Module 1 - Lecture 2: Protein Folding

Secondary Structures

Periodic folding of the polypeptide chain into conserved arrangements through chemical interactions.

Motif

Combinations of the secondary structures

Alpha Helix

Spiral, rod-like structure. Hydrogen bonds connect other amino acid residues to form the alpha helix, four positions away.

Beta Sheet

Collection of associated beta strands. Defined by the pattern of H-bonds forming between the non-variable amino acid side chains, the amino and carboxyl groups.

Loops or Connectors

Bends in the polypeptide backbone that lie between the alpha helix and beta strands.

Coiled-coil Motif

Two alpha helices are wrapped around one another. They are amphipathic, that are determined by the variable R groups of the amino acid residues. Commonly found in DNA binding proteins because it can fit in the grooves of the DNA helix.

Zinc-Finger Motif

Involves an alpha helix and two beta strands (small beta sheet). Held in this position by the precise interaction of conserved amino acid residue. Found in DNA binding proteins, but can bind to RNA molecules as well.

B-Barrel Motif

Large beta sheet that loops back upon itself. Useful for forming a channel or a pore across a hydrophobic membrane. Amphipathic structure.

Helix-loop-helix Motif

Has two small alpha helices, but they are held in a specific orientation relative to each other by non-covalent interactions between specific amino acid resides and a calcium cofactor.

Tertiary Structure

Final three-dimensional structure of a protein

Domain

Functional unit, there is a unique function associated with each part of the protein. They can fold independently of the rest of the protein.

Functional Domains

Associated with a specific activity of the protein. Could be DNA binding domain, enzymatic domain, or a protein-protein interaction domain.

Structural domains

Associated with a recognizable shale or characteristic such as the type of amino acid residues found there

SRC Protein

Important protein in the regulation of the cell cycle. Particular cofactor is ATP

SH3

SRC Homology 3 Domain

SH2

SRC Homology 2 Domain. Recognizes phosphorylated tyrosine residues in other proteins.

Quaternary Structure

Number and organization of subunits within a multiple-protein complex

Multimeric Protein

A complex that consists of multiple distinct polypeptides

Dimer

Two polypeptides/subunits that are associated together

Trimer

Three polypeptides/subunits that are associated together

Homodimer

Complex that contains two identical polypeptides with the same primary sequences and the same tertiary structures

Heterodimer

Complex in which the two associated proteins are different from one another

Acetylations

Addition of an acetyl group that can modify the activity of a protein

Methylation

Addition of an methyl group that can alter gene expression.

Phosphorylation

Addition of a phosphate that iss catalyzed by enzymes called kinases.

Dephosphorylation

Remove the phosphate is mediated by enzymes called phosphatase

Hydroxylation

Addition of OH group and is important for changing the structure of proteins

Carboxylation

Addition of carboxyl group, changes the properties of amino acid residues by adding a negative change

Glycosylation

Addition of a carbohydrate, important for protecting proteins from proteolysis and for proper protein folding

Lipidation

Addition of lipid molecules onto a polypeptide, important for anchoring proteins to hydrophobic bio-membranes

Sickle Cell Anemia

Associated with a protein called hemoglobin. Causes the red blood cell to be stretched which then gets them stuck in capillaries and individuals don’t get enough oxygen