Title

Knob-Socket Model: A novel method of predicting protein stability

Poster Number

04B

Lead Author Major

Biological Sciences

Lead Author Status

Senior

Second Author Major

Biochemistry

Second Author Status

Senior

Third Author Major

Biochemistry

Third Author Status

Junior

Fourth Author Major

Bioengineering

Fourth Author Status

Junior

Fifth Author Major

Biochemistry

Fifth Author Status

Junior

Format

Poster Presentation

Faculty Mentor Name

Jerry Tsai

Faculty Mentor Email

jtsai@pacific.edu

Faculty Mentor Department

Chemistry

Additional Faculty Mentor Name

Hyun Joo

Additional Faculty Mentor Email

hjoo@pacific.edu

Additional Faculty Mentor Department

Chemistry

Graduate Student Mentor Name

Taylor Rabara

Graduate Student Mentor Email

taylor.rabara@gmail.com

Graduate Student Mentor Department

Chemistry

Additional Mentors

Melina Huey, m_huey@u.pacific.edu, Chemistry department

Abstract/Artist Statement

The Tsai laboratory developed a novel description of protein tertiary packing called the Knob-Socket Model. This model describes protein packing at the tertiary and quaternary levels of protein structure as involving a four-residue tetrahedral motif. The motif consists of a three-amino acid socket from one piece of a secondary structure that can be packed by a single amino acid knob from another piece of a secondary structure. A protein a-helix, named KSα1.1, was designed to validate the Knob-Socket Model, using the packing code derived by the Protein Data Bank. To computationally predict the packing of peptide chains, propensity libraries were used based on the amino acid composition of the knob-socket motif from these known secondary structures. So, the amino acid composition of sockets favors or disfavors a-helical formation. These a-helical propensity libraries were used to design KSα1.1, and also predict the effect of point mutations on the KSα1.1 structure. So, the KSα1.1 mutants were classified as having a potentially higher or lower a-helical character in comparison to the wild-type protein. Corresponding point mutant variants of the KSα1.1 protein were created through site-directed mutagenesis. Using circular dichroism (CD) analysis, the a-helicity of the mutant proteins were characterized. The a-helical character of the mutated proteins in comparison to the wild type KSα1.1 were then compared to the original prediction made from the propensity library. Using raw data collected from the CD graphs, deconvolution studies were conducted through different protein analysis programs in order to quantify and calculate the KSα1.1 a-helical content of each mutant. Additionally, an increase of the a-helical character of a protein indicates a more stable structure in comparison to the wild type protein. To further determine structural stability, proteins were placed through both chemical and thermal denaturation studies. The future aims of this project include creating, analyzing, and characterizing proteins with double mutations.

Location

DeRosa University Center, Ballroom

Start Date

28-4-2018 1:00 PM

End Date

28-4-2018 3:00 PM

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Apr 28th, 1:00 PM Apr 28th, 3:00 PM

Knob-Socket Model: A novel method of predicting protein stability

DeRosa University Center, Ballroom

The Tsai laboratory developed a novel description of protein tertiary packing called the Knob-Socket Model. This model describes protein packing at the tertiary and quaternary levels of protein structure as involving a four-residue tetrahedral motif. The motif consists of a three-amino acid socket from one piece of a secondary structure that can be packed by a single amino acid knob from another piece of a secondary structure. A protein a-helix, named KSα1.1, was designed to validate the Knob-Socket Model, using the packing code derived by the Protein Data Bank. To computationally predict the packing of peptide chains, propensity libraries were used based on the amino acid composition of the knob-socket motif from these known secondary structures. So, the amino acid composition of sockets favors or disfavors a-helical formation. These a-helical propensity libraries were used to design KSα1.1, and also predict the effect of point mutations on the KSα1.1 structure. So, the KSα1.1 mutants were classified as having a potentially higher or lower a-helical character in comparison to the wild-type protein. Corresponding point mutant variants of the KSα1.1 protein were created through site-directed mutagenesis. Using circular dichroism (CD) analysis, the a-helicity of the mutant proteins were characterized. The a-helical character of the mutated proteins in comparison to the wild type KSα1.1 were then compared to the original prediction made from the propensity library. Using raw data collected from the CD graphs, deconvolution studies were conducted through different protein analysis programs in order to quantify and calculate the KSα1.1 a-helical content of each mutant. Additionally, an increase of the a-helical character of a protein indicates a more stable structure in comparison to the wild type protein. To further determine structural stability, proteins were placed through both chemical and thermal denaturation studies. The future aims of this project include creating, analyzing, and characterizing proteins with double mutations.