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John Tileston Edsall, M.D. - Related publications

Biochemistry Harvard University, Cambridge, MA, United States 
Protein Physical Chemistry
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Kolos JM, Pomplun S, Jung S, Rieß B, Purder PL, Voll AM, Merz S, Gnatzy M, Geiger TM, Quist-Løkken I, Jatzlau J, Knaus P, Holien T, Bracher A, Meyners C, et al. Picomolar FKBP inhibitors enabled by a single water-displacing methyl group in bicyclic [4.3.1] aza-amides. Chemical Science. 12: 14758-14765. PMID 34820091 DOI: 10.1039/d1sc04638a   
2021 Sheikh AY, Mattei A, Miglani Bhardwaj R, Hong RS, Abraham NS, Schneider-Rauber G, Engstrom KM, Diwan M, Henry RF, Gao Y, Juarez V, Jordan E, DeGoey DA, Hutchins CW. Implications of the Conformationally Flexible, Macrocyclic Structure of the First-Generation, Direct-Acting Anti-Viral Paritaprevir on Its Solid Form Complexity and Chameleonic Behavior. Journal of the American Chemical Society. PMID 34637297 DOI: 10.1021/jacs.1c06837   
2021 Catalano C, Al Mughram MH, Guo Y, Kellogg GE. 3D interaction homology: Hydropathic interaction environments of serine and cysteine are strikingly different and their roles adapt in membrane proteins. Current Research in Structural Biology. 3: 239-256. PMID 34693344 DOI: 10.1016/j.crstbi.2021.09.002   
2021 Zagotta WN, Sim BS, Nhim AK, Raza MM, Evans EG, Venkatesh Y, Jones CM, Mehl RA, Petersson EJ, Gordon SE. An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET. Elife. 10. PMID 34623258 DOI: 10.7554/eLife.70236   
2021 Agarwal N, Jaiswal N, Gulati K, Gangele K, Nagar N, Kumar D, Poluri KM. Molecular Insights into Conformational Heterogeneity and Enhanced Structural Integrity of DNA Binding Protein Hup at Low pH. Biochemistry. PMID 34665609 DOI: 10.1021/acs.biochem.1c00395   
2021 Sun Z, Zheng S, Zhao H, Niu Z, Lu Y, Pan Y, Yang Y. To improve the predictions of binding residues with DNA, RNA, carbohydrate, and peptide via multi-task deep neural networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 34637380 DOI: 10.1109/TCBB.2021.3118916   
2021 Vankayala SL, Warrensford LC, Pittman AR, Pollard BC, Kearns FL, Larkin JD, Woodcock HL. CIFDock: A novel CHARMM-based flexible receptor-flexible ligand docking protocol. Journal of Computational Chemistry. PMID 34741467 DOI: 10.1002/jcc.26759   
2021 Sanejouand YH. Normal-mode driven exploration of protein domain motions. Journal of Computational Chemistry. 42: 2250-2257. PMID 34599620 DOI: 10.1002/jcc.26755   
2021 Correia VG, Trovão F, Pinheiro BA, Brás JLA, Silva LM, Nunes C, Coimbra MA, Liu Y, Feizi T, Fontes CMGA, Mulloy B, Chai W, Carvalho AL, Palma AS. Mapping Molecular Recognition of β1,3-1,4-Glucans by a Surface Glycan-Binding Protein from the Human Gut Symbiont Bacteroides ovatus. Microbiology Spectrum. e0182621. PMID 34817219 DOI: 10.1128/Spectrum.01826-21   
2021 Hussain M, Cummins MC, Endo-Streeter S, Sondek J, Kuhlman B. Designer proteins that competitively inhibit Gα by targeting its effector site. The Journal of Biological Chemistry. 101348. PMID 34715131 DOI: 10.1016/j.jbc.2021.101348   
2021 Suleman M, Yousafi Q, Ali J, Ali SS, Hussain Z, Ali S, Waseem M, Iqbal A, Ahmad S, Khan A, Wang Y, Wei DQ. Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Computers in Biology and Medicine. 138: 104936. PMID 34655895 DOI: 10.1016/j.compbiomed.2021.104936   
2021 Heltberg ML, Miné-Hattab J, Taddei A, Walczak AM, Mora T. Physical observables to determine the nature of membrane-less cellular sub-compartments. Elife. 10. PMID 34677123 DOI: 10.7554/eLife.69181   
2021 Islam MA, Rallabandi VPS, Mohammed S, Srinivasan S, Natarajan S, Dudekula DB, Park J. Screening of β1- and β2-Adrenergic Receptor Modulators through Advanced Pharmacoinformatics and Machine Learning Approaches. International Journal of Molecular Sciences. 22. PMID 34681845 DOI: 10.3390/ijms222011191   
2021 Seok J, Hong J, Park J, Kim KJ. Structural analysis of the peptidoglycan editing factor PdeF from Bacillus cereus ATCC 14579. Biochemical and Biophysical Research Communications. 583: 43-48. PMID 34735878 DOI: 10.1016/j.bbrc.2021.10.051   
2021 Jang H, Lee C, Hwang Y, Lee SJ. Concanavalin A: coordination diversity to xenobiotic metal ions and biological consequences. Dalton Transactions (Cambridge, England : 2003). PMID 34806716 DOI: 10.1039/d1dt03501k   
2021 Pan Z, Huang J, Zhuang W. Protein-Ligand Binding Molecular Details Revealed by Terahertz Optical Kerr Spectroscopy: A Simulation Study. Jacs Au. 1: 1788-1797. PMID 34723281 DOI: 10.1021/jacsau.1c00356   
2021 Wang R, Zhang L, Chi Y, Chi Y. Forces involved in freeze-induced egg yolk gelation: Effects of various bond dissociation reagents on gel properties and protein structure changes. Food Chemistry. 371: 131190. PMID 34583175 DOI: 10.1016/j.foodchem.2021.131190   
2021 Jia Z, Liu C, Chen Y, Jiang H, Wang Z, Yao J, Yang J, Zhu J, Zhang B, Yuchi Z. Crystal structures of the SARS-CoV-2 nucleocapsid protein C-terminal domain and development of nucleocapsid-targeting nanobodies. The Febs Journal. PMID 34665939 DOI: 10.1111/febs.16239   
2021 Guo L, Dutton OJ, Kucukdisli M, Davy M, Wagnières O, Butts CP, Myers EL, Aggarwal VK. Conformationally Controlled Linear and Helical Hydrocarbons Bearing Extended Side Chains. Journal of the American Chemical Society. PMID 34590479 DOI: 10.1021/jacs.1c07778   
2021 He T, Liu J, Wang JP. Development of a Dihydropteroate Synthase-Based Fluorescence Polarization Assay for Detection of Sulfonamides and Studying Its Recognition Mechanism. Journal of Agricultural and Food Chemistry. PMID 34783550 DOI: 10.1021/acs.jafc.1c05674   
2021 Akawa OB, Soremekun OS, Olotu FA, Soliman MES. Atomistic insights into the selective therapeutic activity of 6-(2,4-difluorophenoxy)-5-((ethylmethyl)pyridine-3-yl)-8-methylpyrrolo[1,2-a]pyrazin-1(2H)-one towards bromodomain-containing proteins. Computational Biology and Chemistry. 95: 107592. PMID 34710811 DOI: 10.1016/j.compbiolchem.2021.107592   
2021 Lamichhane TR, Ghimire MP. Evaluation of SARS-CoV-2 main protease and inhibitor interactions using dihedral angle distributions and radial distribution function. Heliyon. 7: e08220. PMID 34693066 DOI: 10.1016/j.heliyon.2021.e08220   
2021 Gaurav M, Natesh A, Arundhati A, Mariam D. Biochemical aspects of hemoglobin-xenobiotic interactions and their implications in drug discovery. Biochimie. 191: 154-163. PMID 34474139 DOI: 10.1016/j.biochi.2021.08.006   
2021 Tabandeh S, Lemus CE, Leon L. Deciphering the Role of π-Interactions in Polyelectrolyte Complexes Using Rationally Designed Peptides. Polymers. 13. PMID 34202468 DOI: 10.3390/polym13132074   
2021 Foloppe N, Chen IJ. The reorganization energy of compounds upon binding to proteins, from dynamic and solvated bound and unbound states. Bioorganic & Medicinal Chemistry. 51: 116464. PMID 34798378 DOI: 10.1016/j.bmc.2021.116464   
2021 Meng D, Zhang L, Wang Q, Zhang Y, Sun Y, Zhang H, Wang Z, Zhou Z, Yang R. Self-Assembly of Phycoerythrin with Oligochitosan by Electrostatic Interaction for Stabilization of Phycoerythrin. Journal of Agricultural and Food Chemistry. PMID 34669400 DOI: 10.1021/acs.jafc.1c05205   
2021 Raj N, Click T, Yang H, Chu JW. Mechanical couplings of protein backbone and side chains exhibit scale-free network properties and specific hotspots for function. Computational and Structural Biotechnology Journal. 19: 5309-5320. PMID 34765086 DOI: 10.1016/j.csbj.2021.09.004   
2021 Alvi SS, Nabi R, Khan MS, Akhter F, Ahmad S, Khan MS. Glycyrrhizic Acid Scavenges Reactive Carbonyl Species and Attenuates Glycation-Induced Multiple Protein Modification: An and Study. Oxidative Medicine and Cellular Longevity. 2021: 7086951. PMID 34712386 DOI: 10.1155/2021/7086951   
2021 Wang H, Xia X, Yin X, Liu H, Chen Q, Kong B. Investigation of molecular mechanisms of interaction between myofibrillar proteins and 1-heptanol by multiple spectroscopy and molecular docking methods. International Journal of Biological Macromolecules. PMID 34710478 DOI: 10.1016/j.ijbiomac.2021.10.105   
2021 Evangelista W, Knapp J, Zandarashvili L, Esadze A, White MA, Gribenko AV, Lee JC. Signal Transmission in Cyclic AMP Receptor Protein for Survival in Extreme Acidic Conditions. Biochemistry. PMID 34605636 DOI: 10.1021/acs.biochem.1c00388   
2021 Gomes DC, Teixeira SCM, Leão JB, Razinkov VI, Qi W, Rodrigues MA, Roberts CJ. Monitoring of Protein Unfolding/Structural States under Cold High-Pressure Stress. Molecular Pharmaceutics. PMID 34699230 DOI: 10.1021/acs.molpharmaceut.1c00604   
2021 Kumar A, Kumar P, Saumya KU, Giri R. Investigating the conformational dynamics of SARS-CoV-2 NSP6 protein with emphasis on non-transmembrane 91-112 & 231-290 regions. Microbial Pathogenesis. 161: 105236. PMID 34648928 DOI: 10.1016/j.micpath.2021.105236   
2021 Perišić O, Wriggers W. Mechanism for the Unfolding of the TOP7 Protein in Steered Molecular Dynamics Simulations as Revealed by Mutual Information Analysis. Frontiers in Molecular Biosciences. 8: 696609. PMID 34660691 DOI: 10.3389/fmolb.2021.696609   
2021 Heyne M, Shirian J, Cohen I, Peleg Y, Radisky ES, Papo N, Shifman JM. Climbing Up and Down Binding Landscapes through Deep Mutational Scanning of Three Homologous Protein-Protein Complexes. Journal of the American Chemical Society. PMID 34609866 DOI: 10.1021/jacs.1c08707   
2021 Hassankalhori M, Bolcato G, Bissaro M, Sturlese M, Moro S. Shedding Light on the Molecular Recognition of Sub-Kilodalton Macrocyclic Peptides on Thrombin by Supervised Molecular Dynamics. Frontiers in Molecular Biosciences. 8: 707661. PMID 34532343 DOI: 10.3389/fmolb.2021.707661   
2021 Parker JB, Tenorio CA, Blaber M. The ubiquitous buried water in the beta-trefoil architecture contributes to the folding nucleus and ~20% of the folding enthalpy. Protein Science : a Publication of the Protein Society. PMID 34562298 DOI: 10.1002/pro.4192   
2021 Jiang L, Sun Q, Li L, Lu F, Liu F. Molecular Insights into the Inhibitory Effect of GV971 Components Derived from Marine Acidic Oligosaccharides against the Conformational Transition of Aβ42 Monomers. Acs Chemical Neuroscience. PMID 34565139 DOI: 10.1021/acschemneuro.1c00555   
2021 Contessoto VG, Ferreira PHB, Chahine J, Leite VBP, Oliveira RJ. Small Neutral Crowding Solute Effects on Protein Folding Thermodynamic Stability and Kinetics. The Journal of Physical Chemistry. B. PMID 34644091 DOI: 10.1021/acs.jpcb.1c07663   
2021 Zhang W, Liu M, Dupont RL, Huang K, Yu L, Liu S, Wang X, Wang C. Conservation and Identity Selection of Cationic Residues Flanking the Hydrophobic Regions in Intermediate Filament Superfamily. Frontiers in Chemistry. 9: 752630. PMID 34540811 DOI: 10.3389/fchem.2021.752630   
2021 Milorey B, Schwalbe H, O'Neill N, Schweitzer-Stenner R. Repeating Aspartic Acid Residues Prefer Turn-like Conformations in the Unfolded State: Implications for Early Protein Folding. The Journal of Physical Chemistry. B. PMID 34619031 DOI: 10.1021/acs.jpcb.1c06472   
2021 Wang Z, Zheng L, Liu Y, Qu Y, Li YQ, Zhao M, Mu Y, Li W. OnionNet-2: A Convolutional Neural Network Model for Predicting Protein-Ligand Binding Affinity Based on Residue-Atom Contacting Shells. Frontiers in Chemistry. 9: 753002. PMID 34778208 DOI: 10.3389/fchem.2021.753002   
2021 Li H, Dong S, Duan L. Difference in the binding mechanisms of ABT-263/43b with Bcl-xL/Bcl-2: computational perspective on the accurate binding free energy analysis. Journal of Molecular Modeling. 27: 317. PMID 34633547 DOI: 10.1007/s00894-021-04924-9   
2021 Prieto VA, Namitz KEW, Showalter SA. Transient Electrostatic Interactions between Fcp1 and Rap74 Bias the Conformational Ensemble of the Complex with Minimal Impact on Binding Affinity. The Journal of Physical Chemistry. B. 125: 10917-10927. PMID 34550709 DOI: 10.1021/acs.jpcb.1c05131   
2021 Tanramluk D*, Pakotiprapha D, Phoochaijaroen S, Chantravisut P, Thampradid S, Vanichtanankul J, Narupiyakul L, Akavipat R, Yuvaniyama J. MANORAA: A machine learning platform to guide protein-ligand design by anchors and influential distances. Structure. PMID 34614393 DOI: 10.1016/j.str.2021.09.004   
2021 Zhao Q, Yuan JJ, Hu F, Qian C, Tian CF, Wang JT, Gao D, Yi W, Wang HB. Isolation, physicochemical, and structure-function relationship of the hydrophobic variant of Fc-fusion proteins that bind to TNF-α receptor, HS002 and HS002A. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. 1186: 123026. PMID 34781108 DOI: 10.1016/j.jchromb.2021.123026   
2021 Fucci IJ, Byrd RA. nightshift: A Python program for plotting simulated NMR spectra from assigned chemical shifts from the Biological Magnetic Resonance Data Bank. Protein Science : a Publication of the Protein Society. PMID 34516045 DOI: 10.1002/pro.4181   
2021 Patel MH, Dolinska MB, Sergeev YV. Tyrp1 Mutant Variants Associated with OCA3: Computational Characterization of Protein Stability and Ligand Binding. International Journal of Molecular Sciences. 22. PMID 34638544 DOI: 10.3390/ijms221910203   
2021 Zhao X, Luo S, Huang K, Xiong D, Zhang JZH, Duan L. Targeting mechanism for SARS-CoV-2 : interaction and key groups of TMPRSS2 toward four potential drugs. Nanoscale. PMID 34787160 DOI: 10.1039/d1nr06313h   
2021 Tang C, Tan B, Sun X. Elucidation of Interaction between Whey Proteins and Proanthocyanidins and Its Protective Effects on Proanthocyanidins during In-Vitro Digestion and Storage. Molecules (Basel, Switzerland). 26. PMID 34576939 DOI: 10.3390/molecules26185468   
2021 Zegota MM, Müller MA, Lantzberg B, Kizilsavas G, Coelho JAS, Moscariello P, Martínez-Negro M, Morsbach S, Gois PMP, Wagner M, Ng DYW, Kuan SL, Weil T. Dual Stimuli-Responsive Dynamic Covalent Peptide Tags: Toward Sequence-Controlled Release in Tumor-like Microenvironments. Journal of the American Chemical Society. PMID 34632780 DOI: 10.1021/jacs.1c06559