Protein structure


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Protein structure and its details

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Protein structure

  1. 1. Protein Structure - Sailee Gurav (M.Sc. Biochemistry Part -1)
  2. 2.    It‟s completely defined & predictable. Each amino acid in one of these giant macromolecules is located at a specific site within the structure , giving the protein the precise shape. It can be described at several levels of organization , each emphasizing a different aspect & each dependent on different types of interactions.
  3. 3.  It‟s simply the sequence of the amino acid polymer.  1 dimensional.  By convention, written from amino end to carboxyl end.  It is important as it is the foundation in which ultimately the higher structures of the protein are determined, and thus the function of the protein.
  4. 4.  It is a local, regularly occurring structure in proteins and is mainly formed through hydrogen bonds between backbone atoms.  Pauling & Corey studied the secondary structures and proposed 2 conformations. The α helix and β sheets.
  5. 5. Right-handed coiled or spiral conformation (helix) 3.6 residues per turn stabilized by hydrogen bonds Hydrogen bonding between C' = O of residue n and NH of residue n + 4 All C'O and NH groups are joined by H-bonds. Except: Terminal NH and C'O groups
  6. 6.  α-helix is tightly packed  Almost no free space within the helix  Amino acid side chains are on the outside of the helix  Roughly point “downwards”  Resembles branches of a Christmas tree  Most common location of α helices is along the protein periphery  One side facing the solution (exterior)  One side facing hydrophobic interior
  7. 7. α-helix Also called the 4₁₃ π-helix Very loosely coiled Hbonding pattern n + 5 Raerly found in nature. 310-helix Very tightley coiled Hbonding pattern n+3 rarely found in nature
  8. 8.  Beta sheets are another major structural element in globular proteins containing 20–28 % of all residues  The basic unit of a beta sheet is a beta strand with approximate backbone dihedral angles phi = -120 and psi = +120  Two types: anti-parallel and parallel strand.  Due to the extended nature of the chain, no significant intra-segment hydrogen bonds and van der Waals interactions between atoms of neighboring residues.  Sometimes called the beta "pleated" sheet since sequentially neighboring Ca atoms are alternately above and below the plane of the sheet
  9. 9. Main-chain NH and O atoms within a b sheet are hydrogen bonded to each other. The amino acids in successive strands have alternating directions (anti-parallel).
  10. 10.  Antiparallel beta sheets are considered intrinsically more stable than parallel sheets due to the more optimal orientation of the interstrand hydrogen bonds
  11. 11.  Different types  Hairpin loops – often between anti-parallel beta strands  Omega loops – beginning and end close (6-16 residues)  Extended loops – more than 16 residues  Secondary structures are joined together by additional structures called loops.  These patterns are called motifs  Defining motifs-small, specific combinations of secondary structure elements
  12. 12. A supersecondary structure is a compact three-dimensional protein structure of several adjacent elements of secondary structure that is smaller than a protein domain or a subunit
  13. 13.  Tertiary structures is defined as the overall arrangement of polypeptide chains in three-dimensional space, describing how secondary structures arrange into supersecondary structures that in turn arrange into domains and domains into tertiary structures.  Components:  Motif : a recognizable subcomponent of the fold – several motifs usually comprise a domain  Fold: used differently in different contexts – most broadly a reproducible and recognizable 3 dimensional arrangement  Domain: a compact and self folding component of the protein that usually represents a discreet structural and functional unit
  14. 14.  Tertiary structures can be divided into three main classes: a domain b domains a/b domains  The domain is the unit of tertiary structure
  15. 15.  In globular proteins  Tertiary interactions are frequently stabilized by sequestration of hydrophobic amino acid residues in the protein core  Consequent enrichment of charged or hydrophilic residues on the protein's water-exposed surface.  In secreted proteins  disulfide bonds between cysteine residue helps to maintain the protein's tertiary structure
  16. 16. They describes the arrangement of sub-units in a protein consisting of more than one polypeptide chain, where the sub-units may be identical or different.  The sub-units in a quaternary structure are held together by non-covalent interactions where the „contact regions‟ between the sub-units resemble the interior of tertiary structure proteins as being hydrophobic.  These structures cannot have mirror image superpositioning resulting in symmetrical distribution of the sub-units in the quaternary structure. 
  17. 17. Poly proline -II helix in proteins: Structure & Function. The polyproline type II (PPII) helix in recent years has emerged clearly as a structural class not only of fibrillar proteins but also of the folded and unfolded proteins.  The left-handed, extended PPII helix represents the only frequently occurring regular structure .  Natively unfolded proteins have a high content of the PPII helices identified by spectroscopic methods.  PPII is favorable for protein-protein and protein-nucleic acid interactions and plays a major role in signal transduction and protein complex assembly. 
  18. 18.    PPII helices do not necessarily contain proline, but proline has high PPII propensity. PPII helices are involved in transcription, cell motility, self-assembly, elasticity, and bacterial and viral pathogenesis, & has an important structural role in amyloidogenic proteins. PPII helices are not always assigned in experimentally solved structures, & they are rarely used in protein structure modeling.
  19. 19.       Lehninger Principles Of Biochemistry, Fourth Edition. Biochemistry, by Voet & Voet, 3rd edition. Harper’s Illustrated Biochemistry, 26th edition. Biochemistry , by Dr.U.Satyanarayana.