Molecular Biology & Biochemistry 694:407& 115:511

Protein Structure

Sept. 13th, 2005, Lecture

Special thanks for this lecture goes to Dr. Gabriel Fenteany, Department of Chemistry, University of Illinois at Chicago (www.chem.uic.edu/fenteany/teaching/452), whose slides I liberally borrowed!

3-D Structure of Myoglobin

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Importance of Proteins

• Main catalysts in biochemistry: enzymes (involved in virtually every biochemical reaction)

• Structural components of cells (both inside and outside of cells in tissues)

• Regulatory functions (if/when a cell divides, which genes are expressed, etc.)

• Carrier and transport functions (ions, small molecules)

Levels of Protein Structure

• Primary Structure - amino acid sequence in a polypeptide

• Secondary Structure - local spatial arrangement of a polypeptide’s backbone atoms without regard to side chain conformation (e. g., -helices and -sheets)

• Tertiary Structure - three-dimensional structure of entire polypeptide

• Quaternary Structure - spatial arrangement of subunits of proteins composed of multiple polypeptides (protein complexes)

Structure of -amino acids

The 20 Amino Acids Found in Proteins

Stereochemistry of -amino acids

Stereoisomers of -amino acids

All amino acids are chiral except glycine.

All amino acids in proteins are L-amino acids.

Properties of Cysteine Side Chain

Side chains with -SH or -OH can ionize, making them more nucleophilic.

Oxidation between pair of cysteine side chains results in disulfide bond formation.

oxidation

reduction

HCH3N+

CH2

COO-

SHHCH3N+

CH2

COO-

SSCH2CH

H3N+ COO-

+ 2H+

+ 2e-

CH

H3N+CH2

COO-

SH

CH

H3N+CH2

COO-

SH

H++

pKa = 8.3

CH

H3N+CH2

COO-

S-

Note: in cells, oxidative disulfide formation normally proceeds via a thiol-disulfide exchange reaction, with (for example) a natural tripeptide such as glutathione:

R’-SH + R”-SH + G-SS-G

R’-SH + R”-SS-G + G-SH

R’-SS-G + R”-SH + G-SH

R’-SS-R” + 2 G-SH

G-SS-G = oxidated glutathioneG-SH = reducted glutathione

Absorption of UV Light by Aromatic Amino Acids

Formation of a Peptide

Planarity of Peptide (Amide) Bond

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cis and trans Isomers

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The trans isomer is generally more stable because of steric crowding of side chains in cis conformation.

“Peptides”• Short polymers of amino acids• Each unit is called a residue• 2 residues - “dipeptide”• 3 residues - “tripeptide”• 12-20 residues - “oligopeptide”• Many residues - “polypeptide”

Examples of Oligopeptides

N- and C-Termini May Be Modified in Proteins

Primary Structure of Bovine InsulinFirst protein to be fully sequenced;Fred Sanger, 1953. For this, he won his first Nobel Prize (his second was for the Sanger dideoxy method of DNA sequencing).

Evolution and Conservation of Protein Sequences

Almost all human genetic diseases involve the disruption of a protein in the body.

Typically, the harmful phenotype(s) of disease-causing lesions in a protein gene are caused by effects on (a) the level of expression of the protein, (b) the activity of the protein, or (c) the folding of the protein.

[Note: Some effects may be different in different tissues for the same mutation! For example, some alpha-1-antitrypsin mutations exert harmful effects in the lungs (emphysema) due to lack of anti-elastase activity, and different harmful effects in the liver (cirrhosis) due to folding/sorting problems.]