secondary structure of proteins : turns and helices
DESCRIPTION
Secondary structure of proteins : turns and helices. Levels of protein structure organization. Peptide bond geometry. Hybrid of two canonical structures. 60%40%. Electronic structure of peptide bond. Peptide bond: planarity. - PowerPoint PPT PresentationTRANSCRIPT
SECONDARY STRUCTURE OF PROTEINS: TURNS AND
HELICES
Levels of protein structure organization
60% 40%
Hybrid of two canonical structures
Peptide bond geometry
Electronic structure of peptide bond
Peptide bond: planarity
The partially double character of the peptide bond results in
•planarity of peptide groups
•their relatively large dipole moment
Side chain conformations: the angles
1=0
1 2 3
Dihedrals with which to describe polypeptide geometry
main chain
side chain
Skan z wykresem energii
Peptide group: cis-trans isomerization
Because of peptide group planarity, main chain conformation is effectively defined by the and angles.
Side chain conformations
The dihedral angles with which to describe the geometry of disulfide bridges
Some and pairs are not allowed due to steric overlap (e.g, ==0o)
The Ramachandran map
Conformations of a terminally-blocked amino-acid residue
C7eq
C7ax
E Zimmerman, Pottle, Nemethy, Scheraga, Macromolecules, 10, 1-9 (1977)
Energy maps of Ac-Ala-NHMe and Ac-Gly-AHMe obtained with the ECEPP/2 force field
Energy curve of Ac-Pro-NHMe obtained with the ECEPP/2 force field
L-Pro-68o
Energy minima of therminally-blocked alanine with the ECEPP/2 force field
Elements of protein secondary structure
• Turns (local)• Loops (local)• Helices (periodic)• Sheets (periodic)• Statistical coil (not regular)
- and -turns
-turn (i+1=-79o, i+1=69o) -turns
Types of -turns in proteins
Hutchinson and Thornton, Protein Sci., 3, 2207-2216 (1994)
Older classification
Lewis, Momany, Scheraga, Biochim. Biophys. Acta, 303, 211-229 (1973)
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
i+1=-60o, i+1=120o, i+2=80o, i+1=0o i+1=60o, i+1=-120o, i+2=-80o, i+1=0o
i+1=-80o, i+1=80o, i+2=80o, i+2=-80o
i+1|80o, |i+2|<60o
i+1|60o, |i+2|180o
cis-proline
Helical structures-helical structure predicted by L. Pauling; the name was given after classification of X-ray diagrams.
Helices do have handedness.
Average parameters of helical structures
TypeH-bond Turns
closed by H-bond
radius
Geometrical parameters of helices
Idealized hydrogen-bonded helical structures: 310-helix (left), -helix (middle), -helix (right)
-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.
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
Helix deformation (kink)
Example from myoglobin structure. The kink angle is up to 20o
Additional H-bonds with water molecules
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
NH
C-OONo amide hydrogen
Helix breaking by Pro residues
Ring constraint
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
-helices always have a large dipole moment
Side chain arrangement in helices
Contact interactions occur between the side chains separated by 3 residues in amino-acid sequence
Schematic representation -helices: helical wheel
3.6 residues per turn = a residue every 100o.
Examples of helical wheels
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
download cytochrome B562
Length of -helices in proteins10-17 amino acids on average (3-5 turns); however much longer helices occur in muscle proteins (myosin, actin)
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.
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
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
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
The -helix