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Andrew D. Miranker - Related publications

Molecular Biophysics and Biochemistry Yale University, New Haven, CT 
Protein Folding and Dynamics, Structural Biology
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Chakraborty R, Dey S, Sil P, Paul SS, Bhattacharyya D, Bhunia A, Sengupta J, Chattopadhyay K. Conformational distortion in a fibril-forming oligomer arrests alpha-Synuclein fibrillation and minimizes its toxic effects. Communications Biology. 4: 518. PMID 33941845 DOI: 10.1038/s42003-021-02026-z   
2021 Somberg NH, Gelenter MD, Hong M. Comparative analysis of C chemical shifts of β-sheet amyloid proteins and outer membrane proteins. Journal of Biomolecular Nmr. PMID 33844106 DOI: 10.1007/s10858-021-00364-y   
2021 Jhaveri A, Maisuria D, Varga M, Mohammadyani D, Johnson ME. Thermodynamics and Free Energy Landscape of BAR-Domain Dimerization from Molecular Simulations. The Journal of Physical Chemistry. B. PMID 33826319 DOI: 10.1021/acs.jpcb.0c10992   
2021 Roy R, Paul S. Potential of ATP toward Prevention of hIAPP Oligomerization and Destabilization of hIAPP Protofibrils: An In Silico Perspective. The Journal of Physical Chemistry. B. PMID 33792323 DOI: 10.1021/acs.jpcb.1c00313   
2021 Lamers S, Feng Q, Cheng Y, Yu S, Sun B, Lukman M, Jiang J, Ruiz-Carrillo D. Structural and kinetic characterization of glutaminyl cyclase. Biological Chemistry. PMID 33823093 DOI: 10.1515/hsz-2020-0298   
2021 Ploetz EA, Karunaweera S, Smith PE. Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Applications of KBFF20. Journal of Chemical Theory and Computation. PMID 33878264 DOI: 10.1021/acs.jctc.1c00076   
2021 Waibl F, Fernández-Quintero ML, Kamenik AS, Kraml J, Hofer F, Kettenberger H, Georges G, Liedl KR. Conformational Ensembles of Antibodies Determine Their Hydrophobicity. Biophysical Journal. 120: 143-157. PMID 33220303 DOI: 10.1016/j.bpj.2020.11.010   
2021 Bera S, Dong X, Krishnarjuna B, Raab SA, Hales DA, Ji W, Tang Y, Shimon LJW, Ramamoorthy A, Clemmer DE, Wei G, Gazit E. Solid-state packing dictates the unexpected solubility of aromatic peptides. Cell Reports. Physical Science. 2: 100391. PMID 33928264 DOI: 10.1016/j.xcrp.2021.100391   
2021 Dawson WM, Lang EJM, Rhys GG, Shelley KL, Williams C, Brady RL, Crump MP, Mulholland AJ, Woolfson DN. Structural resolution of switchable states of a de novo peptide assembly. Nature Communications. 12: 1530. PMID 33750792 DOI: 10.1038/s41467-021-21851-8   
2021 Rhys GG, Dawson WM, Beesley JL, Martin FJO, Brady RL, Thomson AR, Woolfson DN. How Coiled-Coil Assemblies Accommodate Multiple Aromatic Residues. Biomacromolecules. PMID 33881308 DOI: 10.1021/acs.biomac.1c00131   
2021 Feng CJ, Sinitskiy A, Pande V, Tokmakoff A. Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity. The Journal of Physical Chemistry. B. PMID 33929849 DOI: 10.1021/acs.jpcb.1c00399   
2021 Zou J, Xiao S, Simmerling C, Raleigh DP. Quantitative Analysis of Protein Unfolded State Energetics: Experimental and Computational Studies Demonstrate That Non-Native Side-Chain Interactions Stabilize Local Native Backbone Structure. The Journal of Physical Chemistry. B. PMID 33779182 DOI: 10.1021/acs.jpcb.0c08922   
2021 Kaplan AR, Olson R, Alexandrescu AT. Protein Yoga: Conformational Versatility of the Hemolysin II C-terminal Domain Detailed by NMR Structures for Multiple States. Protein Science : a Publication of the Protein Society. PMID 33733504 DOI: 10.1002/pro.4066   
2021 Bhatia S, Krishnamoorthy G, Udgaonkar JB. Resolving Site-Specific Heterogeneity of the Unfolded State under Folding Conditions. The Journal of Physical Chemistry Letters. 3295-3302. PMID 33764778 DOI: 10.1021/acs.jpclett.1c00098   
2021 Zhuang Y, Bureau HR, Lopez C, Bucher R, Quirk S, Hernandez R. Energetics and structure of alanine-rich α-helices via Adaptive Steered Molecular Dynamics (ASMD). Biophysical Journal. PMID 33775636 DOI: 10.1016/j.bpj.2021.03.017   
2021 Erickson DP, Dunbar M, Hamed E, Ozturk OK, Campanella OH, Keten S, Hamaker BR. Atomistic Modeling of Peptide Aggregation and β-Sheet Structuring in Corn Zein for Viscoelasticity. Biomacromolecules. PMID 33844506 DOI: 10.1021/acs.biomac.0c01558   
2021 El Khoury Y, Le Breton G, Cunha AV, Jansen TLC, van Wilderen LJGW, Bredenbeck J. Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c. The Journal of Chemical Physics. 154: 124201. PMID 33810651 DOI: 10.1063/5.0039969   
2021 Fu R, Rooney MT, Zhang R, Cotten ML. Coordination of Redox Ions within a Membrane-Binding Peptide: A Tale of Aromatic Rings. The Journal of Physical Chemistry Letters. 4392-4399. PMID 33939920 DOI: 10.1021/acs.jpclett.1c00636   
2021 Egli J, Esposito C, Müri M, Riniker S, Wennemers H. Influence of Lipidation on the Folding and Stability of Collagen Triple Helices-An Experimental and Theoretical Study. Journal of the American Chemical Society. 143: 5937-5942. PMID 33830753 DOI: 10.1021/jacs.1c01512   
2021 Nasreen K, Parray ZA, Shamsi A, Ahmad F, Ahmed A, Malik A, Lakhrm NA, Hassan MI, Islam A. Crowding Milleu stabilizes apo-myoglobin against chemical-induced denaturation: Dominance of hardcore repulsions in the heme devoid protein. International Journal of Biological Macromolecules. PMID 33744250 DOI: 10.1016/j.ijbiomac.2021.03.089   
2021 Nasreen K, Parray ZA, Shamsi A, Ahmad F, Ahmed A, Malik A, Lakhrm NA, Hassan MI, Islam A. Crowding Milleu stabilizes apo-myoglobin against chemical-induced denaturation: Dominance of hardcore repulsions in the heme devoid protein. International Journal of Biological Macromolecules. PMID 33744250 DOI: 10.1016/j.ijbiomac.2021.03.089   
2021 Wu X, Ma Y, Zhao K, Zhang J, Sun Y, Li Y, Dong X, Hu H, Liu J, Wang J, Zhang X, Li B, Wang H, Li D, Sun B, et al. The structure of a minimum amyloid fibril core formed by necroptosis-mediating RHIM of human RIPK3. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33790016 DOI: 10.1073/pnas.2022933118   
2021 Paissoni C, Puri S, Wang I, Chen SY, Camilloni C, Hsu SD. Converging experimental and computational views of the knotting mechanism of a small knotted protein. Biophysical Journal. PMID 33812848 DOI: 10.1016/j.bpj.2021.03.032   
2021 Jain R, Muneeruddin K, Anderson J, Harms MJ, Shaffer SA, Matthews CR. A conserved folding nucleus sculpts the free energy landscape of bacterial and archaeal orthologs from a divergent TIM barrel family. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33875592 DOI: 10.1073/pnas.2019571118   
2021 Badasyan A, Valant M, Grdadolnik J, Uversky VN. The Finite Size Effects and Two-State Paradigm of Protein Folding. International Journal of Molecular Sciences. 22. PMID 33671738 DOI: 10.3390/ijms22042184   
2021 Worthy HL, Williamson LJ, Auhim HS, Leppla SH, Sastalla I, Jones DD, Rizkallah PJ, Berry C. The Crystal Structure of HblL. Toxins. 13. PMID 33807365 DOI: 10.3390/toxins13040253   
2021 Su A, Tabata Y, Aoki K, Sada A, Ohki R, Nagatoishi S, Tsumoto K, Wang S, Otani Y, Ohwada T. Elaboration of non-naturally occurring helical tripeptides as p53-MDM2/MDMX interaction inhibitors. Chemical & Pharmaceutical Bulletin. PMID 33952867 DOI: 10.1248/cpb.c21-00238   
2021 Mbianda J, Bakail M, André C, Moal G, Perrin ME, Pinna G, Guerois R, Becher F, Legrand P, Traoré S, Douat C, Guichard G, Ochsenbein F. Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity. Science Advances. 7. PMID 33741589 DOI: 10.1126/sciadv.abd9153   
2021 Monzon AM, Bonato P, Necci M, Tosatto SCE, Piovesan D. FLIPPER: Predicting and Characterizing Linear Interacting Peptides in the Protein Data Bank. Journal of Molecular Biology. 433: 166900. PMID 33647288 DOI: 10.1016/j.jmb.2021.166900   
2021 Pedchenko V, Boudko SP, Barber M, Mikhailova T, Saus J, Harmange JC, Hudson BG. Collagen IV dysfunction in glomerular basement membrane diseases. III. A functional framework for α345 hexamer assembly. The Journal of Biological Chemistry. 100592. PMID 33775696 DOI: 10.1016/j.jbc.2021.100592   
2021 Jin Y, Kotler JLM, Wang S, Huang B, Halpin JC, Street TO. The ER chaperones BiP and Grp94 regulate the formation of insulin-like growth factor 2 (IGF2) oligomers. Journal of Molecular Biology. 166963. PMID 33811917 DOI: 10.1016/j.jmb.2021.166963   
2021 Blaber M. Cooperative hydrophobic core interactions in the β-trefoil architecture. Protein Science : a Publication of the Protein Society. PMID 33686691 DOI: 10.1002/pro.4059   
2021 Mishra P, Patni D, Jha SK. A pH-dependent protein stability switch coupled to the perturbed pKa of a single ionizable residue. Biophysical Chemistry. 274: 106591. PMID 33895555 DOI: 10.1016/j.bpc.2021.106591   
2021 Hsu DJ, Leshchev D, Kosheleva I, Kohlstedt KL, Chen LX. Unfolding bovine α-lactalbumin with T-jump: Characterizing disordered intermediates via time-resolved x-ray solution scattering and molecular dynamics simulations. The Journal of Chemical Physics. 154: 105101. PMID 33722011 DOI: 10.1063/5.0039194   
2021 Wang L, Cao C, Zuo S. Protein secondary structure assignment using pc-polyline and convolutional neural network. Proteins. PMID 33780034 DOI: 10.1002/prot.26079   
2021 Kaur H, Jakob RP, Marzinek JK, Green R, Imai Y, Bolla JR, Agustoni E, Robinson CV, Bond PJ, Lewis K, Maier T, Hiller S. The antibiotic darobactin mimics a β-strand to inhibit outer membrane insertase. Nature. PMID 33854236 DOI: 10.1038/s41586-021-03455-w   
2021 Yan NL, Santos-Martins D, Nair R, Chu A, Wilson IA, Johnson KA, Forli S, Morgan GJ, Petrassi HM, Kelly JW. Discovery of Potent Coumarin-Based Kinetic Stabilizers of Amyloidogenic Immunoglobulin Light Chains Using Structure-Based Design. Journal of Medicinal Chemistry. PMID 33939422 DOI: 10.1021/acs.jmedchem.1c00339   
2021 Niu C, Du Y, Kaltashov IA. Towards better understanding of the heparin role in NETosis: feasibility of using native mass spectrometry to monitor interactions of neutrophil elastase with heparin oligomers. International Journal of Mass Spectrometry. 463. PMID 33692650 DOI: 10.1016/j.ijms.2021.116550   
2021 Sagar A, Jeffries CM, Petoukhov MV, Svergun DI, Bernadó P. Comment on the Optimal Parameters to Derive Intrinsically Disordered Protein Conformational Ensembles from Small-Angle X-ray Scattering Data Using the Ensemble Optimization Method. Journal of Chemical Theory and Computation. PMID 33725442 DOI: 10.1021/acs.jctc.1c00014   
2021 Moritsugu K, Takeuchi K, Kamiya N, Higo J, Yasumatsu I, Fukunishi Y, Fukuda I. Flexibility and Cell Permeability of Cyclic Ras-Inhibitor Peptides Revealed by the Coupled Nosé-Hoover Equation. Journal of Chemical Information and Modeling. 61: 1921-1930. PMID 33835817 DOI: 10.1021/acs.jcim.0c01427   
2021 Teixeira AL, Alves NA. The high stability of the three-helix bundle UBA domain of p62 protein as revealed by molecular dynamics simulations. Journal of Molecular Modeling. 27: 102. PMID 33665744 DOI: 10.1007/s00894-021-04698-0   
2021 Khamari L, Pramanik U, Shekhar S, Mohanakumar S, Mukherjee S. Thermal Reversibility and Structural Stability in Lysozyme Induced by Epirubicin Hydrochloride. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 33703900 DOI: 10.1021/acs.langmuir.1c00179   
2021 Dias D'Andréa É, Sebastian Retel J, Diehl A, Schmieder P, Oschkinat H, Ricardo Pires J. NMR structure and dynamics of Q4DY78, a conserved kinetoplasid-specific protein from Trypanosoma cruzi. Journal of Structural Biology. 107715. PMID 33705979 DOI: 10.1016/j.jsb.2021.107715   
2021 Eccleston RC, Pollock DD, Goldstein RA. Selection for cooperativity causes epistasis predominately between native contacts and enables epistasis-based structure reconstruction. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33879570 DOI: 10.1073/pnas.2010057118   
2021 Sikkema HR, Poolman B. In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy. Scientific Reports. 11: 5756. PMID 33707507 DOI: 10.1038/s41598-021-85003-0   
2021 Pramanick I, Sengupta N, Mishra S, Pandey S, Girish N, Das A, Dutta S. Conformational flexibility and structural variability of SARS-CoV2 S protein. Structure (London, England : 1993). PMID 33932324 DOI: 10.1016/j.str.2021.04.006   
2021 Egelman EH, Wang F. Cryo-EM is a powerful tool, but helical applications can have pitfalls. Soft Matter. PMID 33729271 DOI: 10.1039/d1sm00282a   
2021 Hou XN, Sekiyama N, Ohtani Y, Yang F, Miyanoiri Y, Akagi KI, Su XC, Tochio H. Conformational space sampled by domain reorientation of linear diubiquitin reflected in its binding mode for target proteins. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. PMID 33928740 DOI: 10.1002/cphc.202100187   
2021 Pipercevic J, Jakob RP, Righetto RD, Goldie KN, Stahlberg H, Maier T, Hiller S. Identification of a Dps contamination in Mitomycin-C-induced expression of Colicin Ia. Biochimica Et Biophysica Acta. Biomembranes. 1863: 183607. PMID 33775657 DOI: 10.1016/j.bbamem.2021.183607   
2021 Walti MA, Kotler SA, Clore GM. Probing the interaction of huntingtin exon-1 polypeptides with the chaperonin nanomachine GroEL. Chembiochem : a European Journal of Chemical Biology. PMID 33644966 DOI: 10.1002/cbic.202100055