Investigating Bias in Protein Properties Inferred via Ancestral Sequence Reconstruction

Simple item page
dc.contributor.authorRickett, Abraham "Bram" James
dc.date.accessioned2017-10-12T14:37:01Z
dc.date.available2017-10-12T14:37:01Z
dc.date.issued2017
dc.description49 pages. A thesis presented to the Department of Chemistry & Biochemistry and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2017
dc.description.abstractAncestral Sequence Reconstruction (ASR) is a powerful technique used by researchers to study ancient proteins and their evolution. It is, however, an approximation based on incomplete information and simplifying assumptions about the evolutionary process. It is therefore important to understand and control sources of error in ASR studies. One possible source of error is electrostatics. We formulate and analyze the electrostatics of 14 distinct protein families, each containing PDB structures of reconstructed ancestral proteins and their modern descendants We observe electrostatic abnormalities in some ancestral families, however these abnormalities are not statistically significant in the context of the entire sample. Simulated evolution analyses suggest that reconstruction can generate sequences with less extreme electrostatic character compared to the known original sequence. High charge optimality is not easily recoverable through posterior probability sampling. Existence of electrostatic bias is ultimately not disproven, and should be explored further with larger samples and more rigorous analytical methods.en_US
dc.identifier.urihttps://hdl.handle.net/1794/22884
dc.language.isoen_US
dc.publisherUniversity of Oregon
dc.rightsCreative Commons BY-NC-ND 4.0-US
dc.subjectProteinen_US
dc.subjectElectrostaticsen_US
dc.subjectReconstructionen_US
dc.subjectAncestralen_US
dc.subjectEvolutionen_US
dc.subjectBiasen_US
dc.titleInvestigating Bias in Protein Properties Inferred via Ancestral Sequence Reconstruction
dc.typeThesis/Dissertation

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Final_Thesis_Rickett.pdf
Size:
508.27 KB
Format:
Adobe Portable Document Format
Download

Collections

Clark Honors College Theses