The contribution of electrostatic interactions to the collapse of oligoglycine in water

Protein solubility and conformational stability are a result of a balance of interactions both within a protein and between protein and solvent. The electrostatic solvation free energy of oligoglycines, models for the peptide backbone, becomes more favorable with an increasing length, yet longer peptides collapse due to the formation of favorable intrapeptide interactions between CO dipoles, in some cases without hydrogen bonds. The strongly repulsive solvent cavity formation is balanced by van der Waals attractions and electrostatic contributions. In order to investigate the competition between solvent exclusion and charge interactions we simulate the collapse of a long oligoglycine comprised of 15 residues while scaling the charges on the peptide from zero to fully charged. We examine the effect this has on the conformational properties of the peptide. We also describe the approximate thermodynamic changes that occur during the scaling both in terms of intrapeptide potentials and peptide-water potentials, and estimate the electrostatic solvation free energy of the system.Comment: 10 pages, 7 figure

Dynamic simulations of water at constant chemical potential

The grand molecular dynamics (GMD) method has been extended and applied to examine the density dependence of the chemical potential of a three-site water model. The method couples a classical system to a chemical potential reservoir of particles via an ansatz Lagrangian. Equilibrium properties such as structure and thermodynamics, as well as dynamic properties such as time correlations and diffusion constants, in open systems at a constant chemical potential, are preserved with this method. The average number of molecules converges in a reasonable amount of computational effort and provides a way to estimate the chemical potential of a given model force field

Osmolyte solutions and protein folding

In this brief review we discuss the evolution of recent thought regarding the role and mechanism of osmolytes with respect to protein stability. Osmolytes are naturally occurring intracellular compounds that change the protein folding landscape. Contributions from experiments are considered in the context of current theory and simulation results

Archaeosperma arnoldii-A Cupulate Seed from the Upper Devonian of North America

139-154http://deepblue.lib.umich.edu/bitstream/2027.42/48427/2/ID275.pd