17. (20 pts) The generic Ramachandran plots for all amino acids and glycine are
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17. (20 pts) The generic Ramachandran plots for all amino acids and glycine are shown below Darker regions are more favored than lighter colored regions. Individual points correspond to measured angles from a glycoside hydrolase. General (6 pts) Explain what a Ramachandran plot is; to what do the axis of the Ramachandran plot correspond? a. b. (6 pts) Label the plots where you would expect to find amino acids taking a-helical and ?-sheet conformations on the generic Ramachandran plot. (5 pts) Why is the Ramachandran plot for glycine so different than that for generic amino acids? c. d. (3 pts) On the blank sets of axis below, Sketch the Ramachandran plot for a polymer of 2-amino-2-methyl-propionic acid (2AMPA). 2AMPA is similar to alanine except that instead of a hydrogen on the alpha-carbon (see below), there is a second methyl group 180 CH3 O ?-? ?? 2AMPA 180 180 180Explanation / Answer
Q. a Ramchandran plot has axis psi ? Vs phi ?
Phi ? value is the angle of rotation about bond between ?- carbon atom and nitrogen atom.
Psi ? value is the angle of rotation about bond between ?-carbon atom and carbonyl carbon atom.
The clockwise rotation of each amino acid around these bonds allows protein to fold in many different ways. The ? and ? angles determine path of polypeptide chain. In any case ,entire path of peptide backbone in a protein is known if the ? and ? rotation angles are all specified. Some values of these angles are not allowed due to steric interference between nonbonded atoms.
A typical Ramchandran plot is combination of all phi and psi possible values. These allowed values can be visualized on two dimentional plot called as ramchandran diagram.
Q.b the amino acid residues in an ? helical confirmation on ramchandran plot have confirmations with ?= 600 and ? = -450 to -500
Q. a Ramchandran plot has axis psi ? Vs phi ?
Phi ? value is the angle of rotation about bond between ?- carbon atom and nitrogen atom.
Psi ? value is the angle of rotation about bond between ?-carbon atom and carbonyl carbon atom.
The clockwise rotation of each amino acid around these bonds allows protein to fold in many different ways. The ? and ? angles determine path of polypeptide chain. In any case ,entire path of peptide backbone in a protein is known if the ? and ? rotation angles are all specified. Some values of these angles are not allowed due to steric interference between nonbonded atoms.
A typical Ramchandran plot is combination of all phi and psi possible values. These allowed values can be visualized on two dimentional plot called as ramchandran diagram.
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