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Specific Inhibition of β-Secretase Processing of the Alzheimer Disease Amyloid Precursor Protein.
It is reported that β-secretase has a higher affinity for Neuregulin than it does for APP, and it is shown that non-amyloid substrates are processed by β- secretase in an endocytosis-independent manner. Expand
Atomistic simulation of NO dioxygenation in group I truncated hemoglobin.
NO dioxygenation, i.e., the oxidation of nitric oxide to nitrate by oxygen-bound truncated hemoglobin (trHbN) is studied using reactive molecular dynamics simulations and suggests that residues Tyr33 and Gln58 preorient the reactive ligands through a highly dynamical H-bonding network which facilitates the reaction. Expand
Nitric oxide dynamics in truncated hemoglobin: docking sites, migration pathways, and vibrational spectroscopy from molecular dynamics simulations.
From extensive molecular dynamics simulations of nitric oxide dynamics and migration in the trHbN of Mycobacterium tuberculosis, it is found that Phe(62) is directly involved in controlling ligand migration. Expand
Structural and mechanistic insight into substrate binding from the conformational dynamics in apo and substrate-bound DapE enzyme.
The essential dynamics of the apo enzyme and the enzyme-substrate complex are extracted from the principal component analysis of the simulations of these two systems where the first two principal components are analyzed in detail. Expand
Synthesis, Structure, Electrochemical, and Spectroscopic Properties of Hetero-Bimetallic Ru(II)/Fe(II)-Alkynyl Organometallic Complexes.
The redox and NIR absorption features indicate that the mixed-valence system of the heterobinuclear dyads belongs to a Robin and Day "class II" system and two well-separated reversible redox waves as a result of successive oxidation of the ferrocenyl and Ru(II) redox centers. Expand
Dynamics in the active site of β-secretase: a network analysis of atomistic simulations.
A unified network analysis of the complexes of BACE with the three states of the substrate provides an estimation of the activation free energy associated with the structural rearrangements that involve only noncovalent interactions. Expand
Quantitative analysis of ligand migration from transition networks.
This work uses transition network analysis for the first time to investigate ligand migration in truncated hemoglobin (trHbN) and obtain kinetic information about the docking-site dynamics in the protein and suggests that residues Tyr33 and Gln58 stabilize the NO ligand in the Xe2 docking site of trHbn, thus facilitating the efficiency of the NO detoxification reaction. Expand
The relativistic E × E Jahn–Teller effect revisited
The vibronic Hamiltonian describing linear Jahn–Teller coupling as well as spin–orbit coupling in systems of trigonal symmetry is derived in the diabatic spin–orbital representation, employing theExpand
The structural and energetic aspects of substrate binding and the mechanism of action of the DapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) investigated using a hybrid QM/MM
The mechanism of action of the DapE catalyzed SDAP hydrolysis is investigated employing a hybrid QM/MM computational method and a conformational change in the side chain of Asp100 is observed which facilitates the enzymatic action by lowering the activation energy and leads to the formation of a new intermediate during the catalytic reaction. Expand
Structural diversity of copper(I) complexes formed by pyrrole- and dipyrrolylmethane-based diphosphine ligands with cu-X···HN hydrogen bonds.
In contrast to the PNP pincer ligand, the dipyrrolyl-diphosphine ligand (PNNP) adopts chelation as well as bridging coordination modes with Cu(I) atoms, indicating its flexibility of bonding. Expand