Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR–Cas9
Ł Nierzwicki, KW East, JM Binz, RV Hsu, M Ahsan… - Nature …, 2022 - nature.com
At the core of the CRISPR–Cas9 genome-editing technology, the endonuclease Cas9
introduces site-specific breaks in DNA. However, precise mechanistic information to …
introduces site-specific breaks in DNA. However, precise mechanistic information to …
Twisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes
The CRISPR-associated protein 9 (Cas9) has been engineered as a precise gene editing
tool to make double-strand breaks. CRISPR-associated protein 9 binds the folded guide …
tool to make double-strand breaks. CRISPR-associated protein 9 binds the folded guide …
Pairing structural reconstruction with catalytic competence to evaluate the mechanisms of key enzymes in the folate‐mediated one‐carbon pathway
Mammalian metabolism comprises a series of interlinking pathways that include two major
cycles: the folate and methionine cycles. The folate‐mediated metabolic cycle uses several …
cycles: the folate and methionine cycles. The folate‐mediated metabolic cycle uses several …
The electronic structure of genome editors from the first principles
Ab-initio molecular dynamics enables following the dynamics of biological systems from the
first principles, describing the electronic structure and offering the opportunity to" watch" the …
first principles, describing the electronic structure and offering the opportunity to" watch" the …
Leveraging QM/MM and Molecular Dynamics Simulations to Decipher the Reaction Mechanism of the Cas9 HNH Domain to Investigate Off-Target Effects
Y Maghsoud, VM Jayasinghe-Arachchige… - Journal of Chemical …, 2023 - ACS Publications
The clustered regularly interspaced short palindromic repeats (CRISPR) technology is an
RNA-guided targeted genome-editing tool using Cas family proteins. Two magnesium …
RNA-guided targeted genome-editing tool using Cas family proteins. Two magnesium …
Molecular dynamics-derived descriptor informs the impact of mutation on the catalytic turnover number in lactonase across substrates
Molecular dynamics simulations have been extensively employed to reveal the roles of
protein dynamics in mediating enzyme catalysis. However, simulation-derived predictive …
protein dynamics in mediating enzyme catalysis. However, simulation-derived predictive …
An interaction network in Bacillus subtilis coproporphyrinogen oxidase is essential for the oxidation of protoporphyrinogen IX
B Wang, L Sun, X Wen, Z Xi - Proteins: Structure, Function, and …, 2023 - Wiley Online Library
Coproporphyrinogen oxidase (CPO) plays important role in the biosynthesis of heme by
catalyzing the coproporphyrinogen III to coproporphyrin III. However, in earlier research, it …
catalyzing the coproporphyrinogen III to coproporphyrin III. However, in earlier research, it …
The catalytic mechanism of the mitochondrial methylenetetrahydrofolate dehydrogenase/cyclohydrolase (MTHFD2)
Methylenetetrahydrofolate dehydrogenase/cyclohydrolase (MTHFD2) is a new drug target
that is expressed in cancer cells but not in normal adult cells, which provides an Achilles …
that is expressed in cancer cells but not in normal adult cells, which provides an Achilles …
Deciphering the Thermodynamic Landscape of CRISPR/Cas9: Insights into Enhancing Gene Editing Precision and Efficiency
The thermodynamic landscape of the CRISPR/Cas9 system plays a crucial role in
understanding and optimizing the performance of this revolutionary genome-editing …
understanding and optimizing the performance of this revolutionary genome-editing …
Molecular basis of the reaction mechanism of the methyltransferase HENMT1
PIWI-interacting RNAs (piRNAs) are important for ensuring the integrity of the germline. 3'-
terminal 2'-O-methylation is essential for piRNA maturation and to protect them from …
terminal 2'-O-methylation is essential for piRNA maturation and to protect them from …