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STRUCTURE OF PROTEINS

STRUCTURE OF PROTEINS. Vladimíra Kvasnicová. The figure was adopted from: J.Koolman, K.H.R ö hm / Color Atlas of Biochemistry, 2 nd edition, Thieme 2005. Syllabus of the lecture. amino acids found in proteins peptides description of stucture of proteins classification of proteins

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STRUCTURE OF PROTEINS

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  1. STRUCTURE OF PROTEINS Vladimíra Kvasnicová

  2. The figure was adopted from: J.Koolman, K.H.Röhm / Color Atlas of Biochemistry, 2nd edition, Thieme 2005

  3. Syllabus of the lecture • amino acids found in proteins • peptides • description of stucture of proteins • classification of proteins • physicochemical properties of proteins

  4. Chemical nature of proteins • biopolymers of amino acids • macromolecules (Mr > 10 000) The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

  5. Amino acids in proteins • 21 proteinogenic AAs • other AAs are formed by a posttranslational modification L--aminocarboxylic acids The figures were adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

  6. Amino acids belong amongoptical active compounds 2 enantiomers: L- a D- The figure was found at http://www.imb-jena.de/~rake/Bioinformatics_WEB/gifs/amino_acids_chiral.gif (October 2007)

  7. The figure was adopted from http://webschoolsolutions.com/biotech/macro.htm (2006)

  8. The figure was adopted from http://webschoolsolutions.com/biotech/macro.htm (2006)

  9. Modified amino acids The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

  10. Essential amino acids • essential in a diet, they are not synthetized in a human body • branched chain AAs (Val, Leu, Ile) • aromatic AAs (Phe, Trp) • basic AAs (Lys, Arg, His) • Thr, Met

  11. Side chains of AAs determine final properties of proteins Isoelectric point (pI) = pH value at which the net charge of a compound is zero pI = (pKCOOH + pKNH3+) / 2 Solutions of AAs belong among ampholytes (= amphoteric electrolytes) „AMPHION“ The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

  12. The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

  13. Absorption of UV radiation • Tyr and Trp strongly absorb in 250 – 300 nm → spectrophotometric determination Ability to bind other compounds • Ser, Thr, (Tyr) ← phosphate or saccharide • Asn ← saccharide Formation of disulfide bonds (oxidation/reduction): • 2 Cys-SH → Cys-S-S-Cys („cystine“)

  14. Important reactions of AAs • dissociation (formation of salts) • decarboxylation → biogenic amines • transamination → 2-oxoacids • oxidative deamination → 2-oxoacids • formation of peptide bonds→peptides or proteins

  15. Peptides and proteins • contain 2 or more AAs bound bypeptide bond(s) • common names are used • systematic names: AA1-yl-AA2-yl-AA3 oligopeptides: 2 – 10 AMK polypeptides:  10 AMK proteins: polypeptides of Mr  10 000

  16. border: polypeptide /protein is not sharp (~ 50 AAs) • AAs are bound by peptide bonds • the order of AAs in a chain(= primary structure) is given by a genetic information • the order of AAs is reportedfromN- to C- terminal The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

  17. Description of structure of proteins • the macromolecule contains various AAs,in an exactly defined order and quantity • spacial arrangement and biological functionare DEPENDENTon the amino acid composition • native protein biological active conformation

  18. side chains ofAAsinfluence a finalstructure of proteins The figure was adopted from http://fig.cox.miami.edu/~cmallery/255/255prot/fig5x5.jpg (2007)

  19. the peptide chain has a special space arrangement: • only some proteins are composed of subunits(= quaternary structure) The figure was adopted from Albert L. Lehninger et al.: Principles of Biochemistry, ISBN 0-87901-500-4

  20. Bonds found in proteins • covalent • peptide bond -CO-NH- • disulfide bond -S-S- • noncovalent interactions • hydrogen bonds -H.....O--H.....N- • hydrophobic interactions nonpolar side chains • ionic interactions -COO- / +H3N-

  21. Primary structure of proteins = order of amino acids • read: from N- to C- end • it is coded on a genetic level • stabilization: peptide bonds The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

  22. Secondary structure of proteins = spatial arrangement of the polypeptide chain given by rotation of the planar peptide bonds around-carbons stabilization:hydrogen bondsbetween –CO- and -NH- of the peptide bonds real proteins: different parts of the polypeptide chain exist in various secondary structures The figure was adopted from http://fig.cox.miami.edu/~cmallery/150/protein/sf3x10b.jpg (October 2007)

  23. The figure was adopted from http://fig.cox.miami.edu/~cmallery/150/protein/5x20.jpg (October 2007)

  24. Helical structure (helix) • various types of the spiral:different steepness, direction of rotation, number of AAs per turn • peptide bond planes are parallelto the axis of the helix with R- perpendicular to it • H-bonds are formed between AAs found above and below themselves the most common: • -helix (right-handed) • collagen helix (left-handed, steeper) The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

  25. -pleated sheet (-structure) • direction of parts of the polypeptide chain is eitherparallel or antiparallel N→ C N→ C N→ C C → N • R- are placed above orbelow the plane of the sheet • H-bonds are formed between peptide bonds of the neighboring parts of the polypeptide chain • it brings strength to proteins The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

  26. -bend (reverse or -turn) • reverse the direction of a polypeptide chain, helping it form a compact, globular shape • often connect successive strands of antiparallel sheets Nonrepetitive secondary structure • loop or coil conformation • not random but less regular structure than - or - • one half of a protein molecule exist in it

  27. Tertiary structure of proteins = spatial arrangement of the secondary structures (folding of domains) stabilization:between side chains of AAs • hydrogen bonds • ionic (electrostatic) interactions • hydrophobic interactions • disulfide bonds

  28. tertiary structure secondary structures The figure was adopted from http://fig.cox.miami.edu/~cmallery/150/protein/5x20.jpg (October 2007)

  29. -helix -sheet motif: barrel The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

  30. Classification of proteins according to their tertiary structure • globular proteins(spheroproteins) • spheroidal shape • both secondary structures are abundant • fibrous proteins(scleroproteins) • rod-like shape • one secondary structure predominates • e.g. -keratin, collagen

  31. Quaternary structure of proteins = oligomeric structure of a protein(2 or more subunits ~ monomers) • i.e. the structure is found only in proteinscomposed from 2 or more chains (subunits) • stabilization: noncovalent interactions • the proteins have an „allosteric effect“

  32. The figure was adopted from http://fig.cox.miami.edu/~cmallery/150/protein/5x23.jpg (October 2007)

  33. SUMMARYof protein structure description The figure was adopted from http://fig.cox.miami.edu/~cmallery/150/protein/5x24.jpg (October 2007)

  34. a functionis related to the spatial structure IT DEPENDS ON AMINO ACIDS COMPOSITION functional domains funkční domény The figure was adopted from http://fig.cox.miami.edu/~cmallery/255/255prot/ecb4x19.jpg (October 2007)

  35. Classification of proteins • by localization in an organism • intra- / extracellular • by function • structural / biological active • by shape • globular / fibrous • by chemical composition • simple / complex (conjugated) proteins

  36. →conjugated proteins contein polypeptide chain (= apoprotein) + prosthetic group • glycoproteins • metalloproteins • hemoproteins • phosphoproteins • nucleoproteins • (lipoproteins) The figure was adopted from http://connection.lww.com/Products/porth7e/documents/Ch24/jpg/24_002.jpg (October 2007)

  37. protein mus be properly foldedNATIVE PROTEIN The figure was adopted from Alberts, B. a kol.: Základy buněčné biologie. Úvod do molekulární biologie buňky. Espero Publishing, s.r.o., Ústí nad Labem, 1998. ISBN 80-902906-0-4

  38. Physicochemical properties • water solubility depends on the structure • proteins form colloidal solutions(viscosity, sedimentation, light dispersion) colloidal-osmotic pressure = onkotic pressure • proteins can be salting-out of the solution(~ water sheet removing)

  39. proteins can be denaturated • heat, whipping, shaking, radiation • strong pH changes, salt of heavy metals, organic solvents, detergents The figure was adopted from http://stallion.abac.peachnet.edu/sm/kmccrae/BIOL2050/Ch1-13/JpegArt1-13/05jpeg/05-06_denaturation_1.jpg (October 2007)

  40. proteins act as antigensformation of antibodies • proteins give positive reactionwith biuret reagent

  41. proteins strongly absorb UV radiation

  42. proteins are ampholytes -COOH -COO- + H+ -NH2 + H+ -NH3+ under physiological pH proteins are negatively charged ANIONS

  43. Determination of proteinsin a laboratory • chemical reacion of peptide bonds with biuret reagent - spectrophotometry • complementary reaction with an antibody - immunochemistry • separation in an electric field- electrophoresis • denaturation

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