AVS 50th International Symposium
    Biomaterial Interfaces Wednesday Sessions
       Session BI-WeM

Paper BI-WeM2
Molecular Simulation Studies of Protein and DNA Interactions with Surfaces

Wednesday, November 5, 2003, 8:40 am, Room 317

Session: Bionanoscale Analysis: Theory to Experiment
Presenter: S. Jiang, University of Washington
Authors: J. Zheng, University of Washington
J. Zhou, University of Washington
J.P. Sullivan, University of Washington
L. Zhang, University of Washington
S. Jiang, University of Washington
Correspondent: Click to Email
Molecular-level understanding of protein behavior on surfaces will facilitate the development of biomaterials with superior biocompatibility and biosensors with high sensitivity and specificity. In this work, we report various molecular simulation studies of non-fouling mechanism, protein orientation/conformation on surfaces, molecular recognition, and DNA chips. First of all, molecular dynamics (MD) simulations are performed to study lysozyme interactions with SAMs presenting oligo (ethylene glycol) (OEG) groups in the presence of explicit water molecules and ions. The behavior of water at protein/SAM interfaces is characterized by self-diffusion coefficient, order parameter, hydrogen bonding, and radial distribution. The effects of surface (charge, hydrophobicity, and defect), solvent, pH, and ion strength will be taken into account. Results from this work will shed light on non-fouling mechanism at the atomic-scale level and guide the design of better biocompatible materials and biosensors. Second, Monte Carlo simulations are performed to study IgG orientation on positively charged NH2 and negatively charged COOH terminated self-assembled monolayers (SAMs) on Au(111). Simulations are confirmed by experimental results from surface plasmon resonance (SPR) biosensor and time-of-flight secondary ion mass spectrometry (ToF-SIMS). Third, MD simulations are performed to study molecular conformation of cytochrome c on charged SAMs in the presence of explicit water molecules and ions. The ability to predict protein orientation and conformation will enable one to control and manipulate protein behavior on surfaces, important for biomaterials and biosensors. Fourth, hybrid molecular simulations are performed to study the unbinding pathway of biotin/avidin interactions at the atomic force microscopy time scale. Finally, MD simulations are performed to study the molecular packing of thiolated ssDNA and dsDNA on Au(111) and then mixed DNA and OEG SAMs.