LECTURE 5
Protein Structure
Proteins make up 50% of the dry weight of cells.
Proteins are linear, unbranched polymers of amino acids joined by peptide bonds formed via dehydration synthesis reactions (Figure 3.16; see also Web figure).
Amino acid composition of proteins: Proteins can be broken down in the laboratory by acid hydrolysis to yield a mixture of amino acids.
Chromatography of this mixture separates the various amino acids to reveal the amounts and kinds of amino acids in the original protein.
Amino acid composition reveals nothing about amino acid sequence.
Proteins are, structurally speaking, the most sophisticated molecules known.
They consist of one or more polypeptide chains.
Individual polypeptide chains range in size from 100 or so amino acid residues to nearly 27,000 amino acid residues.
The average size of polypeptide chains is about 270 residues.
Levels of protein structure (Figure 3.17)
1. Primary (1° ) structure: the N® C sequence of amino acids in a protein; amino acid sequence
2. Secondary (2° ) structure: a -helices and b -pleated sheets formed by H-bonding interactions between amino acids
3. Tertiary (3° ) structure: protein folding
4. Quaternary (4° ) structure: The association of 2 or more polypeptide chains to form a multimeric assembly. Each polypeptide chain is referred to as a subunit or monomer.
Primary structure of proteins:
The amino acid sequence is unique for any given protein (Web figure of ribonuclease (RNase) - 124 residues, beginning with Lys and ending at position 124 with Val)
A protein of n residues has 20n possible amino acid sequences.
RNase represents 1 of 20124 possible sequence arrangements for a protein of 124 residues.
There is not nearly enough matter in the universe to make one molecule each of the 20124 possible amino acid sequence arrangements for a protein this size.
How secondary structures arise:
Constraints on protein structure:
1. The amide plane: the peptide bond has partial double-bonded character
2. Maximizing the number of H bonds: H-bond formation is essential to the establishment of secondary structure
Only 2 secondary structural motifs permit the formation of 2 H bonds per peptide ensemble (the maximal number) (Web figure)
1. The a -helix
2. The b -pleated sheet
Proteins can be grouped into 3 basic classes on the basis of shape (Web figure)
1. Fibrous: regular, linear structures (fibers), usually water-insoluble. Example: collagen
2. Globular: roughly spherical, folded so that hydrophobic amino acids are on the inside, hydrophilic amino acids are on the outside; very soluble. Example: Myoglobin
3. Membrane: roughly spherical, folded so that hydrophobic amino acids are on the outside (on the inside, hydrophilic amino acids may be arranged to form channels for transport of substances through the protein); very insoluble in water, but ideal for insertion into a membrane.
Example: Bacteriorhodopsin
Tertiary Structure of Proteins: Protein folding: the folding of elements of secondary structure to form a compact, globular molecule
Tertiary structure is stabilized by H bonds, ionic bonds, S-S (disulfide) bridges, and hydrophobic interactions
The driving force in protein folding: To minimize the protein's solvent-accessible surface area
Hydrophobic R groups buried inside
Hydrophilic R groups exposed on outside for interaction with solvent
No protein is stable as a single-layered structure
Conformation º the arrangement of a molecule in 3-dimensional space; the overall precise 3-dimensional architecture of a molecule
What determines conformation?
The denaturation and renaturation of RNase (Nobel Prize for Christian Anfinsen) See also Figure 3.20
The information for the conformation of a protein is intrinsic in its 1° structure (amino acid sequence), which in turn is programmed within its gene, a stretch of nucleotides in DNA.
Protein folding: The outstanding intellectual issue in contemporary molecular biology.
We don't know yet how the information represented by the amino acid sequence of a protein directs its folding into the proper conformation.
Proteins know how to fold, even if we don't know how they do it.
Quaternary Structure: When 2 or more polypeptides interact to form a larger protein structure.
Here again the driving force is burial of solvent-accessible surface area (in this case, surface areas on the folded subunits)
Examples:
Hemoglobin (Hb) (Figure 3.19) is a tetramer with an a 2b 2 organization:
2 a -subunits = 2 a -globin chains
2 b -subunits = 2 b -globin chains
each subunit » 16.5 kD, Hb » 65 kD
Immunoglobulin G (IgG or g -globulin): also a 2b 2, but the chains are called L and H, for"light" and"heavy", respectively, so IgG is H2L2. IgG » 150 kD:
L chains » 25 kD; H chains » 50 kD
Glutamine Synthetase (GS), an enzyme
GS (600 kD) is an a 12 dodecamer of identical 50-kD subunits