SECONDARY STRUCTURE OF PROTEINS: HELICES, SHEETS, SUPERSECONDARY STRUCTURE

Levels of protein structure organization

60%40% Hybrid of two canonical structures Peptide bond geometry

Dihedrals with which to describe polypeptide geometry main chain side chain

Because of peptide group planarity, main chain conformation is effectively defined by the  and  angles.

The Ramachandran map

Conformations of a terminally-blocked amino-acid residue C 7 eq C 7 ax E Zimmerman, Pottle, Nemethy, Scheraga, Macromolecules, 10, 1-9 (1977)

A Ramachandran plot for BPTI (M6.10)

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  -68 o

Dominant  -turns

Types of  -turns in proteins Hutchinson and Thornton, Protein Sci., 3, (1994)

Older classification Lewis, Momany, Scheraga, Biochim. Biophys. Acta, 303, (1973)

 i+1 =-60 o,  i+1 =-30 o,  i+2 =-90 o,  i+2 =0 o  i+1 =60 o,  i+1 =30 o,  i+2 =90 o,  i+2 =0 o  i+1 =-60 o,  i+1 =-30 o,  i+2 =-60 o,  i+2 =-30 o  i+1 =60 o,  i+1 =30 o,  i+2 =60 o,  i+2 =30 o

 i+1 =-60 o,  i+1 =120 o,  i+2 =80 o,  i+1 =0 o  i+1 =60 o,  i+1 =-120 o,  i+2 =-80 o,  i+1 =0 o

 i+1 =-80 o,  i+1 =80 o,  i+2 =80 o,  i+2 =-80 o

 i+1 |  80 o, |  i+2 |<60 o  i+1 |  60 o, |  i+2 |  180 o cis-proline

Hydrogen bond geometry in  -turns Average for  - turns  -turn Asx-type  -turns Type of structure

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 Type H-bond Size of the ring closed by the H-bond radius Geometrical parameters of helices

Idealized hydrogen-bonded helical structures: helix (left),  -helix (middle),  -helix (right)

Criterion for hydrogen bonding: the DSSP formula q N =q O =-0.42 e ; q H =q C =+0.20 e Kabsch W, Sander C (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features". Biopolymers 22 (12): 2577–637 Define Secondary Structure of Proteins

Schematic representation  -helices: helical wheel 3.6 residues per turn = a residue every 100 o.

Examples of helical wheels

Amphipatic (or amphiphilic) helices Hydrophobic Hydrophilic hydrophilic head group aliphatic 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 proteins 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.

Structure  residues/turn translation/residue  -helix helix  -helix Polyproline I Polyproline II Polyproline III The ,  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).PDB Deca-glycine in PPII and PPI without hydrogen atoms, spacefill modells, CPK colouring PPI-PRO.PDB PPII-PRO.PDB

The  -helix

Comparison of  - helical and  - sheet structure

 -sheet structures Alpha, Beta, … I got ALL the letters up here, baby! 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.

A single  -strand

An example of  -sheet

Antiparallel sheet (L6-7) The side chains have alternating arrangement; usually hydrophobic on one and hydrophilic on the opposite site resulting in a bilayer 2TRX.PDB

Parallel sheet (L6-7) The amino acid R groups face up & down from a beta sheet 2TRX.PDB

Structure  Residues/turn Translation/residue Antiparallel  Parallel   -helix helix  -helix Polyproline I Polyproline II Polyproline III 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)  -sheets

1/3 peptide-bond dipole is parallel to strand direction for parallel  -sheets 1/15 peptide-bond dipole is parallel to strand direction for antiparallel  -sheets Dipole moment of  -sheets

The  -sheets are stabilized by long-range hydrogen bonds and side chain contacts

 -sheets are pleated

Backbone hydrogen bonds in  -sheets are by about 0.1 Å shorter from those in  -helices and more linear (160 o ) than the helical structures (157 o )  -sheets are not initiated by any specific residue types Pro residues are rare inside  -strands; one exception is dendrotoxin K (1DTK) And the ruffles add flavor!

 -sheet chirality Because of interactions between the side chains of the neighboring strands, the  -strands have left-handed chirality which results in the right twist of the  -sheets N-end C-end

The degree of twist is determined by the tendency to save the intrachain hydrogen bonds in the presence of side-chain crowding

anti-parallel parallel ‘twisted’ The geometry of twisted  -sheets

The geometry of parallel  twisted  sheets thioredoxin trioseposphate isomerase

Parallel  - structures occur mostly in  proteins where the  -sheet is covered by  -helical helices

Geometry of antiparallel   sheets (mostly outside proteins and between domains) twisted (coiled) Multistrand twisted Cyllinders Threestrand with a  -bulge Three strand helicoidal Cupola (dome)

Example of a coiled two-strand antiparallel  -sheet TERMOLIZYNA-RASMOL Stereoscopic views of some examples of two-strand, coiled antiparallel  -structures: a) pancreatic trypsin inhibitor, b) lactate dehydrogenase, c) thermolysin.

Example of a three-strand antiparallel  -structure The central strand is least deformed Ribonuclease A

A fragment of the antiparallel  -cyllinder in chymotrypsin, with local deviations from the ideal  -structure. Note that the divergence of the strands near cyllinder edge which occurrs to relieve local strains results in twisting the strands. The geometry of twisted)  structures  In cyllindrical antiparallel  -sheets  (as in parallel  -sheets  ) strand conformation at cyllinder ends is often irregular. The interstrand angle depends on the number of strands in a cyllinder.

Example of a cyllindrical (  -barrel) structure

Large antiparallel  -sheets: twisted planes not barrels 2CNA (3CNA) and 3BCL Concavalin

 -bulges

Local  -state at the bulging residue X 2 1

Four types of  -bulges Classical ,  angles of residue 1 as for  structures; those for residue 2 and X for  -structures G1 Link of a  - and turn structure Gly almost exclusively at position 1 Broad Larger H-bond distances between the consecutive  strands GX Strong preference for Gly at position X

 -sheet amphipacity 1B9C - RASMOL The hydrophobic and hydrophilic side chains are arranged on alternative sides of a  - sheet.

Length of  -sheets in proteins 20 Å (6 aa residues)/strand on average, corresponding to single domain length Usually up to do 6  -strands (about 25 Å) Usually and odd number of  -strands because of better accommodation of hydrogen bonds in a  -sheet

antiparallel 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). parallel Covalent interstrand connections in  sheets

antiparallel parallel  -sheet topology in proteins  -hairpin connects the C-end of one strand with the N-end of another strand. If the strands are neighbors in sequence, this connection is denoted as „+1”; if they are separated by one strand it is denoted as „+2”. The cross-over connection denoted as +1x if the connected strands are neioghbors in sequence or +2x if they are second neighbors

Topologia  struktur białkowych

Typical connections in  structures

An example of complex beta-sheets: Silk Fibroin - multiple pleated sheets provide toughness & rigidity to many structural proteins.

 and  connections 1CTF RASMOL Conserved Gly residues and hydrophobic interactions between residues at positions Gly-4 and Gly+3

„Paperclips” Turn structures at the ends of  -helices

PCY RASMOL Green key and  -arch

Secondary Structure Preference Amino acids form chains, the sequence or primary structure. These chains fold in  -helices,  -strands,  -turns, and loops (or for short, helix, strand, turn and loop), the secondary structure. These secondary structure elements fold further to make tertiary structure. There are relations between the physico-chemical characteristics of the amino acids and their secondary structure preference. I.e., the  - branched residues (Ile, Thr, Val) like to sit in  -strands. We will now discuss the 20 ‘natural’ amino acids, and we will later return to the problem of secondary structure preferences.

Secondary Structure Preferences helix strand turn Alanine Arginine Aspartic Acid Asparagine Cysteine Glutamic Acid Glutamine Glycine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tryptophan Tyrosine Valine

Secondary Structure Preferences helix strand turn Alanine Glutamic Acid Glutamine Leucine Lysine Methionine Phenylalanine Subset of helix-lovers. If we forget alanine (I don’t understand that things affair with the helix at all), they share the presence of a (hydrophobic) C- , C-  and C-  (S-  in Met). These hydrophobic atoms pack on top of each other in the helix. That creates a hydrophobic effect.

Secondary Structure Preferences helix strand turn Isoleucine Leucine Phenylalanine Threonine Tryptophan Tyrosine Valine Subset of strand-lovers. These residues either have in common their  - branched nature (Ile, Thr, Val) or their large and hydrophobic character (rest).

Secondary Structure Preferences helix strand turn Aspartic Acid Asparagine Glycine Proline Serine Subset of turn-lovers. Glycine is special because it is so flexible, so it can easily make the sharp turns and bends needed in a  -turn. Proline is special because it is so rigid; you could say that it is pre-bend for the  -turn. Aspartic acid, asparagine, and serine have in common that they have short side chains that can form hydrogen bonds with the own backbone. These hydrogen bonds compensate the energy loss caused by bending the chain into a  -turn.