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Protein Folds

  1. Jan 3, 2010 #1
    Hi everyone

    What do textbooks mean when they say this is a "four fold" protein? The term fold gets used a lot in txtbooks but iit's not formally defined. Can someone help me? Is the term only applied to proteins?

  2. jcsd
  3. Jan 4, 2010 #2
    Can you give a little context as to how the term is being used?

    Quoted from http://en.wikipedia.org/wiki/Genetic_code#Degeneracy_of_the_genetic_code :
    A position of a codon is said to be a fourfold degenerate site if any nucleotide at this position specifies the same amino acid. For example, the third position of the glycine codons (GGA, GGG, GGC, GGU) is a fourfold degenerate site, because all nucleotide substitutions at this site are synonymous; i.e., they do not change the amino acid. Only the third positions of some codons may be fourfold degenerate. A position of a codon is said to be a twofold degenerate site if only two of four possible nucleotides at this position specify the same amino acid. For example, the third position of the glutamic acid codons (GAA, GAG) is a twofold degenerate site. In twofold degenerate sites, the equivalent nucleotides are always either two purines (A/G) or two pyrimidines (C/U), so only transversional substitutions (purine to pyrimidine or pyrimidine to purine) in twofold degenerate sites are nonsynonymous. A position of a codon is said to be a non-degenerate site if any mutation at this position results in amino acid substitution. There is only one threefold degenerate site where changing three of the four nucleotides may have no effect on the amino acid (depending on what it is changed to), while changing the fourth possible nucleotide always results in an amino acid substitution. This is the third position of an isoleucine codon: AUU, AUC, or AUA all encode isoleucine, but AUG encodes methionine. In computation this position is often treated as a twofold degenerate site.

    Or maybe you're talking about primary/secondary/tertiary/quaternary structures?

    Or if you're in some crystallography class, could be talking about determining the correct crystallographic groups (unit cell) http://en.wikipedia.org/wiki/Crystal_system
  4. Jan 8, 2010 #3
    the passage in my book is similar to

    "Despite the need for continued technological advancements in the proteomic field, the technology is developed enough to identify changes in protein abundance between samples. ACADS, a protein encoded by a gene in both the HDL QTL Hdlq1 and the gallstone QTL Lith17 on Chr 5, showed significantly increased protein abundance in SM adult female liver relative to the NZB strain (a 2.6- and a 1.6-fold change from MS and Western analysis, respectively), but no difference in mRNA expression (Table 2). The difference in protein abundance was confirmed by Western blot analysis. Similar results were obtained for FH1, HSD11B1, and NDUFA9 (Table 3, Figures 2 and 3). Finally, our MS data indicate a 4-fold protein increase of APOA2 in NZB relative to SM protein abundance with no mRNA expression difference. A difference in the quantity of APOA2 protein but not in mRNA was reported previously between two different strains (DOOLITTLE et al. 1990). We have previously shown that the gene Apoa2 is responsible for the HDL QTL Hdlq5 (WANG et al. 2004) in mice and associated with HDL levels in human studies (LILJA et al. 2002). " from

    I don't understand what they're referring to with the 4-fold or 2-folds. Thank you so much
  5. Jan 8, 2010 #4
  6. Jan 8, 2010 #5


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    In this context, a 4-fold protein increase means that the levels of protein went up by a factor of 4. It has nothing to do with protein structure.
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