Search Results - "Palermo, Giulia"

Structure and Dynamics of the CRISPR–Cas9 Catalytic Complex by Palermo, Giulia

“…CRISPR–Cas9 is a bacterial immune system with exciting applications for genome editing. In spite of extensive experimental characterization, the active site…”
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All-atom simulations disentangle the functional dynamics underlying gene maturation in the intron lariat spliceosome by Casalino, Lorenzo, Palermo, Giulia, Spinello, Angelo, Rothlisberger, Ursula, Magistrato, Alessandra

“…The spliceosome (SPL) is a majestic macromolecular machinery composed of five small nuclear RNAs and hundreds of proteins. SPL removes noncoding introns from…”
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CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations by Palermo, Giulia, Miao, Yinglong, Walker, Ross C., Jinek, Martin, McCammon, J. Andrew

“…CRISPR-Cas9 has become a facile genome editing technology, yet the structural and mechanistic features underlying its function are unclear. Here, we perform…”
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The Future of Chemistry Through Computations by Palermo, Giulia, Nordén, Bengt

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Enhanced specificity mutations perturb allosteric signaling in CRISPR-Cas9 by Nierzwicki, Lukasz, East, Kyle W, Morzan, Uriel N, Arantes, Pablo R, Batista, Victor S, Lisi, George P, Palermo, Giulia

“…CRISPR-Cas9 (clustered regularly interspaced short palindromic repeat and associated Cas9 protein) is a molecular tool with transformative genome editing…”
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Allosteric Motions of the CRISPR–Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics by East, Kyle W, Newton, Jocelyn C, Morzan, Uriel N, Narkhede, Yogesh B, Acharya, Atanu, Skeens, Erin, Jogl, Gerwald, Batista, Victor S, Palermo, Giulia, Lisi, George P

“…CRISPR–Cas9 is a widely employed genome-editing tool with functionality reliant on the ability of the Cas9 endonuclease to introduce site-specific breaks in…”
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Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules by Nierzwicki, Łukasz, Palermo, Giulia

“…Single-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution…”
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An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a by Saha, Aakash, Ahsan, Mohd, Arantes, Pablo R., Schmitz, Michael, Chanez, Christelle, Jinek, Martin, Palermo, Giulia

“…CRISPR-Cas12a is a powerful RNA-guided genome-editing system that generates double-strand DNA breaks using its single RuvC nuclease domain by a sequential…”
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Fighting COVID-19 Using Molecular Dynamics Simulations by Arantes, Pablo R, Saha, Aakash, Palermo, Giulia

“…Molecular dynamics simulations revealed a promising immune target on the SARS-CoV-2 spike protein, proposing novel strategies for vaccine development…”
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GPU-Enhanced DFTB Metadynamics for Efficiently Predicting Free Energies of Biochemical Systems by Kumar, Anshuman, Arantes, Pablo R, Saha, Aakash, Palermo, Giulia, Wong, Bryan M

“…Metadynamics calculations of large chemical systems with ab initio methods are computationally prohibitive due to the extensive sampling required to simulate…”
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Allosteric cross-talk in chromatin can mediate drug-drug synergy by Adhireksan, Zenita, Palermo, Giulia, Riedel, Tina, Ma, Zhujun, Muhammad, Reyhan, Rothlisberger, Ursula, Dyson, Paul J., Davey, Curt A.

“…Exploitation of drug–drug synergism and allostery could yield superior therapies by capitalizing on the immensely diverse, but highly specific, potential…”
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Movement smoothness in chronic post-stroke individuals walking in an outdoor environment-A cross-sectional study using IMU sensors by Garcia, Flora do Vale, da Cunha, Maira Jaqueline, Schuch, Clarissa Pedrini, Schifino, Giulia Palermo, Balbinot, Gustavo, Pagnussat, Aline Souza

“…Walking speed is often used in the clinic to assess the level of gait impairment following stroke. Nonetheless, post-stroke individuals may employ the same…”
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Acetylcholine-Binding Protein Affinity Profiling of Neurotoxins in Snake Venoms with Parallel Toxin Identification by Palermo, Giulia, Schouten, Wietse M, Alonso, Luis Lago, Ulens, Chris, Kool, Jeroen, Slagboom, Julien

“…Snakebite is considered a concerning issue and a neglected tropical disease. Three-finger toxins (3FTxs) in snake venoms primarily cause neurotoxic effects…”
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NMR and computational methods for molecular resolution of allosteric pathways in enzyme complexes by East, Kyle W., Skeens, Erin, Cui, Jennifer Y., Belato, Helen B., Mitchell, Brandon, Hsu, Rohaine, Batista, Victor S., Palermo, Giulia, Lisi, George P.

“…Allostery is a ubiquitous biological mechanism in which a distant binding site is coupled to and drastically alters the function of a catalytic site in a…”
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Frontiers in CryoEM Modeling by Palermo, Giulia, Sugita, Yuji, Wriggers, Willy, Amaro, Rommie E

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Disruption of electrostatic contacts in the HNH nuclease from a thermophilic Cas9 rewires allosteric motions and enhances high-temperature DNA cleavage by Belato, Helen B, Norbrun, Carmelissa, Luo, Jinping, Pindi, Chinmai, Sinha, Souvik, D'Ordine, Alexandra M, Jogl, Gerwald, Palermo, Giulia, Lisi, George P

“…Allosteric signaling within multidomain proteins is a driver of communication between spatially distant functional sites. Understanding the mechanism of…”
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Corrigendum: Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules by Nierzwicki, Łukasz, Palermo, Giulia

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RNA targeting and cleavage by the type III-Dv CRISPR effector complex by Schwartz, Evan A., Bravo, Jack P. K., Ahsan, Mohd, Macias, Luis A., McCafferty, Caitlyn L., Dangerfield, Tyler L., Walker, Jada N., Brodbelt, Jennifer S., Palermo, Giulia, Fineran, Peter C., Fagerlund, Robert D., Taylor, David W.

“…CRISPR-Cas are adaptive immune systems in bacteria and archaea that utilize CRISPR RNA-guided surveillance complexes to target complementary RNA or DNA for…”
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Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics by Ricci, Clarisse G, Chen, Janice S, Miao, Yinglong, Jinek, Martin, Doudna, Jennifer A, McCammon, J. Andrew, Palermo, Giulia

“…CRISPR-Cas9 is the state-of-the-art technology for editing and manipulating nucleic acids. However, the occurrence of off-target mutations can limit its…”
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Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations by Palermo, Giulia, Miao, Yinglong, Walker, Ross C, Jinek, Martin, McCammon, J. Andrew

“…The CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 system recently emerged as a transformative genome-editing technology that is…”
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