Title

Investigating Rigidity Properties of Protein Cavities

Presenter Information

Christian Walling

Document Type

Oral Presentation

Location

SURC Ballroom C/D

Start Date

15-5-2014

End Date

15-5-2014

Keywords

Proteins, Cavities, Rigidity

Abstract

Proteins are three dimensional molecules that bend and flex to perform a multitude of functions, ranging from cellular repair, to mediating the immune response, to aiding in neuronal signal propagation. Drugs are designed to regulate protein functions and their interactions, which they do by closely associating with cavities or other structurally important features on a protein's surface. Because scientists have not analyzed the properties of protein cavities in a large enough dataset, it is still unclear how, or to what extent, the geometric properties of a protein cavity play in helping to facilitate a protein's function and interaction with other proteins. The ability to analyze the rigidity properties of cavities among a large database of proteins would allow a deeper understanding of how proteins interact with other molecules. As a first step, we want to try and determine if different molecules have distinct cavity properties that distinguish them from other proteins. We have developed a series of custom shell scripts that rely on protein structure data from the Protein Data Bank (PDB) and protein cavity data from our collaborators. To analyze the rigidity properties of our proteins, we use KINARI-Web, a freely-available on-line tool. Our scripts aggregate the cavity and rigidity data of a protein to provide rigidity information about the cavities. This permits us to look at the size, atomic content, and rigidity of many different protein cavities on a large scale to begin understanding their differences, and the properties of their flexibility.

Poster Number

9

Faculty Mentor(s)

Jagodzinski, Filip

Additional Mentoring Department

Computer Science

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May 15th, 8:30 AM May 15th, 11:00 AM

Investigating Rigidity Properties of Protein Cavities

SURC Ballroom C/D

Proteins are three dimensional molecules that bend and flex to perform a multitude of functions, ranging from cellular repair, to mediating the immune response, to aiding in neuronal signal propagation. Drugs are designed to regulate protein functions and their interactions, which they do by closely associating with cavities or other structurally important features on a protein's surface. Because scientists have not analyzed the properties of protein cavities in a large enough dataset, it is still unclear how, or to what extent, the geometric properties of a protein cavity play in helping to facilitate a protein's function and interaction with other proteins. The ability to analyze the rigidity properties of cavities among a large database of proteins would allow a deeper understanding of how proteins interact with other molecules. As a first step, we want to try and determine if different molecules have distinct cavity properties that distinguish them from other proteins. We have developed a series of custom shell scripts that rely on protein structure data from the Protein Data Bank (PDB) and protein cavity data from our collaborators. To analyze the rigidity properties of our proteins, we use KINARI-Web, a freely-available on-line tool. Our scripts aggregate the cavity and rigidity data of a protein to provide rigidity information about the cavities. This permits us to look at the size, atomic content, and rigidity of many different protein cavities on a large scale to begin understanding their differences, and the properties of their flexibility.