Level Description Bonds Primary Sequence of amino acids in proteins Covalent (peptide bonds) Secondary Structural motifs in proteins: α- helix and β-sheet Hydrogen bonds (between NH and CO groups in backbone) Tertiary Folding up of polypeptide chain Various: covalent, ionic, H-bonds, van der Waals, hydrophobic Quaternary Association of protein subunits into larger assemblies Various The peptide bond is rigid and planar Trans 10% Pro has cis conformation Phe-Pro
Three Bonds N-C α bond phi angle (Φ) C α -C bond psiangle (Ψ) Backbone Dihedral Angles O C H N H R Cα C O H R N H CO Φ = -90 o CO H N H R Cα C O H R N HN H Cα O NH Ψ = -90 o Adapted from Introduction to Protein Structure by Branden & Tooze
Certain values of Φ and Ψ are not permitted due to steric hindrance. Observed Glycine
Ramachandran plot for Ala residues β strand: Φ = -119 o, Ψ = 113 o α helix: Φ = -57 o, Ψ = -47 o Ramachandran plot of pyruvate kinase Glycine can have any dihedral angles
α-helix 3 10 helix π-helix Three Regular Polypeptide Helices phi psi α-helix -57.8-47.0 3 10 -helix -74.0-4.0 π-helix -57.1-69.7 Idealized model of the conformations of polyalanine are displayed.
CO (i) to NH (i+4) NH (i) to CO (i-4) 1 2 3 4 5 The α helix is a common protein secondary structure
Helix Wheel Hydrophilic Hydrophobic Amphipathic Helix Dipole NH 3+ L-Amino acid forms right-handed α helix Counterclockwise COO -
α-helix is a dipole moment. Amino acid sequence affects a helix stability 1 2 3 4 5? Interaction between D100 and R103
1 2 3
β strands to β sheet
5 4 2 3 1 1 3 2 4 5
Twist of β Sheet The classical beta sheets originally proposed are planar but most sheets observed in globular proteins are twisted (0 to 30 º/ residue). Antiparallel beta sheets are more often twisted than parallel sheets. This twist is always of the same handedness, but unfortunately, it has been described using two conflicting conventions in the literature. If defined in terms of the progressive twist of the hydrogenbonding direction, the twist is right-handed. Two-stranded beta strands show the largest twists. β-bulge Another irregularity found in antiparallel beta sheets is the hydrogen-bonding of two residues from one strand with one residue from the other called a beta bulge. Bulges are most often found in antiparallel sheets with ~5 % of bulges occurring in parallel strands (Richardson, 1981). Bulges, like "Turns" effect the directionality of the polypeptide chain.
Turns Turns are the third of the three "classical" secondary structures. Approximately one-third of all residues in globular proteins are contained in turns that serve to reverse the direction of the polypeptide chain. This is perhaps not so surprising since the diameter of the average globular protein domain is roughly 25 Å (an extended polypeptide conformation would require ~7 residues to traverse the domain before having to change directions). Turns are located primarily on the protein surface and accordingly contain polar and charged residues. Antibody recognition, phosphorylation, glycosylation, hydroxylation, and intron/exon splicing are found frequently at or adjacent to turns. Turns β turn: 4 residues; CO (1 st residue) to NH (4 th residue) γ turn: 3 residues:? Amino acid residues P and G tend to have turn structure. XPGX
Type I Turn. The hydrogen bond between CO of residue i and NH of residue i+3. The backbone dihedral angles are (-60, -30) and (-90, 0) of residues i+1 and i+2, respectively, for the type I turn. Proline is often found in position i+1 in type I turns as its phi angle is restricted to -60 and its imide nitrogen does not require a hydrogen bond. Glycine is favored in this position in the type II' as it requires a positive (left-handed) phi value. P2G3 Type II Turn. The hydrogen bond between CO of residue i and NH of residue i+3. The backbone dihedral angles are (-60, 120) and (80, 0) of residues i+1 and i+2, respectively, for the type II turn. Glycine is favored in this position in the type II' as it requires a positive (lefthanded) phi value.
Type III Turn. The hydrogen bond between CO of residue i and NH of residue i+3. This is a single turn of right-handed (III) and left-handed (III') 3 10 helix. The backbone dihedral angles are (-60, -30) and (- 60, -30) of residues i+1 and i+2, respectively, for the classical type III turn. Gamma Turn The hydrogen bond between CO of residue i and NH of residue i+2. The dihedral angles of residue i+1 are (70, - 60) and (-70, 60) for phi and psi of the classical and inverse gamma turns.
Loop regions are at the surface of protein molecules Loops In Leszczynski & Rose (1986), out of 67 proteins surveyed, they tabulated 26 % helix, 19% sheet, 26 % turns and 21 % in loops. These loop structures contain between 6 and 16 residues and are compact and globular in structure. Like turns, they generally contain polar residues and hence are predominantly at the protein surface.
Common secondary structures have characteristic bond angles and amino acid content Preferred Residues for β Sheet and Turns Eight most common residues for beta-sheet Val, Ile, Tyr, Trp, Phe, Leu, Cys, Thr Eight least common residues for beta-sheet Glu, Asp, Pro, Ser, Lys, Gly, Ala, Asn Eight most common residues for turns Gly, Asn, Pro, Asp, Ser, Cys, Tyr, Lys Eight least common residues for turns Ile, Val, Met, Leu, Phe, Ala, Glu, Trp
Globular proteins have common structural patterns tertiary structure domain motif secondary structure primary structure Motif or supersecondary structure: A commonly occuring substructure, usually comprising two to three secondary structures. Super Secondary Structures (Motifs) Simple combinations of a few secondary structure elements with a specific geometric arrangement are called super secondary structures or motifs. They may have functional and structural significance. Common motifs: Helix-turn-helix β-hairpin, β-meander β-barrel, Geek key βαβ
Helix-Turn-Helix Motif Two α helices that are connected by a short loop region in a specific geometric arrangement constitute a helix-turn-helix motif. (a) the DNA-binding motif and (b) the calciumbinding motif, which are present in many proteins whose function is regulated by calcium. EF-hand Calcium-binding Motif The calcium atom is bound to one of the motifs in the muscle protein troponin-c through six oxygen atoms: one each from the side chains of Asp (D) 9, Asn (N) 11, and Asp (D) 13; one from the main chain of residue 15; and two from the side chain of Glu (E) 20. In addition, a water molecule (W) is bound to the calcium atom.
Amino Acid Sequences of EF-hand Motifs 1 3 5 7 9 12 The side chains of hydrophobic residues on the flanking helices form a hydrophobic core between the α helices The β Hairpin Motif Bovine Trypsin Inhibitor Snake Venom Erabutoxin The hairpin motif is very frequent in β sheets and is built up from two adjacent β strands that are joined by a loop region.
Greek Key Motif The Greek key motif is found in antiparallel β sheets when four adjacent β strands are arranged in the pattern shown as a topology diagram in (a). The three dimensional structure of the enzyme Staphylococcus Nuclease shown in (b) in blue and red is also a Greek key motif. Forming Greek Key Motif Suggested folding pathway from a hairpin-like structure to the Greek key motif. Beta strands 2 and 3 fold over such that strand 2 is aligned adjacent and antiparallel to strand 1.
β-hairpin motif? Greek key motif
Greek key motif staphylococcus nuclease Topology diagram aspartate transcarbamoylase flavodoxin: redox protein plastocyanin: electron carrier
β α β Motif Two adjacent parallel β strands are usually connected by an α helix from the C-terminus of strand 1 to the N- terminus of strand 2. Most protein structures that contain parallel β sheets are built up from combinations of such β α β motifs. β α β motif right hand left hand
β α β Handedness The β α β motif can in principle have two "hands." (a) This connection with the helix above the sheet is found in almost all proteins and is called right-handed because it has the same hand as a right-handed α helix. (b) The left-handed connection with the helix below the sheet.
Domains are built from structural motifs triosephosphate isomerase protein structure P53 domain motif DNA-binding domain sheet-turn-helix secondary structure α-helix & β-sheet & turn primary structure linear chain
Structural domains in the polypeptide troponin c Domains are regions of contiguous polypeptide chain that have been described as compact, local, and semi-independent units.