Part I : Introduction to Protein Structure


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Part I : Introduction to Protein Structure

  1. 1. Part I : Introduction to Protein Structure Mohamed Ramadan Hassan Manager of Research & Development Laboratory Quality Control Department VACSERA
  2. 2. Overview  What are the Importance of Protein Structure ?  The Basics of Protein Structure  Levels of Protein Structure  Classification of Protein Structure
  3. 3. Overview  What are the Importance of Protein Structure ?  The Basics of Protein Structure  Levels of Protein Structure  Classification of Protein Structure
  4. 4. What are the Importance of Protein Structure ? In the factory of living cells, proteins are the workers, performing a variety of biological tasks.  Each protein has a particular 3D structure that brings into close proximity residues that are far apart in the amino acid sequence. “ Structure implies Function “ Each protein adopts a particular folding pattern that determines its function.  During normal cells life, most newly synthesized proteins fold spontaneously.   Sequenc Structure Function
  5. 5. Common Characters of Proteins  Physical Characters Hydrophobic residues tends to be buried inside the structure. Hydrophilic residues tends to be exposed to the solvent.  Electrostatic Characters Hydrogen bonding between +ve and –ve Charged atoms distantly separated, e.g.; – N and – O atoms which help to stabilize the structure.  Structural Characters Covalent bonding between – SH groups in 2 Cysteine residues in two different chains or in the same chain.
  6. 6. Anfinsen’s Thermodynamic Hypothesis “ The three-dimensional structure of a native protein in its normal physiological environment is the one in which the Gibbs free energy of the whole system is the lowest one; that is, that the native conformation is determined by the totality of interatomic interactions and hence by the amino acid sequence, in a given environment. “ ---- Anfinsen’s Nobel Lecture, 1972
  7. 7. Overview  Why Protein Structure ?  The Basics of Protein Structure  Levels of Protein Structure  Classification of Protein Structure
  8. 8. The Basics of Protein Structure  Proteins are linear heteropolymers.  Contains one or more polypeptide chains.  Repeat units are 20 natural amino acids.  Total Number of Amino acids from few 10s - 1000s.   Proteins enormously varied in 3D shapes ( “ folds ” ) in order to perform their biological activity. L-amino acids are the naturally occurring configuration in living organisms.
  9. 9. Common Structure of L-Amino Acid Cα is a chiral center : i.e.; Has 4 chemically different groups attached to it. Side Chain = H , CH3 , …. R C - ---- --------------------- ------------------ H ------------------------------------------ N Cα O ---- + ------------------------- H ------------------ Backbone --------------------------------------------------- ------------------------------Amino Atom lost during Peptide bond formation --- -------------------------------------H Atom lost ----Carboxylate H During Peptide bond formation -------------------------- O
  10. 10. Aliphatic residues Hydrocarbon side chains Alanine Ala or A Valine Val or V Leucine Leu or L Only heavy atoms are usually shown ( i.e.; no hydrogens atoms ). Also, residues lacks one oxygen atom in the carboxylate group.
  11. 11. Aromatic residues
  12. 12. Charged residues These contain side chains that are charged under physiological conditions, i.e. pH 7.0: Acidic – negative charge.  Basic – positive charge.
  13. 13. Polar residues
  14. 14. The odd couple Can form cisPeptide bonds
  15. 15. Formation of Polypeptide Chain
  16. 16. Backbone torsion angles
  17. 17. Overview  Why Protein Structure ?  The Basics of Protein Structure  Levels of Protein Structure  Classification of Protein Structure
  18. 18. Levels of Protein Structure Zero Structure  Amino acid composition, i.e.; percentage of each single amino acid which can be translated to number of each one ( no structural information ). Primary Structure  This is simply the order of covalent linkages along the polypeptide chain, i.e.; the sequence itself. MHGYRTPRSKTDYGCQILETRAS
  19. 19. Levels of Protein Structure Secondary Structure  Local organization of protein backbone:- e.g.; α-helix, β-strand (which assemble into β-sheet), turn and interconnecting loop.
  20. 20. Secondary Structure The α-helix   Myoglobin is the first structure predicted (Pauling, Corey, Branson 1951) and experimentally solved (Kendrew et. al. 1958). It is one of the most closely packed arrangement of residues.  Turn: 3.6 residues.  Pitch: 5.4 Å/turn.  Rise: 1.5 Å/residue.  Dipole: start +ve and end –ve.
  21. 21. Secondary Structure Properties of the α-helix   Side chains project outwards: proline only fits the start. Amphipathicity if solvent exposed: hydrophilic residues in cyan; hydrophobic residues in magenta.
  22. 22. Secondary Structure The β-sheet   Side chains project alternately up or down. Backbone almost fully extended: thus one of the most loosely packed arrangements of residues.
  23. 23. Secondary Structure Topologies of β-sheets
  24. 24. Levels of Protein Structure Tertiary Structure   Packing of secondary structure elements into a compact spatial unit. “Fold” or domain this is the level to which structure prediction is currently possible.
  25. 25. Driving forces in protein folding    Stabilization by forming hydrogen bonds. Exposing hydrophilic residues ( charged and polar side chains ) and burying hydrophobic residues ( aliphatic and aromatic side chains ). For small proteins ( usually < 75 residues ). Formation of disulfide bridges. Interactions with metal ions.
  26. 26. The disulfide bond  It equals disulfide bridges.  Mostly in extracellular proteins.   Formed by oxidation of the SH (thiol) group of cysteine residues. Covalent bond between the Sγ (or ‘SG’) atoms of two cysteine residues.
  27. 27. Levels of Protein Structure Quaternary Structure   Assembly of homo- or heteromeric protein chains. Usually the functional unit of a protein, especially for enzymes.
  28. 28. Overview  Why Protein Structure ?  The Basics of Protein Structure  Levels of Protein Structure  Classification of Protein Structure
  29. 29. Classification of Protein Structure All-α (helical) All-β (sheet)
  30. 30. Classification of Protein Structure α/β (parallel β-sheet) α+β (antiparallel β-sheet) Most popular class
  31. 31. What is meant by “Domain” Structure     A domain is a compact folding unit of protein structure, usually associated with a function. It is usually a “fold” - in the case of monomeric soluble proteins. Comprises normally only one protein chain: rare examples involving 2 chains are known. Domains can be shared between different proteins.
  32. 32. Homologous Folds    Hemoglobin and erythrocruorin: 31% sequence identity. Normally at least 25% sequence identity. Identical or closely related functions.
  33. 33. Analogous Folds    Hemoglobin and phycocyanin: 9% sequence identity. Structural architechture quite similar. Function not conserved.
  34. 34. (I) Structural Comparison Facts     Proteins adopt only a limited number of folds. Homologous sequences show structures: variations are mainly in regions. very similar non-conserved In the absence of sequence homology, some folds are preferred by vastly different sequences. There are striking regularities in the way in which secondary structures are assembled ( Levitt & Chothia , 1976 ).
  35. 35. (II) Structural Comparison Facts   The “active site” (a collection of functionally critical residues) is remarkably conserved, even when the protein fold is different. Structural models (especially those based on homology) provides insights into possible function for new proteins. Implications for that :Protein engineering. Ligand/Drug design. Function assignment for genomic data.