Week 9: Computational modeling of peptides and proteins . Understand and be able
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Question
Week 9: Computational modeling of peptides and proteins . Understand and be able to identify different interactions that factor into peptide/protein folding (e.g, hydrogen bonding, salt bridge interactions, disulfide bonding. Be able to predict these interactions given a peptide structure. -Understand basic molecular geometry in a peptide. What is the bond angle between amide N, C, and O atoms? Why is the angle like this? . What is the geometry like in an alpha helix? What intermolecular forces lead to the formation of a helix? What about for a beta sheet?Explanation / Answer
Due to the resonance all the peptide bonds are nearly planar in the protein structures , and making it rigid which helps in the reducing of the degrees of freedom of the polypeptide during theprotein folding.
The peptide bond nearly always has the trans configuration since it is more favourable than cis. Due to the sterics the trans are always more stable resulting in the optimal NCO bond angle of 125 degrees.
The geometry of the alpha helix repeats itself every 5.4 Angstroms along the helix axis, having a pitch of 5,4 angstorms.. Alpha-helices have 36 amino acids and would form 10 turns. The separation of residues along the helix axis is 5.4/3.6 or 1.5 Angstroms, ie the alpha-helix has the increase per residue of 1.5 Angstroms.In the sheet every C=O and N-H group is hydrogen-bonded to a peptide bond 4 residues away imposing a very robust and stable arrangement. The peptide planes are roughly parallel with the helix axis and the dipoles within the helix are aligned, ie all C=O groups point in the same direction and all N-H groups point the other way ..
The alpha sheet have a signature phi-psi value of -60 and -50 degrees respectively.
THe alpha sheet is formed keeping in the hydrogen bonding which plays the pivotal role among the weak interactions to stablize the secondary structure. It is the coils and turns in the structure with the H-bonding that makes the secondary structure.
For the beta sheet the structure is formed by the association of parallel beta strands linked together by the H-bonding. THese structures are also sometimes stabilized by the protein-protein interactions, bound metal ions. The hydrogen bonds are between the N-H group of one amino acid and the C=O group of another. Large aromatic amino acids, like tryptophan, tyrosine, and phenylalanine are often found in the middle of these sheets. The signature Ramachandran plot degrees are between -60 to -120, 100-190 degrees.
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