Biochem Lecture 17- Protein Families

C. Alpha keratin and tropomyosin

- Alpha keratin is found in the epidermal layer of skin, in nails and hair; tropomyosin is found in muscle fiber. - Both are fibrous proteins with REPETITIVE SEVEN AMINO ACID SEGMENTS. - The 1st and 4th amino acids are hydrophobic - The 5th and 7th are polar residues. - the 7 amino acids represent two turns of the helix and thereby form a POLAR AND APOLAR side of the helix. - The APOLAR edges align with one or two other helices to form a SUPERHELIX. -These superhelical structures are crosslinked with other superhelical structures to form FIBRILS.

A. Collagen- Amino Acid composition

- Collagen makes up 74% of skin protein, and is a major component of most cells. - It contains a large percentage of modified amino acids. - The amino acids (P,G,A) make up over 55% of its composition.

DNA binding proteins

- DNA is a substrate for many proteins and enzymes. These proteins are involved in maintaining the structure of DNA (Histones), disrupting DNA, synthesizing DNA (DNA polymerases), degrading DNA (nucleases), regulating gene transcription (transcription factors) and replication (topoisomerases), and synthesizing mRNA (RNA polymerases). - Although the entire DNA based genome varies in nucleotide sequence throughout, it has a generalized ALPHA-HELICAL structure throughout; this leads to the formation of a major and minor groove in the helix. - . This generalized structure enables DNA binding proteins to share common molecular strategies (Structural motifs) to bind to DNA. However, most DNA binding proteins bind to rare and highly specific DNA sequences. - This specificity, however, is realized by subtle differences in the DNA and protein structure within the common structural motifs.

B. Elastin

- Fibrous proteins that gives tissues and organs the ability to stretch. However, IT SHARES NO SIMILARITY to the structure of collagen EXCEPT for the formation of ALLYSINE cross linkages. - It LACKS secondary structure and exists as an unordered flexible coil.

D. Lipoproteins

- Function to carry hydrophobic compounds through aqueous environments and have specific metabolic roles. - Each type of lipoprotein can be characterized by- mass, size, chemical composition, density and physiological role. - The structure of the complex is maintained by NON-COVALENT FORCES. - The protein components of these lipoprotein particles are called APOLIPOPROTEINS, and are associated with specific lipoproteins.

Leucine Zipper

- It is found on alpha helices, and is formed when multiple leucines line a single side of the helix. This arrangement occurs when the leucine residues are spaced 7 amino acids apart( (LX6LX6LX6LX6LX6). - In this sequence, the leucines make up every amino acid residue on one side of the helix. - The leucine rich helix interacts with another to form a stable protein-protein interaction. - The leucine zipper region of the protein does not bind to DNA but rather an R and K rich region adjacent to the leucine zipper binds to the negatively charged phosphate backbone of the DNA. - DNA proteins that bind by this motif include fos, jun and myc.

D1. Generalized structure of lipoproteins

- Lipoproteins form spherical structures with the neutral lipids occupying the interior. - Amphoteric lipids and lipoproteins make up the outer shell (20 angstroms thick): The SMALLER the particle, the HIGHER the density. Lipoproteins have a high helical content, with the helical regions being AMPHIPATHIC: The hydrophobic side interacts with the core, the hydrophilic side interacts with the phospholipid head groups and the aqueous milieu.

Lysine conversion

- Lysine is converted to 5-hydroxylysine, then glycosylated following protein synthesis but prior to folding.

E. Glycoproteins

- Many membrane-bound proteins (blood antigen system, plasma proteins and hormones) are glycosylated. - Antigenic sites are often glycoproteins. The carbohydrates serve as both identification signals and signaling molecules for contact inhibition. Some glycoproteins contain as much as 85% carbs. - The carbohydrates are typically located on the EXTERIOR OF THE CELL OR PROTEIN SURFACE. - They are added POSTTRANSCRIPTIONALLY in the Golgi and ER. - The carbs are added to either asparagine residues (N-glycosidic linkages) or to Ser/Thr residues (O- glycosidic linkages). Type III linkages are found in collagen, and involve hydroxylysine. - The degree to which hemoglobin is glycosylated can be used to follow changes in blood glucose concentrations.

Proline conversion

- Proline is converted to hydroxyproline and is found uniquely in collagen. - This conversion is DEPENDENT on Vitamin C. - Scurvy results from impaired collagen synthesis.

Common structural motifs found in DNA binding proteins

1. Helix-turn-helix 2. Zinc Finger motif 3. Leucine zipper

Helix-turn-helix

A helix present in the DNA binding protein (recognition helix) binds to the major groove by non-covalent interactions. The proteins exist as dimers and therefore two contacts are made with the DNA per single protein molecule. eg., TATA binding protein

Zinc finger motif

A zinc atom is bound by two CYSTEINE and two HISTIDINE residues to form a loop. It has an alpha helical region that binds into the major groove. eg., p53-DNA complex

Glycine

Glycine in every third residue is needed to allow different chains to be in close proximity in the structure.

Fibrous Protein

These are usually long rod-shaped insoluble proteins that form cellular infrastructure and include proteins like collagen, keratin and tropomyosin.

I. Non-Globular Proteins

These proteins are not water soluble- including fibrous proteins, lipoproteins and glycoproteins. Many of these types of proteins have specialized function.

Immunoglobin Characteristics

They are glycoproteins that consist of 4 polypeptide chains; Two light chains (220 aa) of identical sequence combine with two heavy chains (400 aa) of identical sequence to form an (LH)2 structure. • The L and H chains are covalently bound by disulfide bonds. • Only the H-chain is glycosylated The amino terminal regions of the antibody are highly variable among individual antibodies and are termed the variable regions (Vh, Vl). Within the variable regions are hypervariable regions or complementary-determining regions (CDRs). These regions form the antigen-binding site. The carboxyterminal region are highly homologous in the L and H chains and are termed the constant regions (C regions). The C regions are required for the binding of complement proteins and for crossing the placental membrane.

Alanine Conversion

to allysine

Immunoglobin Superfamily

• antibodies are produced as a defense mechanism to remove foreign compounds (antigens) from circulation. Generally, each antibody recognizes a single antigen. • The antibody recognizes a compounds as foreign and binds to the "antigenic determinant". • Each human can produce an estimated 10 million different antibodies, however, the structure of each antibody is highly similar.