Structural Biochemistry/Protein Terms

Structural Biochemistry Protein Terms

• PRIMARY STRUCTURE: The primary structure of a protein is the sequence of amino acids in the polypeptide. These amino acids are covalently bonded through peptide bonds.
• SECONDARY STRUCTURE: The secondary structure of a protein regards the folding of the chain of amino acids into organized sub-structures like an alpha helix, beta pleated sheet, beta turn, or omega loop. This organizational scheme is held together primarily by hydrogen bonds.
• TERTIARY STRUCTURE: The tertiary structure of a protein involves the three dimensional arrangement of a single polypeptide chain, which includes hydrophobic and hydrophilic interactions, disulfide and hydrogen bonds (non-covalent bonds), salt bridges, and motifs.
• QUATERNARY STRUCTURE: The quaternary structure of a protein is the general arrangement and assembly of several polypeptide chains into subunits. When multiple subunits are stabilized by non-covalent interactions the resulting complex is called a multimer.
• ALIPHATIC: A hydrocarbon chain that is not aromatic.
• PEPTIDE BOND / AMIDE BOND: Involves a condensation reaction that joins two amino acids and requires the input of free energy, but while the bond is thermodynamically unstable it is kinetically favorable as the rate of hydrolysis is quite slow. This bond also has considerable double bond character making amino acids relatively planar.
• DISULFIDE BONDS: These bonds are formed from the oxidation of a pair of cysteine amino acid residues thereby forming cystine and are generally involved in tertiary structure arrangements.
• PROTEIN: A protein is a linear polymer of monomer units called amino acids linked by peptide bonds. Proteins spontaneously fold into a native 3D conformation, have a wide range of functional groups, and are chemically reactive.
• PHI: Phi is the torsion angle that occurs about the rotation of the single bond from nitrogen to the alpha carbon, which allows the protein to rotate to various orientations. Clockwise is considered positive rotation by convention.
• PHOSPHODIESTER BOND: Covalent bond involving a phosphate group and two ester groups. E.g. Bond joining two nucleotides.
• PSI: Psi is the angle of rotation about the single bond between the alpha carbon and the carbonyl group. A clockwise rotation is considered positive by convention and allows proteins to fold into many conformations.
• TORSION ANGLE / DIHEDRAL ANGLE: A torsion angle is the measure of the rotation about a bond between positive and negative 180 degrees. For proteins those angles are called phi and psi and are most easily seen on a Ramachandran Diagram.
• RESIDUE: A residue is an amino acid unit in a polypeptide
• RAMACHANDRAN DIAGRAM: A Ramachandran Diagram is a visual representation of the many compilations of the torsion angles that are allowed and are forbidden in a protein’s configuration due to steric collisions.
• STERIC EXCLUSION: Steric exclusion is the fact that two atoms cannot be in the same place at the same time. This is a powerful organizing principle for protein structure.
• DOMAINS: Domains are globular units of polypeptide chains that fold into two or more compact regions and are typically connected by a flexible segment of polypeptide chain. They are usually considered part of the tertiary structure.
• MOTIFS: A motif is part of the supersecondary structure and describes unique sequences of secondary structure elements present in proteins such as helix-turn-helix or beta ribbon.
• HOMOLOGY – Having a common evolutionary origin. Sometimes used mistakenly to describe similarities between proteins or nucleic acid sequences.
• HOT SPOTS – Essential amino acid deposits of protein-binding sites that have a particularly high binding free energy. Can cluster to form densely packed ‘hot regions’.
• ACTIVE CENTRE – Protein segment that plays a key part in the catalytic reaction of the enzyme function shown by the respective protein.
• BINDING SITE – Amino acid side chains located at the binding interface.
• CENTRAL RESIDUES – Contain catalytic residues (active centres) in addition to binding sites and hit spots.

References

Berg, Jeremy M., Tymoczko, John L., and Stryer, Lubert. Biochemistry. 6th ed. New York, N.Y.: W.H. Freeman and Company, 2007.