Secondary structure of proteins : sheets supersecondary structure. Levels of protein structure organization. Peptide bond geometry. Hybrid of two canonical structures. 60% 40%. Dihedrals with which to describe polypeptide geometry. side chain. main chain.
Hybrid of two canonical structures
Because of peptide group planarity, main chain conformation is effectively defined by the f and y angles.
Zimmerman, Pottle, Nemethy, Scheraga, Macromolecules, 10, 1-9 (1977)
Hutchinson and Thornton, Protein Sci., 3, 2207-2216 (1994)
Lewis, Momany, Scheraga, Biochim. Biophys. Acta, 303, 211-229 (1973)
f fieldi+1=-60o, yi+1=-30o, fi+2=-90o, yi+2=0o
fi+1=60o, yi+1=30o, fi+2=90o, yi+2=0o
fi+1=-60o, yi+1=-30o, fi+2=-60o, yi+2=-30o
fi+1=60o, yi+1=30o, fi+2=60o, yi+2=30o
f fieldi+1=-60o, yi+1=120o, fi+2=80o, yi+1=0o
fi+1=60o, yi+1=-120o, fi+2=-80o, yi+1=0o
f fieldi+1=-80o, yi+1=80o, fi+2=80o, yi+2=-80o
Hydrogen bond geometry in fieldb-turns
Type of structure
Average for b-turns
Helical structures field
a-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
Turns closed by H-bond
310-helix (left), a-helix (middle), p-helix (right)
Schematic representation fielda-helices: helical wheel
3.6 residues per turn = a residue every 100o.
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
Amphipatic helices often interact with lipid membranes
hydrophilic head group
aliphatic carbon chain
download cytochrome B562 field
Length of fielda-helices in proteins
10-17 amino acids on average (3-5 turns); however much longer helices occur in muscle proteins (myosin, actin)
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.
f and y angles of regular and polyproline helices
Deca-glycine in PPII and PPI without hydrogen atoms, spacefill modells, CPK colouring
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).
The spacefill modells, CPK colouring b-helix
Pauling and Corey continued thinking about periodic structures that could satisfy the hydrogen bonding potential of the peptide backbone. They proposed that two extended peptide chains could bond together through alternating hydrogen bonds.
Alpha, Beta, … I got ALL the letters up here, baby!
The side chains have alternating arrangement; usually hydrophobic on one and hydrophilic on the opposite site
resulting in a bilayer
The amino acid R groups face up & down from a beta sheet
Residues/turn spacefill modells, CPK colouring
Distance along axis/turn
A diagram showing the dihedral bond angles for regular polypeptide conformations.Note: omega = 0º is a cis peptide bond and omega = 180º is a trans peptide bond.
Schemes for antiparallel (a) and parallel (b) spacefill modells, CPK colouring b-sheets
b spacefill modells, CPK colouring -sheets are pleated
And the ruffles add flavor! spacefill modells, CPK colouring
b spacefill modells, CPK colouring -sheet chirality
Because of interactions between the side chains of the neighboring strands, the b-strands have left-handed chirality which results in the right twist of the b-sheets
The degree of twist is determined by the tendency to save the intrachain hydrogen bonds in the presence of side-chain crowding
The the intrachain hydrogen bonds in the presence of side-chain crowding geometry of parallel twistedb -sheets
Parallel the intrachain hydrogen bonds in the presence of side-chain crowdingb-structures occur mostly in a/b proteins where the b-sheet is covered by a-helical helices
Geometry of antiparallel the intrachain hydrogen bonds in the presence of side-chain crowding¯b-sheets (mostly outside proteins and between domains)
Threestrand with a b-bulge
Three strand helicoidal
Example of a coiled two-strand antiparallel the intrachain hydrogen bonds in the presence of side-chain crowdingb-sheet
Example of a three-strand antiparallel the intrachain hydrogen bonds in the presence of side-chain crowdingb-structure
Geometria skręconych (ang. the intrachain hydrogen bonds in the presence of side-chain crowdingtwisted) struktur b¯
W powierzchniach cylindrycznych b¯(podobnie jak w b) konformacja nici na końcach cylindra jest często nieregularna
Kąt pod jakim układają się nici na powierzchni cylindra, mierzony między dwiema przeciwległymi nićmi, przybiera różne wartości w zależności od liczby nici
Example of a cyllindrical ( the intrachain hydrogen bonds in the presence of side-chain crowdingb-barrel) structure
Large antiparallel the intrachain hydrogen bonds in the presence of side-chain crowdingb-sheets: twisted planes not barrels
2CNA (3CNA) i 3BCL
b the intrachain hydrogen bonds in the presence of side-chain crowding-bulges
Local the intrachain hydrogen bonds in the presence of side-chain crowdinga-state at the bulging residue
Four types of the intrachain hydrogen bonds in the presence of side-chain crowdingb-bulges
F, Y angles of residue 1 as for a structures; those for residue 2 and X for b-structures
Link of a b- and turn structure
Gly almost exclusively at position 1
Strong preference for Gly at position X
The hydrophobic and hydrophilic side chains are arranged on alternative sides of a b-sheet.
1B9C - RASMOL
Length of the intrachain hydrogen bonds in the presence of side-chain crowdingb-sheets in proteins
20 Å (6 aa residues)/strand on average, corresponding to single domain length
Usually up to do 6 b-strands (about 25 Å)
Usually and odd number of b-strands because of better accommodation of hydrogen bonds in a b-sheet
Covalent the intrachain hydrogen bonds in the presence of side-chain crowdinginterstrandconnectionsinb-sheets
There are two basic categories of connections between the individual strands of a beta sheet (Richardson, 1981). When the backbone enters the same end of the sheet that it left it is called a hairpin connection and when the backbone enters the opposite end it is called a crossover connection.
Crossover connections can be thought of as a type of helical connection of the strand ends. In globular proteins, right-handed crossovers are the rule, although a few examples of left-handed crossovers are available (e.g., subtilisin and glucose phosphate isomerase).
b the intrachain hydrogen bonds in the presence of side-chain crowding-sheet topology in proteins
Topologia the intrachain hydrogen bonds in the presence of side-chain crowdingb struktur białkowych
An example of complex beta-sheets: the intrachain hydrogen bonds in the presence of side-chain crowding
- multiple pleated sheets provide toughness & rigidity to many structural proteins.
a-b the intrachain hydrogen bonds in the presence of side-chain crowding and b-a connections
Conserved Gly residues and hydrophobic interactions between residues at positions Gly-4 and Gly+3
1CTF 100-120 - RASMOL
„Paperclips” the intrachain hydrogen bonds in the presence of side-chain crowding
Green key and the intrachain hydrogen bonds in the presence of side-chain crowdingb-arch
PCY 74-80 - RASMOL
helix strand turn
helix strand turn