Question

1. As we increase our understanding of how proteins fold, we can start making predictions off of the primary amino acid sequence, about how a protein will fold. Use the peptide he answer the following questions: lle-Ala-His-Thr-Tyr-Gly-Pro-Phe-Glu-Ala-Ala-Met-Cys-Lys- 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Trp-Glu-Ala-Gln-Pro-Asp-Gly-Met-Glu-Cys-Ala-Phe-His-Arg 15 16 17 18 19 20 21 22 23 24 25 26 27 28 a. In the amino acid sequence above, where would you predict that bends or B turns would occur (reference specific amino acid numbers)? Briefly explain. b. Where might intrachain disulfide cross-linkages be formed (reference specific amino acid numbers)? C. Assuming that this sequence is part of a larger globular protein, indicate the probable location (the external surface or interior of the protein) of the following amino acid residues: Asp, lle, Thr, Ala, Gin, Lys. Explain your reasoning for each individually.

Answer 1

Ans.(a) Bends or turns are most likely to occure at residue 7 and 19 because pro residue are often (but not always) found at bends in globular folded protein. A bend may also occur at the The residue Cresidue -4) and assuming that this is a portion of a large polypeptide, at the Ile residue (R-I) (b) Interchain disulphide cross-linkage Can form only between residu 13 and 24 ( cys residue)

c.) Amino acids with lonie (charged) on strongly polar neutral groups (eg. Asp, Gly, and Lys in this proteins are located on the external surface, where they interact optimally with solvent water. Residue with non- polas side chain (such as Ala and Ile) are situated in the interior, where they escape the polar environment. The is of intermediate polarity and could be found either in the interion or on the exterion surfall.