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
The peptide bond is rigid and planar carboxyl C 1.24 terminus 153A 146A 132 Amino Inus b)The conformation corresponding to =1800, v=1800 goel when the peptide is in its fully extended conformation The conformation corresponding to o =0, y=0, which is disallowed by the steric overlap between H and o atoms of adjacent peptide planes. (c)
The peptide bond is rigid and planar c) The conformation corresponding to =00 , =00 , which is disallowed by the steric overlap between H and O atoms of adjacent peptide planes. b) The conformation corresponding to =1800 , =1800 , when the peptide is in its fully extended conformation
+180 120 60 0 60 120 -180 180 0 +180 φ( degrees Ramachandran plot for L-Ala residues. Dark blue area reflect conformations that involve no steric overlap and thus are fully allowed; medium blue indicates conformations allowed at the extreme limits for unfavorable atomic contacts; the lightest blue area reflects conformations that are permissible if a little flexibility is allowed in the bond angles
Ramachandran plot for L-Ala residues. Dark blue area reflect conformations that involve no steric overlap and thus are fully allowed; medium blue indicates conformations allowed at the extreme limits for unfavorable atomic contacts; the lightest blue area reflects conformations that are permissible if a little flexibility is allowed in the bond angles
1.3 Protein structures have conventionally been understood at four different levels 1.3.1 The primary structure is the amino acid sequence(including the locations of disulfide bonds). 1.3.2 The secondary structure refers to the regular recurring arrangements of adjacent residues resulting mainly from hydrogen bonding between backbone groups, with a-helices and b-pleated sheets as the two most common ones 1.3.3 The tertiary structure refers to the spatial relationship among all amino acid residues in a polypeptide chain, that is, the complete three dimensional structure 1.3.4 The quaternary structure refers to the spatial arrangements of each subunit in a multisubunit protein, including nature of their contact
1.3 Protein structures have conventionally been understood at four different levels. 1.3.1 The primary structure is the amino acid sequence (including the locations of disulfide bonds). 1.3.2 The secondary structure refers to the regular, recurring arrangements of adjacent residues resulting mainly from hydrogen bonding between backbone groups, with a-helices and b-pleated sheets as the two most common ones. 1.3.3 The tertiary structure refers to the spatial relationship among all amino acid residues in a polypeptide chain, that is, the complete threedimensional structure. 1.3.4 The quaternary structure refers to the spatial arrangements of each subunit in a multisubunit protein, including nature of their contact
Primary Secondary Tertiary Quaternary strueture strueture structure strueture Gly Leu Amino acid residues a helix Polypeptide chain Assembled subunits
2. Protein Secondary Structure 2.1 The likely regular conformations of protein molecules were proposed before they were actually observed This was accomplished by building precise molecular models 2.1.1 Experimental data(from X-ray studies)were closely adhered, interpreted 2.1.2 Single bonds other than the peptide bond in the backbone chain are free to rotate
2. Protein Secondary Structure 2.1 The likely regular conformations of protein molecules were proposed before they were actually observed! This was accomplished by building precise molecular models. 2.1.1 Experimental data (from X-ray studies) were closely adhered, interpreted. 2.1.2 Single bonds other than the peptide bond in the backbone chain are free to rotate
