Interfaces and Interactions: Non-ideal Behavior of Biological Molecules
EMSL Project ID
20898
Abstract
The focus of this project is to achieve an understanding the non-ideal solution behavior of biomolecules at interfaces via multiscale simulation and modeling coupled with experiment. In both device applications as well as in biology, biomacromolecules find themselves in highly nonideal conditions. They function in environments that are not isotropic nor dilute and frequently in the presence of many other species or fields.[1,2] The stability and functionality of biomolecular systems are often dictated by complex environments. Understanding the influence of the liquid and/or solid environment on biological molecules will yield design principles from geobiology to biotechnology to medicinal chemistry. The study of interfaces is a central part of the EMSL mission.Project Details
Project type
Capability Research
Start Date
2006-10-01
End Date
2009-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Chen C, BW Beck, K Krause, TE Weksberg, and BM Pettitt. 2006. "Effects of Dimerization of Serratia marcescens Endonuclease on Water Dynamics." Biopolymers 85(3):241-252.
Chen C ,Pettitt B M 2016. "DNA Shape versus Sequence Variations in the Protein Binding Process" Biophysical Journal 110(3):534–544. 10.1016/j.bpj.2015.11.3527
Dyer K M,Pettitt B M 2013. "Proximal Distributions from Angular Correlations: A Measure of the Onset of Coarse-graining" Journal of Chemical Physics 139():214111. 10.1063/1.4832895
Feng J, K Wong, GC Lynch, X Gao, and B Pettitt. 2007. "Peptide Conformations for a Microarray Surface-Tethered Epitope of the Tumor Suppressor p53." Journal of Physical Chemistry B 111(49):13797-13806. doi:10.1021/jp075051y
Hironori Kokubo and B. Montgomery Pettitt. Preferential solvation in urea solutions at different concentrations: properties from simulation studies. J Phys Chem B, 111:5233-5242, 2007
Hu CY, GC Lynch, H Kokubo, and BM Pettitt. 2010. "Trimethylamine ?-oxide Influence on the Backbone of Proteins: An Oligoglycine Model." Proteins. Structure, Function, and Bioinformatics 78(3):695-704. doi:10.1002/prot.22598
Hu CY, H Kokubo, GC Lynch, DW Bolen, and BM Pettitt. 2010. "Backbone Additivity in the Transfer Model of Protein Salvation." Protein Science 19(5):1011-1022. doi:10.1002/pro.378
Kokubo H, CY Hu, and BM Pettitt. 2011. "Peptide Conformational Preferences in Osmolyte Solutions: Transfer Free Energies of Decaalanine." Journal of the American Chemical Society 133(6):1849 - 1858. doi:10.1021/ja1078128
Kokubo H, J Rosgen, D Bolen, and BM Pettitt. 2007. "Molecular Basis of the Apparent Near Ideality of Urea Solutions." Biophysical Journal 93(10):3392-3407. doi:10.1529/biophysj.107.114181
Kokubo H, RC Harris, D Asthagiri, and BM Pettitt. 2013. "Solvation Free Energies of Alanine Peptides: The Effect of Flexibility." Journal of Physical Chemistry B 117(51):16428-16435. doi:10.1021/jp409693p
N. Choudhury and B. M. Pettitt. On the mechanism of hydrophobic association of nanoscopic solutes. J. Am. Chem. Soc., 127:3556-3567, 2005
Perkyns JS, GC Lynch, JJ Howard, and BM Pettitt. 2010. "Protein Solvation from Theory and Simulation: Exact Treatment of Coulomb Interactions in Three-Dimensional Theories." Journal of Chemical Physics 132(6):064106. doi:10.1063/1.3299277
Randall GL, EL Zechiedrich, and BM Pettitt. 2009. "In the Absence of Writhe, DNA Relieves Torsional Stress with Localized, Sequence-Dependent Structural Failure to Preserve B-form." Nucleic Acids Research 37(16):5568-5577. doi:doi:10.1093/nar/gkp556
Tiffany E. Weksberg, Gillian C. Lynch, Kurt L. Krause, and B. Montgomery Pettitt. Molecular dynamics simulations of trichomonas vaginalis ferredoxin show a loop-cap transition. Biophys J, 92:3337-3345, 2007