Four Levels of Protein Structure

Seite 1

Primary structure describes the linear sequence of amino acid residues in a protein. The sequence of amino acids determines the structural and functional characteristics of the protein. Proteins with very different sequences of amino acids (different primary structures) will have very different properties.

Seite 2

Secondary structure refers to regularities in local conformations that are maintained by hydrogen bonds between imide hydrogens and carbonyl oxygens of AA residues, which are relatively close to one another in the 1 structure. This folding will be driven in part by the tendency of hydrophobic side chains to minimize their contact with water and hydrophilic side chains to maximize their contact with water. Hydrogen bonding and the physical properties of the polypeptide backbone also play an important role. The major secondary structures are -helices and -structures (including -sheets).

2.1) a – Helix

 Pauling and Corey proposed structure.

 The backbone is arranged in a helical coil having about 3.6 AA’s per turn.

 -Helix stabilised by the formation of intrachain hydrogen bonds. The carbonyl (C=O) dipole of AA residue n is hydrogen bonded with the imino (NH) dipole of residue n+4. The three imino groups at one end of the helix and the three carbonyl groups at the other end lack hydrogen-bonding partners within the helix.

 The intrachain H-bonds are parallel to the long axis of the helix.

 Although a single H-bond provides negligible stability, the cumulative effect of numerous intrachain H-bonds stabilize this conformation. -Helix also designated as 3.613 helix, with the subscript designating the number of consecutive atoms present in a closed loop between the interacting O and H atoms (hydrogen bond). The stability of a -helix is affected by the identity of the side chains of the AA residues:

i) AA’s that allow spontaneous stable -helix formation; Ala, Val, Leu, Phe, Met, Asn, and Gln.

ii) Gly destabilises -helical conformations since rotation around its -carbon is unconstrained. Therefore many -helices begin or end with Gly.

iii) AA sequences with large numbers of similar charged R-groups (Lys, Arg, Asp, and Glu) are incompatible with -helical conformations due the repulsion of identically or similarly charged groups.

iv) AA sequences with large numbers of Bulky R-groups (Trp) are incompatible with -helical conformations due steric hindrance between large R-groups.

v) Pro disrupts the -helical conformation. It contains a rigid ring that prevents rotation of the N C bond. In addition Proline has no NH group available to form the intrachain H-bond that are crucial in stabilizing this conformation. Therefore it is found at the ends of -helical conformations.

 In the -keratins of hair, wool, skin, horns, and fingernails, three or seven such -helices may be super coiled around each other to form triple or seven stranded ropes that are stabilised by interchain disulphide linkages.

 In the -keratins all polypeptide chains are parallel i.e. run in the same direction from N-terminal to C-terminal.

CH

C

O

C

O

CH

N

H

Rn

N

H

N

Rn+3

H

CH

C

O

C

O

CH

Rn+4

N

H

N

Rn+4

H

CH

C

O

Rn+2

B.

A.

carbonyl

dipole

imino

dipole

 

N

O

C

 +

 +

 

H

47

2.2 B STRUCTURE

 Structure was proposed Pauling and Corey.

 In a  -strand, each AA residue accounts for about 0.32-0.34nm of the overall length.

  - Sheets consist of multiple  strands arranged in sheets.

  - Sheets may contain 2 to 15  - strands, with an average of 6 AA’s per strand.

 Several insects and spiders produce SILK, a substance that consists of the fibrous protein FIBRION.

 Side by side, polypeptide chains in the  - conformation are arranged in pleated sheet, which are cross-linked by interchain hydrogen bonds.

 All the peptide linkages participate in this cross-linking and thus lend the structure great stability.

 The R-groups lie above and below the planes of the pleated sheet.

 Examining the sequence of fibroin, almost every other residue is Gly and in between these lie either Ser or Ala i.e. [ Gly-Ala-Gly-Ala-Gly-Ser-Gly-Ala-Ala-Gly (Ser-Gly-Ala-Gly-Ala-Gly) 8 ].

 Therefore all the R-groups on one side of the sheet are hydrogen (-H) of Gly whilst most of the R-groups on the other side are either methyl (CH3) of Ala or –CH2OH group of Ser. Fibroin is rich in amino acids having relatively small R-groups, particularly Gly and Ala.

 If the R-groups are bulky or have like charges, the pleated sheet cannot exist because of R-group steric hindrances.

 In fibroin, the adjacent polypeptide chains run in the opposite directions i.e. they are antiparallel.

 In  - keratins, such as fibroin there is no disulphide interchain bonding.

 Although both the antiparallel and parallel  - pleated structures occur, the antiparallel alignment is more stable since the C=O and N-H dipoles are better orientated for optimum interaction. Because pleated sheets are loosely bonded to each other, they slide over each other and this arrangement gives silk its flexibility.

  - Keratins are found in feathers, skin, claws, beaks and scales of most reptiles and birds. Their structure is similar to silk fibroin but exhibits many modifications to provide the exact physical properties needed in different tissues.

Seite 3

Tertiary structure describes the completely folded and compacted polypeptide chain. This may contain one or more globular units or domains. Tertiary structure is stabilized by interactions of side chains of non - neighboring amino acid residues. The formation of tertiary structure brings distant portions of the primary structure close together. The tertiary structure of the protein is influenced by the primary and secondary structure. It is the primary structure of a protein that determines how it will fold into secondary and tertiary structures, and it’s the folding and overall shape of the protein that determines how that protein will function.

 Most of the chemical work of the cell (synthesizing, transporting, metabolizing) is carried out with the aid of an enormous class of globular proteins.

 These are given the name because their polypeptide chains are folded into compact structure very unlike the extended, filamentous forms of the fibrous proteins.

 As it passes through the molecule the polypeptide chain is often locally folded into one or another of the kind of secondary structure. But to make the structure globular and compact, these regions of secondary structure must also be folded on one another. This folding is referred to as the tertiary structure of a protein.

 In globular proteins it is the non-helical regions in the polypeptide chain that allow folding.

 The folding is not random but occurs in a specific fashion, thereby imparting certain specific steric properties to the protein.

 Specific folding is achieved and maintained by a variety of interactions, between one part of the polypeptide chain and another (refer to diagram), namely:i. Hydrogen-bonding

A significant number of H-bonds form within a protein’s interior and on its surface.

e.g. between the -COO of Glu and the phenolic hydroxyl (-OH) group of Tyr.

ii. Hydrophobic Interactions

e.g. Interactions occurring between nonpolar side chains of Val, Leu, Ile, Met and Phe.

iii. Disulfide bonds (covalent bonds)

This is the most prominent of covalent bonds in 3 structures.

iv. Metal-ion coordination complexes

e.g. such as those between a positively charged metal ion and the negatively charged R-groups of Asp and Glu.

v. Electrostatic (Ionic) interactions

These occur between side chains that have oppositely charged ionic groups. E.g. such as those between Lys (+) and Glu () or Arg (+) and Asp ().

Seite 4

Quaternary structure describes the association of two or more polypeptide chains into a multi-subunit or oligomeric protein. The polypeptide chains of an oligomeric protein may be identical or different. Many proteins are made up of several polypeptides. The classic example is hemoglobin. Hemoglobin is a tetramer, consisting of two -globin polypeptides and two -globin subunits.