S James Remington, Ph.D. - Related publications

Affiliations: 
Physics University of Oregon, Eugene, OR, United States 
Area:
X-ray crystallography
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50 most relevant papers in past 60 days:
Year Citation  Score
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 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 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 Rumfeldt J, Kurttila M, Takala H, Ihalainen JA. The hairpin extension controls solvent access to the chromophore binding pocket in a bacterial phytochrome: a UV-vis absorption spectroscopy study. Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society For Photobiology. 20: 1173-1181. PMID 34460093 DOI: 10.1007/s43630-021-00090-2   
2021 Li J, Hou C, Ma X, Guo S, Zhang H, Shi L, Liao C, Zheng B, Ye L, Yang L, He X. Entropy-Enthalpy Compensations Fold Proteins in Precise Ways. International Journal of Molecular Sciences. 22. PMID 34502559 DOI: 10.3390/ijms22179653   
2021 Grahame DAS, Dupuis JH, Bryksa BC, Tanaka T, Yada RY. Improving the alkaline stability of pepsin through rational protein design using renin, an alkaline-stable aspartic protease, as a structural and functional reference. Enzyme and Microbial Technology. 150: 109871. PMID 34489030 DOI: 10.1016/j.enzmictec.2021.109871   
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 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 Mayerthaler F, Feldberg AL, Alfermann J, Sun X, Steinchen W, Yang H, Mootz HD. Intermediary conformations linked to the directionality of the aminoacylation pathway of nonribosomal peptide synthetases. Rsc Chemical Biology. 2: 843-854. PMID 34458813 DOI: 10.1039/d0cb00220h   
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 Sato Y, Matsugami A, Watanabe S, Hayashi F, Arai M, Kigawa T, Nishimura C. Changes in dynamic and static structures of the HIV-1 p24 capsid protein N-domain caused by amino-acid substitution are associated with its viral viability. Protein Science : a Publication of the Protein Society. PMID 34523753 DOI: 10.1002/pro.4184   
2021 Toyama Y, Harkness RW, Kay LE. Dissecting the role of interprotomer cooperativity in the activation of oligomeric high-temperature requirement A2 protein. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34446566 DOI: 10.1073/pnas.2111257118   
2021 Ali MS, Rehman MT, Al-Lohedan HA, AlAjmi MF. Exploration of the binding between cuminol and bovine serum albumin through spectroscopic, molecular docking and molecular dynamics methods. Journal of Biomolecular Structure & Dynamics. 1-9. PMID 34488560 DOI: 10.1080/07391102.2021.1971560   
2021 Zweckstetter M. NMR hawk-eyed view of AlphaFold2 structures. Protein Science : a Publication of the Protein Society. PMID 34469019 DOI: 10.1002/pro.4175   
2021 Gao B, Ji R, Li Z, Su X, Li H, Sun Y, Ji C, Gan J, Li J. Structural analysis and functional study of phosphofructokinase B (PfkB) from Mycobacterium marinum. Biochemical and Biophysical Research Communications. 579: 129-135. PMID 34597996 DOI: 10.1016/j.bbrc.2021.09.051   
2021 Maben Z, Arya R, Georgiadis D, Stratikos E, Stern LJ. Conformational dynamics linked to domain closure and substrate binding explain the ERAP1 allosteric regulation mechanism. Nature Communications. 12: 5302. PMID 34489420 DOI: 10.1038/s41467-021-25564-w   
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 Duarte Neto JMW, Silva JC, Sousa F, Gonçalves OSL, Wanderley MCA, Sarmento B, Lima CA, Neves-Petersen MT, Porto ALF. Structural and functional analysis of broad pH and thermal stable protease from URM 4622. Preparative Biochemistry & Biotechnology. 1-12. PMID 34533419 DOI: 10.1080/10826068.2021.1972429   
2021 Fernández-Quintero ML, Kroell KB, Bacher LM, Loeffler JR, Quoika PK, Georges G, Bujotzek A, Kettenberger H, Liedl KR. Germline-Dependent Antibody Paratope States and Pairing Specific V-V Interface Dynamics. Frontiers in Immunology. 12: 675655. PMID 34447370 DOI: 10.3389/fimmu.2021.675655   
2021 Pinkston J, Jo J, Olsen KJ, Comer D, Glaittli CA, Loria JP, Johnson SJ, Hengge AC. Significant Loop Motions in the SsoPTP Protein Tyrosine Phosphatase Allow for Dual General Acid Functionality. Biochemistry. PMID 34496202 DOI: 10.1021/acs.biochem.1c00365   
2021 Uday RVS, Misra R, Harika A, Dolui S, Saha A, Pal U, Ravichandiran V, Maiti NC. Dabrafenib, idelalisib and nintedanib act as significant allosteric modulator for dengue NS3 protease. Plos One. 16: e0257206. PMID 34506566 DOI: 10.1371/journal.pone.0257206   
2021 Liu W, Chen J, Jin L, Liu ZY, Lu M, Jiang G, Yang Q, Quan C, Nam KH, Xu Y. Functional and structural analysis of catabolite control protein C that responds to citrate. Scientific Reports. 11: 20285. PMID 34645869 DOI: 10.1038/s41598-021-99552-x   
2021 Wong SWK, Liu Z. Conformational variability of loops in the SARS-CoV-2 spike protein. Proteins. PMID 34661307 DOI: 10.1002/prot.26266   
2021 Li Q, Kang C. Structure and Dynamics of Zika Virus Protease and Its Insights into Inhibitor Design. Biomedicines. 9. PMID 34440248 DOI: 10.3390/biomedicines9081044   
2021 Tušar L, Usenik A, Turk B, Turk D. Mechanisms Applied by Protein Inhibitors to Inhibit Cysteine Proteases. International Journal of Molecular Sciences. 22. PMID 33498210 DOI: 10.3390/ijms22030997   
2021 Blundell TL. The first resolution revolution in protein structure analysis: X-ray diffraction of polypeptide conformations and globular protein folds in 1950s and 1960s. Progress in Biophysics and Molecular Biology. PMID 34520786 DOI: 10.1016/j.pbiomolbio.2021.09.002   
2021 Guo M, Rosbottom I, Zhou L, Yong CW, Zhou L, Yin Q, Todorov IT, Errington E, Heng JYY. Triglycine (GGG) Adopts a Polyproline II (pPII) Conformation in Its Hydrated Crystal Form: Revealing the Role of Water in Peptide Crystallization. The Journal of Physical Chemistry Letters. 8416-8422. PMID 34436909 DOI: 10.1021/acs.jpclett.1c01622   
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 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 Koebke KJ, Tebo AG, Manickas EC, Deb A, Penner-Hahn JE, Pecoraro VL. Nitrite reductase activity within an antiparallel de novo scaffold. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 26: 855-862. PMID 34487215 DOI: 10.1007/s00775-021-01889-1   
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 Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. Critical Assessment of Methods of Protein Structure Prediction (CASP) - Round XIV. Proteins. PMID 34533838 DOI: 10.1002/prot.26237   
2021 Yeggoni DP, Dubey S, Mohammad YZ, Rachamallu A, Subramanyam R. Elucidation of binding mechanism of stigmasterol with human serum albumin: a biophysical and molecular dynamics simulation approach. Journal of Biomolecular Structure & Dynamics. 1-13. PMID 34463217 DOI: 10.1080/07391102.2021.1968498   
2021 Poghosyan AH, Shahinyan AA, Kirakosyan GR, Ayvazyan NM, Mamasakhlisov YS, Papoian GA. A molecular dynamics study of protein denaturation induced by sulfonate-based surfactants. Journal of Molecular Modeling. 27: 261. PMID 34432183 DOI: 10.1007/s00894-021-04882-2   
2021 Li S, Hsieh KY, Su SC, Pintilie GD, Zhang K, Chang CI. Molecular basis for ATPase-powered substrate translocation by the Lon AAA+ protease. The Journal of Biological Chemistry. 101239. PMID 34563541 DOI: 10.1016/j.jbc.2021.101239   
2021 Papp D, Szigyártó IC, Nordén B, Perczel A, Beke-Somfai T. Structural Water Stabilizes Protein Motifs in Liquid Protein Phase: The Folding Mechanism of Short β-Sheets Coupled to Phase Transition. International Journal of Molecular Sciences. 22. PMID 34445303 DOI: 10.3390/ijms22168595   
2021 Wang X, Liu D, Shen L, Li F, Li Y, Yang L, Xu T, Tao H, Yao D, Wu L, Hirata K, Bohn LM, Makriyannis A, Liu X, Hua T, et al. A Genetically Encoded F-19 NMR Probe Reveals the Allosteric Modulation Mechanism of Cannabinoid Receptor 1. Journal of the American Chemical Society. PMID 34596399 DOI: 10.1021/jacs.1c06847   
2021 Huang S, Mei H, Lu L, Kuang Z, Heng Y, Xu L, Liang X, Qiu M, Pan X. Conformational transitions of caspase-6 in substrate-induced activation process explored by perturbation-response scanning combined with targeted molecular dynamics. Computational and Structural Biotechnology Journal. 19: 4156-4164. PMID 34527189 DOI: 10.1016/j.csbj.2021.07.017   
2021 Talapati SR, Goyal M, Nataraj V, Pothuganti M, Sreevidya MR, Gore S, Ramachandra M, Antony T, More SS, Rao NK. Structural and binding studies of Cyclin dependent kinase 2 with NU6140 inhibitor. Chemical Biology & Drug Design. PMID 34423559 DOI: 10.1111/cbdd.13941   
2021 Featherston ER, Issertell EJ, Cotruvo JA. Probing Lanmodulin's Lanthanide Recognition via Sensitized Luminescence Yields a Platform for Quantification of Terbium in Acid Mine Drainage. Journal of the American Chemical Society. 143: 14287-14299. PMID 34432449 DOI: 10.1021/jacs.1c06360   
2021 Faragó Z, Mirzahosseini A, Horváth D, Pálla T, Horváth P, Perczel A, Noszál B. Solution Structure and Acid-Base Properties of Reduced α-Conotoxin MI. Chemistry & Biodiversity. e2100464. PMID 34467647 DOI: 10.1002/cbdv.202100464   
2021 Dwivedi R, Samanta P, Sharma P, Zhang F, Mishra SK, Kucheryavy P, Kim SB, Aderibigbe AO, Linhardt RJ, Tandon R, Doerksen RJ, Pomin VH. Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. The Journal of Biological Chemistry. 101207. PMID 34537241 DOI: 10.1016/j.jbc.2021.101207   
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 Li ZJ, Srebnik S, Rojas OJ. Revisiting Cation Complexation and Hydrogen Bonding of Single-Chain Polyguluronate Alginate. Biomacromolecules. PMID 34461721 DOI: 10.1021/acs.biomac.1c00840   
2021 Zhao J, Liu M, Zang J, Yang S, Chen R, Zhao X, Ding L. Molecular docking, 3D-QASR and molecular dynamics simulations of thiazoles Pin1 inhibitors. Journal of Biomolecular Structure & Dynamics. 1-15. PMID 34499020 DOI: 10.1080/07391102.2021.1975568   
2021 Radhakrishnan R, Manna B, Ghosh A. Solvent induced conformational changes for the altered activity of laccase: A molecular dynamics study. Journal of Hazardous Materials. 423: 127123. PMID 34530268 DOI: 10.1016/j.jhazmat.2021.127123   
2021 Dreydoppel M, Dorn B, Modig K, Akke M, Weininger U. Transition-State Compressibility and Activation Volume of Transient Protein Conformational Fluctuations. Jacs Au. 1: 833-842. PMID 34467336 DOI: 10.1021/jacsau.1c00062   
2021 Sahoo S, Dehury B, Narang PK, Raina V, Misra N, Suar M. Comprehensive sequence and structure analysis of algal lipid catabolic enzyme Triacylglycerol lipase: an study to vitalize the development of optimum engineered strains with high lipid productivity. Journal of Biomolecular Structure & Dynamics. 1-19. PMID 34415234 DOI: 10.1080/07391102.2021.1967194   
2021 Xiao T, Sun L, Zhang M, Li Z, Haura EB, Schonbrunn E, Ji H. Synthesis and Structural Characterization of a Monocarboxylic Inhibitor for GRB2 SH2 Domain. Bioorganic & Medicinal Chemistry Letters. 128354. PMID 34506932 DOI: 10.1016/j.bmcl.2021.128354   
2021 Li L, Zhao X, Xu X. Trace the difference driven by unfolding-refolding pathway of myofibrillar protein: Emphasizing the changes on structural and emulsion properties. Food Chemistry. 367: 130688. PMID 34365246 DOI: 10.1016/j.foodchem.2021.130688