20.109:W/F Green Team

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Oral Presentation Outline


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.

Possible Presentation 1


  • Drug Pumps, Opiate Addiction, and Parkinsons Disease
  • Fallacy of Silent Mutations
  • Codon Biases
  • Quote on relevance


  • To Test if Translation Kinetics is responsible for protein mis-folding.


  • Simulate Translation Conditions via Manipulating Codon Bias (in vivo quote)

What do we need to put in eppendorf?

  • X Ray Crystallography


  • Reasons for misfolding

How can we build on these results?

  • Drug Delivery
  • Improved Computation Protein Structure Based on shiz
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)


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


Silent SNP leads to parkinsons disease?

Gerra G, Leonardi C, Cortese E, D'Amore A, Lucchini A, Strepparola G, Serio G, Farina G, Magnelli F, Zaimovic A, Mancini A, Turci M, Manfredini M, Donnini C. 2007. Human Kappa Opioid Receptor Gene (OPRK1) Polymorphism Is Associated With Opiate Addiction. Am J Med Genet Part B.


Although KOR silent polymorphisms may apparently have no consequences on mRNA transcription, post-transcriptional mechanisms, such as mRNA stability, translation efficiency, and regulability may impair the function of kappa receptors system, with increased risk for substance use disorders. In specific, the neurobiological changes induced by mu-kappa opioid imbalance could underlie vulnerable personality traits and risk behavior.