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structure of protins
This document discusses the structure of proteins at four levels: primary, secondary, tertiary, and quaternary. The primary structure refers to the amino acid sequence in the polypeptide chain. Secondary structures include alpha helices and beta sheets formed by hydrogen bonding between amino acids. Tertiary structure describes the overall 3D shape of the protein formed by interactions between amino acid side chains. Quaternary structure applies to proteins composed of multiple polypeptide subunits that combine through non-covalent bonds. The structures are determined through techniques like X-ray crystallography and NMR spectroscopy.
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structure of protins
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- 3. • Proteins arean 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 INTRODUCTION
- 4. PRIMARY STRUCTURE • Theprimary structure of protein refers to the sequence of amino acids present in the polypeptide chain. • Amino acids are covalently linked by peptide bonds. • Each component amino acid in a polypeptide is called a “residue” or “moiety” • By convention, the 10 structure of a protein starts from the amino- terminal (N) end and ends in the carboxyl-terminal (C) end.
- 5. IMPORTANCE OF PRIMARYSTRUCTURE • To predict 20 and 30 structures from sequence homologies with related proteins. (Structure prediction) • Many genetic diseases result from abnormal amino acid sequences. • To understand the molecular mechanism of action of proteins. • To trace evolutionary paths. • End group analysis – Edman degradation. • Gene sequencing method. METHODS OF AMINO ACID SEQUENCE DETERMINATION
- 6. SECONDARY STRUCTURE • Localizedarrangement of adjacent amino acids formed as the polypeptide chain folds. • It consists of • Linus Pauling proposed some essential features of peptide units and polypeptide backbone. They are: – The amide group is rigid and planar as a result of resonance. So rotation about C-N bond is not feasible. – Rotation can take place only about N- Cα and Cα – C bonds. – Trans configuration is more stable than cis for R grps at Cα • From these conclusions Pauling postulated 2 ordered structures α helix and β sheet α-helix β-pleated sheet β-bends Non repetitive structures Super secondary structures
- 7. POLYPEPTIDE CHAIN CONFORMATIONS • Theonly reasonably free movements are rotations around the C α-N bond (measured as ϕ ) and the C α-C bond (measured as Ѱ). • The conformation of the backbone can therefore be described by the torsion angles (also called dihedral angles or rotation angles)
- 8. • Spiral structure •Tightly packed, coiled polypeptide backbone core. • Side chain extend outwards • Stabilized by H bonding b/w carbonyl oxygen and amide hydrogen. • Amino acids per turn – 3.6 • Pitch is 5.4 A • Alpha helical segments are found in many globular proteins like myoglobins, troponin- C etc. ALPHA HELIX H bonding
- 9. • Formed when2 or more polypeptides line up side by side. • Individual polypeptide - β strand • Each β strand is fully extended. • They are stabilized by H bond b/w N-H and carbonyl grps of adjacent chains. BETA PLEATED SHEET 2 types Parallel Anti -Parallel N C N N NC C C
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- 11. EXAMPLES The collagen triplehelix. Silk fibroin beta sheet.
- 12. BETA BENDS • Permitsthe 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 aminoacid residues
- 13. NON REPETITIVE STRUCTURES •A significant portion of globular protein’s structure may be irregular or unique. • They include coils and loops. • Segments of polypeptide chains whose successive residues do not have similar ϕ and Ѱ values are called coils. • Almost all proteins with more than 60 residues contain one or more loops of 6 to 16 residues, called Ω loops. Space-filling model of an Ω loop
- 14. TERTIARY STRUCTURE • Tertiarystructure is the three- dimensional conformation of a polypeptide. • The common features of protein tertiary structure reveal much about the biological functions of the proteins and their evolutionary origins. • The function of a protein depends on its tertiary structure. If this is disrupted, it loses its activity.
- 15. DOMAINS • Polypeptide chainscontaining more than ,200 residues usually fold into two or more globular clusters known as domains. • Fundamental functional and 3 dimensional structure of proteins. • Domains often have a specific function such as the binding of a small molecule. • Many domains are structurally independent units that have the characteristics of small globular proteins. The two-domain protein glyceraldehyde- 3-phosphate dehydrogenase. NAD+
- 16. INTERACTIONS STABILIZING 30 STRUCTURE •This final shape is determined by a variety of bonding interactions between the "side chains" on the amino acids. • Hydrogen bonds • Ionic Bonds • Disulphide Bridges • Hydrophobic Interactions:
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- 18. DETERMINATION OF TERTIARY STRUCTURE •The known protein structures have come to light through: • X-ray crystallographic studies • Nuclear Magnetic Resonance studies • The atomic coordinates of most of these structures are deposited in a database known as the Protein Data Bank (PDB). • It allows the tertiary structures of a variety of proteins to be analyzed and compared.
- 19. • The biologicalfunction of some molecules is determined by multiple polypeptide chains – multimeric proteins. • Arrangement of polypeptide sub unit is called quaternary structure. • Sub units are held together by non covalent interactions. • Eg: Hemoglobin has the subunit composition a2b2 QUATERNARY STRUCTURE Quaternary structure of hemoglobin.
- 20. RECENT DEVELOPMENTS • Ateam of scientists at The Scripps Research Institute and the National Institutes of Health (NIH) has discovered the structure of a protein – dynamin, that pinches off tiny pouches from cell’s outer membranes. • Scientists at the Institute of Structural and Molecular Biology have revealed the structure of a complex protein called FimD that acts as an assembly platform for the pili of cystitis bacteria. • Researchers from the Walter and Eliza Hall Institute have found a structural surprise in a type of protein, Bcl-w ,that encourages cell survival, raising interesting questions about how the proteins function to influence programmed cell death.
- 21. CONCLUSION • Proteins areextraordinarily complex molecules. Of all the molecules encountered in living organisms, proteins have the most diverse functions. • So a basic understanding of the structure of proteins is necessary to comprehend its role in organisms. • Further researches will provide more insight into the structure of several other proteins in the coming year.
- 22. REFERENCE • Voet, Donald;Voet Judith. Biochemistry, 3rd edition, John Wiley and sons. • Champe, Pamela.C, Harvey, Richard A, Ferrier Denise R (2005). Lippincott’s Illustrated Reviews: Biochemistry, 3rd edition. Lippincott William and Wilkins. • McKee Trudy, McKee James R (2003), Biochemistry: The molecular basis of life, 3rd edition, McGraw Hill. • http://esciencenews.com/articles/2011/06/01/new.antibiotics.a. step.closer.with.discovery.bacterial.protein.structure • http://www.eurekalert.org/pub_releases/2010-04/sri- srs042610.php • http://www.physorg.com/news/2011-10-cell-survival-protein- reveals.html