Ronald N. Zuckermann, Ph.D. - Related publications

Affiliations: 
Molecular Foundry Lawrence Berkeley National Laboratory, Berkeley, CA, USA 
Area:
Nanobioscience
Website:
http://www.ronznet.com
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Lu W, Wang S, Liu R, Guan Y, Zhang Y. Human serum albumin-imprinted polymers with high capacity and selectivity for abundant protein depletion. Acta Biomaterialia. PMID 33722786 DOI: 10.1016/j.actbio.2021.03.010   
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 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 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 Hu LB, Hu XQ, Zhang Q, You QD, Jiang ZY. An affinity prediction approach for the ligand of E3 ligase Cbl-b and an insight into substrate binding pattern. Bioorganic & Medicinal Chemistry. 38: 116130. PMID 33848699 DOI: 10.1016/j.bmc.2021.116130   
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 Casillo A, Fabozzi A, Russo Krauss I, Parrilli E, Biggs CI, Gibson MI, Lanzetta R, Appavou MS, Radulescu A, Tutino ML, Paduano L, Corsaro MM. Physicochemical Approach to Understanding the Structure, Conformation, and Activity of Mannan Polysaccharides. Biomacromolecules. PMID 33729771 DOI: 10.1021/acs.biomac.0c01659   
2021 Di Rienzo L, Miotto M, Bò L, Ruocco G, Raimondo D, Milanetti E. Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network. Frontiers in Molecular Biosciences. 8: 626837. PMID 33718433 DOI: 10.3389/fmolb.2021.626837   
2021 Mundlapati VR, Imani Z, Goldsztejn G, Gloaguen E, Brenner V, Le Barbu-Debus K, Zehnacker-Rentien A, Baltaze JP, Robin S, Mons M, Aitken DJ. A theoretical and experimental case study of the hydrogen bonding predilection of S-methylcysteine. Amino Acids. PMID 33743071 DOI: 10.1007/s00726-021-02967-z   
2021 Matsumoto S, Sugimoto N. New Insights into the Functions of Nucleic Acids Controlled by Cellular Microenvironments. Topics in Current Chemistry (Cham). 379: 17. PMID 33782792 DOI: 10.1007/s41061-021-00329-7   
2021 Fowler WC, Deng C, Griffen GM, Teodoro T, Guo AZ, Zaiden M, Gottlieb M, de Pablo JJ, Tirrell MV. Harnessing Peptide Binding to Capture and Reclaim Phosphate. Journal of the American Chemical Society. PMID 33721492 DOI: 10.1021/jacs.1c01241   
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 Ortet PC, Muellers SN, Viarengo-Baker LA, Streu K, Szymczyna BR, Beeler AB, Allen KN, Whitty A. Recapitulating the Binding Affinity of Nrf2 for KEAP1 in a Cyclic Heptapeptide, Guided by NMR, X-ray Crystallography, and Machine Learning. Journal of the American Chemical Society. PMID 33683866 DOI: 10.1021/jacs.0c09799   
2021 Cubuk H, Ozbil M, Cakir Hatir P. Computational analysis of functional monomers used in molecular imprinting for promising COVID-19 detection. Computational & Theoretical Chemistry. 113215. PMID 33747754 DOI: 10.1016/j.comptc.2021.113215   
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 Mizsei R, Li X, Chen WN, Szabo M, Wang JH, Wagner G, Reinherz EL, Mallis RJ. A general chemical crosslinking strategy for structural analyses of weakly interacting proteins applied to preTCR-pMHC complexes. The Journal of Biological Chemistry. 296: 100255. PMID 33837736 DOI: 10.1016/j.jbc.2021.100255   
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 Le HT, Do PC, Le L. Grafting Methionine on 1F1 Ab Increases the Broad-Activity on HA Structural-Conserved Residues of H1, H2, and H3 Influenza a Viruses. Evolutionary Bioinformatics Online. 17: 11769343211003082. PMID 33795930 DOI: 10.1177/11769343211003082   
2021 Feng X, Li F, Ding M, Zhang R, Shi T, Jiang W. Molecular dynamic simulation: Structural insights of multi-stranded curdlan in aqueous solution. Carbohydrate Polymers. 261: 117844. PMID 33766340 DOI: 10.1016/j.carbpol.2021.117844   
2021 Nath P, Goyal A. Structure and dynamics analysis of multi-domain putative β-1,4-glucosidase of family 3 glycoside hydrolase (PsGH3) from Pseudopedobacter saltans. Journal of Molecular Modeling. 27: 106. PMID 33694107 DOI: 10.1007/s00894-021-04721-4   
2021 Mohanty AK, Choudhary S, Kaushik JK, Fisher AJ. Crystal structure of BRP39, a signaling glycoprotein expressed during mammary gland apoptosis at 2.6 Å resolution. Journal of Structural Biology. 107737. PMID 33838225 DOI: 10.1016/j.jsb.2021.107737   
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 Assaiya A, Burada AP, Dhingra S, Kumar J. An overview of the recent advances in cryo-electron microscopy for life sciences. Emerging Topics in Life Sciences. PMID 33760078 DOI: 10.1042/ETLS20200295   
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 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 Hernandes IS, Da Silva HC, Dos Santos HF, De Almeida WB. Unveiling the Molecular Structure of Antimalarial Drugs Chloroquine and Hydroxychloroquine in Solution through Analysis of H NMR Chemical Shifts. The Journal of Physical Chemistry. B. PMID 33760611 DOI: 10.1021/acs.jpcb.1c00609   
2021 Jaskolski M, Dauter Z, Shabalin IG, Gilski M, Brzezinski D, Kowiel M, Rupp B, Wlodawer A. Crystallographic models of SARS-CoV-2 3CL: in-depth assessment of structure quality and validation. Iucrj. 8: 238-256. PMID 33708401 DOI: 10.1107/S2052252521001159   
2021 Lima I, Cino EA. Sequence similarity in 3D for comparison of protein families. Journal of Molecular Graphics & Modelling. 106: 107906. PMID 33848948 DOI: 10.1016/j.jmgm.2021.107906   
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 Mulligan VK, Workman S, Sun T, Rettie S, Li X, Worrall LJ, Craven TW, King DT, Hosseinzadeh P, Watkins AM, Renfrew PD, Guffy S, Labonte JW, Moretti R, Bonneau R, et al. Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33723038 DOI: 10.1073/pnas.2012800118   
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 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 Liu B, Shi H, Al-Hashimi HM. Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids. Current Opinion in Structural Biology. 70: 16-25. PMID 33836446 DOI: 10.1016/j.sbi.2021.02.007   
2021 Luo Z, Luo S, Ju Y, Ding P, Xu J, Gu Q, Zhou H. Structural insights into the ligand recognition and catalysis of the key aminobutanoyltransferase CntL in staphylopine biosynthesis. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 35: e21575. PMID 33826776 DOI: 10.1096/fj.202002287RR   
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 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 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 Gong W, Guerler A, Zhang C, Warner E, Li C, Zhang Y. Integrating multimeric threading with high-throughput experiments for structural interactome of Escherichia coli. Journal of Molecular Biology. 166944. PMID 33741411 DOI: 10.1016/j.jmb.2021.166944   
2021 Fogarty CA, Fadda E. Oligomannose -Glycans 3D Architecture and Its Response to the FcγRIIIa Structural Landscape. The Journal of Physical Chemistry. B. PMID 33661628 DOI: 10.1021/acs.jpcb.1c00304   
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 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 Kang SM, Moon H, Han SW, Kim BW, Kim DH, Kim BM, Lee BJ. Toxin-Activating Stapled Peptides Discovered by Structural Analysis Were Identified as New Therapeutic Candidates That Trigger Antibacterial Activity against in the Model. Microorganisms. 9. PMID 33801872 DOI: 10.3390/microorganisms9030568   
2021 Norn C, Wicky BIM, Juergens D, Liu S, Kim D, Tischer D, Koepnick B, Anishchenko I, , Baker D, Ovchinnikov S. Protein sequence design by conformational landscape optimization. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33712545 DOI: 10.1073/pnas.2017228118   
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 Ren H, Zhang Z, Zhang W, Feng X, Xu L. Prodrug-type antisense oligonucleotides with enhanced nuclease stability and anti-tumour effects. European Journal of Pharmaceutical Sciences : Official Journal of the European Federation For Pharmaceutical Sciences. 105832. PMID 33826934 DOI: 10.1016/j.ejps.2021.105832   
2021 Cho SY, Yoon SI. Structural analysis of the activation and DNA interactions of the response regulator VbrR from Vibrio parahaemolyticus. Biochemical and Biophysical Research Communications. 555: 102-108. PMID 33813268 DOI: 10.1016/j.bbrc.2021.03.114   
2021 Zhang S, Gong W, Han Z, Liu Y, Li C. Insight into Shared Properties and Differential Dynamics and Specificity of Secretory Phospholipase A Family Members. The Journal of Physical Chemistry. B. PMID 33780247 DOI: 10.1021/acs.jpcb.1c01315   
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 Estrada Pabón JD, Haddox HK, Van Aken G, Pendleton IM, Eramian H, Singer JM, Schrier J. The Role of Configurational Entropy in Miniprotein Stability. The Journal of Physical Chemistry. B. PMID 33739115 DOI: 10.1021/acs.jpcb.0c09888   
2021 Desiraju GR. Crystal engineering in IUCrJ: from 'the' crystal structure to 'a' crystal structure. Iucrj. 8: 148-149. PMID 33708389 DOI: 10.1107/S2052252521000993