Title

Polar Group Distribution and Folding Favorability

Poster Number

10B

Lead Author Major

Biochemistry

Lead Author Status

Senior

Second Author Major

Biology

Second Author Status

Junior

Format

Poster Presentation

Faculty Mentor Name

Hyun Joo

Faculty Mentor Email

hjoo@pacific.edu

Faculty Mentor Department

Chemistry

Additional Faculty Mentor Name

Jerry Tsai

Additional Faculty Mentor Email

jtsai@pacific.edu

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

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Apr 29th, 1:00 PM Apr 29th, 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.