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 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 Yu M, Zhao Z, Chen Z, Le S, Yan J. Modulating mechanical stability of heterodimerization between engineered orthogonal helical domains. Nature Communications. 11: 4476. PMID 32900995 DOI: 10.1038/s41467-020-18323-w   
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 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 Kirmizialtin S, Pitici F, Cardenas AE, Elber R, Thirumalai D. Dramatic Shape Changes Occur as Cytochrome Folds. The Journal of Physical Chemistry. B. PMID 32840372 DOI: 10.1021/acs.jpcb.0c05802   
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 Stojanovski BM, Pelc LA, Zuo X, Di Cera E. Zymogen and activated protein C have similar structural architecture. The Journal of Biological Chemistry. PMID 32855236 DOI: 10.1074/jbc.RA120.014789   
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 Plaks JG, Brewer JA, Jacobsen NK, McKenna M, Uzarski JR, Lawton TJ, Filocamo SF, Kaar JL. Rosetta-enabled Structural Prediction of Permissive Loop Insertion Sites in Proteins. Biochemistry. PMID 32970423 DOI: 10.1021/acs.biochem.0c00533   
2020 Oliveira NFB, Pires IDS, Machuqueiro M. Improved GROMOS 54A7 charge sets for phosphorylated Tyr, Ser, and Thr to deal with pH-dependent binding phenomena. Journal of Chemical Theory and Computation. PMID 32809819 DOI: 10.1021/acs.jctc.0c00529   
2020 Smith Z, Ravindra P, Wang Y, Cooley R, Tiwary P. Discovering Protein Conformational Flexibility Through Artificial Intelligence Aided Molecular Dynamics. The Journal of Physical Chemistry. B. PMID 32841026 DOI: 10.1021/acs.jpcb.0c03985   
2020 Cheng Y, Zhang Y, Gong Z, Zhang XH, Li Y, Shi X, Pei Y, You H. High Mechanical Stability and Slow Unfolding Rates Are Prevalent in Parallel-Stranded DNA G-Quadruplexes. The Journal of Physical Chemistry Letters. PMID 32885976 DOI: 10.1021/acs.jpclett.0c02229   
2020 Maffucci I, Laage D, Stirnemann G, Sterpone F. Differences in thermal structural changes and melting between mesophilic and thermophilic dihydrofolate reductase enzymes. Physical Chemistry Chemical Physics : Pccp. 22: 18361-18373. PMID 32789320 DOI: 10.1039/d0cp02738c   
2020 Singewald K, Bogetti X, Sinha K, Rule G, Saxena SK. Double Histidine based EPR measurements at physiological temperatures permit site-specific elucidation of hidden dynamics in enzymes. Angewandte Chemie (International Ed. in English). PMID 32910837 DOI: 10.1002/anie.202009982   
2020 Chrabąszczewska M, Sieradzan AK, Rodziewicz-Motowidło S, Grubb A, Dobson CM, Kumita JR, Kozak M. Structural Characterization of Covalently Stabilized Human Cystatin C Oligomers. International Journal of Molecular Sciences. 21. PMID 32824145 DOI: 10.3390/ijms21165860   
2020 Younas T, Vidallon MLP, Tabor RF, He L. Open-Closed Structure of Light Responsive Protein LOV2 Regulates its Molecular Interaction with Binding Partner. The Journal of Physical Chemistry Letters. PMID 32945680 DOI: 10.1021/acs.jpclett.0c02252   
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 Kuhar N, Umapathy S. Probing the stepwise unfolding of bovine serum albumin using 2D correlation Raman spectroscopic analysis. Analytical Chemistry. PMID 32865392 DOI: 10.1021/acs.analchem.0c02968   
2020 Subramanian S, Golla H, Divakar K, Kannan A, De Sancho D, Naganathan AN. Slow Folding of a Helical Protein: Large Barriers, Strong Internal Friction, or a Shallow, Bumpy Landscape? The Journal of Physical Chemistry. B. PMID 32955882 DOI: 10.1021/acs.jpcb.0c05976   
2020 Iuliano JN, Tolentino Collado J, Gil AA, Ravindran PT, Lukacs A, Shin S, Woroniecka HA, Adamczyk K, Aramini JM, Edupuganti UR, Hall CR, Greetham GM, Sazanovich IV, Clark IP, Daryaee T, et al. Unraveling the Mechanism of a LOV Domain Optogenetic Sensor: A Glutamine Lever Induces Unfolding of the Jα Helix. Acs Chemical Biology. PMID 32880430 DOI: 10.1021/acschembio.0c00543   
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 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 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 Henderson JN, Simmons CR, Fahmi NE, Jeffs JW, Borges CR, Mills JH. Structural insights into how protein environments tune the spectroscopic properties of a non-canonical amino acid fluorophore. Biochemistry. PMID 32845612 DOI: 10.1021/acs.biochem.0c00474   
2020 Sala BM, Le Marchand T, Pintacuda G, Camilloni C, Natalello A, Ricagno S. Conformational Stability and Dynamics in Crystals Recapitulate Protein Behavior in Solution. Biophysical Journal. 119: 978-988. PMID 32758421 DOI: 10.1016/j.bpj.2020.07.015   
2020 Zhang Y, Krieger J, Mikulska-Ruminska K, Kaynak B, Sorzano COS, Carazo JM, Xing J, Bahar I. State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps. Progress in Biophysics and Molecular Biology. PMID 32866476 DOI: 10.1016/j.pbiomolbio.2020.08.006   
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 Perlinska AP, Kalek M, Christian T, Hou YM, Sulkowska JI. Mg-Dependent Methyl Transfer by a Knotted Protein: A Molecular Dynamics Simulation and Quantum Mechanics Study. Acs Catalysis. 10: 8058-8068. PMID 32904895 DOI: 10.1021/acscatal.0c00059   
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 Neelamraju S, Wales DJ, Gosavi S. Protein energy landscape exploration with structure-based models. Current Opinion in Structural Biology. 64: 145-151. PMID 32795948 DOI: 10.1016/j.sbi.2020.07.003   
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 Bandyopadhyay D, Mishra PP. Real-time Monitoring of the Multi-State Conformational Dynamics of Polypurine Reverse Hoogsteen Hairpin (PPRH) to Capture Their Triplex-Affinity for Gene Silencing by smFRET Microspectroscopy. The Journal of Physical Chemistry. B. PMID 32840369 DOI: 10.1021/acs.jpcb.0c05493   
2020 Roy P, Roy S, Sengupta N. Disulfide Reduction Allosterically Destabilizes the β-Ladder Subdomain Assembly within the NS1 Dimer of ZIKV. Biophysical Journal. PMID 32946768 DOI: 10.1016/j.bpj.2020.08.036   
2020 Bayse CA, Marsan ES, Garcia JR, Tran-Thompson AT. Thyroxine binding to type III iodothyronine deiodinase. Scientific Reports. 10: 15401. PMID 32958818 DOI: 10.1038/s41598-020-72243-9   
2020 Guo X, Yu J, Abell AD, Chen X, Yeoh YQ, He Y, Zhou C, Horsley JR. Unravelling structural dynamics within a photoswitchable single-peptide: A step towards multi-modal bio-inspired nanodevices. Angewandte Chemie (International Ed. in English). PMID 32851761 DOI: 10.1002/anie.202004701   
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 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 Lokareddy RK, Ko YH, Hong N, Doll SG, Paduch M, Niederweis M, Kossiakoff AA, Cingolani G. Recognition of an α-helical hairpin in P22 large terminase by a synthetic antibody fragment. Acta Crystallographica. Section D, Structural Biology. 76: 876-888. PMID 32876063 DOI: 10.1107/S2059798320009912   
2020 Lee CW, Lee S, Jeong CS, Hwang J, Chang JH, Choi IG, Kim TD, Park H, Kim HY, Lee JH. Structural insights into the psychrophilic germinal protease PaGPR and its autoinhibitory loop. Journal of Microbiology (Seoul, Korea). 58: 772-779. PMID 32870483 DOI: 10.1007/s12275-020-0292-0   
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