20.109:W/F Green Team

Oral Presentation Outline

Summary

Single nucleotide polymorphisms which are traditionally considered silent (coding for same amino acid) can effect protein folding. We have always been taught to believe that these silent mutations are just that, silent. The fact that they can change protein structure and subsequent function could lead to a much more thorough analysis of DNA mutations and could give us new insight as to how things are mutated.

We want to design a peptide which has several points for silent mutations which are known to create structural differences in proteins. We then want to test the effects of mutating this peptide is humans, yeast and E.coli. Here are the codon biases for these organisms.

SOURCES

Info	Link	Notes
Pearson H. Silent Mutations Speak Up. Nature.	Paper	Overview of Silent SNPs
Richards AJ et al. Missense and silent mutations in COL2A1 result in Stickler syndrome but via different molecular mechanisms. Human Mutation.2007 Apr 16;28(6):639	Paper
A "Silent" Polymorphism in the MDR1 Gene Changes Substrate Specificity Chava Kimchi-Sarfaty, Jung Mi Oh, In-Wha Kim, Zuben E. Sauna, Anna Maria Calcagno, Suresh V. Ambudkar, and Michael M. Gottesman (26 January 2007)	Paper	hypothesize that the presence of a rare codon, marked by the synonymous polymorphism, affects the timing of cotranslational folding and insertion of P-gp into the membrane, thereby altering the structure of substrate and inhibitor interaction sites.
Porcine DJ-1: cloning of PARK7 cDNA, sequence comparison, expression analysis and chromosomal localization K. Larsen, L.B. Madsen, A. Høj, C. Bendixen	Paper	Silent SNP leads to parkinsons disease?