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Bioinformatics

Bioinformatics. Ayesha M. Khan. Structural Bioinformatics. Structure study is an abstraction All which we study is an abstraction to make comprehension of a complex entity more straightforward Structure is better conserved than sequence It can adopt a wide range of mutations

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Bioinformatics

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  1. Bioinformatics Ayesha M. Khan

  2. Structural Bioinformatics • Structure study is an abstraction All which we study is an abstraction to make comprehension of a complex entity more straightforward • Structure is better conserved than sequence • It can adopt a wide range of mutations • Physical forces favor certain structures

  3. Protein structure basics • It is the amino acid sequence that “exclusively” determines the 3D structure of a protein • 20 amino acids – modifications do occur post translationally

  4. It is the properties of the R group that determine the property of the AA and ultimately the protein • Different schemes exist for describing the properties • Hydrophobicity, polarity and charge are common measures Chirality– amino acids are enatiomorphs, only the L form is found in naturally forming proteins. Some enzymes can produce D amino acids

  5. Amino acid classification

  6. Peptide bond • Individual amino acids form a polypeptide chain • Such a chain is a component of a hierarchy for describing macromolecular structure • The chain has its own set of attributes • The peptide linkage is planar and rigid

  7. Geometry of the chain • A dihedral/torsion angle is defined by four consecutively bonded atoms • There are three repeating torsion angles along the backbone chain called phi, psi and omega.

  8. Geometry of the chain (contd) Omega is the rotation around the peptide bond it is planar and is 180 under ideal conditions

  9. Ramachandran plot • The values of phi and psi are constrained to certain values based on steric clashes of the R group. Thus these values show characteristic patterns as defined by the Ramachandranplot. • Plot of Psi vs Phi is called a Ramachandran plot (after G. N. Ramachandran) or conformational map.

  10. Ramachandranplot (contd) White areas correspond to conformations which are sterically disallowed for all amino acids except glycine which is unique in that it lacks a side chain. The red regions correspond to conformations where there are no stericclashes: i,.e.,theseare the allowed regions namely the alpha-helical and beta-sheet conformations. The yellow areas show the allowed regions if the atoms are allowed to come a little closer together.

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