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- Publications
- Influence
Aging mechanism of soman inhibited acetylcholinesterase.
- Gulseher Sarah Sirin, Y. Zhou, Lee Lior-Hoffmann, S. Wang, Y. Zhang
- Chemistry, Medicine
- The journal of physical chemistry. B
- 28 September 2012
Acetylcholinesterase (AChE) is a crucial enzyme in the cholinergic nervous system that hydrolyzes neurotransmitter acetylcholine (ACh) and terminates synaptic signals. The catalytic serine of AChE… Expand
Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface
A new practical approach to studying enzyme reactions by combining ab initio QM/MM calculations with free energy perturbation is presented. An efficient iterative optimization procedure has been… Expand
A challenge for density functionals: Self-interaction error increases for systems with a noninteger number of electrons
The difficulty of widely used density functionals in describing the dissociation behavior of some homonuclear and heteronuclear diatomic radicals is analyzed. It is shown that the self-interaction… Expand
Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study.
- Y. Zhang, J. Kua, J. McCammon
- Chemistry, Medicine
- Journal of the American Chemical Society
- 10 August 2002
The initial step of the acylation reaction catalyzed by acetylcholinesterase (AChE) has been studied by a combined ab initio quantum mechanical/molecular mechanical (QM/MM) approach. The reaction… Expand
How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study.
- Y. Cheng, Y. Zhang, J. McCammon
- Chemistry, Medicine
- Journal of the American Chemical Society
- 15 January 2005
We have carried out density functional theory QM/MM calculations on the catalytic subunit of cAMP-dependent protein kinase (PKA). The QM/MM calculations indicate that the phosphorylation reaction… Expand
Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: an ab initio QM/MM-FE study with multiple initial structures.
Histone lysine methylation is emerging as an important mechanism to regulate chromatin structure and gene activity. To provide theoretical understanding of its reaction mechanism and product… Expand
Zinc chelation with hydroxamate in histone deacetylases modulated by water access to the linker binding channel.
- Ruibo Wu, Z. Lu, Zexing Cao, Y. Zhang
- Chemistry, Medicine
- Journal of the American Chemical Society
- 1 April 2011
It is of significant biological interest and medical importance to develop class- and isoform-selective histone deacetylase (HDAC) modulators. The impact of the linker component on HDAC inhibition… Expand
Improving scoring‐docking‐screening powers of protein–ligand scoring functions using random forest
TLDR
Catalytic reaction mechanism of acetylcholinesterase determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations.
Acetylcholinesterase (AChE) is a remarkably efficient serine hydrolase responsible for the termination of impulse signaling at cholinergic synapses. By employing Born-Oppenheimer molecular dynamics… Expand