Research Interests:

Alpha Helical Scaffold Proteins in Arabidopsis thaliana

We use computer-assisted bioinformatic techniques to discover and characterize “alpha helical scaffold proteins” in the model plant Arabidopsis thaliana.  These proteins are important in cell signal transduction pathways in development, cell cycle regulation, and response to environmental stresses.

New Research Collaborations

We are very excited to have Dr. David Cummings as a new member of our faculty.  Dr. Cummings, who is a PLNU alumnus, comes to us from the U.S. Department of Energy’s Idaho National Laboratory where his interests were focused on the physiology and ecology of bacteria involved in the clean-up of environmental toxins.  During the course of his first year, Dr. Cummings has established a new program involving PLNU students looking at bacteria native to the Tijuana River Estuary and their roles in metal cycling in the sediments.  I will work with him to establish the genetic patterns of interrelatedness and evolution of these microbes by examination of the structures of their small subunit rRNA molecules.  In another project, we are examining the newly sequenced genome of the acid-loving iron-reducing bacterium Acidiphilium cryptum.  The goal is to discover and characterize genes involved in electron transport in order to identify novel mechanisms used by this organism for iron reduction and energy generation.

Student Research Projects

Summer 2005:

Students Directed by David Kerk
Thomas Bravo, Cedar Glen, CA; Richard Trager, Visalia, CA

My students use computer-assisted bioinformatic techniques to discover and characterize “alpha helical scaffold proteins” in the model plant Arabidopsis thaliana.  These proteins are important in cell signal transduction pathways in development, cell cycle regulation, and response to environmental stresses. 

This summer Richard continued work that he began last academic year as a University Honors Scholar.  Richard used computer programs to simulate in 3D the binding of candidate scaffold proteins to known peptide ligands (portions of larger interacting proteins).  Thomas used custom programs written by Richard, as well as programs from other researchers, to identify and characterize classes of scaffold proteins not previously investigated in detail.  We continued to interact closely with our collaborator, Dr. Terry Conley, at Oklahoma City University.  Dr. Conley and his students use biochemical and molecular/genetic techniques to identify the functions of scaffold genes, which we have discovered and characterized from the bioinformatic perspective, in whole plants.

Summer 2004:

Students Directed by David Kerk
Matt Alexander, San Diego, CA; Megan McGlothlin, Bakersfield, CA; Richard Trager, Visalia, CA

My students use computer-assisted bioinformatic techniques to discover and characterize “alpha helical scaffold proteins” in the model plant Arabidopsis thaliana.  These proteins are important in cell signal transduction pathways in development, cell cycle regulation, and response to environmental stresses. 

Richard used computer programs he wrote to do mass “genome scale” searches for different classes of new candidate scaffolding proteins using the entire Arabidopsis protein database.  Megan and Matt characterized the domain architecture of the candidates, focusing on multi-repeat “blocks” likely to be functionally important in ligand binding.  Matt and Richard developed a statistical tool within MS Excel that allowed us to assess the significance of candidate sequence regions.  Matt utilized molecular modeling software suites to examine the three dimensional structures of important scaffold proteins, and potential binding interactions with important ligands.  Richard is continuing that work this academic year as a University Honors Scholar.

Summer 2003:

Students Directed by David Kerk
Matt Alexander, San Diego, CA; Megan McGlothlin, Bakersfield, CA; Flor Rodriguez, Los Angeles, CA;  Richard Trager, Visalia, CA

My students use computer-assisted bioinformatic techniques to discover and characterize “alpha helical scaffold proteins” in the model plant Arabidopsis thaliana.  These proteins are important in cell signal transduction pathways in development, cell cycle regulation, and response to environmental stresses.  Flor and Megan worked on defining the architecture of protein domains in previously annotated scaffold proteins.  Richard wrote computer programs enabling us to perform a mass “genome scale” search of the entire Arabidopsis protein database for new candidate scaffolding proteins.  Matt utilized molecular modeling software suites to examine the three dimensional structures of important scaffold proteins, and potential binding interactions with important ligands.

Student Honors Project

Academic Year 2004 - 2005
 

Title

TPR HSP90 PEPTIDE IN SILICO DOCKING SIMULATIONS
Richard Trager*, Matt Alexander, Megan McGlothlin (David Kerk), Point Loma Nazarene University, Dept of Biology, 3900 Lomaland Dr, San Diego, CA 92106

Abstract

TPR proteins are molecular scaffolds, which utilize a curved surface constructed from multiple copies of a degenerate 34 amino acid (“tetratricopeptide”) motif.  A pattern of conserved hydrophobic residues stabilizes the multiple alpha helices within the interaction surface, while conserved polar and charged residues interact with substrate proteins.  A subclass of TPR proteins in animals and plants act as molecular co-chaperones, binding to Hsp70 and Hsp90.  The latter is thought to be particularly important in signal transduction pathways.  We are identifying and characterizing TPR proteins in the model plant Arabidopsis.  Based on a high degree of sequence similarity to animal Hsp90 binding proteins, certain Arabidopsis proteins would be expected to share this property.  A solved co-crystal structure is available of a TPR domain from the human protein “Hop” bound to a C-terminal Hsp90 peptide.  We have constructed a homology model of an Arabidopsis homologue of Hop, and used simulated protein-peptide docking to examine predictions of its interactions with the Hsp90 peptide.  Procedures developed to produce and evaluate this docking will be used with a larger group of putative Arabidopsis Hsp90 binding proteins.  The predictions of this bioinformatic analysis will then provide the research community with a set of specific hypotheses for experimental testing.

External Grants

• NSF ROA: "Functional Annotation of Protein Phosphatases in Arabidopsis  thaliana"(Award number DBI-9975808/PTLOMA):  $15,700, Summer 2000
• NSF ROA: "Characterization of Protein Kinases in Arabidopsis thaliana Genomic Sequence" (Award number DBI-9975808/PTLOMA): $21,900, Summer 2001
• NSF ROA: "Bioinformatic Characterization of Protein Phosphatases in Arabidopsis thaliana and Other Plants" (Award number DBI-9975808/PTLOMA): $23,462, Summer  2002
• NSF Arabidopsis 2010: RUI: "Functional Genomics of Alpha-Helical Scaffold Proteins in Arabidopsis thaliana” Award No. MCB-0209686: $625,000, 2002
• NSF Grant No.MCB-0209686, Amendment No.001, Proposal No.MCB-0330810: $5,000, Summer 2003
• NSF Grant No.MCB-0209686, Amendment No.003, Proposal No.MCB-0401736: $7,100, Dec 2003