Chapter 6 The Three-dimensional Structure of Proteins
Chapter 6 The Three-dimensional Structure of Proteins
1. General studies of the peptide bond 1.1 The peptide(o=C-n-) bond was found to be shorter than the c-n bond in a simple amine and atoms attached are coplanar. 1.1.1 This was revealed by x-ray diffraction studies of amino acids and of simple dipeptides and tripeptides. 1.1.2 The peptide(amide) bond was found to be about 1.32 A(C-N single bond, 1.49 c=n double bond, 1.27), thus having partial double bond feature(should be rigid and unable to rotate freely)
1. General studies of the peptide bond 1.1 The peptide (O=C-N-H) bond was found to be shorter than the C-N bond in a simple amine and atoms attached are coplanar. 1.1.1 This was revealed by X-ray diffraction studies of amino acids and of simple dipeptides and tripeptides. 1.1.2 The peptide (amide) bond was found to be about 1.32 Å (C-N single bond, 1.49; C=N double bond, 1.27), thus having partial double bond feature (should be rigid and unable to rotate freely)
1.1.3 The partial double bond feature is a result of partial sharing(resonance) of electrons between the carbonyl oxygen and amide nitrogen 1.1.4 The atoms attached to the peptide bond are coplanar with the oxygen and hydrogen atom in trans positions. 1. 2 X-ray studies of a-keratin(the fibrous protein making up hair and wool) revealed a repeating unit of 5.4 A(Astury in the 1930s)
1.1.3 The partial double bond feature is a result of partial sharing (resonance) of electrons between the carbonyl oxygen and amide nitrogen. 1.1.4 The atoms attached to the peptide bond are coplanar with the oxygen and hydrogen atom in trans positions. 1.2 X-ray studies of a-keratin (the fibrous protein making up hair and wool) revealed a repeating unit of 5.4 Å (Astury in the 1930s)
The carbonyl oxygen has a partial negative charge and the amide nitrogen a partial positive charge, setting up a small electric dipole. Virtually all peptide bonds in proteins occur in this trans configuration; an exception is noted in Igure 6-8b F O O H H H
1.2 The backbone conformation of a peptide can be defined by two sets of rotation angles 1.2.1 The rotation angles around the n-ca bonds are labeled as phi(o), and around ca-c bonds are psi (y) 1.2.2 By convention, both phi and psi are defined aso degree in the conformation when the two peptide planes connected to the same a carbon are in the same plane. 1.2.3 In principle, phi and psi can have any value between-180 and +180 degrees. 1.2. 4 The conformation of the main chain is completely defined when phi and psi are specified for each residue in the chain
1.2 The backbone conformation of a peptide can be defined by two sets of rotation angles. 1.2.1 The rotation angles around the N-Ca bonds are labeled as phi (), and around Ca-C bonds are psi (). 1.2.2 By convention, both phi and psi are defined as 0 degree in the conformation when the two peptide planes connected to the same a carbon are in the same plane. 1.2.3 In principle, phi and psi can have any value between -180 and +180 degrees. 1.2.4 The conformation of the main chain is completely defined when phi and psi are specified for each residue in the chain