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Protein Sequence Prediction

1. You wish to use the Chou-Fasman method to predict the secondary structure of the following protein sequence:

MCPQLNWKAYVKSAGARNLKGN

a. Moving from left to right in the protein sequence, use the Chou-Fasman method to scan for the first group of six consecutive amino acids that are predicted to nucleate an alpha helix. Do not propagate the alpha helix. Write the sequence that you identified below.

b. List the names of two alternative secondary structure prediction methods that could be used to predict the secondary structure of this protein sequence.

2. Write the name of the tertiary (3D) structure prediction method that would work best to predict the structure of a protein that does not have a sequence homologue in the PDB structure database.

3. Which of the following peptides could be generated from a complete trypsin digestion (i.e., no missed cleavages) of a sample protein?

A. LHEKLEK
B. PELVPNF
C. NPILMGK
D.RAVDEEL

4. Which of the following statements about the MALDI ionization method is correct?

A. MALDI MS spectra are less complex to analyze than equivalent ESI MS spectra
B. MALDI uses a laser to ionize the protein/peptide sam ple
C. MALDI requires the co-crystallization of the protein/peptide sample with a matrix
D. All of the above
E. None of the above

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1. You wish to use the Chou-Fasman method to predict the secondary structure of the following protein sequence:

MCPQLNWKAYVKSAGARNLKGN

a. Moving from left to right in the protein sequence, use the Chou-Fasman method to scan for the first group of six consecutive amino acids that are predicted to nucleate an alpha helix. Do not propagate the alpha helix. Write the sequence that you identified below.

Before beginning this question you should read the following paper which describes the Chou-Fasman methodology: http://www.waset.org/journals/waset/v48/v48-178.pdf

The Chou-Fasman method of secondary structure prediction depends on assigning a set of prediction values to an amino acid (AA) residue and then applying a simple algorithm to those numbers. Scan through the peptide and identify AAs where 4 out of 6 contiguous AAs have P(a-helix) > 100. That region is declared an alpha-helix. Extend the helix in both directions until a set of four contiguous residues that have an average P(a-helix) < 100 is reached. That is ...

Solution Summary

There are four questions broken up into sub-questions related to protein sequencing. The questions are answered in full with links to references that were used to generate the answers and for additional reading and study.

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