Lecture 2 Secondary and sidechain structures James Chou BCMP201 Spring 2008
Images from Petsko & Ringe, Protein Structure and Function. Branden & Tooze, Introduction to Protein Structure. Richardson, J. S. & Richardson, D. C. Principles and Patterns of Protein Conformation.
IUPAC definition of dihedral angles Definition of φ (AB-CD) dihedral angle A A B C D +! D B C φ (AB-CD) is + if clockwise - if counterclockwise #! " 360 if! >180! = $ %! + 360 if! < "180
Polypeptide structure can be described by backbone dihedral angles Variable backbone dihedrals '! i C i"1 " N i " C i # "C i '! i N i " C i # " C i ' " N i +1 Peptide plane dihedral! i,i +1 C i " # C i ' " # N i +1 # C i +1 ω tends to be planar due to delocalization of the C π electron and the nitrogen lone pair.! =180 0 ±10 0
Secondary structures are local backbone structures with repeating φ and ψ Common examples: α helix β strands The Ramachandran plot, or ψ vs. φ plot, is the best way to view secondary structures in terms of the backbone dihedral angles.
Regular α helix right-handed! = "60 0, # = "40 0
α helix! = "60 0, # = "40 0 right handed, clockwise looking down from the N-terminus H-bond between O of residue i and HN of residue i+4 N 3.6 residues 5.4 A H-bond C Pauling et al., PNAS, 1951
Why are α helices right-handed in nature? right handed left handed HB of Arg7 O of Arg7 O of Arg7 HB of Arg7 less steric collision more steric collision
Some residues have the left-handed helical φ and ψ left-handed! = +60 0, " = +40 0
Glycines frequently have positive φ angles Take home question Why do glycines often have the left-handed dihedrals! = +60, " = +40?
Helix electric dipole moment -0.42 ~ 3.5 Debye +0.42-0.20 +0.20 1 Debye =10!18 esu cm e! 1 angs = 4.8!10 "18 esu cm Wada, Adv. in Biophysics, 9, 1-63 (1976) Helix dipole can coordinate phosphate or sulphate binding
Example: the sulphate-binding protein (PDB code: 1SBP) SO 4 -
A single helix in solution is not stable. It must be stabilized by packing with other structural elements. Examples of stabilization of helix by helix-helix packing H-bond energy ~ 7 kj/mol, similar to the thermal energy in water. Thus H-bonds are not enough to keep a single helix stably locked.
Representation of helix by the helix wheel http://cti.itc.virginia.edu/~cmg/demo/wheel/wheelapp.html
Other unusual helical structures right-handed 3 10 helix! = "49 0, # = "26 0
3 10 helix 3 residues per turn H-bond (i,i+3)!," = #49,#26 α helix 3.6 residues per turn H-bond (i,i+4)!," = #60,#40 π helix 4.1 residues per turn H-bond (i,i+5)!," = #55,#70
Beginning and end of an α helix N-cap: The first residue of an α helix has non-helical Φ,Ψ dihedral angles, but participates, through its main-chain C=O group, in intra-helical hydrogen bonds. The side chain of the N-cap residue frequently accepts a hydrogen bond from the mainchain NH of the N3 residue. C-cap: The last residue of an α-helix has non-helical Φ,Ψ dihedral angles, but participates, through its main-chain N-H group, in intra-helical hydrogen bonds. The C-cap residue is often in the left-handed 3 10 helix conformation. Take home question What are the more likely amino acids for the N-cap? How about the C-cap?
! = "135 0, # = 135 0 β strands
β strands are NOT fully extended polypeptide chains Fully extended peptide! = "180 0, # = 180 0 Anti-parallel β strands are slightly more stable than parallel β strands. 6 Å! = "140 0, # = 135 0! = "120 0, # = 115 0
Example: thioredoxin from E. coli
A single sheet in solution is also not stable. It must be stabilized by packing with helices or other sheets. dihydrofolate reductase V domain of Ig light chain retinol-binding protein
Non-repetitive structure: turns type I, most common type II, 2nd most common α helix 3 10 helix poly-pro Gly, left-handed 3 10 helix H-bond H-bond
Turns in antiparallel β strands type I type II
Ca trace of ubiquitin Protein sidechain conformation
not staggered staggered Example: valine χ 1 trans 180 +gauche 60 -gauche -60
Definition of sidechain χ 1 rotamer Regular, Ser Val, Ile, Thr -60 Hα -60 Hα CA-CB bond Hβ 2 C Hβ 1 Cγ / Oγ N Hβ C Cγ2 Cγ1/ Oγ1 N +60 Hα +60 Hα Hβ 1 Hβ 2 Cγ2 Hβ C N C N Cγ / Oγ Cγ1/ Oγ1 180 Hα 180 Hα Cγ / Oγ Hβ 1 Cγ1/ Oγ1 Cγ2 C N C N Hβ 2 Hβ
Sidechain conformation is dependent on backbone secondary structures due mainly to steric hindrance. Example of steric hindrance in determining the conformation of pentane (Dunbrack & Karplus, Nat. Struct. Biol., 1994).! 1 = 180,! 2 = 180, 0.00 kj/mol! 1 = 68,! 2 = 177, 3.6 kj/mol! 1 = 65,! 2 = 65, 7.5 kj/mol! 1 = 78,! 2 = 84, 14.9 kj/mol
Different values of φ and ψ yield different amount of steric hindrance at a given χ 1. Dunbrack & Karplus, Nat. Struct. Biol., 1994
(φ,ψ) dependent χ 1 preference for Valine Valine χ 1 = 180 Valine χ 1 = -60 http://dunbrack.fccc.edu/bbdep/confanalysis.php#bbdepgraph
(φ,ψ) dependent χ 1 preference for Isoleucine Isoleucine χ 1 = 180 Isoleucine χ 1 = -60
Effect of special residues on the backbone structure Gly often terminates an α helix, ~1/3 of all helices finish with Gly N- and C-terminal ends of the helix Gly C-cap
Proline also causes distortion or termination of helices N- and C-terminal ends of the helix Note: the closed ring constraints φ to be near -60
Proline causes a kink in α helix Proline in tight turns preceded by trans peptides No H-bond
cis - trans isomerization of proline X-X peptide 99.9% trans 0.1% cis X-Pro peptide ~70% trans ~30% cis
cis - trans isomerization of Proline in a turn
Polyproline helices type I!," = #75, 160 3.3 residues per turn, right-handed, cis type II!," = #75, 150 3 residues per turn, left-handed, trans collagen (GPP) n