Protein Primer
Protein basics
Amino acids are chiral in the L configuration. They are zwitterions (separate positive and negative groups) and are formed in a condensation reaction between an amine and carboxyl group.
- Primary structure: Amino acids
- Secondary structure: Local elements (alpha helices and beta sheets)
- Tertiary structure: Structural units (folded) with a hydrophobic core
- Quaternary structure: Multiple polypeptides (e.g. receptor complex)
Hydrophobic forces are the single strongest driving force in protein tertiary conformation.
Alpha chains: Polypeptide strands with left-handed helical conformation
Alpha helices: Right handed
Collagen
Most common protein in mammals. Sequence has lots of Gly, Pro, and 4-hydroxyproline (modified pro). 3 alpha chains wrap around each other to form tropocollagen. This triple-helix is very strong which is why collagen is so strong, grouping together to form fibrils. Fibril cross linking relies on Lysine (Lys), 5-hydroxylysine (HyLys), and His residues and is dependent on lysyl (Lysine) oxidase.
Types of collagen:
- Tendon
- Skin
- Cartilage/bone
- Cornea
Clinical Peals
Osteogenesis imperfecta
AKA brittle bone disease. Causes by defective type I collagen. A point mutation is sufficient to reduce collagen stability and produce an autosomal dominant disease.
Ehlers-Danlos
A group of diseases which are characterized by hyper flexibility of joints and skin. Some types characterized by lysyl hydroxylase deficiency.
Lathyrism (osteolathyrism)
Stems from ingestion of poisonous sweet pea seeds which inactivate lysyl oxidase. Leads to abnormalities in bones, joints, and large blood vessels.
Scurvy
Blood vessel hemorrhage, tooth loss, poor wound healing, bone degeneration, and eventually heart failure. Stems from vitamin c deficiency required as a cofactor for prolyl (Proline) and lysyl hydroxylase.
Post-translational modifications
Almost all polypeptides are processed to remove the amino terminal. Met resides will cleave the peptide bonds.
Transport to ER
Proteins bound for the ER are tagged with a signal peptide.
- Translation in cytoplasm
- Signal recognition particle (SRP) bind the signal peptide / docks ribosome on ER membrane
- Translation coupled with translocation into ER lumen
- Signal peptide is cleaved co-translationally (before release from ribosome) by signal peptidase
Insulin
Pancreas synthesizes preproinsulin (immature insulin) which has a pre-peptide, polypeptide A, a pro-peptide, and polypeptide B. Removal of pre/pro peptide yields insulin.
Propeptide: A part of the polypeptide which much be removed to get the mature form.
Zymogens
Are inactive pro-enzymes which have auto-inhibitory pro-peptides. Usually have the suffix -ogen (e.g. fibrinogen becomes fibrin).
Glycoproteins
N-linked glycosylation
Important for protein folding in the ER lumen, recognized by the calnexin/calreticulin chaperone system. The sugar is attached to a polypeptide at an Asn residue. The glycan is added co-translationally. All N-linked glycans have a mannose-rich core.
O-linked glycosylation
Sugar is attached via a Ser or Thr residue, which happens after the protein is fully folded and entered the golgi.
Proteoglycans
Glycoproteins which have a lot of carbs. Core has at least one glycosaminoglycan. These form the basement membrane or extracellular matrix.
Aggrecan
A main proteoglycan of cartilage which can form huge complexes. Has a core protein with its N-terminal rich in N-linked oligosaccharides, a central region rich in O-linked sulfate chains, and a C-terminal rich in chondroitin sulfate.
Its brushlike structure and numerous negative charges capture water which act as a shock absorber when compressed.
Ubiquitylation
Ubiquitin is often added to proteins which need to be degraded by the 26S proteosome. Phosphorylation → ubiquitylation → degradation.
Enzymes involved in activation:
- Ubiquitin activating enzyme E1
- Ubiquitin activating enzyme E2
- Ubiquitin ligase E3 (this picks the target)
Histone code
Modifications help determine which parts of DNA will undergo transcription.