Chapter 5 The Three-dimensional Structure of proteins
Chapter 5 The Three-dimensional Structure of Proteins
1. Early studies on the peptide(protein) structure 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 c-N double bond, 1.27) thus having partiar'< found to be about 1. A(C-N single bond, 1.49; double bond feature(should be rigid and unable to rotate freely)
1. Early studies on the peptide (protein) structure 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)
1.3 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 ma king 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
Carboxyl 124A terminus 1.53AC 146A 132A Amin terminus H (b)
2. The likely regular conformations of protein molecules were proposed before they were actually observed! 2.1 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. The likely regular conformations of protein molecules were proposed before they were actually observed! 2.1 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
2.2 The simplest arrangement of the polypeptide chain was proposed to be a helical structure called a-helix (Pauling and corey, 1951) 2.2.1 The polypeptide backbone is tightly wound around the long axis(rodlike). 2.2.2R groups protrude outward from the helical backbone 2.2.3 A single turn of the helix(corresponding to the repeating unit in a-keratin) extends about 5.6 Angstroms, including 3.6 residues(each residue arises 1.5 a and rotate 100 degrees about the helix axis)
2.2 The simplest arrangement of the polypeptide chain was proposed to be a helical structure called a-helix (Pauling and Corey, 1951) 2.2.1 The polypeptide backbone is tightly wound around the long axis (rodlike). 2.2.2 R groups protrude outward from the helical backbone. 2.2.3 A single turn of the helix (corresponding to the repeating unit in a-keratin) extends about 5.6 Angstroms, including 3.6 residues (each residue arises 1.5 Å and rotate 100 degrees about the helix axis)
2.2. 4 The model made optimal use of internal hydrogen bonding for structure stabilization 2.2.5 Each carbonyl oxygen of the residue n is hydrogen bonded to the nh group of residue(n+4) 2.2.6 The residues forming one a-helix must all be one type of stereoisomers(either L-or D-) 2.2L amino acids can be used to build either right- or left-handed a-helices(the helix spiraling away clockwise or counterclockwise respectively)
2.2.4 The model made optimal use of internal hydrogen bonding for structure stabilization. 2.2.5 Each carbonyl oxygen of the residue n is hydrogen bonded to the NH group of residue (n+4). 2.2.6 The residues forming one a-helix must all be one type of stereoisomers (either L- or D-). 2.2.7 L amino acids can be used to build either right- or left-handed a-helices (the helix spiraling away clockwise or counterclockwise respectively)
C N O C C C N H R (c)
+180 120 60 60 -120 180 -180 +180 φ( degrees)
