Protein structure and classification for BSc/Msc/NET:-

Primary structure of protein:-

·        Primary structure of protein is linnear sequence of amino acid from amino to carboxyl terminal.

·        It arises from covalent linkage of individual amino acid via peptide bond.

·        While nucleic acid carry the genetic information, The primary function of protein is to execute the task directed by that information.

Primary structure is stabilized largly by weak interaction:-

Stability:- Stability can be defined as the tendency to maintain native conformation.

The interaction that stabilizes protein conformation can be classified in 2 classes:-

(1)Covalent interaction :-

·        Peptide bond

·        Disulfide bond

(2)Non covalent interaction

·         Hydrogen bond

·        Van-der waal's interaction

·        Ionic interaction

·        Hydrophobic interaction.

Peptide bond:-  In late 1930s linus pauling an Robert corey laid down the foundation for our current understanding of protein structure.

            c alpha-----------------c----------n----------------c alpha

X-Ray diffraction studies of some protein showed that peptide C-N bond is somewhat shorter than normal C-N bond.

and it is concluded that cause of partial double bond character peptide bond cannot rotate freely.

Sedondary structure of protein:-

·        Primary structure of protein leads to the secondary structure, The local conformation of polypeptide chain or spatial relationship of amino acid residue that are close together in primary sequence.

·        In globular protein the three basic subunit of protein structure are  Alpha helix, Beta sheet and turns.

·        They can be homopolymer and heteropolymer.

·        Homopolymer are consistent conformation and because of this uniformity they are more attractive candidate for initial studies of protein structure.

·        Hydrogen bonding is mainly responsible for the formation of secondary structure.

3.613-Alpha helix:-

·        3.613/Helix It is the most comman secondary structure it can be right handed or left handed.

·        Right handed is most common and left handed is rare.

·        The (translation) distance between two amino acid is 1.5 angstrom and 0.15 nm.

·         R-group do not participate in hydrogen bonding.

·        Amid hydrogen(N-H) and carboxyl oxygen(c=o) participate in hydrogen bonding.

·        Generally 1^st and 4^th amino acid take part in H-bonding.(n)+(n+1).

·        Glycin and proline cannot participate in h-bonding because they destablizes the helical conformation.

Beta pleated sheet:-

·        It is the most common secondary structure.

·        It is extended conformation.

·        If alpha helix is converted into beta strand its lenghth will increase.

·        Hydrogen bonding occure between carboxyl oxygen (C=O) and amide hydrogen(N-H).

·        Nature of hydrogen bonding is straight in antiparallel and tilted (zig-zag)  in parallel.

·        Antiparallel conformation is most common.EG:- Silk , Fibroin and Spider web.

Turns:-

·        They are also the secondary structure.

·        4-5 amino acid generally participate.

·        They are stabilized by hydrogen bonding.

·        They are proline and glycine rich.

·        They u-shaped and found on the surface of globular protein.

·        They can be classified as:-

          

        TERTIARY STRUCTURE

·        The tertiary structure represent’s. the folded polypeptide chain(they are complexes of secondary structure).

·        It is defined as the spatial arrangement of amino acid residue that are widely separated in the primary structure/sequence or more succinetly as the overall topology formed by the polypeptide.

·        Structure involve a compact molecule composed of secondary structural motif with little irregular structure.

·        Disorder or irregular structure in protein or linker region connecting one or more domain’s.

·        The tertiary structures arises from linking together secondary structures forming a compact globular molecule.

·        Element’s of secondary structure interact via H-bond as in beta-sheet.

·        They have both covalent and non covalent interaction.Covalent interaction = Disulphide interaction.

And covalent interactions are:- Hydrogen bond, van-der waals interaction,ionic interaction,hydrophobic interaction.

Tertiary structure(Domain):-

·        These are the unit of tertiary structure.

·        They are independently folded functional unit.EG:-DNA pol.1.(5’-3’)Exonuclease,(5’-3’)polymerase activity,(5’-3’)proofeading activity.

Tertiary structure(Motif):-Example:-

·        Super secondary structure.

·        Beta Alpha Beta.

·        Beta meander.

·        Greek key motif

         Quaternary structure:-

·        More than one polypeptide participate

·        It produces multimeric proteins.

·        If monomer are identical it is homomultimere .

·        If monomer are non-identical it is heteromultimere.

·        Covalent interaction are interchain disulfide bond.

·        Non covalent are hydroen bond,van-der waals interaction,hydrophobic interaction,ionic interaction.

·        example:- haemoglobin.

Protein solubility:-     Solubility of proteins depend on PH,Nature of  solvent,temperature,Salt concentration.

(1)PH:-    Suppose there is protein “y” and its isoelectric ph is 8.

In PH-8 protein y contain both positive and negative charge.

When we take protein Y in PH-2 we got high concentration of proton and and protonation of protein y occur and there will be net positive charge which repel each others and protein solubility will increase. Similar thing will happen at Ph-11.at which there is net  negative charge and protein get solubilized.

          At isoelectric PH protein will have both positive and negative charge thus aggregation of protein occur and solubility decreases.

Nature of solvent:-   If solvents dielectric constant is high then water solubility will be high.

And if solvent dielectric constant is ;low then solubility will also be low.

Waters dielectric is 80 and thus its solubility is high.

Temperature:-  At low temperature kinetic energy of molecule is low thus van-der waals interaction is high and solubility decreases. and at high temperature kinetic energy of molecule is high and thus van – der waals interaction is low and solubility increases.

Fibrous protein:-

·        They long and rod shaped protein.

·        They are less soluble in aqueous solution because of presence of non-polar amino acid.

·        They have structural and protective function.

·        They contain mainly a single secondary structure.

·        Example:- keratin, collagen, elastine.

Keratin found in nail and hair.

Globular protein:-   

·        They are spherical protein and soluble in aqueous solution.

·        Non-polar amino acid found in anterior surface and polar hydrophilic amino acid found on outer surface.

·        They contain many type of secondary structure example:-haemoglobin (Hb), myoglobin(Mb).

                                      

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                                                                              Published by   - Prakash kaushik.