Molecular simulations of beta-amyloid protein near hydrated lipids (PECASE).

Technical Report · Thu Dec 01 04:00:00 EST 2005

DOI:https://doi.org/10.2172/876519· OSTI ID:876519

Thompson, Aidan Patrick; Han, Kunwoo ^[1]; Ford, David M. ^[2]

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1. Texas A&M University, College Station, TX
2. Texas A&M University, College Station, TX

We performed molecular dynamics simulations of beta-amyloid (A{beta}) protein and A{beta} fragment(31-42) in bulk water and near hydrated lipids to study the mechanism of neurotoxicity associated with the aggregation of the protein. We constructed full atomistic models using Cerius2 and ran simulations using LAMMPS. MD simulations with different conformations and positions of the protein fragment were performed. Thermodynamic properties were compared with previous literature and the results were analyzed. Longer simulations and data analyses based on the free energy profiles along the distance between the protein and the interface are ongoing.

• Research Organization: Sandia National Laboratories
• Sponsoring Organization: USDOE
• DOE Contract Number: AC04-94AL85000
• OSTI ID: 876519
• Report Number(s): SAND2005-7497
• Country of Publication: United States
• Language: English

Related Subjects

Molecular dynamics-Simulation methods.
59 BASIC BIOLOGICAL SCIENCES
FREE ENERGY
LIPIDS
MOLECULAR DYNAMICS METHOD
PROTEINS
Protein-analysis.
SIMULATION
THERMODYNAMIC PROPERTIES
Thermodynamic properties.
WATER