☰

Giulia Palermo - Publications

Affiliations: 
2013-2015 Department of Bioengineering University of California, Riverside, Riverside, CA, United States 
Tree Info Similar researchers PubMed Report error

66 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Molina Vargas AM, Sinha S, Osborn R, Arantes PR, Patel A, Dewhurst S, Hardy DJ, Cameron A, Palermo G, O'Connell MR. New design strategies for ultra-specific CRISPR-Cas13a-based RNA detection with single-nucleotide mismatch sensitivity. Nucleic Acids Research. PMID 38033324 DOI: 10.1093/nar/gkad1132  0.702
2023 Sinha S, Molina Vargas AM, Arantes PR, Patel A, O'Connell MR, Palermo G. Unveiling the RNA-mediated allosteric activation discloses functional hotspots in CRISPR-Cas13a. Nucleic Acids Research. PMID 38033317 DOI: 10.1093/nar/gkad1127  0.71
2023 Wang J, Maschietto F, Qiu T, Arantes PR, Skeens E, Palermo G, Lisi GP, Batista VS. Substrate-independent activation pathways of the CRISPR-Cas9 HNH nuclease. Biophysical Journal. PMID 37936350 DOI: 10.1016/j.bpj.2023.11.005  0.662
2023 Skeens E, Sinha S, Ahsan M, D'Ordine AM, Jogl G, Palermo G, Lisi GP. High-Fidelity, Hyper-Accurate, and Evolved Mutants Rewire Atomic Level Communication in CRISPR-Cas9. Biorxiv : the Preprint Server For Biology. PMID 37662375 DOI: 10.1101/2023.08.25.554853  0.405
2023 Vargas AMM, Osborn R, Sinha S, Arantes PR, Patel A, Dewhurst S, Palermo G, O'Connell MR. New design strategies for ultra-specific CRISPR-Cas13a-based RNA-diagnostic tools with single-nucleotide mismatch sensitivity. Biorxiv : the Preprint Server For Biology. PMID 37547020 DOI: 10.1101/2023.07.26.550755  0.704
2023 Sinha S, Molina Vargas AM, Arantes PR, Patel A, O'Connell MR, Palermo G. RNA-mediated Allosteric Activation in CRISPR-Cas13a. Biorxiv : the Preprint Server For Biology. PMID 37546822 DOI: 10.1101/2023.07.27.550797  0.712
2023 Taylor D, Schwartz E, Bravo J, Ahsan M, Macias L, McCafferty C, Dangerfield T, Walker J, Brodbelt J, Palermo G, Fineran P, Fagerlund R. Type III CRISPR-Cas effectors act as protein-assisted ribozymes during RNA cleavage. Research Square. PMID 37163044 DOI: 10.21203/rs.3.rs-2837968/v1  0.319
2023 Sinha S, Pindi C, Ahsan M, Arantes PR, Palermo G. Machines on Genes through the Computational Microscope. Journal of Chemical Theory and Computation. PMID 36947696 DOI: 10.1021/acs.jctc.2c01313  0.677
2023 Nierzwicki Ł, Ahsan M, Palermo G. The Electronic Structure of Genome Editors from the First Principles. Electronic Structure (Bristol, England). 5. PMID 36926635 DOI: 10.1088/2516-1075/acb410  0.366
2023 Kumar A, Arantes PR, Saha A, Palermo G, Wong BM. GPU-Enhanced DFTB Metadynamics for Efficiently Predicting Free Energies of Biochemical Systems. Molecules (Basel, Switzerland). 28. PMID 36770943 DOI: 10.3390/molecules28031277  0.744
2023 Wang J, Arantes PR, Ahsan M, Sinha S, Kyro GW, Maschietto F, Allen B, Skeens E, Lisi GP, Batista VS, Palermo G. Twisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes. Frontiers in Molecular Biosciences. 9: 1072733. PMID 36699705 DOI: 10.3389/fmolb.2022.1072733  0.725
2022 Nierzwicki Ł, East KW, Binz JM, Hsu RV, Ahsan M, Arantes PR, Skeens E, Pacesa M, Jinek M, Lisi GP, Palermo G. Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR-Cas9. Nature Catalysis. 5: 912-922. PMID 36778082 DOI: 10.1038/s41929-022-00848-6  0.733
2022 Pacesa M, Lin CH, Cléry A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M. Structural basis for Cas9 off-target activity. Cell. 185: 4067-4081.e21. PMID 36306733 DOI: 10.1016/j.cell.2022.09.026  0.779
2022 Rossetti M, Merlo R, Bagheri N, Moscone D, Valenti A, Saha A, Arantes PR, Ippodrino R, Ricci F, Treglia I, Delibato E, van der Oost J, Palermo G, Perugino G, Porchetta A. Enhancement of CRISPR/Cas12a trans-cleavage activity using hairpin DNA reporters. Nucleic Acids Research. PMID 35822842 DOI: 10.1093/nar/gkac578  0.784
2022 Saha A, Arantes PR, Palermo G. Dynamics and mechanisms of CRISPR-Cas9 through the lens of computational methods. Current Opinion in Structural Biology. 75: 102400. PMID 35689914 DOI: 10.1016/j.sbi.2022.102400  0.804
2022 Wang J, Skeens E, Arantes PR, Maschietto F, Allen B, Kyro GW, Lisi GP, Palermo G, Batista VS. Structural Basis for Reduced Dynamics of Three Engineered HNH Endonuclease Lys-to-Ala Mutants for the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Associated 9 (CRISPR/Cas9) Enzyme. Biochemistry. PMID 35420793 DOI: 10.1021/acs.biochem.2c00127  0.729
2022 Arantes PR, Patel AC, Palermo G. Emerging Methods and Applications to Decrypt Allostery in Proteins and Nucleic Acids. Journal of Molecular Biology. 167518. PMID 35240127 DOI: 10.1016/j.jmb.2022.167518  0.701
2021 Nierzwicki L, East KW, Morzan UN, Arantes PR, Batista VS, Lisi GP, Palermo G. Enhanced specificity mutations perturb allosteric signaling in CRISPR-Cas9. Elife. 10. PMID 34908530 DOI: 10.7554/eLife.73601  0.688
2021 Wang J, Arantes PR, Bhattarai A, Hsu RV, Pawnikar S, Huang YM, Palermo G, Miao Y. Gaussian accelerated molecular dynamics (GaMD): principles and applications. Wiley Interdisciplinary Reviews. Computational Molecular Science. 11. PMID 34899998 DOI: 10.1002/wcms.1521  0.689
2021 Belato HB, D'Ordine AM, Nierzwicki L, Arantes PR, Jogl G, Palermo G, Lisi GP. Structural and dynamic insights into the HNH nuclease of divergent Cas9 species. Journal of Structural Biology. 214: 107814. PMID 34871741 DOI: 10.1016/j.jsb.2021.107814  0.724
2021 Nierzwicki Ł, Arantes PR, Saha A, Palermo G. Establishing the allosteric mechanism in CRISPR-Cas9. Wiley Interdisciplinary Reviews. Computational Molecular Science. 11. PMID 34322166 DOI: 10.1002/wcms.1503  0.808
2021 Palermo G, Spinello A, Saha A, Magistrato A. Frontiers of metal-coordinating drug design. Expert Opinion On Drug Discovery. 16: 497-511. PMID 33874825 DOI: 10.1080/17460441.2021.1851188  0.748
2021 Narkhede YB, Gautam AK, Hsu RV, Rodriguez W, Zewde NT, Harrison RES, Arantes PR, Gaieb Z, Gorham RD, Kieslich C, Morikis D, Sahu A, Palermo G. Role of Electrostatic Hotspots in the Selectivity of Complement Control Proteins Toward Human and Bovine Complement Inhibition. Frontiers in Molecular Biosciences. 8: 618068. PMID 33829039 DOI: 10.3389/fmolb.2021.618068  0.635
2020 Casalino L, Nierzwicki Ł, Jinek M, Palermo G. Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Molecular Dynamics. Acs Catalysis. 10: 13596-13605. PMID 33520346 DOI: 10.1021/acscatal.0c03566  0.372
2020 Arantes PR, Saha A, Palermo G. Fighting COVID-19 Using Molecular Dynamics Simulations. Acs Central Science. 6: 1654-1656. PMID 33140032 DOI: 10.1021/acscentsci.0c01236  0.769
2020 Saha A, Arantes PR, Hsu RV, Narkhede YB, Jinek M, Palermo G. Molecular Dynamics Reveals a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12a. Journal of Chemical Information and Modeling. PMID 33107304 DOI: 10.1021/acs.jcim.0c00929  0.798
2020 Palermo G, Bonvin AMJJ, Dal Peraro M, Amaro RE, Tozzini V. Editorial: Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations. Frontiers in Molecular Biosciences. 7: 194. PMID 33005628 DOI: 10.3389/Fmolb.2020.00194  0.321
2020 Cui JY, Zhang F, Nierzwicki L, Palermo G, Linhardt RJ, Lisi GP. Mapping the Structural and Dynamic Determinants of pH-Sensitive Heparin Binding to Granulocyte Macrophage Colony Stimulating Factor. Biochemistry. PMID 32897051 DOI: 10.1021/Acs.Biochem.0C00538  0.37
2020 Mitchell BP, Hsu RV, Medrano MA, Zewde NT, Narkhede YB, Palermo G. Spontaneous Embedding of DNA Mismatches Within the RNA:DNA Hybrid of CRISPR-Cas9. Frontiers in Molecular Biosciences. 7: 39. PMID 32258048 DOI: 10.3389/Fmolb.2020.00039  0.494
2020 Palermo G, Casalino L, Jinek M. Two-Metal Ion Mechanism of DNA Cleavage in CRISPR-Cas9 Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.528  0.321
2019 East KW, Newton JC, Morzan UN, Narkhede Y, Acharya A, Skeens E, Jogl G, Batista VS, Palermo G, Lisi GP. Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics. Journal of the American Chemical Society. PMID 31885264 DOI: 10.2210/Pdb6O56/Pdb  0.511
2019 East KW, Skeens E, Cui JY, Belato HB, Mitchell B, Hsu R, Batista VS, Palermo G, Lisi GP. NMR and computational methods for molecular resolution of allosteric pathways in enzyme complexes. Biophysical Reviews. PMID 31838649 DOI: 10.1007/S12551-019-00609-Z  0.41
2019 Borišek J, Saltalamacchia A, Gallì A, Palermo G, Molteni E, Malcovati L, Magistrato A. Disclosing the Impact of Carcinogenic SF3b Mutations on Pre-mRNA Recognition Via All-Atom Simulations. Biomolecules. 9. PMID 31640290 DOI: 10.3390/biom9100633  0.61
2019 Palermo G, Ricci CG, McCammon JA. The invisible dance of CRISPR-Cas9. Simulations unveil the molecular side of the gene-editing revolution. Physics Today. 72: 30-36. PMID 31511751 DOI: 10.1063/Pt.3.4182  0.51
2019 Vanni S, Riccardi L, Palermo G, De Vivo M. Structure and Dynamics of the Acyl Chains in the Membrane Trafficking and Enzymatic Processing of Lipids. Accounts of Chemical Research. PMID 31364837 DOI: 10.1021/Acs.Accounts.9B00134  0.324
2019 Ricci CG, Chen JS, Miao Y, Jinek M, Doudna JA, McCammon JA, Palermo G. Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics. Acs Central Science. 5: 651-662. PMID 31041385 DOI: 10.1021/Acscentsci.9B00020  0.615
2019 Palermo G, Casalino L, Magistrato A, Andrew McCammon J. Understanding the mechanistic basis of non-coding RNA through molecular dynamics simulations. Journal of Structural Biology. PMID 30880083 DOI: 10.1016/J.Jsb.2019.03.004  0.688
2019 Palermo G. Structure and Dynamics of the CRISPR-Cas9 Catalytic Complex. Journal of Chemical Information and Modeling. PMID 30763088 DOI: 10.1021/Acs.Jcim.8B00988  0.508
2019 Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, ... ... Palermo G, et al. Allostery in Its Many Disguises: From Theory to Applications. Structure (London, England : 1993). PMID 30744993 DOI: 10.1016/J.Str.2019.01.003  0.617
2019 Palermo G. Dissecting Structure and Function of DNA·RNA Hybrids Chem. 5: 1364-1366. DOI: 10.1016/J.Chempr.2019.05.015  0.305
2019 Palermo G, Gravina Ricci C, Rivalta I, Batista VS, McCammon JA. An Allosteric Signaling Governs the CRISPR-Cas9 Function Biophysical Journal. 116: 485a. DOI: 10.1016/J.Bpj.2018.11.2619  0.406
2019 Palermo G, Gravina Ricci C, Chen JS, Miao Y, Jinek M, Doudna JA, McCammon JA. Molecular Mechanism of Off-Target Effects in CRISPR-Cas9 Biophysical Journal. 116: 319a. DOI: 10.1016/J.Bpj.2018.11.1731  0.606
2019 Casalino L, Palermo G, Spinello A, Roethlisberger U, Magistrato A. Pre-mRNA Splicing: The Gene Maturation Symphony of the Intron Lariat Spliceosome Revealed by Molecular Dynamics Simulations Biophysical Journal. 116: 299a. DOI: 10.1016/J.Bpj.2018.11.1619  0.768
2018 Palermo G, Chen JS, Ricci CG, Rivalta I, Jinek M, Batista VS, Doudna JA, McCammon JA. Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain. Quarterly Reviews of Biophysics. 51: e9. PMID 30912489 DOI: 10.1017/S0033583518000070  0.574
2018 Palermo G, Chen JS, Ricci CG, Rivalta I, Jinek M, Batista VS, Doudna JA, McCammon JA. Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain. Quarterly Reviews of Biophysics. 51. PMID 30555184 DOI: 10.1017/S0033583518000070  0.626
2018 Casalino L, Palermo G, Spinello A, Rothlisberger U, Magistrato A. All-atom simulations disentangle the functional dynamics underlying gene maturation in the intron lariat spliceosome. Proceedings of the National Academy of Sciences of the United States of America. PMID 29891649 DOI: 10.1073/Pnas.1802963115  0.652
2018 Palermo G, Ricci C, Miao Y, Jinek M, McCammon JA. A PAM-Induced Signalling Activates the Communication between HNH and RUVC in CRISPR-Cas9 Biophysical Journal. 114: 250a. DOI: 10.1016/J.Bpj.2017.11.1391  0.4
2017 Palermo G, G Ricci C, Fernando A, Basak R, Jinek M, Rivalta I, Batista VS, McCammon JA. PAM-induced allostery activates CRISPR-Cas9. Journal of the American Chemical Society. PMID 28764328 DOI: 10.1021/Jacs.7B05313  0.628
2017 Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Proceedings of the National Academy of Sciences of the United States of America. PMID 28652374 DOI: 10.1073/Pnas.1707645114  0.634
2017 Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. CRISPR-Cas9: Computational Insights Toward Improved Genome Editing Biophysical Journal. 112: 72a. DOI: 10.1016/J.Bpj.2016.11.432  0.63
2016 Casalino L, Palermo G, Abdurakhmonova N, Rothlisberger U, Magistrato A. Development of Site-Specific Mg(2+)-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations. Journal of Chemical Theory and Computation. PMID 28001405 DOI: 10.1021/Acs.Jctc.6B00905  0.642
2016 Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations. Acs Central Science. 2: 756-763. PMID 27800559 DOI: 10.1021/Acscentsci.6B00218  0.63
2016 Casalino L, Palermo G, Rothlisberger U, Magistrato A. Who Activates the Nucleophile in Ribozyme Catalysis? An Answer from the Splicing Mechanism of Group II Introns. Journal of the American Chemical Society. 138: 10374-7. PMID 27309711 DOI: 10.1021/Jacs.6B01363  0.637
2016 Ma Z, Palermo G, Adhireksan Z, Murray BS, von Erlach T, Dyson PJ, Rothlisberger U, Davey CA. An Organometallic Compound which Exhibits a DNA Topology-Dependent One-Stranded Intercalation Mode. Angewandte Chemie (International Ed. in English). PMID 27184539 DOI: 10.1002/Anie.201602145  0.388
2016 Palermo G, Magistrato A, Riedel T, von Erlach T, Davey CA, Dyson PJ, Rothlisberger U. Fighting Cancer with Transition Metal Complexes: From Naked DNA to Protein and Chromatin Targeting Strategies. Chemmedchem. 11: 1199-210. PMID 26634638 DOI: 10.1002/Cmdc.201500478  0.687
2016 Palermo G, Ma Z, Murray BS, Dyson PJ, Davey CA, Rothlisberger U. Molecular Mechanism of Chromatin Targeting by a Potent Anticancer Agent Acting at the Nucleosome Core Particle Biophysical Journal. 110: 68a-69a. DOI: 10.1016/J.Bpj.2015.11.434  0.305
2016 Palermo G, Bauer I, Campomanes P, Cavalli A, Armirotti A, Girotto S, Vivo MD, Rothlisberger U. Molecular Simulations Integrated with Experiments Unravel the Key Factors of Lipid Selection in Fatty Acid Amide Hydrolase and Suggest A General Mechanism of Lipid-Processing in the Parent Enzymes Biophysical Journal. 110: 202a-203a. DOI: 10.1016/J.Bpj.2015.11.1131  0.31
2015 Palermo G, Favia AD, Convertino M, De Vivo M. The Molecular Basis for Dual Fatty Acid Amide Hydrolase (FAAH)/Cyclooxygenase (COX) Inhibition. Chemmedchem. PMID 26593700 DOI: 10.1002/Cmdc.201500507  0.342
2015 Palermo G, Minniti E, Greco ML, Riccardi L, Simoni E, Convertino M, Marchetti C, Rosini M, Sissi C, Minarini A, De Vivo M. An optimized polyamine moiety boosts the potency of human type II topoisomerase poisons as quantified by comparative analysis centered on the clinical candidate F14512. Chemical Communications (Cambridge, England). 51: 14310-3. PMID 26234198 DOI: 10.1039/C5Cc05065K  0.323
2015 Palermo G, Bauer I, Campomanes P, Cavalli A, Armirotti A, Girotto S, Rothlisberger U, De Vivo M. Keys to Lipid Selection in Fatty Acid Amide Hydrolase Catalysis: Structural Flexibility, Gating Residues and Multiple Binding Pockets. Plos Computational Biology. 11: e1004231. PMID 26111155 DOI: 10.1371/Journal.Pcbi.1004231  0.377
2015 Palermo G, Cavalli A, Klein ML, Alfonso-Prieto M, Dal Peraro M, De Vivo M. Catalytic metal ions and enzymatic processing of DNA and RNA. Accounts of Chemical Research. 48: 220-8. PMID 25590654 DOI: 10.1021/Ar500314J  0.518
2015 Palermo G, Rothlisberger U, Cavalli A, De Vivo M. Computational insights into function and inhibition of fatty acid amide hydrolase. European Journal of Medicinal Chemistry. 91: 15-26. PMID 25240419 DOI: 10.1016/J.Ejmech.2014.09.037  0.337
2015 Palermo G, Campomanes P, Cavalli A, Rothlisberger U, De Vivo M. Anandamide hydrolysis in FAAH reveals a dual strategy for efficient enzyme-assisted amide bond cleavage via nitrogen inversion. The Journal of Physical Chemistry. B. 119: 789-801. PMID 25205244 DOI: 10.1021/Jp5052276  0.362
2013 Palermo G, Campomanes P, Neri M, Piomelli D, Cavalli A, Rothlisberger U, De Vivo M. Wagging the Tail: Essential Role of Substrate Flexibility in FAAH Catalysis. Journal of Chemical Theory and Computation. 9: 1202-13. PMID 26588763 DOI: 10.1021/Ct300611Q  0.352
2013 Palermo G, Stenta M, Cavalli A, Dal Peraro M, De Vivo M. Molecular Simulations Highlight the Role of Metals in Catalysis and Inhibition of Type II Topoisomerase. Journal of Chemical Theory and Computation. 9: 857-62. PMID 26588728 DOI: 10.1021/Ct300691U  0.373
2011 Brunk E, Ashari N, Athri P, Campomanes P, de Carvalho FF, Curchod BF, Diamantis P, Doemer M, Garrec J, Laktionov A, Micciarelli M, Neri M, Palermo G, Penfold TJ, Vanni S, et al. Pushing the frontiers of first-principles based computer simulations of chemical and biological systems. Chimia. 65: 667-71. PMID 22026176 DOI: 10.2533/Chimia.2011.667  0.4
Show low-probability matches.