Proteins

Protein Structure

• Every protein has a three-dimensional structure that reflects its function.

• Protein structure is stabilized by multiple weakinteractions. Hydrophobic interactions are the major contributors to stabilizing the globular form of most soluble proteins; hydrogen bonds and ionic interactions ar optimized in the specific structures that are thermodynamically most stable.

• The nature of the covalent bonds in the polypeptide backbone places constraints on structure. The peptide bond has a partial doublebond character that keeps the entire six-atom peptide group in a rigid planar configuration. The NOC and COC bonds can rotate to assume bond angles of and , respectively.

Alpha helix

• In this structure the polypeptide backbone is tightly wound around an imaginary axis drawn longitudinally through the middle of the helix

• R groups of the amino acid residues protrude outward from the helical backbone

• The repeating unit is a single turn of the helix, which extends about 5.4 Å along the long axis

• Each helical turn includes 3.6 amino acid residues

• Helical twist is right handed

Why alpha helix

• The structure is stabilized by a hydrogen bond between the hydrogen atom attached to the electronegative nitrogen atom of a peptide linkage and the electronegative carbonyl oxygen atom of the fourth amino acid on the amino-terminal side of that peptide bond

• Each successive turn of the helix is held to adjacent turns by three to four hydrogen bonds

• All the hydrogen bonds combined give the entire helical structure considerable stability.

• Positively charged amino acids are often found three residues away from negatively charged amino acids, permitting the formation of an ion pair

• Two aromatic amino acid residues are often similarly spaced, resulting in a hydrophobic interaction

Beta sheets

• The backbone of the polypeptide chain is extended into a zigzag rather than helical structure

• The zigzag polypeptide chains can be arranged side by side to form a structure resembling a series of pleats

• Hydrogen bonds are formed between adjacent segments of polypeptide chain

• The R groups of adjacent amino acids protrude from the zigzag structure in opposite directions

Turns or loops

• These are the connecting elements that link successive runs of helix or conformation

• The structure is a 180 turn involving four amino acid residues