Methods of determination of protein structure

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Architecture of Proteins

  • Shape - globular or fibrous

  • The levels of protein structure

  • - Primary - sequence

  • - Secondary - local structures - H-bonds

  • - Tertiary - overall 3-dimensional shape

  • - Quaternary - subunit organization

What forces determine the structure?

  • Primary structure - determined by covalent bonds

  • Secondary, Tertiary, Quaternary structures - all determined by weak forces

  • Weak forces - H-bonds, ionic interactions, van der Waals interactions, hydrophobic interactions

Other Chemical Groups in Proteins

  • Proteins may be "conjugated" with other chemical groups

  • If the non-amino acid part of the protein is important to its function, it is called a prosthetic group.

  • Glycoprotein, lipoprotein, nucleoprotein, phosphoprotein, metalloprotein, hemoprotein, flavoprotein.

Steric Constraints on phi & psi

  • Unfavorable orbital overlap precludes some combinations of phi and psi

  • phi = 180, psi = 0 is unfavorable

  • phi = 0, psi = 0 is unfavorable

  • phi = 0, psi = 180 is unfavorable

Classes of Secondary Structure

  • All these are local structures that are stabilized by hydrogen bonds

  • Alpha helix

  • Other helices

  • Beta sheet (composed of "beta strands")

  • Tight turns

  • Beta bulge

The Alpha Helix

  • First proposed by Linus Pauling and Robert Corey in 1951

  • Identified in keratin by Max Perutz

  • A ubiquitous component of proteins

  • Stabilized by H-bonds

The Beta-Pleated Sheet

  • Composed of beta strands

  • Also first postulated by Pauling and Corey, 1951

  • Strands may be parallel or antiparallel

  • Rise per residue:

    • 3.47 Angstroms for antiparallel strands
    • 3.25 Angstroms for parallel strands
    • Each strand of a beta sheet may be pictured as a helix with two residues per turn

The Beta Turn

  • allows the peptide chain to reverse direction

  • carbonyl C of one residue is H-bonded to the amide proton of a residue three residues away

  • proline and glycine are prevalent in beta turns

What are the structural and functional advantages driving quaternary association?

  • Stability: reduction of surface to volume ratio

  • Genetic economy and efficiency

  • Bringing catalytic sites together

  • Cooperativity

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