Computer Simulations of Protein-Nanomaterial Interactions
EMSL Project ID
35413
Abstract
The development of nanotechnology has led to an increasing interest in interfacing biological molecules with nanomaterials. Proteins have been used to functionalize nanomaterials controlling their synthesis, assembly and influencing their properties for applications from biosensing to delivery. In turn, the surface chemistry of a nanoparticle also influences the structure and function of the adsorbed proteins. Some specific interactions between nanomaterials and proteins in living cells have recently been shown to be cause of a series of adverse health effects. Therefore, the understanding of the molecular basis of how nanomaterial properties affect protein structure and function becomes imperative for the design of not only smart bionanocomposites with biosensing or delivery properties, but also to ensure the safety of the designed nanomaterials.This proposal seeks high performance computing allocation for the development and application of computational methodologies aiming at the characterization of the effects of nanomaterials on protein structure, stability and dynamics. The rationale of such interactions will be drawn based on a variety of simulations specifically involving i) the adsorption of cell-surface receptors and plasma proteins to silica, polysterene and asbestos particulates; and, ii) the effect of enzyme confinement on mesoporous silica. This effort involves a synergistic collaboration between experiment al and computational teams at PNNL (Computational Biology and Bioinformatics, EMSL and Biological Sciences) and Ohio State University.
Project Details
Project type
Capability Research
Start Date
2009-10-01
End Date
2012-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Boily JF, and RD Lins. 2009. "Electrostatic Cooperativity of Hydroxyl Groups at Metal Oxide Surfaces." Journal of Physical Chemistry C 113(38):16568-16570. doi:10.1021/jp906124a
Franca EF, LC Freitas, and RD Lins. 2011. "Chitosan Molecular Structure as a Function of N-Acetylation." Biopolymers 95(7):448 - 460. doi:10.1002/bip.21602
Gomes, D.E.B. PhD Thesis
Gomes DEB, RD Lins, PG Pascutti, C Lei, and TA Soares. 2010. "The Role of Non-Bonded Interactions in the Conformational Dynamics of Organophosphorous Hydrolase Adsorbed onto Functionalized Mesoporous Silica Surfaces." Journal of Physical Chemistry B 114(1):531-540.
Gomes DE, RD Lins, PG Pascutti, C Lei, and TA Soares. 2011. "Conformational Variability of Organophosphorus Hydrolase upon Soman and Paraoxon Binding ." Journal of Physical Chemistry B 115(51):15389-15398. doi:10.1021/jp208787g
Kirschner KN, RD Lins, A Maass, and TA Soares. 2012. "A Glycam-Based Force Field for Simulations of Lipopolysaccharide Membranes: Parametrization and Validation." Journal of Chemical Theory and Computation 8(11):4719-4731. doi:10.1021/ct300534j
Lower S, S Lamlertthon, N Casillas-Ituarte, RD Lins, R Yongsunthon, ES Taylor, A DiBartola, C Edmondson, LM McIntyre, LB Reller, YA Que, R Ros, B Lower, and V Fowler, Jr.. 2011. "Polymorphisms in Fibronectin Binding Protein A of Staphylococcus Aureus are Associated with Infection of Cardiovascular Devices." Proceedings of the National Academy of Sciences of the United States of America 108(45):18372–18377 . doi:10.1073/pnas.1109071108
Pontes FJ, VH Rusu, TA Soares, and RD Lins. 2012. "The Effect of Temperature, Cations, and Number of Acyl Chains on the Lamellar to Non-Lamellar Transition in Lipid-A Membranes: A Microscopic View." Journal of Chemical Theory and Computation 8(10):3830-3838. doi:10.1021/ct300084v