Protein Structure – Part-2 Pauling Rules The bond lengths and bond angles should be distorted as little as possible. No two atoms should approach one another more closely than is allowed by their van der Walls radii. The amide group must remain planar and in trans configuration. Some kind of noncovalent bonding is necessary to stabilize a regular folding. The most likely bond is hydrogen bond between amide protons and carbonyl oxygen. The preferred conformations must be those that allow maximum amount of hydrogen bonding.

Protein Secondary Structure Polypeptide chains can fold into regular structures such as the alpha helix, the beta-sheet, and turns and loops. α-Helix The polypeptide backbone is tightly wound around an imaginary axis drawn longitudinally through the middle of the helix, forming the inner part of the rod and the side chains extend outward in a helical array (Fig-1, Fig-6).

Fig-1.

α-Helix is stabilized by hydrogen bonds between the -NH- & -CO- groups of the main chain. -CO- group of each amino acid forms a hydrogen bond with the –NH- group of the amino acid that is situated 4 residues ahead in the sequence (Fig-2). Fig.2. Hydrogen-Bonding Scheme For an α helix.

The screw sense of an alpha helix is right handed in essentially all proteins. Right handed helices are energetically more favorable because there is less steric clash between the side chains and the backbone. Five different kinds of constraints affect the stability of an α-helix: 1. The electrostatic repulsion (or attraction) between successive amino acid residues with charged R groups 2. The bulkiness of adjacent R groups 3. The interactions between R groups spaced three (or four) residues apart 4. The occurrence of Pro and Gly residues 5. The interaction between amino acid residues at the ends of the helical segment and the electric dipole inherent to the α-helix. The tendency of a given segment of a polypeptide chain to fold up as an α-helix therefore depends on the identity and sequence of amino acid residues within the segment.

Beta Sheets Beta Sheets are stabilized by hydrogen bonding between polypeptide strands It is composed of two or more polypeptide chains called β strands. A β strand is almost fully extended rather than being tightly coiled as in the α-helix. The distance between adjacent amino acids along a β strand is approximately 3.5 A o in contrast to a distance of 1.5 A o along an α- helix. The side chains of adjacent amino acids point in opposite directions. Adjacent chains in a β sheet can run in the same direction (parallel β sheet- Fig. 3a) or in opposite directions ( antiparallel β sheet- Fig. 3b)

Fig- 3a For each amino acid, the –NH- group is bonded to the –CO- group of one amino acid on the adjacent strand, whereas –CO- group is hydrogen bonded to –NH- group on the amino acid two residues farther along the chain.

Fig.- 3b The –NH- group and the –CO- group of each amino acid are respectively bonded to –CO- group and –NH- group of a partner on the adjacent chain.

Many strands, typically four or five but as many as 10 or more, can come together in β sheets. Such β sheets can be purely parallel, purely antiparallel, or mixed. Fig.4. Two types of β sheet structures. (A) An antiparallel β sheet (B) A parallel β sheet

Polypeptide chains can turn direction by making reverse turns and loops which give protein a compact and globular shape (Fig.5 a,b). Fig.5a. Structure of a Reverse Turn. The CO group of residue i of the polypeptide chain is hydrogen bonded to the NH group of residue i + 3 to stabilize the turn.

Fig.5b.Loops on a Protein Surface. A part of an antibody molecule has surface loops (shown in red) that mediate interactions with other molecules. Turns and loops invariably lie on the surfaces of proteins and thus often participate in interaction between protein and other molecules.

Fig.6. Secondary structure elements The regular conformation of the polypeptide backbone observed in the α helix and the β sheet. (A, B, and C) The α helix. The N–H of every peptide bond is hydrogen-bonded to the C=O of a neighboring peptide bond located four peptide bonds away in the same chain. (D, E, and F) The β sheet. In this example, adjacent peptide chains run in opposite (antiparallel) directions. The individual polypeptide chains (strands) in a β sheet are held together by hydrogen- bonding between peptide bonds in different strands, and the amino acid side chains in each strand alternately project above and below the plane of the sheet. (A) and (D) show all the atoms in the polypeptide backbone, but the amino acid side chains are truncated and denoted by R. In contrast, (B) and (E) show the backbone atoms only, while (C) and (F) display the shorthand symbols that are used to represent the α helix and the β sheet in ribbon drawings of proteins

Tertiary Structure The compact, asymmetric 3-D structure that individual polypeptide attain is called tertiary structure (Fig-7) The tertiary structures of water soluble proteins have common features- a) An interior formed of amino acids with hydrophobic side chains. b) A surface formed largely of hydrophilic amino acids that interact with the aqueous environment. The driving force for the formation of the tertiary structure of water soluble proteins is the hydrophobic interactions between the interior residues. Proteins which exist in hydrophobic environment display the inverse distribution- Hydrophobic on surface and Hydrophilic interior.

Domain Certain combinations of α-helices and β sheets pack together to form compactly folded globular units, each of which is called a domain. Domains are usually constructed from a certain section of polypeptide chain that contains between amino acids, and they seem to be the modular units from which proteins are constructed. Motifs Certain combinations of secondary structure (α-helices and β sheets to make a globular structure) occur repeatedly in the core of many related proteins and frequently exhibit similar functions. These combinations are called motifs.

Fig.7

Factors influencing tertiary structures Electrostatic interactions (positive and negatively charged side chain Internal H-bond (Ser OH and Asp C=O ) Van der Walls interactions- the interior is tightly packed, allowing for maximum contact between side chain atoms. Hydrophobic effect- Entropy (unfavorable conformation), Intramolecular (side group interaction, and Cooperativity (burial of hydrophobic groups)

Quaternary Structure Polypeptide chains can assemble into multisubunit structures giving rise to quaternary structure. Proteins containing more than one polypeptide chain display quaternary structure. Each individual polypeptide chain is called a subunit. Quaternary structure can be as simple as two identical subunits or as complex as dozens of different subunits. In most cases, the subunits are held together by non covalent bonds and interactions.

Fig-8