9-protein structure amino acids and peptides.pptx

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1. By . Dr. Elrasheed Eltaher Osman CHEMISTRY , STRUCTURE AND FUNCTION OF PROTEINS

2. The objectives Definition of proteins Functions of proteins Classification of protein Protein structural levels CLASSIFICATION ACCORDING TO Solubility Shape Biological function Three dimensional structure Nutritional values NEW CLASSIFICATION

3. Proteins

4. 2006-2007 Proteins Multipurpose molecules

5. What is proteins: Is the most structurally & functionally diverse group of biomolecules that result from polymerization of amino acids

6. Proteins Structure: monomer = amino acids 20 different amino acids polymer = polypeptide protein can be one or more polypeptide chains folded & bonded together large & complex molecules Has 3-D {dimensional} shape

7. Functions of proteins : involved in almost everything Enzymes (pepsin, polymerase, etc.) Structure (keratin, collagen) Carriers & transport ( membrane channels) Receptors & binding ( defense antibodies) Contraction ( actin & myosin) Signaling (hormones: insulin) Storage (bean seed proteins)

8. Classification of proteins

9. OL Why classify proteins Number of solved structures grow rapidly Generate overview of structure types Detect similarities (evolutionary relationships) Set up prediction benchmarks

10. Classified according to Solubility Shape Biological function Three dimensional structure Nutritional values

11. Example According to the shape classified as 1- fibrous 2- globular According to solubility 1-albumin 2-globulin 3- histone

12. According to the biological functions classified as Structural Catalytic Immunological Transporter Channel Receptor Regulatory

13. Protein structural levels

14. Levels of Protein Structure Primary Secondary Tertiary Quaternary Assembly Folding Packing Interaction S T R U C T U R E P R O C E S S

15. Protein structure levels 1- Primary structure 2- Secondary structure 3- Tertiary structure 4- Quaternary structure

16. Primary structure of protein Is the amino acids sequences Joint by peptide bond Include any location of disulfide bridge

17. Secondary structure of protein Is spatial conformation that brought near by amino acids residues together Can be 1- Regular 2- Irregular

18. The regular secondary structures include 1- α - helix 2- β -pleated sheets 3- β -turn

19. α -helix is an equal winding of the polypeptide around a common axis forming regular coil

20. α -helix

21. β -pleated sheets is the looping of polypeptide to and fro to form parallel and anti-parallel sheets

22. Β -turn is regular bending of polypeptide that changing it is direction

23. Forces stabilized the secondary structure Hydrogen bonds Van Der Waal forces

24. Class/Motif Class = secondary structure composition, e.g. all , all , segregated +, mixed / Motif = small, specific combinations of secondary structure elements, e.g.  -  -  loop

25. Tertiary structure of protein Is spatial conformation of polypeptide in such away that far distant amino acids brought together Some protein are biologically active at tertiary structure levels

26. Forces stabilized tertiary structure include Hydrogen bond Hydrophobic interaction Electrostatic bonds Van Der Waal forces Disulfide bridge

27. Domain Is special conformation in tertiary structure having special function containing special motifs

28. Quaternary structure of protein Protein consisting of more than one polypeptide called subunit Stabilized by the following forces Hydrogen bonds Electrostatic bond Disulfide bridge

29. Subunits Is the whole polypeptide that does not function unless joint other polypeptide to form functional protein and is called (mere)

30. New Classification of protein

31. According to three dimensional structure classified as SCOP Manual classification (A Murzin ) CATH Semi manual classification (C rengo ) FSSP Automatic classification (L Holm)

32. Computational Determination and Analysis CATH ( C lass, A rchitecture, T opology, H omologous superfamily ) SCOP ( S tructural C lassification O f P roteins) FSSP ( F old classification based on S tructure- S tructure alignment of P roteins)

33. SCOP Manual classification Class Folds Superfamilies Families Murzin et al 1995

34. Each Class may be divided into one or more folds Proteins which have the same (>~50%) secondary structure elements arranged in the same order in the protein chain and in three dimensions are classified as having the same fold

35. Superfamilies A superfamily contains proteins which are thought to be evolutionarily related due to Sequence Function Special structural features

36. Families are subdivision of supefamilies Contains members whose relationship is readily recognizable from the sequence (>~25% sequence identity)

37. CATH Levels Class Architecture This level is unique to CATH (~30 is defined) Topology ~Fold(/ superfamily ) in SCOP Homologous Superfamily ~ Superfamily (/family) in SCOP