O Proteins are the macromolecules made up of long chains of one or more amino acid residues. O Proteins are the primary constituents of all living matter and they are found in all living cells. O They perform several important biological functions.
Outline of Structure O Proteins are basically the polypeptide chains of amino acids. O The amino acids are linked to each other by a peptide bond.
O The protein molecule may exist in 4
different types of structures.
2 13-05-2024
Different structures of proteins Primary Structure Secondary Structure Tertiary Structure Quaternary Structure
PRIMARY STRUCTURE: 1. This involves the linear arrangement of amino acids in a polypeptide chain. 2. It represents number, nature, sequence of amino acids in a polypeptide chain. 3. All the properties of a protein molecule are determined directly or indirectly by the primary structure. 4. Any folding or catalytic activity of protein depends on the proper primary structure
3 13-05-2024
SECONDARY STRUCTURE The folding of linear polypeptide chain into a specific arrangement, represents secondary structure of protein molecules. It is of two types: (i) Alpha helix: The polypeptide forms a spiral staircase with 3.6 amino acids per turn. The coil is held together by hydrogen bonds. (ii) Beta-Pleated Sheet: Hydrogen bonding occurs at right angles to
TERTIARY STRUCTURE The final three dimensional structure of a protein due to further folding of its polypeptide chain is called as tertiary structure. Folding of proteins occur to maximize stability. The stabilizing interactions that occur in folding are: (i) Covalent bonds (ii) Hydrogen bonds (iii) Van der waal forces (iv) Electrostatic interactions
4 13-05-2024
QUATERNARY STRUCTURE The quaternary structure involves non covalent interactions of two or more polypeptide chains. The individual chain in quaternary structure is called a subunit. It describes the way in which subunits are placed in space. The interactions that hold together are: (i) Hydrophobic interactions (ii) Hydrogen bonding (iii) Electrostatic interactions For e.g.. Haemoglobin
A protein may also be classified as:
Fibrous Proteins Globular Proteins
1. These are tough, 1. These are colloidal, usually insoluble in usually soluble in water. water. 2. They have long, 2. These are folded thread like into roughly spherical structures that shapes. tend to lie side by 3. These are related side to form fibers to many life- E.g.: Keratin, processes functions. Collagen etc. E.g.: Insulin, Fibrinogen etc.
5 13-05-2024
What are proteinmotifs?
O Proteinmotifs are the supersecondary structures which occur in many unrelated globular proteins. O These are the partially stable arrangements of several elements of secondary structure and connections between them. O Recognized motifs range from simple to complex ones, sometimes appearing in repeating units or combinations. A single large motif may
Structural Organization in Proteinmotifs O The proteinmotifs can be of given structures: (i) motif: It is the right handed crossover connection between two consecutive parallel strands of a -sheet and an incorporated - helix.
(ii) -hairpin motif
It consists of antiparallel -sheets and is formed by sequential segments of polypeptides that are
6 13-05-2024
O motif: It consists of two successive anti-parallel -helices packed against each other, with their axes inclined so as to permit their contacting side chains to interdigitate efficiently. E.g. -keratin
O Greek Key motif:
It resembles the ornamental design, commonly seen in ancient Greece. -hairpin is folded over to form a four stranded anti-parallel -
Domains O Polypeptide chains that consist of more than ~200 residues usually fold into two or more globular clusters known as domains, which often give these proteins a bi- or multilobal appearance. O Most domains contain 100-200 Amino Acid residues and have an average diameter of ~25 Angstrom. O Domains are therefore structurally independent units each having the characteristics of a small globular protein. O Small molecule binding sites often occur in multi domain proteins in clefts between domains, which help in functioning.
7 13-05-2024
Structure of Domains
/ barrels /- domains Open - Classification sheets on the basis of -domains structure
-domains
O -domains: Only -helix motifs are involved to form a domain. E.g.: cytochrome b562
O -domains: These contain 4 to >10 predominantly antiparallel -strands that are arranged into two sheets that pack against each other. Inherent curvature of sheets often cause them to roll up into -barrels
8 13-05-2024
Some -barrels topologies
O Up and Down -barrels: It consists of 8 successive antiparallel strands that are arranged like the staves of a barrel. E.g.: Retinol Binding Protein
O In -B crystallin the domain consists of two
Greek key motifs which thereby constitute an alternative way of connecting the sheets.
O Swiss roll barrel
4-segment - hairpin rolled up to an 8- stranded antiparallel -barrels of different topology. E.g.: Peptide-N4-(N-acetyl- -D- glucosaminyl) asparagine amidase F.
Up and Down - barrels
-B crystallin
Swiss roll barrel
9 13-05-2024
/-domains O / barrels A central parallel or mixed – sheet is flanked by –helices. The / –barrel is remarkably regular structure that consists of 8-stranded parallel – barrel concentric with an outer barrel of 8 –helices. Each –strand is approximately antiparallel to the succeeding –helix and all are inclined at around some angle to barrel axis. E.g.: Triose Phosphate Isomerase (TIM)
O Open -sheets These are known as doubly wound sheets These consist of three layers of polypeptide backbone interspersed by regions of hydrophobic side chains. They have been observed to contain 4-10 –strands with 6 strands being the most common.
A topological switch point is
a point where chain reverses its winding direction. Since TSP can occur between any consecutive –helix and –strand, doubly wound
10 13-05-2024
Folds O Groups of motifs combine in overlapping and non-overlapping ways to form the tertiary structure of a domain, which is called a fold.
O The number of possible different folds would seem
to be unlimited.
O Few protein folds have been recognized as unique.
Most proteins of known-structure have folds that also occur in unrelated proteins.
O Theoretical considerations suggest there are less
than 8000 naturally occurring folds, of these ~1200 have been determined, with around half of the proteins of known structure belonging to only 20 fold groups.
Conclusion O Proteins are polypeptide chain, consisting of amino acids linked together by peptide bond. O The protein molecule may have a primary, secondary, tertiary or quaternary structure. O Proteinmotifs are the supersecondary structures, which are partially stable arrangements of secondary structures. O Domains are the globular clusters of proteins consisting of long chains of amino acids O Folds are overlapping or non-
