Homology modeling and molecular dynamics simulations of lymphotactin

Homology modeling and molecular dynamics simulations of transmembrane domain structure of human neuronal nicotinic acetylcholine receptor.

A three-dimensional model of the transmembrane domain of a neuronal-type nicotinic acetylcholine receptor (nAChR), (alpha4)2(beta2)3, was constructed from a homology structure of the muscle-type nAChR recently determined by cryo-electron microscopy. The neuronal channel model was embedded in a fully hydrated DMPC lipid bilayer, and molecular-dynamics simulations were performed for 5 ns. A compa...

Modeling Nanocomposites for Molecular Dynamics (md) Simulations

Regioselectivity of CYP2B6: homology modeling, molecular dynamics simulation, docking.

Human cytochrome P450 (CYP) 2B6 activates the anticancer prodrug cyclophosphamide (CPA) by 4-hydroxylation. In contrast, the same enzyme catalyzes N-deethylation of a structural isomer, the prodrug ifosfamide (IFA), thus causing severe adverse drug effects. To model the molecular interactions leading to a switch in regioselectivity, the structure of CYP2B6 was modeled based on the structure of ...

Molecular Modeling –mid Simulations- Protein Structure and Dynamics

Introduction Rapid advances in computer technology have led to the development of increasing successful molecular simulations of protein structural dynamics that are intrinsic to biological processes. These simulations have resulted in the development of novel models and methods that increasingly agree with experimental observations; suggest new experiments and insights into biological mechanis...

Modeling of annexin A2—Membrane interactions by molecular dynamics simulations

The annexins are a family of Ca2+-regulated phospholipid binding proteins that are involved in membrane domain organization and membrane trafficking. Although they are widely studied and crystal structures are available for several soluble annexins their mode of membrane association has never been studied at the molecular level. Here we obtained molecular information on the annexin-membrane int...