Investigating Rigidity Properties of Protein Cavities
Document Type
Oral Presentation
Campus where you would like to present
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.
Recommended Citation
Walling, Christian, "Investigating Rigidity Properties of Protein Cavities" (2014). Symposium Of University Research and Creative Expression (SOURCE). 55.
https://digitalcommons.cwu.edu/source/2014/posters/55
Poster Number
9
Additional Mentoring Department
Computer Science
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.
Faculty Mentor(s)
Jagodzinski, Filip