Van der Ende, B: Molecular Dynamics Simulations of the NeuTr

Neu is a membrane-bound protein whose structure includes a single helix which spans the width of a cellular membrane. It is a growth factor receptor which dimerizes (forms pairs) when signaling cell growth and proliferation. Key mutations at a specific location in the transmembrane domain (TMD) of the neu protein have been demonstrated to result in permanent dimerization of mutated pairs, and are simultaneously associated with the formation of cancerous tumors. The physical effects of these key point mutations that lead to such permanent dimerization are not known. Atomistic molecular dynamics (MD) simulations, whereby Newton‘s equations of motion are numerically solved for the atoms in the neu TMD and its surrounding membrane environment, provide further physical insight into this important problem. This book reviews the MD simulation method as well as previous work characterizing the neu protein; the book further examines the results of detailed MD simulations of native and mutant neu TMDs in hydrated membrane environments. The reader should have some basic background in biophysical chemistry, Newtonian dynamics, and statistical mechanics.