![RAMACHANDRAN PLOT
• also known as a Ramachandran diagram or a [φ,ψ]
plot
• originally developed in 1963 by G. N. Ramachandran](https://image.slidesharecdn.com/secondarystructureofprotein-180411194709/85/Secondary-Structure-Of-Protein-Repeating-structure-of-protein-35-320.jpg)
Secondary Structure Of Protein (Repeating structure of protein)
- 1. STRUCTURE OF PROTEIN AMRUTHA K H I MSc ZOOLOGY UC COLLEGE
- 2. INTRODUCTION • Proteins are an important class of biological macromolecules which are the polymers of amino acids. • Biochemists have distinguished several levels of structural organization of proteins. They are: – Primary structure – Secondary structure – Tertiary structure – Quaternary structure
- 4. SECONDARY STRUCTURE • Segments of the polypeptide strands repeatedly coil or fold in a pattern which contribute to overall confirmation. • It consists of • It is the three dimensional form of local segments of proteins, is non linear. α-helix Collagen helix β-pleated sheet β-bends Non repetitive structures Super secondary structures
- 5. • The concept of secondary structure was first introduced by Kaj Ulrik Linderstrøm-Lang at Stanford in 1952. • Formed and stabilized by hydrogen bonding, electrostatic and van der Waals interactions
- 6. • Regular local structures formed by single strands of peptide chain due to constraints on backbone conformation
- 7. ALPHA HELIX
- 8. • Pauling and Corey found that a polypeptide chain with planar peptide bonds would form a right handed helical structure by simple twist from α-carbon-to- nitrogen and α-carbon-to-carbonyl carbon bonds. This helical structure is α-helix. • Also called classic Pauling–Corey–Branson α-helix
- 9. STRUCTURE OF THE α-helix 1. A ribbon depiction with the α-carbon and side chains 2.Side view of ball and stick version depicts H bonds between NH and CO
- 10. 3.A cross-section view of α-helix 4.Tightly-packed interior core of α-helix
- 12. Properties of α-helix • It is a rod like structure. • Tightly packed, coiled polypeptide backbone core • Stabilized by H bonding b/w NH and CO groups. • Side chain extend outwards • Amino acids per turn of helix – 3.6 • Pitch is 5.4A • Hence it gives rise per residue of 5.4/3.6 =1.5 A, this is the identity period of α-helix. • Amino acid residues in α-helix have confirmations with Ø=- 60 ˚and ψ=-45˚ to -50˚ • Alpha helical segments are found in many globular proteins like myoglobins, troponin- C etc.
- 13. • Carbonyl group of every peptide bond is in a position to form a hydrogen bond with NH group of peptide bond in the next turn of helix-hence. contribute to the stability of helix • In aqueous environment an isolated α-helix is not stable. • Coiled coil-2 identical α-helix having repeated arrangement of non-polar side chain will twist around each other gradually & forms a stable structure. • Coiled coil is found in fibrous proteins.
- 14. • α-helix is seen in α-keratin, found in skin and its appendages such as hair, nails etc. • Basic structural unit of α-keratin is 3 right handed helical polypeptide in left handed coil, stabilized by cross linking disulfide bond.
- 15. • Destabilization of α-helix can occur as follows :- I. Prolyl residue cannot participate in α-helix structure, so creates a sharp bend in helix II. Negatively charged side chain repels one another III. Steric hindrance imposed by R-groups IV. Lack of side chain on glycine allows great degree of rotation about amino acids α- carbon.
- 17. BETA PLEATED SHEET • Identified by Pauling and Corey. • Formation depends on intermolecular H bond • Formed by parallel alignment of no: of polypeptide chains • Individual polypeptide - β strand • They are stabilized by H bond b/w N-H and carbonyl groups of adjacent chains.
- 18. •Parallel: H bonded neighboring polypeptide aligned in same N-to- C terminus direction, repeat period is shorter •Anti parallel: H bonded neighboring polypeptide aligned in opposite N-to-C direction.
- 19. α-helix BETAPLEATEDSHEET Polypeptide chain is called beta strand, fully extended confirmation Polypeptide chain is tightly coiled Axial distance b/w adjacent amino acid is 3.5 A Axial distance b/w adjacent amino acid is 1.5 A Stabilized by H bonds b/w NH and CO in different polypeptide Stabilized by H bonds b/w NH and CO in same polypeptide
- 20. EXAMPLE-Silk fibroin • Anti parallel pleated sheet structure, stable. • Member of a class of fibrillar protein called α- keratin
- 21. RANDOM COIL • 3rd type of secondary structure • When a polypeptide contains adjacent buly residue or charged residue, repulsion b/w these groups causes polypeptide to assume random coil configuration • Lack a well-defined structure Other seconday structures are:- 1. β turn 2. Collagen helix
- 22. β turn • Also called β bend or hairpin bend • Found in the surface of protein, also called reverse turns
- 23. • Permits the change of direction of the peptide chain to get a folded structure. • It gives a protein globularity rather than linearity. • H bond stabilizes the beta bend structure • Proline and Glycine are frequently found in beta turns. • Beta turns often promote the formation of antiparallel beta sheets. • Occur at protein surfaces. • Involve four successive amino acid residues
- 24. Collagen helix • Also called type-2 helix. • Most abundant protein in mammals. • Principal structural element of the human body makes up 25-30% of all the body protein. • Found in connective tissues such as tendons,cartilage,cornea of eye etc • Contain 3 helical polypeptide nearly 1000 residues long. • Amino acid sequence structure is remarkably regular, nearly every 3rd residue is a glycine • It contains 4-hydroxyproline(Hyp) • The % composition is given as:- Gly(35%),Ala(11%) & Pro+Hyp (25%)
- 25. STRUCTURE OF THE COLLAGEN • Rod-shaped molecule,3000A long & 15A diameter • H bonds absent, instead stabilized by steric repulsion of pyrrolidone rings of proline and hydroxyproline residues. • 3 strands wind each other and forms superhelix,this is known as collegen triple helix • Tight wrapping provides great tensile strength ,no capacity to stretch
- 27. Tropocollagen molecule •Collagen fibrils with 3 stranded polypeptide units •Arranged head-to-tail in parallel bundles. •Each unit of tropocollagen is about 1.5 nm wide and 300 nm long. •Series of complex covalent crosslink are formed within and between the tropocollegen,making it strong mature collagen. •This is the reason for rigid brittle connective tissue in old people.
- 28. • Homotrimers- if all 3 amino acid sequence is identical • Heterotrimers-2 chains are identical and the 3rd differ
- 29. An electron micrograph of collagen from skin
- 30. Genetic disorders of collagen • This shows the close relationship between amino acid sequence and 3D structure of protein. • 2 main disorders seen are :- Ehlers-Danlos (E-D) syndrome. Osteogenesis imperfecta Ehlers-Danlos syndrome • characterized by loose joints. • group of 10 different collagen deficiency diseases. • Causes fragility,hyeredxtensibily of skin. • Caused by defect of type III collagen • Arises because glycine is replaced by serine.
- 31. The “India-rubber man” of circus fame had an E-D syndrome.
- 32. Osteogenesis imperfecta(OI) • Also called brittle bone disease. • abnormal (fragile) bone formation in human babies. • Arises because glycine is replaced by cysteine. • Defect in the synthesis of type-I collagen • Numerous fractures and severe bone deformity; small stature with underdeveloped lungs.
- 35. RAMACHANDRAN PLOT • also known as a Ramachandran diagram or a [φ,ψ] plot • originally developed in 1963 by G. N. Ramachandran
- 36. • way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure. • A dihedral angle is the angle between two intersecting planes
- 37. • The phi angle is the angle around the -N-CA- bond (where 'CA' is the alpha-carbon) • The psi angle is the angle around the -CA-C- bond. • The omega angle is the angle around the -C-N- bond (i.e. the peptide bond)
- 38. • • • . White regions : Sterically disallowed for all amino acids except glycine. Red regions : allowed regions namely the a-helical and b-sheet conformations. Yellow areas : outer limit
- 39. Uses • can be used in two somewhat different ways • First to show in theory which values, or conformation of the ψ and φ angles are possible for an amino-acid residue in a protein. • second is to show the empirical distribution of data points observed in a single structure