Title

A Knob-Socket Analysis of a Protein Folding Pathway

Poster Number

29

Lead Author Major

Biochemistry

Format

Poster Presentation

Faculty Mentor Name

Jerry Tsai

Faculty Mentor Department

Chemistry

Additional Faculty Mentor Name

Hyun Joo

Abstract/Artist Statement

The protein-folding problem remains a challenge in the field of molecular biology. Here, we utilize a protein tertiary structure motif, the knob-socket, to study protein folding. The knobsocket motif is a collection of four amino acids arranged in a tetrahedron. Three amino acids in the tetrahedron, local in sequence, form the socket while a residue non-local in sequence participates as the knob. Previous studies have shown that the knob-socket motif presents a unique and informative way to understand the packing of amino acids in proteins. The utility of the knob-socket model is the ability to project protein tertiary structure onto two-dimensional lattices of repeating sockets, leading to clear and intuitive representations of packing in proteins. In this project, we focus on the mapping of protein structures onto two-dimensional lattices in conjunction with phi-value analysis, an experimental technique used to probe the transition state of proteins, to recognize the necessary interactions for protein-folding. We present Knob-Socket Topology Maps for wildtype and mutant barnase. Observations from these maps and their associated phi-values, it was noted that a few structures were retained in all proteins and had fairly high phi values. The residue F7 packs into the beta-sheet around the region K98, T99, and T100. Also, the turn involving S91-L95 and R69 was in every single variant of the barnase proteins. This is a strong indication that the packing of these residues are crucial to the folding mechanics. These lessons help advance our studies of the protein folding pathway and provide significant implications towards the importance of the knob-socket motif in protein structure.

Location

DeRosa University Center, Ballroom

Start Date

25-4-2015 10:00 AM

End Date

25-4-2015 12:00 PM

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Apr 25th, 10:00 AM Apr 25th, 12:00 PM

A Knob-Socket Analysis of a Protein Folding Pathway

DeRosa University Center, Ballroom

The protein-folding problem remains a challenge in the field of molecular biology. Here, we utilize a protein tertiary structure motif, the knob-socket, to study protein folding. The knobsocket motif is a collection of four amino acids arranged in a tetrahedron. Three amino acids in the tetrahedron, local in sequence, form the socket while a residue non-local in sequence participates as the knob. Previous studies have shown that the knob-socket motif presents a unique and informative way to understand the packing of amino acids in proteins. The utility of the knob-socket model is the ability to project protein tertiary structure onto two-dimensional lattices of repeating sockets, leading to clear and intuitive representations of packing in proteins. In this project, we focus on the mapping of protein structures onto two-dimensional lattices in conjunction with phi-value analysis, an experimental technique used to probe the transition state of proteins, to recognize the necessary interactions for protein-folding. We present Knob-Socket Topology Maps for wildtype and mutant barnase. Observations from these maps and their associated phi-values, it was noted that a few structures were retained in all proteins and had fairly high phi values. The residue F7 packs into the beta-sheet around the region K98, T99, and T100. Also, the turn involving S91-L95 and R69 was in every single variant of the barnase proteins. This is a strong indication that the packing of these residues are crucial to the folding mechanics. These lessons help advance our studies of the protein folding pathway and provide significant implications towards the importance of the knob-socket motif in protein structure.