CHMI E.R. Gauthier, Ph.D. 1 CHMI 2227E Biochemistry I Proteins: - Tertiary structure

CHMI E.R. Gauthier, Ph.D. 2 Tertiary structure

CHMI E.R. Gauthier, Ph.D. 3 Tertiary structure Secondary structure:  Involves a single type of structure:  -helix  -pleated sheet  Presence of interactions between amino acids that are close together in the primary structure  Main type of interaction: H bonds.  Necessary but not sufficient to make a functional protein. Tertiary structure:  Involves the folding, in space, of the whole polypeptide chain;  Involves several elements of seconday structures, whichy interact together through different interaction forces/bonds: H bonds Electrostatic interactions Van der Waals interactions Hydrophobic interactions Disulfide-bonds  Absolutely required for a protein to be active.  Two main types of tertiary structures exist: Fibrous (e.g. collagen) Globular (e.g. myoglobin) myoglobin Collagen

CHMI E.R. Gauthier, Ph.D. 4 Tertiary structure Interaction forces For proteins in an aqueous environment:  Hydrophobic amino acids are buried in the interior of the structure;  Hydrophilic amino acids are exposed to the solvent; Conversely, membrane- bound proteins are exposed to an hydrophobic environment:  Hydrophobic amino acids are exposed;  Hydrophilic amino acids are buried inside. butane.chem.uiuc.edu/cyerkes/chem104A_S07/Lecture_Notes_104/lect28c.html Check this one out:

CHMI E.R. Gauthier, Ph.D. 5 Tertiary structure Protein folding occurs in specific steps:  Some individual elements of secondary structure are first formed;  A few elements of secondary structure cluster together to form conserved folding motifs;  These bundles of secondary structure then form domains, which fold independently of the rest of the protein;  Finally, several domains interact to form the final, functional 3-D structure of the protein. Any given protein will always adopt the same functional 3-D structure. A B

CHMI E.R. Gauthier, Ph.D. 6 Tertiary structure Folding motifs - 1

CHMI E.R. Gauthier, Ph.D. 7 Tertiary structure Folding motifs - 2

CHMI E.R. Gauthier, Ph.D. 8 Tertiary structure Protein domains – Pyruvate kinase Domain 1 Domain 2 Domain 3

CHMI E.R. Gauthier, Ph.D. 9 Tertiary structure 1. Myoglobin Found in muscles Binds the oxygen required for aerobic metabolism; Associated with a heme group, which is actually responsible for binding oxygen;  -turn Proline

CHMI E.R. Gauthier, Ph.D. 10 Tertiary structure 1. Myoglobin Cross-sectional view Hydrophilic amino acids: Blue Hydrophobic amino acids: Yellow

CHMI E.R. Gauthier, Ph.D. 11 Tertiary structure 2. Porin – a membrane-bound protein Hydrophilic amino acids: Blue Hydrophobic amino acids: Yellow

CHMI E.R. Gauthier, Ph.D. 12 Tertiary structure Chaperones For some proteins, folding requires the help of other proteins called chaperones; Chaperones generally work by binding to exposed hydrophobic patches on the unfolded protein, preventing aggregation and irreversible inactivation.

CHMI E.R. Gauthier, Ph.D. 13 Tertiary structure Protein denaturation Proteins can be denatured by treatments that destroy the interaction forces required for the adoption of the proper 3-D structure:  Heat  pH  Solvent  Urea/guadinium: breaks up H-bonds   -ME Check this one out:

CHMI E.R. Gauthier, Ph.D. 14 Tertiary structure Protein denaturation The fact that ribonuclease can be reversibly denatured and renatured in vitro shows that the information required for the proper folding of a protein resides in its primary structure.

CHMI E.R. Gauthier, Ph.D. 15 Examples of proteins 1. Green fluorescent protein Protein found in the jelly fish; Has the unique property to emit a green light; Different variants were produced by genetic engineering to produce red, yellow, cyan, blue light. Extremely useful in cell biology: one can tag it to her/his protein of interest and follow the protein in the cell using fluorescence microscopy.

CHMI E.R. Gauthier, Ph.D. 16 Examples of proteins 1. Green fluorescent protein Light!

CHMI E.R. Gauthier, Ph.D. 17 Examples of proteins 1. Green fluorescent protein Golgi apparatus Nucleus

CHMI E.R. Gauthier, Ph.D. 18 Examples of proteins 1. Green fluorescent protein

CHMI E.R. Gauthier, Ph.D. 19 Examples of proteins 2. Prion proteins Normal form = PrP c Toxic form = PrP sc

CHMI E.R. Gauthier, Ph.D. 20 Examples of proteins 2. Prion proteins Fiber aggregation

CHMI E.R. Gauthier, Ph.D. 21 Important web site: