Computational Studies for the Design of Metalloenzyme Mimics
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Macrophage migration inhibitory factor (MIF) is a multifunctional protein and a major mediator of innate immunity. Although X-ray crystallography revealed that MIF exists as a homotrimer, its oligomerization state in vivo and the factors governing its olig ...
Ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and hydrolyzes the phosphodiester linkages that form the backbone of the RNA strand in RNA x DNA hybrids. This enzyme is implicated in replication initiation and DNA topology ...
Caspases are fundamental targets for pharmaceutical interventions in a variety of diseases involving disregulated apoptosis. Here, we present a quantum mechanics/mol. mechanics Car-Parrinello study of key steps of the enzymic reaction for a representative ...
Recently, a novel metal Mg2+-dependent phosphatase activity has been discovered in the N-terminal domain of the soluble epoxide hydrolase (sEH), opening a new branch of fatty acid metabolism and providing an additional site for drug targeting. Importantly, ...
Organometallic ruthenium(II)-arene (RA) antitumour compounds of the general type [Ru(II)(η6-arene)(X)2(pta)], RA-pta, and [Ru(II)(η6-arene)X(en)], RA-en, (X=leaving group; pta=1,3,5-triaza-7-phosphaadamantane, en=ethylenediamine) have been investigated com ...
Histone deacetylases (HDACs) constitute an important family of zinc-dependent enzymes responsible for catalyzing the cleavage of acetyl groups from acetyl-lysine residues in histone N-terminal tails. HDACs can potentially play a key role treating various c ...
This thesis describes the application of the quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello methodology to two systems of high biological interest: (a) The potassium channel KcsA from Streptomyces lividans and (b) The DNA repair enzyme EndoIV ...
Hypothetical hydroxide and proton migration along the linear water chain in Aquaporin GlpF from Escherichia coli are studied by ab initio Car-Parrinello mol. dynamics simulations. It is found that the protein stabilizes a bipolar single file of water. The ...
A parallel study of the radical-copper enzyme Galactose Oxidase (GOase) and a low mol. wt. analog of the active site (Wang et. al. , Science 279, 537 (1998)) was performed with dynamical d. functional and mixed quantum-classical (QM/MM) calcns. This combin ...
A parallel study of the radical copper enzyme galactose oxidase (GOase) and a low mol. wt. analog of the active site was performed with dynamic d. functional and mixed quantum-classical calcns. This combined approach enables a direct comparison of the prop ...