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SECONDARY STRUCTURE OF PROTEINS: TURNS AND
HELICES
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Levels of protein structure organization
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60% 40%
Hybrid of two canonical structures
Peptide bond geometry
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Electronic structure of peptide bond
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Peptide bond: planarity
The partially double character of the peptide bond results in
•planarity of peptide groups
•their relatively large dipole moment
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Side chain conformations: the angles
1=0
1 2 3
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Dihedrals with which to describe polypeptide geometry
main chain
side chain
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Skan z wykresem energii
Peptide group: cis-trans isomerization
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Because of peptide group planarity, main chain conformation is effectively defined by the and angles.
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Side chain conformations
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The dihedral angles with which to describe the geometry of disulfide bridges
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Some and pairs are not allowed due to steric overlap (e.g, ==0o)
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The Ramachandran map
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Conformations of a terminally-blocked amino-acid residue
C7eq
C7ax
E Zimmerman, Pottle, Nemethy, Scheraga, Macromolecules, 10, 1-9 (1977)
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Energy maps of Ac-Ala-NHMe and Ac-Gly-AHMe obtained with the ECEPP/2 force field
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Energy curve of Ac-Pro-NHMe obtained with the ECEPP/2 force field
L-Pro-68o
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Energy minima of therminally-blocked alanine with the ECEPP/2 force field
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Elements of protein secondary structure
• Turns (local)• Loops (local)• Helices (periodic)• Sheets (periodic)• Statistical coil (not regular)
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- and -turns
-turn (i+1=-79o, i+1=69o) -turns
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Types of -turns in proteins
Hutchinson and Thornton, Protein Sci., 3, 2207-2216 (1994)
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Older classification
Lewis, Momany, Scheraga, Biochim. Biophys. Acta, 303, 211-229 (1973)
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i+1=-60o, i+1=-30o, i+2=-90o, i+2=0o i+1=60o, i+1=30o, i+2=90o, i+2=0o
i+1=-60o, i+1=-30o, i+2=-60o, i+2=-30o i+1=60o, i+1=30o, i+2=60o, i+2=30o
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i+1=-60o, i+1=120o, i+2=80o, i+1=0o i+1=60o, i+1=-120o, i+2=-80o, i+1=0o
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i+1=-80o, i+1=80o, i+2=80o, i+2=-80o
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i+1|80o, |i+2|<60o
i+1|60o, |i+2|180o
cis-proline
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Helical structures-helical structure predicted by L. Pauling; the name was given after classification of X-ray diagrams.
Helices do have handedness.
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Average parameters of helical structures
TypeH-bond Turns
closed by H-bond
radius
Geometrical parameters of helices
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Idealized hydrogen-bonded helical structures: 310-helix (left), -helix (middle), -helix (right)
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-helices: deformationsbifurcated or mismatched H-bonds disrupt periodic structure
Bifurcated hydrogen bonds (1,4 and 1,5) at helix ends.
1,3-, and 1,4-hydrogen bonds at helix ends.
1,6-hydrogen bonds at helix ends.
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Zniekształcenia -helisdodatkowe wiązania wodorowe na końcachhelis (wiązanie wodorowe rozwidlonelub zmiana wiązania wodorowego)
Bifurcated hydrogen bonds (1,4 and 1,5) at the N-terminums of helix A of thermolysin.
Bifurcated hydrogen bonds (1,4 and 1,5) at the C-terminums of helix D of carboxypeptidase.
1,6 and 2,5 hydrogen bonds at the C-terminus of helix A in lysosyme
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Helix deformation (kink)
Example from myoglobin structure. The kink angle is up to 20o
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Additional H-bonds with water molecules
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Other factors resulting in helix deformation
1. Deformation is forced because of tertiary structure (crowding).
2. Strong H-bonding (e.g., between side chains).
3. Helix breakers inside; Pro will result in a kink for sure and Gly almost always but small polar amino acids such as Ser and Thr also can.
Kink inside an -helix in phosphoglyceryl aldehyde dehydrogenase
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NH
C-OONo amide hydrogen
Helix breaking by Pro residues
Ring constraint
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Helix cappingIzolowana 12-resztowa -helisa posiada 12 grup donorowych NH oraz 12 grup akceptorowych CO wiązania wodorowego (w obrębie łańcucha głównego). W 12 resztowej helisie może utworzyć się tylko 8 wewnątrzcząsteczkowych wiązań wodorowych. N- i C-Końcowy fragment helisy zawiera więc 4 wolne donory NH i 4 wolne akceptory CO wiązań wodorowych. Kompensacją tej niedogodności jest występowanie polarnych reszt aa na N- i C-końcu helisy. N- i C-Końcowe fragmenty helis wykazują dodatkowo różne preferencje co do określonych reszt aa.
...-N’’-N’-Ncap-N1-N2-N3-...........................-C3-C2-C1-Ccap-C’-C’’-...
The first and the last residue are the capping residues
The N1 and C1 residues possess and angle values typical of an a-helix
About 48% residues in Ncap-N1-N2-N3 fragments and about 35% of residues in -C3-C2-C1-Ccap- fragments forms hydrogen bonds in which side-chain groups take part.
Residue preferences to occur at end or close-to-end positions
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-helices always have a large dipole moment
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Side chain arrangement in helices
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Contact interactions occur between the side chains separated by 3 residues in amino-acid sequence
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Schematic representation -helices: helical wheel
3.6 residues per turn = a residue every 100o.
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Examples of helical wheels
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Amphipatic (or amphiphilic) helices
Hydrophobic
Hydrophilic
hydrophilic head groupaliphatic carbon chain lipid
bilayer
Amphipatic helices often interact with lipid membranes
One side contains hydrophobic amino-acids, the other one hydrophilic ones.
In globular proteins, the hydrophilic side is exposed to the solvent and the hydrophobic side is packed against the inside of the globule
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Length of -helices in proteins10-17 amino acids on average (3-5 turns); however much longer helices occur in muscle proteins (myosin, actin)
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Proline helices (without H-bonds)
Polyproline helices I, II, and III (PI, PII, and PIII): contain proline and glycine residues and are left-handed.
PII is the building block of collagen; has also been postulated as the conformation of polypeptide chains at initial folding stages.
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C2 (half-chair) conformations of C-endo L-proline
CS (envelope) conformation of C-endo L-proline peptide group at the trans position with respect to C-H (=120o), as in collagene
CS (envelope) of C-egzo L-proline with the peptide group at the cis’ orientation with respect to C-H (=-60o)
Polyproline ring conformations
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Structure residues/turn turns/residue
-helix -57 -47 180 +3.6 1.5
310-helix -49 -26 180 +3.0 2.0
-helix -57 -70 180 +4.4 1.15
Polyproline I -83 +158 0 +3.33 1.9
Polyproline II -78 +149 180 -3.0 3.12
Polyproline III -80 +150 180 +3.0 3.1
and angles of regular and polyproline helices
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Poly-L-proline in PPII conformation, viewed parallel to the helix axis, presented as sticks, without H-atoms. (PDB)It can be seen, that the PPII helix has a 3-fold symmetry, and every 4th residue is in the same position (at a distance of 9.3 Å from each other).
Deca-glycine in PPII and PPI without hydrogen atoms, spacefill modells, CPK colouring
PPI-PRO.PDB
PPII-PRO.PDB
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The -helix