   
2020 Huang S, Li H, Liu Y, Yang L, Wang D, Xiao Q. Investigations of conformational structure and enzymatic activity of trypsin after its binding interaction with graphene oxide. Journal of Hazardous Materials. 392: 122285. PMID 32105952 DOI: 10.1016/j.jhazmat.2020.122285   
2020 Sauer MF, Sevy AM, Crowe JE, Meiler J. Multi-state design of flexible proteins predicts sequences optimal for conformational change. Plos Computational Biology. 16: e1007339. PMID 32032348 DOI: 10.1371/journal.pcbi.1007339   
2020 Bai C, Lao Z, Chen Y, Tang Y, Wei G. Pristine and Hydroxylated Fullerenes Prevent the Aggregation of Human Islet Amyloid Polypeptide and Display Different Inhibitory Mechanisms. Frontiers in Chemistry. 8: 51. PMID 32117877 DOI: 10.3389/fchem.2020.00051   
2020 Minh Hung H, Nguyen MT, Tran PT, Truong VK, Chapman J, Quynh Anh LH, Derreumaux P, Vu VV, Ngo ST. Impact of the Astaxanthin, Betanin and EGCG Compounds on Small Oligomers of the Amyloid Aβ40 Peptide. Journal of Chemical Information and Modeling. PMID 32105466 DOI: 10.1021/acs.jcim.9b01074   
2020 Swain BC, Mukherjee SK, Rout J, Sakshi, Mishra PP, Mukherjee M, Tripathy U. A spectroscopic and computational intervention of interaction of lysozyme with 6-mercaptopurine. Analytical and Bioanalytical Chemistry. PMID 32055906 DOI: 10.1007/s00216-020-02483-1   
2020 Fargason T, Wang T, De Silva NIU, Zhang Z, McKelvey H, Knapp T, Zaharias S, Zhang J. Amide additives improve RDC measurements in polyacrylamide. Journal of Biomolecular Nmr. PMID 32056065 DOI: 10.1007/s10858-020-00305-1   
2020 Madsen D, Jørgensen FP, Palmer D, Roux M, Olsen JV, Bols M, Schoffelen S, Diness F, Meldal M. Design and Combinatorial Development of Shield-1 Peptide Mimetics Binding to Destabilized FKBP12. Acs Combinatorial Science. PMID 32027120 DOI: 10.1021/acscombsci.9b00197   
2020 Heifetz A, Morao I, Babu MM, James T, Southey MW, Fedorov DG, Aldeghi M, Bodkin MJ, Townsend-Nicholson A. Characterising Inter-helical Interactions of G Protein-Coupled Receptors with the Fragment Molecular Orbital Method. Journal of Chemical Theory and Computation. PMID 32096994 DOI: 10.1021/acs.jctc.9b01136   
2020 Xu Y, Dai T, Huang K, Liang L, Liu C, Chen J. Analyses on the binding interaction between rice glutelin and conjugated linoleic acid by multi-spectroscopy and computational docking simulation. Journal of Food Science and Technology. 57: 886-894. PMID 32123409 DOI: 10.1007/s13197-019-04121-w   
2020 Shi W, Lemoine JM, Shawky AA, Singha M, Pu L, Yang S, Ramanujam J, Brylinski M. BionoiNet: Ligand-binding site classification with off-the-shelf deep neural network. Bioinformatics (Oxford, England). PMID 32053156 DOI: 10.1093/bioinformatics/btaa094   
2020 Jain M, Muthukumaran J, Singh AK. Structural and Functional characterization of Chitin binding Lectin from : Insights from Phylogenetic analysis, Protein structure prediction, Molecular docking and Molecular dynamics simulation. Journal of Biomolecular Structure & Dynamics. 1-33. PMID 32116131 DOI: 10.1080/07391102.2020.1737234   
2020 Allert MJ, Hellinga HW. Describing complex structure-function relationships in biomolecules at equilibrium. Journal of Molecular Biology. PMID 31940471 DOI: 10.1016/j.jmb.2019.12.039   
2020 Hardenbrook NJ, Liu S, Zhou K, Ghosal K, Hong Zhou Z, Krantz BA. Atomic structures of anthrax toxin protective antigen channels bound to partially unfolded lethal and edema factors. Nature Communications. 11: 840. PMID 32047164 DOI: 10.1038/s41467-020-14658-6   
2020 Hentzen NB, Islami V, Köhler M, Zenobi R, Wennemers H. A Lateral Salt Bridge for the Specific Assembly of an ABC-Type Collagen Heterotrimer. Journal of the American Chemical Society. PMID 31971793 DOI: 10.1021/jacs.9b13037