Title

A Knob-Socket Model of Amino Acid Sequence Changes on Alpha Helical Stability and Structure

Poster Number

20B

Lead Author Major

Biochemistry, Spanish

Lead Author Status

Senior

Format

Poster Presentation

Faculty Mentor Name

Jerry Tsai

Faculty Mentor Email

jtsai@pacific.edu

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

Abstract/Artist Statement

The Knob-Socket Model is a protein-packing model that explains how amino acid residues pack with each other. For alpha helices, the KS model describes how individual amino acids can contribute to a protein’s alpha-helicity and stability. The model is based on a construct consisting of a 3 amino acid residue socket on one alpha-helix that can be packed with a 1 amino acid residue knob from another alpha-helix. Sockets that are packed with a knob are considered to be “filled” and favor inter-helical interactions. Sockets that are not packed with a knob are considered “free”, meaning they favor intra-helical interactions. Lastly, certain combinations of amino acids are “non”, meaning an alpha-helical structure is not favored. The KS model can then be used in conjunction with a socket propensity library in de novo protein design. A novel alpha-helical protein KSa1.1 was built using this KS approach to be a parallel homodimer. Site-directed mutagenesis was performed in order to study the effects of single and double mutations on alpha-helicity and stability. A single mutation can affect the six sockets surrounding the amino acid residue, which forms a Rabara hexagon. The change in total socket propensity can be used to predict an increase or decrease in alpha-helicity and therefore stability in comparison to the wild-type protein. From previous studies, these predictions were shown to be consistent with experimental data from Circular Dichroism and denaturation studies. In addition, double mutations consisting of non-overlapping Rabara hexagons were computationally and experimentally determined to be additive in terms of alpha-helicity. For double mutations exhibiting overlapping Rabara hexagons, there are two sockets that overlap between the two Rabara hexagons, while the rest of the sockets maintain the same propensities as seen in their single mutations. These changes in propensities of the two sockets can affect the total socket propensities of the two hexagons. This study seeks to explain how double mutations resulting in overlapping Rabara hexagons affect KSa1.1 alpha-helicity and stability. To determine if the computational data is consistent with the experimental data, as is seen with single mutations and double mutations displaying non-overlapping Rabara hexagons, Rabara hexagon propensities will be correlated with measurements of secondary structure and stability.

Location

DeRosa University Center Ballroom

Start Date

27-4-2018 10:00 AM

End Date

27-4-2018 12:00 PM

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Apr 27th, 10:00 AM Apr 27th, 12:00 PM

A Knob-Socket Model of Amino Acid Sequence Changes on Alpha Helical Stability and Structure

DeRosa University Center Ballroom

The Knob-Socket Model is a protein-packing model that explains how amino acid residues pack with each other. For alpha helices, the KS model describes how individual amino acids can contribute to a protein’s alpha-helicity and stability. The model is based on a construct consisting of a 3 amino acid residue socket on one alpha-helix that can be packed with a 1 amino acid residue knob from another alpha-helix. Sockets that are packed with a knob are considered to be “filled” and favor inter-helical interactions. Sockets that are not packed with a knob are considered “free”, meaning they favor intra-helical interactions. Lastly, certain combinations of amino acids are “non”, meaning an alpha-helical structure is not favored. The KS model can then be used in conjunction with a socket propensity library in de novo protein design. A novel alpha-helical protein KSa1.1 was built using this KS approach to be a parallel homodimer. Site-directed mutagenesis was performed in order to study the effects of single and double mutations on alpha-helicity and stability. A single mutation can affect the six sockets surrounding the amino acid residue, which forms a Rabara hexagon. The change in total socket propensity can be used to predict an increase or decrease in alpha-helicity and therefore stability in comparison to the wild-type protein. From previous studies, these predictions were shown to be consistent with experimental data from Circular Dichroism and denaturation studies. In addition, double mutations consisting of non-overlapping Rabara hexagons were computationally and experimentally determined to be additive in terms of alpha-helicity. For double mutations exhibiting overlapping Rabara hexagons, there are two sockets that overlap between the two Rabara hexagons, while the rest of the sockets maintain the same propensities as seen in their single mutations. These changes in propensities of the two sockets can affect the total socket propensities of the two hexagons. This study seeks to explain how double mutations resulting in overlapping Rabara hexagons affect KSa1.1 alpha-helicity and stability. To determine if the computational data is consistent with the experimental data, as is seen with single mutations and double mutations displaying non-overlapping Rabara hexagons, Rabara hexagon propensities will be correlated with measurements of secondary structure and stability.