Download Biological Chemistry II: Problem Set 1

Biological Chemistry II: Problem Set 1
1.
(a) Tropomyosin, a 70 kDa muscle protein, is a double-stranded, α helical coiled coil.
How long is the molecule?
(b) A 40 amino acid peptide fragment forms a two-stranded, antiparallel β-sheet with a
hairpin loop consisting of 4 residues. What is the largest dimension of this motif?
(c) Although β-hairpin structures are often unstable in solution, incorporation of D-ProXaa sequences has been found to promote autonomous hairpin formation in aqueous
solution. The corresponding L-Pro-containing sequences are completely disordered.
Why?
2.
Poly-L-leucine is α helical in organic solvents like dioxane, whereas poly-L-isoleucine
adopts another conformation. Why do these amino acids, which possess the same type
and number of atoms, exhibit completely different helical propensities?
3.
The conformation of poly-L-lysine is pH dependent. At relatively high pH values, the
polymer adopts a predominantly helical structure, but at acidic and neutral pH it exists
as a random coil. Furthermore, at high temperatures the helix converts to an aggregated
antiparallel β sheet. Explain these observations.
4.
(a) Define identity, similarity and homology.
(b) What percent sequence identity do you expect for two non-homologous proteins of
identical length, if you assume that all 20 proteinogenic amino acids occur with equal
frequency and are distributed uniformly over the length of the protein?
(c) BLAST searches are performed to identify proteins having similar amino acid
sequences. A BLAST tutorial can be found at http://www.ncbi.nlm.nih.gov/BLAST/,
which describes how the program works. Explain the difference between the following
BLAST subroutines:
blastp, blastn, blastx, tblastn, tblastx
(d) Find the sequence for the Bacillus subtilis chorismate mutase (BsCM) in the “Protein
knowledgebase“ on the ExPASy Molecular Biology Server (www.expasy.org).
Determine the number of subunits BsCM has and their length.
(e) At the very bottom of the ExPASy data sheet for BsCM there is a link to BLAST
submission on ExPASy/SIB. Use this link and the blastp subroutine to search for similar
proteins. What is the sequence identity between BsCM and the chorismate mutase from
Bacillus halodurans? Is the sequence identity high? What conclusions can you reach
regarding the structural similarity of the two proteins?
(f) Alignments can be made to facilitate comparisons of similar amino acid sequences.
Click on the box in front of the first ten sequences found in (e) and initiate “Clustal W
alignment” above the box by hitting “submit query”. You have to click “Run Clustal
W“ again on the newly opened page. The alignment can be viewed in the results
window (clustalw aln). Asterisks indicate conserved amino acid residues. Why is it
significant that certain residues are conserved?
Biological Chemistry II: LITERATURE
Lecture 1: Protein Structure & Stability
General
Voet, Voet & Pratt: Chapter 6
Stryer: Chapter 2
Branden & Tooze: Chapters 1 & 2
Creighton, Chapters 4 & 5
Secondary Structure Prediction
Chou & Fassman, Annu. Rev. Biochem.1978, 47, 258
Blaber et al., Science 1993, 260, 1637
Protein stability
Lim & Sauer, Nature 1989, 339, 31
Eriksson et al., Science 1992, 255, 178