Abstract

The main goal of this project is to investigate the evolutionary constraints that govern the natural selection of partially collapsed, flexible proteins and protein domains. To accomplish this goal we have selected a model system based on a conserved flexible linker from the 70kDa subunit of replication protein A (RPA70). We will use this model system to determine if and how natural selection works to preserve the structure and function of partially collapsed, flexible proteins and protein domains through the following specific aims: 1) Characterize the structure, dynamics, and function of the linkers from several RPA70 homologues and determine the functional consequences of linker swapping; 2) Investigate the allowable sequence space of the RPA70 flexible linkers by experimental evolution and by conducting a broad survey of eukaryotic linker sequences; 3) Use the results of specific aims 1 and 2 to formulate rules that permit the identification and alignment of flexible sequences as well as the de novo design of sequences that function as linkers. While the presence and importance of partially collapsed, flexible proteins and protein domains in nature as well established, this proposal marks the first systematic empirical investigation into their evolutionary constraints and patterns.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Exploratory Grants (P20)
Project #
1P20RR016448-01
Application #
6574013
Study Section
Special Emphasis Panel (ZRR1)
Project Start
2002-02-23
Project End
2007-01-31
Budget Start
Budget End
Support Year
1
Fiscal Year
2002
Total Cost
Indirect Cost

  Institution

Name
University of Idaho
Department
Type
DUNS #
City
Moscow
State
ID
Country
United States
Zip Code
83844

  Publications

Ruffley, Megan; Smith, Megan L; Espíndola, Anahí et al. (2018) Combining allele frequency and tree-based approaches improves phylogeographic inference from natural history collections. Mol Ecol 27:1012-1024
Chernikova, Diana A; Madan, Juliette C; Housman, Molly L et al. (2018) The premature infant gut microbiome during the first 6 weeks of life differs based on gestational maturity at birth. Pediatr Res 84:71-79
Smith, Stephanie A; Benardini 3rd, James N; Anderl, David et al. (2017) Identification and Characterization of Early Mission Phase Microorganisms Residing on the Mars Science Laboratory and Assessment of Their Potential to Survive Mars-like Conditions. Astrobiology 17:253-265
Marx, Hannah E; Dentant, Cédric; Renaud, Julien et al. (2017) Riders in the sky (islands): using a mega-phylogenetic approach to understand plant species distribution and coexistence at the altitudinal limits of angiosperm plant life. J Biogeogr 44:2618-2630
Yano, Hirokazu; Wegrzyn, Katarznya; Loftie-Eaton, Wesley et al. (2016) Evolved plasmid-host interactions reduce plasmid interference cost. Mol Microbiol 101:743-56
Sarver, Brice A J; Demboski, John R; Good, Jeffrey M et al. (2016) Comparative Phylogenomic Assessment of Mitochondrial Introgression among Several Species of Chipmunks (TAMIAS). Genome Biol Evol :
Stockmann, Chris; Ampofo, Krow; Pavia, Andrew T et al. (2016) Clinical and Epidemiological Evidence of the Red Queen Hypothesis in Pneumococcal Serotype Dynamics. Clin Infect Dis 63:619-626
Loftie-Eaton, Wesley; Yano, Hirokazu; Burleigh, Stephen et al. (2016) Evolutionary Paths That Expand Plasmid Host-Range: Implications for Spread of Antibiotic Resistance. Mol Biol Evol 33:885-97
Uribe-Convers, Simon; Settles, Matthew L; Tank, David C (2016) A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae). PLoS One 11:e0148203
Chernikova, Diana A; Koestler, Devin C; Hoen, Anne Gatewood et al. (2016) Fetal exposures and perinatal influences on the stool microbiota of premature infants. J Matern Fetal Neonatal Med 29:99-105

Showing the most recent 10 out of 196 publications