Overview. The peptide bond. Page 1

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1 Overview Secondary structure: the conformation of the peptide backbone The peptide bond, steric implications Steric hindrance and sterically allowed conformations. Ramachandran diagrams Side chain conformations Backbone hydrogen bonding Recurring regular structures of the backbone Alfa helix, other helices Beta sheet Reccuring irregular structures: Turns The peptide bond Delocalization; double bond character: Resonance structures: O N C! H C! O N + or C! H! " O N H!+ Consequences: C! Geometry of the trans peptide bond Shorter than ordinary C-N bond Very limited rotation around C-N-bond; O,C,N,H in one plane Cis-trans isomerism Permanent dipole; polar - + Page 1

2 cis- och trans peptides Trans, common Cis, rare (cis-prolin [X-cisPro-]) H O R H N R H H R O R H N H Proline Trans-proline Cis-proline Page 2

3 Two conformational degrees of freedom for each residue For each residue, the backbone conformation can be specified by the torsion angles φ and ψ O i-1 Res. nr. i C β i R C i-1 φ C α i ψ N i+1 N i C i H i O i N i H i φ C i φ=0 when C α i -C i trans to N i -H i O i ψ=0 when C α i -N i trans to C i -O i C α i C i Ψ N i N i+1 Petsko&Ringe fig. 1.9 Steric hindrance and van der Waals distances Repulsion between electron clouds proportional to (1/r) 12 ; atoms can be regarded as hard spheres Observed distances (Å) Contact Normal Extreme H.. H H.. O H.. N H.. C O.. O O.. N O.. C N.. N N.. C C.. C Schultz & Schirmer: Principles of Protein Structure Page 3

4 Steric hindrance and allowed conformation (φ,ψ) for glycine residue φ=0, ψ=80 φ ψ φ=0, ψ=180 φ=0, ψ=90 φ=0, ψ=0 φ=-180, ψ=0 φ=-90, ψ=0 Shultz & Schirmer, Principles of protein structure A β-carbon imposes further restrictions Sidechain in all amino acids except glycine φ ψ φ about 130; O n-1 - C β ψ about -100; N n-1, H n-1 - C β φ ψ Efter Shultz & Schirmer, Principles of protein structure Page 4

5 Energy as function of geometry-a more detailed calculation Potential energy diagram for alanine residie (geometry of peptide bond and bond legnths fixed; Shultz och Schirmer: Principles of Protein Structure) > 0 kcal/mol -1-0 kcal/mol kcal mol kcal/mol kcal/mol Bridge region; Steric repulsion between N i och H i+1 compensated by favourable dipoledipole interaction φ=-90, ψ=0 δ + δ δ + δ Efter Shultz & Schirmer, Principles of protein structure Experimental φ and ψ: Ramachandran diagrams Ca 5 % of all residues with β- carbon ( Gly) in forbidden areas Ramachandrandiagram for 13 proteins (2500 residues) Realistic calculations need to take into account - Peptide bond torsion: ( Ω < 12 o increses energy < 1 kcal/ mol) Small variations of bond angles and lengths are OK energywise Efter Shultz och Schirmer: Principles of Protein Structure Page 5

6 Conformational preferences of residues as Ramachandran diagrams Examples Hovmöller et al; Description of side chain conformation with torsional angles Denoted χ 1, χ 2... χ 1 i χ 2 i Från Schultz & Schirmer: Principles of Protein Structure Page 6

7 Nomenclature for side chains Figur av Jon Cooper, PPS Side chain conformations χ 1 Most frequent ; Cγ opposite carbonyl carbon χ 2 Second most common (not Val, Ile) Cα Uncommon; however Ser, Thr (H-bond Oγbackbone) Oftast som χ 1 Med Cγ sp 2 (Phe, Tyr, Trp, His...) ± 90 grader (?) H H Cβ Figur av Jon Cooper, PPS Page 7

8 Exemples of observed rotamerer preferences Val Ile His χ 1 χ 1 χ 2 χ 2 Repetition of φ and ψ produces helixes Parameters to describe a helix Units per turn, n (positive for right-anded; negative for left-handed Distance along axis per turn, p (pitch) Radius p d Alternatives Angle between units; 360/n Distance along axis per unit, d=p/n r Page 8

9 Helix structures p=0 p p p p n=5 n=4 n=3 n=2 n=-3 not chiral n does not need to be an integer except when p=0 Figur av Irving Geis, från Voet och voet, Biochemistry Torsional angles and helix parameters Helix parameters d and n for helixes obtained by assigning same torsional angles ψ and φ to residues in a polypeptide chain ψ d n φ From Shultz och Schirmer: Principles of Protein Structure Page 9

10 Secondary structure Structure that can be described using only the backbone torsional angles φ och ψ No steric hindrance involving backbone or C β Backbone carbonyl and amides involved in hydrogen bonding to backbone Hydrogen bonding possibilitites i! i+1 i ribbon i helix i+4 α helix i+5 π helix Figur av Irving Geis, hämtad ur Matthews & van Holde, Biochemistry Page 10

11 Helix structures (Helical parameters for various secondary structures) Table 5-1. Linear Groups Formed by Polypeptide Chains (Schultz och Schirmer, Principles of Protein Structure) Residues per Rise per Radius of turn n and residue helix r Linear group Observed chirality d (A) (A) Planar parallel sheet Rare ± Planar antiparallel sheet Rare ± Twisted parallel or Abundant antiparallel sheet Helix Small pieces a(r)-helix (right-handed) Abundant a(l)-helix (left-handed) Hypothetical IT-Helix Hypothetical Collagen-helix In fibers See also Petsko&Ringe fig Stick model: Hydrogen bonding Alpha helix Spacefilling model (CPK) From top i+4 i i+1 i+3 i+2 i+4 i i+1 i+2 Common; accounts for about 35 % of all structure Suitable radius for good van der Waals interaction Side chains point away from each other; minimal steric hindrance Pesko&Ringe fig 1.13 Page 11

12 3.10 helix Hydrogen bonding CPK-model Top view Rare ca. 3 % short fragments (1-3 hydrogen bonds) (φ,ψ)=(-74,-4), borderline Radius smaller than van der Waals distance Sidechains not will spaced evenly Dipole moment Addition of permanent dipole moments of peptide bonds produces net dipole moment for alpha helixes; ( about +0.5 i C-terminus och -0.5 i N- terminus) Some preference for negatively charged sidechains at the N-terminus and for positively charged side chains at the C-terminus. Phosphate binding oftan at N-terminus of alpha helix Figur av Doc. Kurt Berndt, Karolinska Institute; se Bränden& Tooze s. 16 Page 12

13 Amphiphatic alpha helixes Perodicity in sequence (period ov 3-4 residues) can produce) amphiphilic helix. Strongly amphiphilic alpha heices can be recognized by hydrophobic moment: Helical wheel diagram N R F C-term D S Non<polar Polar Charged Take the hydrophobicity of each residue as the length of a vector directed from the helix as the sidechain. The length of the vector sum is called hyrdophobic moment I L N-term G G L D Alcohol dehydrogenase: Ile-Gln-Asp-Gly-Phe-Asp-Leu-Leu-Arg-Ser-Gly Petsko&Ringe fig Amphiphilic alpha helix in mellitin (bee venom). Efter Gennis, Biomembranes β-structure About 2 residues /turn; planar One β-strand: Always together with other strands; carbonyl oxygens and amide nitrogens hydrogen bonded Page 13

14 Association av β-strands with hydrogen bonds produces a planar structure, β pleated sheet (β-sheet) Almost ideal β- structurer från glutathion reductase From the side β-strands can be parallel or antiparallel Parallell beta structure Antiparallell beta structure!! Petsko&Ringe fig Page 14

15 Most β-strands are twisted n -2.3 β-sheet becomes twisted; propellerlike structure Strands will form an angle of about 25 degrees Schultz och schirmer, Principles of Protein Structure Twisted β-structure ( thioredoxin) From top From side Page 15

16 Turns - Connections between antiparallel beta strands -mostly short (2-5 residues) Type I turn! (Note that turn nomenclature is not consistent) 1,4 2 G 3 Page 16

17 Type II turn 1,4 3 2 Liten bit 3.10-helix Petsko&Ringe fig 1.12 Gamma turn: hydrogen bond from O(i) till H(i+2) Som 2.7 ribbon i vätebindningsöversikten. Endast en rest som inte ingår i förbundna betasträngar. stereoisomerer Figurer av Kurt Berndt, Karlinska Institutet (PPS), Page 17

18 Conformational preferences for residues in turn region Gly (>50 % of turn residues) Other Page 18