Exploring the Homeodomain Sequence Space by Comparison of Natural Homologues to Consensus

Faculty Mentor

Mark V. C. dela Cerna

Location

Savannah Ballroom

Type of Research

On-going

Session Format

Poster Presentation

College

College of Science & Mathematics

Department

Biochemistry, Chemistry, and Physics

Abstract

Understanding the molecular determinants of a protein’s function is essential in the development of de novo sequences, as well as the optimization of the naturally occurring ones. Coupled with this necessity, enhancing the stability of a protein allows for the easy adaptability of these peptides as environmental catalysts or purifying agents for contamination capture. For this purpose, the Homeodomain (HD) family was selected to study the effects of sequence mutations to a protein’s function, stability, activity, and dynamics. Previous studies have shown the non-additivity behavior of a natural Homeodomain (HD) protein by the introduction of single-point mutations towards consensus based upon charge, residue burial, and family sequence conservation [1]. Abovementioned results have also indicated the substantial role of weakly conserved positions to protein stability, as well as the necessity of the background sequence to stabilize the introduced mutations. To study the effects. In addition, Singular Value Decomposition (SVD) analysis of the HD family surfaces the evolutionary segregation of the family into five different subtypes [2]. Under the derived eigenvector field from SVD analysis, the proximity of the sub-family and their respective homologues towards consensus (CHD) can be derived. Representatives from each of the clusters were selected, and their structure, dynamics, stability, and binding affinity towards a consensus DNA sequence were studied to analyze the differences in structure, dynamics, activity, and function across the family.  Molecular simulations were run in tandem to assess the predictive potential in silico of these types of studies.

Program Description

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Start Date

4-21-2026 1:30 PM

End Date

4-21-2026 3:30 PM

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Apr 21st, 1:30 PM Apr 21st, 3:30 PM

Exploring the Homeodomain Sequence Space by Comparison of Natural Homologues to Consensus

Savannah Ballroom

Understanding the molecular determinants of a protein’s function is essential in the development of de novo sequences, as well as the optimization of the naturally occurring ones. Coupled with this necessity, enhancing the stability of a protein allows for the easy adaptability of these peptides as environmental catalysts or purifying agents for contamination capture. For this purpose, the Homeodomain (HD) family was selected to study the effects of sequence mutations to a protein’s function, stability, activity, and dynamics. Previous studies have shown the non-additivity behavior of a natural Homeodomain (HD) protein by the introduction of single-point mutations towards consensus based upon charge, residue burial, and family sequence conservation [1]. Abovementioned results have also indicated the substantial role of weakly conserved positions to protein stability, as well as the necessity of the background sequence to stabilize the introduced mutations. To study the effects. In addition, Singular Value Decomposition (SVD) analysis of the HD family surfaces the evolutionary segregation of the family into five different subtypes [2]. Under the derived eigenvector field from SVD analysis, the proximity of the sub-family and their respective homologues towards consensus (CHD) can be derived. Representatives from each of the clusters were selected, and their structure, dynamics, stability, and binding affinity towards a consensus DNA sequence were studied to analyze the differences in structure, dynamics, activity, and function across the family.  Molecular simulations were run in tandem to assess the predictive potential in silico of these types of studies.