Polar Group Distribution and Folding Favorability
Poster Number
10B
Format
Poster Presentation
Faculty Mentor Name
Hyun Joo
Faculty Mentor Department
Chemistry
Additional Faculty Mentor Name
Jerry Tsai
Additional Faculty Mentor Department
Chemistry
Abstract/Artist Statement
The hydrophobic effect drives the folding of proteins into their native states within cells by maximizing water entropy versus that of the protein. To accomplish this level of water contact, polar residues have a higher tendency to be placed on the surface of proteins as opposed to hydrophobic ones that pack on the interior. Since the hydrophobic effect is not yet well understood, novel models aim at characterizing its dynamics. One way to elucidate the entropic force of water driving protein folding is through molecular dynamics simulations, which approximate the degrees of freedom of a folded protein interacting with itself via intramolecular forces as well as the solvation shell waters via intermolecular forces. Our focus lies in utilizing a library of protein molecular simulations in order to analyze the molecular manner by which water interacts with the protein’s hydrophobic and hydrophilic regions. Hydrogen bonding paths which link polar groups on the protein surfaces are one way to characterize the entropic favorability of water around certain types of amino acid residues. As a quantitative measure, the radial distribution function of polar nitrogen and oxygen atoms on the protein surface connected through a hydrogen bonded water network in comparison with the radial distribution of water oxygen atoms describes the propensity of interacting waters with polar groups in certain types of protein structure. For example, alpha helices have been found to be well solvated whereas beta sheets tend to have less of an interaction with surrounding waters. Together, these functions, among others, help piece together different aspects of how the hydrophobic effect drives the folding of proteins in such a way that maximizes the entropy of water overall and leads to the most stable protein conformation possible.
Location
DeRosa University Center, Ballroom
Start Date
29-4-2017 1:00 PM
End Date
29-4-2017 3:00 PM
Polar Group Distribution and Folding Favorability
DeRosa University Center, Ballroom
The hydrophobic effect drives the folding of proteins into their native states within cells by maximizing water entropy versus that of the protein. To accomplish this level of water contact, polar residues have a higher tendency to be placed on the surface of proteins as opposed to hydrophobic ones that pack on the interior. Since the hydrophobic effect is not yet well understood, novel models aim at characterizing its dynamics. One way to elucidate the entropic force of water driving protein folding is through molecular dynamics simulations, which approximate the degrees of freedom of a folded protein interacting with itself via intramolecular forces as well as the solvation shell waters via intermolecular forces. Our focus lies in utilizing a library of protein molecular simulations in order to analyze the molecular manner by which water interacts with the protein’s hydrophobic and hydrophilic regions. Hydrogen bonding paths which link polar groups on the protein surfaces are one way to characterize the entropic favorability of water around certain types of amino acid residues. As a quantitative measure, the radial distribution function of polar nitrogen and oxygen atoms on the protein surface connected through a hydrogen bonded water network in comparison with the radial distribution of water oxygen atoms describes the propensity of interacting waters with polar groups in certain types of protein structure. For example, alpha helices have been found to be well solvated whereas beta sheets tend to have less of an interaction with surrounding waters. Together, these functions, among others, help piece together different aspects of how the hydrophobic effect drives the folding of proteins in such a way that maximizes the entropy of water overall and leads to the most stable protein conformation possible.