Protein backbone Biochemical view: basic repeating unit is NH—CαH—C’=O We can also look at repeating units from Cα to Cα Interesting properties: Bond lengths almost equal in all groups, in all proteins Bond angles almost equal in all groups, in all proteins A Cα atom belongs to two units All atoms in an unit coplanar Preferable when describing structural properties

Protein backbone Geometric/Structural view: polypeptide chain divided into Peptide units Cα atom and carboxyl group of residue i Amino group and Cα atom of residue i+1 Are rigid groups Rotation on bond C-N is prevented by energy barrier Peptide units are joined by covalent bonds between Cα atoms. Thus Peptides can rotate along 2 bonds: N-Cα and Cα-C Two dihedral angles for each unit: Ф (Phi) and Ψ (Psi) Two degrees of freedom per unit Determine the conformation of the backbone

Dihedral angles and regular structures Repeating values of Ф and Ψ along the main chain result in regular structure repeating values of Ф =-57o and Ψ =-47o give a right-handed helical fold (α-helix) repetitive values of Ф[-110,-140] and Ψ[+110,+135] give sub chains with conformations that allow interactions between nearby parallel segments (β-sheet) Most combinations of Ф and Ψ angles are not allowed Allowed conformations plotted as 2-D chart Ramachandran plot

Secondary Structure defined by patterns of hydrogen bonds between backbone amide groups sidechain-mainchain and sidechain-sidechain hydrogen bonds are irrelevant The amino acids in the interior/core of a globular protein have hydrophobic side chains Water soluble proteins fold to pack hydrophobic side chain into interior Results in hydrophobic core and hydrophilic surface The main chain must fold into interior, too Main chain is hydrophilic: N--H: hydrogen bond donor C=O: hydrogen bond acceptor These groups must be neutralized by formation of H bonds  secondary structure Secondary structure α-helices β-sheets form rigid and stable frameworks

α-Helix Righthanded coiled conformation Has between 4 to 40 residues backbone N-H group i+4 forms hydrogen bonding with backbone C = O group i 3.6 residues per turn (5.4 Å, 1.5 Å per residue) Variations, with chain more loosely or tightly coiled are possible (i+3 or i+5 instead of i+4) but not often backbone (φ, ψ) dihedral angles around (-60o,-45o) Sum of φ and ψ angles of consecutive residues about 105o Has between 4 to 40 residues All H bonds point in the same direction Aligned along helical axis Dipole moments for residues are aligned along axis Net dipole for α-helix (+ at N-H end and – at C=O end)

Representations (cartoon, backbone trace, space filling)

β-sheets Combination of several regions of the chain (not chain adjacent): β-strands Parallel: all amino acids go in same direction Evenly spaced H bonds Antiparallel: amino acids in successive strands alternate directions Alternate narrowly/widely spaced H bonds Mixed β-sheet also exist Have twisted strands: right-handed twist (always) β-strand: 5 to 10 residues long Almost fully extended

Representations (bond, cartoon, ribbon)

From secondary structure to structure Protein structure: built from secondary structures Connected by loop regions Various lengths Irregular shape Are at the surface of the protein Reach in charged and polar residues Easier to predict! In homologous proteins almost always insertions and deletions occur in the loop regions.

Structure Motifs Secondary structures  connected to form motifs α-helices and β-sheets in a motif Adjacent in the 3-dimensional structure Connected bu loop regions Combinations of motifs and secondary structures  domains

Native conformation: direct consequence of Tertiary structure: Arrangement of secondary structure Structural domains Quaternary structure More than one polypeptide folded together Native conformation: direct consequence of primary structure chemical environment water based oily interior of a cell membrane So far, no reliable computational method exists to predict the native structure from the amino acid sequence

Structure Classes Protein structure  four classes: α-domains core built up only from α-helices β-domains core built up only from (usually 2) antiparallel β-sheets α/β-domains mostly β-α-β motifs (mostly) parallel β-sheets surrounded by α-helices α+β-domains (few cases) antiparallel β-sheet packed against α-helices