structure of proteins
there are 4 organizational levels of proteins: Primary, secondary, tertiary and quaternary structure. By analyzing these 4 organizational levels, we can consider how complex would be the protein.
primary structure of proteins
the sequence of amino acids in a protein. and these amino acids joined by peptide bonds. Note that proteins with abnormal amino acid sequences may cause genetic diseases.
Figure 1. amino acid sequence of Bovine insulin
peptide bond
Peptide-bond formation is the linking of two amino acids which is accompanied by the loss of a molecule of water.
Figure 2. formation of peptide bond
how we can name the peptide in the sequence, the free amino end (N-terminal) is written to the left and the free carboxyl end (C-terminal) to the right, the sequences are read from the N- to the C-terminal of the peptide.
characteristics of peptide bonds
figure 3. resonance structure of peptide bond
figure 4. Typical bond lengths within a peptide unit
figure 5. Peptide bonds are planar
figure 6.Trans and cis peptide bonds
secondary structure of proteins
The polypeptide backbone forms a regular arrangement of amino acids that are located near to each other in the linear sequence.
Mainly including α-helix, β-sheet, β-bend (reverse turn), and omega (Ω)-loop.
α-helix
Described in 1930 by Pauling and Corey, the α-helix is the most common polypeptide helices are found in nature. It is a spiral structure, consisting of a tightly packed, coiled polypeptide backbone core, with the side chains of the component amino acids extending outward from the central axis to avoid interfering sterically with each other.
An α-helix is stabilized by extensive hydrogen bonding between the peptide-bond carbonyl oxygens and amide hydrogens that are part of the polypeptide backbone. Hydrogen bonds are individually weak, but they collectively serve to stabilize the helix.
Figure 7. A largely α helical protein. Ferritin, an iron-storage protein, is built from a bundle of α helices.
Figure 8. An α-helical coiled coil. The two helices wind around one another to from a superhelix. Such structure are found in many proteins including keratin in hair, quills, claws, and horns.
in each turn there are 3.6 amino acids, there are also some amino acids that disrupt the α-helixes:
proline which is not geometrically compatible with the right handed spiral of the alpha helix and it inserts kink in the chain.
charged amino acids (acidic or basic amino acids) which forms ionic bonds or electrostatically repelling.
amino acids with bulky side chains, such as tryptophan, or amino acids, such as valine or isoleucine, that branch at the β-carbon (the first carbon in the R group, next to the α-carbon) can interfere with formation of the α-helix if they are present in large numbers.
β-sheet
β-sheet is another form of secondary structure, the surfaces appear extended and “pleated”. Composed of two or more peptide chains or segments of polypeptide chains. Three types of β-sheet are as follow: parallel (with the N-termini together), antiparallel sheets (with the N-terminal and C-terminal ends alternating), and the mixed form.
Figure 9. An antiparallel β sheet. Adjacent β strands run in opposite directions. Hydrogen bonds between NH and CO groups connect each amino acid to a single amino acid on an adjacent strand, stabilizing the structure.
Figure 10. A parallel β sheet. Adjacent β strands run in the same direction. Hydrogen bonds connect each amino acid on one strand with two different amino acids on the adjacent strand.
Figure 11. Structure of a mixed β sheet
β-bend (turn)
β-bend (turn) reverse the direction of a polypeptide chain, helping it form a compact, globular shape. Often connect successive strands of antiparallel β- sheets. Found on the surface of protein molecules often including Pro, Gly, and charged residues and stabilized by hydrogen and ionic bonds.
Figure 12. Structure of a β- bend. The CO group of residue i of the polypeptide chain is hydrogen bonded to the NH group of residue i+3 to stabilize the turn.
Ω-loop
Ω-loop is Nonrepetitive secondary structure: loop or coil conformation, less regular structure.
figure 13. Loops on a protein surface. A part of an antibody molecule has surface loops that mediate interactions with other molecules.
Tertiary structure of globular proteins
“Tertiary” refers both to the folding of domains (the basic units of structure and function) and to the final arrangement of domains in the polypeptide. The structure of globular proteins in aqueous solution is compact, with a high density (close packing) of the atoms in the core of the molecule. Hydrophobic side chains are buried in the interior, whereas hydrophilic groups are generally found on the surface of the molecule. Noncovalent bonds (interactions) stabilize the structure.
Figure 14. Three-dimensional structure of myoglobin.
Domains
Domains are the fundamental functional and three-dimensional structural units of polypeptides. Polypeptide chains that are greater than 200 amino acids in length generally consist of two or more domains. combinations of motifs and independently folding, each domain has the characteristics of a small, compact globular protein.
figure 15. Protein domains. Antibodies (IgGs) contain two Fab domains which can bind antigens.
the following are interactions stabilizing tertiary structure:
Disulfide bonds: interchain or intrachain
Hydrophobic interactions: between nonpolar side chains, energetically most favorable.
Hydrogen bonds: inside molecules and with aqueous solvent (which enhances the solubility of the protein).
Ionic interactions: negatively charged groups interact with positively charged groups.
Quaternary structure of proteins
Some proteins may consist of two or more polypeptide chains (each chain called a subunit). The arrangement of these polypeptide subunits is called the quaternary structure.
Figure 16. Quaternary structure of G protein. The G protein comprises three subunits( a,β,g), which plays important roles in cell signaling.
Figure 17. The levels of protein structure
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