Olivier Dalmas - Related publications

Affiliations: 
2014 University of Chicago, Chicago, IL 
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Song KC, Molina AV, Chen R, Gagnon IA, Koh YH, Roux B, Sosnick TR. Folding and misfolding of potassium channel monomers during assembly and tetramerization. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34413192 DOI: 10.1073/pnas.2103674118   
2021 de Souza Degenhardt MF, Vitale PAM, Abiko LA, Zacharias M, Sattler M, Oliveira CLP, Salinas RK. Molecular insights on CALX-CBD12 inter-domain dynamics from MD simulations, RDCs and SAXS. Biophysical Journal. PMID 34310942 DOI: 10.1016/j.bpj.2021.07.022   
2021 Xue J, Han Y, Baniasadi H, Zeng W, Pei J, Grishin NV, Wang J, Tu BP, Jiang Y. TMEM120A is a coenzyme A-binding membrane protein with structural similarities to ELOVL fatty acid elongase. Elife. 10. PMID 34374645 DOI: 10.7554/eLife.71220   
2021 Lento C, Wilson DJ. Subsecond Time-Resolved Mass Spectrometry in Dynamic Structural Biology. Chemical Reviews. PMID 34324314 DOI: 10.1021/acs.chemrev.1c00222   
2021 Röpke M, Riepl D, Saura P, Di Luca A, Mühlbauer ME, Jussupow A, Gamiz-Hernandez AP, Kaila VRI. Deactivation blocks proton pathways in the mitochondrial complex I. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34272275 DOI: 10.1073/pnas.2019498118   
2021 Neupane K, Zhao M, Lyons A, Munshi S, Ileperuma SM, Ritchie DB, Hoffer NQ, Narayan A, Woodside MT. Structural dynamics of single SARS-CoV-2 pseudoknot molecules reveal topologically distinct conformers. Nature Communications. 12: 4749. PMID 34362921 DOI: 10.1038/s41467-021-25085-6   
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 Gupta C, Khaniya U, Vant JW, Shekhar M, Mao J, Gunner MR, Singharoy A. Poor Person's pH Simulation of Membrane Proteins. Methods in Molecular Biology (Clifton, N.J.). 2315: 197-217. PMID 34302678 DOI: 10.1007/978-1-0716-1468-6_12   
2021 Gupta C, Khaniya U, Vant JW, Shekhar M, Mao J, Gunner MR, Singharoy A. Poor Person's pH Simulation of Membrane Proteins. Methods in Molecular Biology (Clifton, N.J.). 2315: 197-217. PMID 34302678 DOI: 10.1007/978-1-0716-1468-6_12   
2021 Malliavin TE. Tandem domain structure determination based on a systematic enumeration of conformations. Scientific Reports. 11: 16925. PMID 34413388 DOI: 10.1038/s41598-021-96370-z   
2021 An X, Bai Q, Bing Z, Liu H, Yao X. Insights into the molecular mechanism of positive cooperativity between partial agonist MK-8666 and full allosteric agonist AP8 of hGPR40 by Gaussian accelerated molecular dynamics (GaMD) simulations. Computational and Structural Biotechnology Journal. 19: 3978-3989. PMID 34377364 DOI: 10.1016/j.csbj.2021.07.008   
2021 Dingfelder F, Macocco I, Benke S, Nettels D, Faccioli P, Schuler B. Slow Escape from a Helical Misfolded State of the Pore-Forming Toxin Cytolysin A. Jacs Au. 1: 1217-1230. PMID 34467360 DOI: 10.1021/jacsau.1c00175   
2021 Cymer F, Schneider D. Small Residues Inhibit Homo-Dimerization of the Human Carbonic Anhydrase XII Transmembrane Domain. Membranes. 11. PMID 34357162 DOI: 10.3390/membranes11070512   
2021 Scholl D, Sigoillot M, Overtus M, Martinez RC, Martens C, Wang Y, Pardon E, Laeremans T, Garcia-Pino A, Steyaert J, Sheppard DN, Hendrix J, Govaerts C. A topological switch in CFTR modulates channel activity and sensitivity to unfolding. Nature Chemical Biology. PMID 34341587 DOI: 10.1038/s41589-021-00844-0   
2021 Muguruza-Montero A, Ramis R, Nuñez E, Ballesteros OR, Ibarluzea MG, Araujo A, M-Alicante S, Urrutia J, Leonardo A, Bergara A, Villarroel A. Do calmodulin binding IQ motifs have built-in capping domains? Protein Science : a Publication of the Protein Society. PMID 34392571 DOI: 10.1002/pro.4170   
2021 Williams JK, Wang B, Sam A, Hoop CL, Case DA, Baum J. Molecular Dynamics Analysis of a Flexible Loop at the Binding Interface of the SARS-CoV-2 Spike Protein Receptor-Binding Domain. Proteins. PMID 34375467 DOI: 10.1002/prot.26208   
2021 Sobti M, Ueno H, Noji H, Stewart AG. The six steps of the complete F-ATPase rotary catalytic cycle. Nature Communications. 12: 4690. PMID 34344897 DOI: 10.1038/s41467-021-25029-0   
2021 Wang W, Gao Y, Tang Y, Zhou X, Lai Y, Zhou S, Zhang Y, Yang X, Liu F, Guddat LW, Wang Q, Rao Z, Gong H. Cryo-EM structure of mycobacterial cytochrome bd reveals two oxygen access channels. Nature Communications. 12: 4621. PMID 34330928 DOI: 10.1038/s41467-021-24924-w   
2021 Wang Q, Wang L, Zhang Y, Zhang X, Zhang L, Shang W, Bai F. Probing the Allosteric Inhibition Mechanism of a Spike Protein Using Molecular Dynamics Simulations and Active Compound Identifications. Journal of Medicinal Chemistry. PMID 34415156 DOI: 10.1021/acs.jmedchem.1c00320   
2021 Voith von Voithenberg L, Barth A, Trauschke V, Demarco B, Tyagi S, Koehler C, Lemke EA, Lamb DC. Comparative analysis of the coordinated motion of Hsp70s from different organelles observed by single-molecule three-color FRET. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34389669 DOI: 10.1073/pnas.2025578118   
2021 Tanaka M, Kato T, Oda M. Conformational changes of α-helical peptides with different hydrophobic residues induced by metal-ion binding. Biophysical Chemistry. 277: 106661. PMID 34388679 DOI: 10.1016/j.bpc.2021.106661   
2021 Sanches K, Wai DCC, Norton RS. Conformational dynamics in peptide toxins: Implications for receptor interactions and molecular design. Toxicon : Official Journal of the International Society On Toxinology. 201: 127-140. PMID 34454969 DOI: 10.1016/j.toxicon.2021.08.020   
2021 Chen E, Reiss K, Shah D, Manjula R, Allen B, Murphy EL, Murphy JW, Batista VS, Bhandari V, Lolis EJ, Lisi GP. A Structurally Preserved Allosteric Site in the MIF Superfamily Affects Enzymatic Activity and CD74 Activation in D-dopachrome Tautomerase. The Journal of Biological Chemistry. 101061. PMID 34384784 DOI: 10.1016/j.jbc.2021.101061   
2021 Ye X, Mayne L, Englander SW. A conserved strategy for structure change and energy transduction in Hsp104 and other AAA+ protein motors. The Journal of Biological Chemistry. 101066. PMID 34384781 DOI: 10.1016/j.jbc.2021.101066   
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 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 Chen X, Wang L, Cui Q, Ding Z, Han L, Kou Y, Zhang W, Wang H, Jia X, Dai M, Shi Z, Li Y, Li X, Geng Y. Structural insights into the activation of human calcium-sensing receptor. Elife. 10. PMID 34467854 DOI: 10.7554/eLife.68578   
2021 Ultsch M, Holliday MJ, Gerhardy S, Moran P, Scales SJ, Gupta N, Oltrabella F, Chiu C, Fairbrother W, Eigenbrot C, Kirchhofer D. Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif. Communications Biology. 4: 916. PMID 34316015 DOI: 10.1038/s42003-021-02387-5   
2021 Shen R, Crean RM, Johnson SJ, Kamerlin SCL, Hengge AC. Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases. Jacs Au. 1: 646-659. PMID 34308419 DOI: 10.1021/jacsau.1c00054   
2021 Markham KJ, Tikhonova EB, Scarpa AC, Hariharan P, Katsube S, Guan L. Complete cysteine-scanning mutagenesis of the Salmonella typhimurium melibiose permease. The Journal of Biological Chemistry. 101090. PMID 34416232 DOI: 10.1016/j.jbc.2021.101090   
2021 Ikoma M, Nakasone Y, Terazima M. Photoreaction of photoactivated adenylate cyclase from cyanobacterium Microcoleus chthonoplastes. Journal of Photochemistry and Photobiology. B, Biology. 221: 112252. PMID 34265548 DOI: 10.1016/j.jphotobiol.2021.112252   
2021 Pimpão C, Wragg D, Bonsignore R, Aikman B, Pedersen PA, Leoni S, Soveral G, Casini A. Mechanisms of irreversible aquaporin-10 inhibition by organogold compounds studied by combined biophysical methods and atomistic simulations. Metallomics : Integrated Biometal Science. PMID 34468767 DOI: 10.1093/mtomcs/mfab053   
2021 Brotzakis ZF, Löhr T, Vendruscolo M. Determination of intermediate state structures in the opening pathway of SARS-CoV-2 spike using cryo-electron microscopy. Chemical Science. 12: 9168-9175. PMID 34276947 DOI: 10.1039/d1sc00244a   
2021 Kumar A, Chakraborty D, Mugnai ML, Straub JE, Thirumalai D. Sequence Determines the Switch in the Fibril Forming Regions in the Low-Complexity FUS Protein and Its Variants. The Journal of Physical Chemistry Letters. 9026-9032. PMID 34516126 DOI: 10.1021/acs.jpclett.1c02310   
2021 Dubrow A, Kim I, Topo E, Cho JH. Understanding the Binding Transition State After the Conformational Selection Step: The Second Half of the Molecular Recognition Process Between NS1 of the 1918 Influenza Virus and Host p85β. Frontiers in Molecular Biosciences. 8: 716477. PMID 34307465 DOI: 10.3389/fmolb.2021.716477   
2021 Dubrow A, Kim I, Topo E, Cho JH. Understanding the Binding Transition State After the Conformational Selection Step: The Second Half of the Molecular Recognition Process Between NS1 of the 1918 Influenza Virus and Host p85β. Frontiers in Molecular Biosciences. 8: 716477. PMID 34307465 DOI: 10.3389/fmolb.2021.716477   
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 Walker B, Jing Z, Ren P. Molecular dynamics free energy simulations of ATP:Mg and ADP:Mg using the polarizable force field AMOEBA. Molecular Simulation. 47: 439-448. PMID 34421214 DOI: 10.1080/08927022.2020.1725003   
2021 Zhang Y, Watanabe S, Tsutsumi A, Kadokura H, Kikkawa M, Inaba K. Cryo-EM analysis provides new mechanistic insight into ATP binding to Ca -ATPase SERCA2b. The Embo Journal. e108482. PMID 34459010 DOI: 10.15252/embj.2021108482   
2021 Volkov VV, Heinz H, Perry CC. Anchoring of a hydrophobic heptapeptide (AFILPTG) on silica facilitates peptide unfolding at the abiotic-biotic interface. Physical Chemistry Chemical Physics : Pccp. PMID 34382985 DOI: 10.1039/d1cp02072b   
2021 Sudha G, Bassot C, Lamb J, Shu N, Huang Y, Elofsson A. The evolutionary history of topological variations in the CPA/AT transporters. Plos Computational Biology. 17: e1009278. PMID 34403419 DOI: 10.1371/journal.pcbi.1009278   
2021 Sun J, Li Z, Yang N. Mechanism of the Conformational Change of the Protein Methyltransferase SMYD3: A Molecular Dynamics Simulation Study. International Journal of Molecular Sciences. 22. PMID 34281237 DOI: 10.3390/ijms22137185   
2021 Sun J, Li Z, Yang N. Mechanism of the Conformational Change of the Protein Methyltransferase SMYD3: A Molecular Dynamics Simulation Study. International Journal of Molecular Sciences. 22. PMID 34281237 DOI: 10.3390/ijms22137185   
2021 Brewer A, Zhang L. Binding free energy calculation of human beta defensin 3 with negatively charged lipid bilayer using free energy perturbation method. Biophysical Chemistry. 277: 106662. PMID 34399250 DOI: 10.1016/j.bpc.2021.106662   
2021 Rong Y, Jiang J, Gao Y, Guo J, Song D, Liu W, Zhang M, Zhao Y, Xiao B, Liu Z. TMEM120A contains a specific coenzyme A-binding site and might not mediate poking- or stretch-induced channel activities in cells. Elife. 10. PMID 34409941 DOI: 10.7554/eLife.71474   
2021 Nguyen ML, Byun J, Cho BK. The Role of the 1,2,3-Triazolyl Heterocycle in the Helical Columnar Assembly and Electric Field Response. The Journal of Physical Chemistry. B. PMID 34342228 DOI: 10.1021/acs.jpcb.1c05301   
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 Kumar A, Singh R, Ghosh B, Makde RD. Crystal structure of aspartyl dipeptidase from Xenopus laevis revealed ligand binding induced loop ordering and catalytic triad assembly. Proteins. PMID 34431561 DOI: 10.1002/prot.26220   
2021 Bibbe JM, Vriend G. Motions around conserved helical weak spots facilitate GPCR activation. Proteins. PMID 34272892 DOI: 10.1002/prot.26179   
2021 Braun L, Schoen I, Vogel V. PIP-induced membrane binding of the Vinculin tail competes with its other binding partners. Biophysical Journal. PMID 34411575 DOI: 10.1016/j.bpj.2021.08.018