Protein Life Cycle Flashcards
Cytoplasmic Crowding
Two fold effect: retards unfolding but enhances aggregation
Hydrophobic residues can be pushed aside and form aggregates instead of actual protein
Physical factors that influence unfolding equilibrium
Denaturing: pH (lysosome, acidosis, bone remodeling, nerve synapses)
Ionic strength: salt
Pressure: Proteins running through blood
Temperature
Osmotic pressure
Urea (kidneys)
Osmolytes
Cause nonspecific effect on all proteins they encounter
Higher concentrations
Enhance protein folding
AA: Proline, Alanine, Taurine
Polyols: Sorbitol, Glycerol
Methylamines: TMAO, betaine
Kidney Cells and Stress
Cell up/downregulates osmolytes to compensate for changing urea and salt concentrations
ER and Protein Processing
Oxidizing: Disulfide bonds and glycosylation
Increase protein stability
Covalent Osmolytes
Very effective for protein stabilization
~50% of proteins are naturally glycosylated
Allergens
Proteins that are so stable they can survive digestion.
Must be >25 AA for it to be allergen
Ovomucoid: egg white allergen. (disulfide bonds, glycosylation)
You cannot unfold these proteins, meaning there’s a recognizable chunk that your immune system cant recognize.
Things larger than 25 AA, the immune system can recognize, which is what causes the allergic reaction.
Chaperones
Protein that the cell makes to help other proteins fold up
Interact often with misfolded or unfolded
Heat shock proteins
Can transport across membrane
Control activities of some proteins
Chaperonin
Class of chaperones that assist with folding of proteins using ATP
Central cavity
TriC = structure of humans
GroEL = E. coli
Interacts with about 10% of new proteins
Protein Turnover
1-2% degradation each day
Proteasome
Short half life, transient function, abnormal or damaged
Lysosome
Longer half life, “housekeeping” function, membrane
Lysosomal degradation
Autophagy: nonselective, slow, constitutive
Chaperone-mediated autophagy: selective, 30% of cytosolic proteins, hsc73 binding to KFERQ motifs (bind to, recognize, haul to lysosome), unfolded protein transported into lysosome
Cathepsin Proteases
> 12, found in the lysosome
Constitutive and tissue specific (some are protein specific, some found in all lysosomes)
broad, overlapping substrate specificities
Proteasome
Cytosol and nucleus
Neutral pH
Ubiquitin tags on protein targets
Requires ATP
Proteosome Pathway
Ubiquitin binds to protein through ATP use
Ubiquitin-protein is bound to proteasome
ATP used again to degrade protein
Ubiquitin is recycled
Ubiquitin Tagging
E1 + ubiquitin: 1 activator protein, ATP required
E2 + ubiquitin: Several carrier isoforms
E3 + target protein + ubiquitin
E3 special because recognizes target protein and ubiquitin
>500 ligase proteins
Ubiquitinylation
Covalent attachment at lysine side chain (N)
Amide bond with Ubq (C)
1 Ubq is not enough: need 4 in order to be broken down by proteosome
Structure of Proteosome
Stacked rings
Three separate protease in middle rings
Each recognizes a different AA cleavage site
Protein Turnover (AA)
75% of free amino acids are recycled into new proteins
25% AA are metabolized
> 1. Nitrogen excreted as urea
>2. Carbon components “burned” for energy
Proteasome and Cancer
Induces death of cancer cells
Few effects on normal cells
Bortezomib: approved for relapsed multiple myeloma
Inhibits activity of proteasome
ER: Unfolded Protein Response
Types of stress: unfolded proteins in ER (mutation or improper glycosylation) ROS or UV damage Low amino acids Heat (fever) Hypoxia High free fatty acids
Stress sensed, cell physiology changes >
recovery or apoptosis
BiP
Chaperone that senses stress
Normally binds sensor proteins
Inactive: BiP is bound to sensor
Active: BiP is unbound, can interact and send signals
At lease three sensor proteins, each with its own pathway of sending messages to the nucleus.
Sensor stretches across ER membrane & is released in ER lumen to interact with unfolded proteins
Cellular Responses
- Inhibit global translation (quit making more protein, only going to make the problem worse)
- Activate transcription/translation of:
ERAD proteins: that assist with degradation of misfolded proteins in ER (includes ubiquitin system)
Chaperones (upregulates)
AA transporters (upregulates- to have more building blocks to build proteins from)
Oxidative stress protection
Ex. of temperature causing protein denaturation
Tachycardia develops when a child runs a fever
Ligand
Includes co-factors
Specific to only some proteins, will not bind to all
Binding a ligand will stabilize the protein conformation
Chemical environment of body
pH and ionic strength frequently change
Some areas are designed to unfold proteins (intestinal tract, lysosome)
The body is influenced by a high density of macromolecules
Aquaporins
Transport water
Catalase and superoxide dismutase
Regulate redox reactions
Multi-drug transporters
Transport hydrophobic ligands across membrane
Histidine (sensing)
charged side chain is able to sense pH changes near 7
Hemoglobin
Cannot bind O2 without heme
Can bind up to 4 O2 molecules
