SUPERSECONDARY STRUCTURE, DOMAINS AND

TERTIARY STRUCTURE

Levels of protein structure organization

Between secondary and tertiary structure

• Supersecondary structure: arrangement of elements of same or different secondary structure into motifs; a motif is usually not stable by itself.

• Domains: A domain is an independent unit, usually stable by itself; it can comprise the whole protein or a part of the protein.

The Ramachandran map

Conformations of a terminally-blocked amino-acid residue

C7eq

C7ax

E Zimmerman, Pottle, Nemethy, Scheraga, Macromolecules, 10, 1-9 (1977)

Secondary Structure Preferences• helix strand turn• Alanine 1.42 0.83 0.66 • Glutamic Acid 1.39 1.17 0.74 • Glutamine 1.11 1.10 0.98• Leucine 1.41 1.30 0.59• Lysine 1.14 0.74 1.01• Methionine 1.45 1.05 0.60• Phenylalanine 1.13 1.38 0.60

• 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 1.08 1.60 0.47• Leucine 1.41 1.30 0.59• Phenylalanine 1.13 1.38 0.60• Threonine 0.83 1.19 0.96• Tryptophan 1.08 1.37 0.96• Tyrosine 0.69 1.47 1.14• Valine 1.06 1.70 0.50

• 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 1.01 0.54 1.46• Asparagine 0.67 0.89 1.56• Glycine 0.57 0.75 1.56• Proline 0.57 0.55 1.52• Serine 0.77 0.75 1.43

• 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.

Dominant -turns

Idealized hydrogen-bonded helical structures: 310-helix (left), -helix (middle), -helix (right)

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 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

Length of -helices in proteins

10-17 amino acids on average (3-5 turns); however much longer helices occur in muscle proteins (myosin, actin)

Antiparallel sheet (L6-7)

The side chains have alternating arrangement; usually hydrophobic on one and hydrophilic on the opposite siteresulting 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 Distance along axis/turn

Antiparallel -139 +135 -178 2.0 3.4

Parallel -119 +113 180 2.0 3.2

-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

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

-sheets are pleated

-sheet chiralityBecause 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

Length of -sheets in proteins20 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

Structural motifs (supersecondary structure)

• -hairpin I • -hairpin II• -corner)• helix hairpin• - corner• E-F hand• helix-turn-helix (HTH) motif• three-helix bundle• four-helix bundle• helix--hairpin (zinc finger

motif)• motif• motif (Rossman fold

• -meander• greek key motif• Swiss, jellyroll or -sandwich

motif• horseshoe motif• -propellor• -helix

Example of a -hairpin in bovine pancreatic trypsin inhibitor– BPTI.

Example of a protein with two -hairpins: erabutoxin from whale.

Example of a -meander: -spectrin SH3 domain (1BK2)

Example of a -hairpin: tryptophan zipper (1LE0)

Helix Hairpin

Alpha alpha corner (L7.24)

E-F Hand motif

Because of high content of acidic amino-acid residues with side chains pointing inside the loop, the EF-hand motif constitutes a calcium-binding scaffold in troponin, calmodulin, etc.

Helix E

helix F

Troponin C with four EF motifs that bind calcium ions.

The Helix-Turn-Helix motif

• This motif is characteristic of proteins binding to the major DNA grove.• The proteins containing this motif recongize palindromic DNA sequences.• The second helix is responsible for nucleotide sequence recognition.

The Helix-Turn-Helix motif

Three-helix bundle (1BDD) Four-helix bundle (3M9H)

The -helix--hairpin motif (zinc finger)

-- Motif (very important and very frequent)

Hydrophobic core between -helix and -sheet

horseshoe

The Greek Key Motif

The Greek-key motif as seen in proteins

Example of a protein with two Greek key motifs: crystallin C.

                                                                      

Four Greek key motifs arranged into two -barrels.

RASMOL - gcrysb.pdb

The jellyroll topology

Example of a protein with jellyroll topology: Carbohydrate-Binding Module Family 28 from Clostridium josui Cel5A (3ACI)

Example of a -barrel (red fluorescent protein; 3NED)

The -helix

Example of a -propellor motif : Thermostable PQQ-dependent Soluble Aldose Sugar Dehydrogenase (3DAS)

Classification of three-dimensional structures of protein

Richardson’s classification

– -helices are only or dominant secondary-structure elements (e.g., ferritin, myoglobin)

– -sheets are only or dominant elements (e.g., lipocain)

– contain strongly interacting helices and sheets

+ structures – contain weakly interacting or separated helices and sheets

Structural Classification Of Proteins

This is a hierarchical classification scheme with the following 4 levels:

1. Families – one family is comprised by proteins related structurally, evolutionally, and functionally.

2. Superfamoilies – A superfamily is comprised by families of substantially related by structure and function.

3. Folds – Superfamilies with common topology of the main portion of the chain.

4. Classes - Groups of folds characterized by secondary structure: (mainly -helices), (mainly-sheets), (-helices and -sheets strongly interacting), (-helices and -weakly interacting or not interacting), multidomain proteins (non-homologous proteins with vert diverse folds).

SCOP classification

[ http://scop.mrc-lmb.cam.ac.uk/scop/ ]

CATH classification (Class (C), Architecture(A), Topology(T), Homologous superfamily (H))

Four hierarchy levels:

1. Class (Level C): according to the content of secondary structure type , , ( and +), weakly or undefined secondary structure.

2. Architecture. (Level A) – Orientation and connection topology between secondary structure elements.

3. Topology. (Level T) – based on fold type.

4. Homoloous superfamilies. (Level H) – high homology indicating a common anscestor:

- >30% sequence identity OR

- > 20% sequence identiy and 60% structural homology OR

- > 60% structural homology and similar domains have similar function.

• Class(C)

derived from secondary structure

content is assigned automatically

• Architecture(A)

describes the gross orientation of

secondary structures,

independent of connectivity.

• Topology(T)

clusters structures according to

their topological connections and

numbers of secondary structures

• Homologous superfamily (H)

[ http://www.biochem.ucl.ac.uk/bsm/cath_new/ ]

Protein periodic table

W. Taylor and M. Hill

-sheets: rectangles and circles; —helics: filled circles

Layers