Pallav Kosuri - Related publications

Affiliations: 
Harvard University, Cambridge, MA, United States 
Area:
Molecular biophysics
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Zhang P, Wang D, Yang W, Marszalek PE. Piecewise All-Atom Steered Molecular Dynamics Simulations Reveal Key Secondary Structures in the Luciferase Mechanical Unfolding Pathway. Biophysical Journal. PMID 33130123 DOI: 10.1016/j.bpj.2020.10.023   
2020 Tang WS, Fawzi NL, Mittal J. Refining All-Atom Protein Force Fields for Polar-Rich, Prion-like, Low-Complexity Intrinsically Disordered Proteins. The Journal of Physical Chemistry. B. PMID 33078950 DOI: 10.1021/acs.jpcb.0c07545   
2020 Bergues-Pupo AE, Lipowsky R, Vila Verde A. Unfolding mechanism and free energy landscape of single, stable, alpha helices at low pull speeds. Soft Matter. PMID 33030193 DOI: 10.1039/d0sm01166e   
2020 Heilmann N, Wolf M, Kozlowska M, Sedghamiz E, Setzler J, Brieg M, Wenzel W. Sampling of the conformational landscape of small proteins with Monte Carlo methods. Scientific Reports. 10: 18211. PMID 33097750 DOI: 10.1038/s41598-020-75239-7   
2020 Campos LA, Sadqi M, Muñoz V. Lessons about Protein Folding and Binding from Archetypal Folds. Accounts of Chemical Research. PMID 32914959 DOI: 10.1021/acs.accounts.0c00322   
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 Chen X, Rajasekaran N, Liu K, Kaiser CM. Synthesis runs counter to directional folding of a nascent protein domain. Nature Communications. 11: 5096. PMID 33037221 DOI: 10.1038/s41467-020-18921-8   
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 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 Henry L, Panman MR, Isaksson L, Claesson E, Kosheleva I, Henning R, Westenhoff S, Berntsson O. Real-time tracking of protein unfolding with time-resolved x-ray solution scattering. Structural Dynamics (Melville, N.Y.). 7: 054702. PMID 32984436 DOI: 10.1063/4.0000013   
2020 Mendelman N, Zerbetto M, Buck M, Meirovitch E. Conformational Entropy from Mobile Bond Vectors in Proteins: A Viewpoint that Unifies NMR-Relaxation-Theory and Molecular-Dynamics-Simulation Approaches. The Journal of Physical Chemistry. B. PMID 32981310 DOI: 10.1021/acs.jpcb.0c05846   
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/j.sbi.2020.10.005   
2020 Sowińska A, Vasquez L, Żaczek S, Manna RN, Tuñón I, Dybala-Defratyka A. Seeking the Source of Catalytic Efficiency of Lindane Dehydrochlorinase, LinA. The Journal of Physical Chemistry. B. PMID 33146535 DOI: 10.1021/acs.jpcb.0c08976   
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 Aoki-Shioi N, Jobichen C, Sivaraman J, Kini RM. Unusual quaternary structure of a homodimeric synergistic-type toxin from mamba snake venom defines its molecular evolution. The Biochemical Journal. PMID 33000863 DOI: 10.1042/BCJ20200529   
2020 Lai CH, Chang CC, Chuang HC, Tan TH, Lyu PC. Structural Insights into the Active Site Formation of DUSP22 in N-loop-containing Protein Tyrosine Phosphatases. International Journal of Molecular Sciences. 21. PMID 33053837 DOI: 10.3390/ijms21207515   
2020 Røjel N, Kari J, Sørensen TH, Badino SF, Morth JP, Schaller K, Cavaleiro AM, Borch K, Westh P. Substrate binding in the processive cellulase Cel7A: Transition state of complexation and roles of conserved tryptophan residues. The Journal of Biological Chemistry. 295: 1454-1463. PMID 31848226 DOI: 10.1074/jbc.RA119.011420   
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 Nandi T, Desai A, Ainavarapu SRK. The unfolding transition state of ubiquitin with charged residues has higher energy than that with hydrophobic residues. Physical Chemistry Chemical Physics : Pccp. PMID 33026000 DOI: 10.1039/d0cp03876h   
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   
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 Smith LJ, van Gunsteren WF, Hansen N. On the Use of Side-Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study using Hen Lysozyme. Chembiochem : a European Journal of Chemical Biology. PMID 33146424 DOI: 10.1002/cbic.202000674   
2020 Fenner K, Redgate A, Brancaleon L. A 200 nanoseconds all-atom simulation of the pH-dependent EF loop transition in bovine β-lactoglobulin. The role of the orientation of the E89 side chain. Journal of Biomolecular Structure & Dynamics. 1-16. PMID 32909899 DOI: 10.1080/07391102.2020.1817785   
2020 Chen Z, Huang J, Pu H, Qi Y, Fang C, Shu G. Analysis of the complexation process between starch molecules and trilinolenin. International Journal of Biological Macromolecules. PMID 32987075 DOI: 10.1016/j.ijbiomac.2020.09.139   
2020 Chakravorty A, Higham J, Henchman RH. Entropy of Proteins Using Multiscale Cell Correlation. Journal of Chemical Information and Modeling. PMID 32955869 DOI: 10.1021/acs.jcim.0c00611   
2020 Muthuramalingam M, Whittier SK, Lovell S, Battaile KP, Tachiyama S, Johnson DK, Picking WL, Picking WD. The Structures of SctK and SctD from Pseudomonas aeruginosa Reveal the Interface of the Type III Secretion System Basal Body and Sorting Platform. Journal of Molecular Biology. PMID 33122003 DOI: 10.1016/j.jmb.2020.10.027   
2020 Yagi-Utsumi M, Chandak MS, Yanaka S, Hiranyakorn M, Nakamura T, Kato K, Kuwajima K. Residual Structure of Unfolded Ubiquitin as Revealed by Hydrogen/Deuterium-Exchange 2D NMR. Biophysical Journal. PMID 33142107 DOI: 10.1016/j.bpj.2020.10.003   
2020 Hinostroza F, Neely A, Araya-Duran I, Marabolí V, Canan J, Rojas M, Aguayo D, Latorre R, González-Nilo FD, Cárdenas AM. Dynamin-2 R465W mutation induces long range perturbation in highly ordered oligomeric structures. Scientific Reports. 10: 18151. PMID 33097808 DOI: 10.1038/s41598-020-75216-0   
2020 Chashmniam S, Teixeria JMC, Paniagua JC, Pons M. A methionine chemical shift based order parameter characterizing global protein dynamics. Chembiochem : a European Journal of Chemical Biology. PMID 33166021 DOI: 10.1002/cbic.202000701   
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 Zhao Y, Zhao Y, Peng B, Zhang L. Dynamic behavior of biomaterials uncovered by cryo-electron microscopy. Combinatorial Chemistry & High Throughput Screening. PMID 33019925 DOI: 10.2174/1386207323666201005100653   
2020 Wingert B, Krieger J, Li H, Bahar I. Adaptability and specificity: how do proteins balance opposing needs to achieve function? Current Opinion in Structural Biology. 67: 25-32. PMID 33053463 DOI: 10.1016/j.sbi.2020.08.009   
2020 Sharma V, Shing B, Hernandez-Alvarez L, Debnath A, Podust LM. . Molecular Pharmacology. PMID 33008918 DOI: 10.1124/molpharm.120.000092   
2020 Nagpal S, Luong TDN, Sadqi M, Muñoz V. Downhill (Un)Folding Coupled to Binding as a Mechanism for Engineering Broadband Protein Conformational Transducers. Acs Synthetic Biology. 9: 2427-2439. PMID 32822536 DOI: 10.1021/acssynbio.0c00190   
2020 Shimamoto S, Fukutsuji M, Osumi T, Goto M, Toyoda H, Hidaka Y. Topological Regulation of the Bioactive Conformation of a Disulfide-Rich Peptide, Heat-Stable Enterotoxin. Molecules (Basel, Switzerland). 25. PMID 33096591 DOI: 10.3390/molecules25204798   
2020 Liu Q, He QT, Lyu X, Yang F, Zhu ZL, Xiao P, Yang Z, Zhang F, Yang ZY, Wang XY, Sun P, Wang QW, Qu CX, Gong Z, Lin JY, et al. DeSiphering receptor core-induced and ligand-dependent conformational changes in arrestin via genetic encoded trimethylsilyl H-NMR probe. Nature Communications. 11: 4857. PMID 32978402 DOI: 10.1038/s41467-020-18433-5   
2020 Catipovic MA, Rapoport TA. Protease protection assays show polypeptide movement into the SecY channel by power strokes of the SecA ATPase. Embo Reports. e50905. PMID 32969592 DOI: 10.15252/embr.202050905   
2020 Yoder N, Jalali-Yazdi F, Noreng S, Houser A, Baconguis I, Gouaux E. Light-coupled cryo-plunger for time-resolved cryo-EM. Journal of Structural Biology. 212: 107624. PMID 32950604 DOI: 10.1016/j.jsb.2020.107624   
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 Iwata T, Yamada D, Mikuni K, Agata K, Hitomi K, Getzoff ED, Kandori H. ATP binding promotes light-induced structural changes to the protein moiety of cryptochrome 1. Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society For Photobiology. 19: 1326-1331. PMID 32935701 DOI: 10.1039/d0pp00003e   
2020 Li F, Tang Y. The activation mechanism of peroxidase by ultrasound. Ultrasonics Sonochemistry. 71: 105362. PMID 33096324 DOI: 10.1016/j.ultsonch.2020.105362   
2020 Rowe SJ, Mecaskey RJ, Nasef M, Talton RC, Sharkey RE, Halliday JC, Dunkle JA. Shared requirements for key residues in the antibiotic resistance enzymes ErmC and ErmE suggest a common mode of RNA recognition. The Journal of Biological Chemistry. PMID 33020182 DOI: 10.1074/jbc.RA120.014280   
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 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 Goldsztejn G, Mundlapati VR, Brenner V, Gloaguen E, Mons M, Cabezas C, León I, Alonso JL. Intrinsic folding of the cysteine residue: competition between folded and extended forms mediated by the -SH group. Physical Chemistry Chemical Physics : Pccp. 22: 20284-20294. PMID 32966425 DOI: 10.1039/d0cp03136d   
2020 Raninga N, Nayeem SM, Gupta S, Mullick R, Pandita E, Das S, Deep S, Sau AK. Stimulation of GMP formation in hGBP1 is mediated by W79 and its effect on the antiviral activity. The Febs Journal. PMID 33113220 DOI: 10.1111/febs.15611   
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 Tian Y, Liu C, Xue W, Wang Z. Crosslinked Recombinant-Ara h 1 Catalyzed by Microbial Transglutaminase: Preparation, Structural Characterization and Allergic Assessment. Foods (Basel, Switzerland). 9. PMID 33096617 DOI: 10.3390/foods9101508   
2020 Oliva F, Flores-Canales JC, Pieraccini S, Morelli CF, Sironi M, Schiøtt B. Simulating Multiple Substrate-Binding Events by γ-Glutamyltransferase Using Accelerated Molecular Dynamics. The Journal of Physical Chemistry. B. PMID 33112625 DOI: 10.1021/acs.jpcb.0c06907   
2020 Zohib M, Maheshwari D, Pal RK, Freitag-Pohl S, Biswal BK, Pohl E, Arora A. Crystal structure of the GDP-bound GTPase domain of Rab5a from Leishmania donovani. Acta Crystallographica. Section F, Structural Biology Communications. 76: 544-556. PMID 33135673 DOI: 10.1107/S2053230X20013722