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Protein Sequence Prediction

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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.

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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https://brainmass.com/biology/protein-structure-and-synthesis/protein-sequence-prediction-535223

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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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See Also This Related BrainMass Solution

Mass Spectrometry Predicting Protein Sequences

This assignment focuses on the methodology of peptide mass finger printing (PMF) and use of mass spectrum analysis software. The lecture notes provide a good foundation for this but you will have to carry out additional personal research to effectively answer the questions. The learning objective of the assignment is to give you an appreciation of the importance of bioinformatics and mass spectrometry in biomedical research technologies. Both mass spectrometry and bioinformatics are important skills in this area.

Please complete the following tasks:

The spectrum in the attached picture is a PMF profile obtained from a spot cut out of a 2 dimensional electrophoresis gel.

1) Identify the protein that produced the attached PMF mass spectrum, you may use any online resource to do this but I suggest the MASCOT server is a good place to start. The profile was produced using trypsin and is derived from a human cell lysate. List the amino acid sequence of each fragment.

2) The MASCOT server lists a number of chemical modifications for peptides. Which of these are likely to have occurred due to the electrophoresis used to isolate the protein? What effect will these have on the protein's mass?

3) Using dot points, outline the processes used to produce the PMF profile starting from protein lysate.

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