Lecture 6: Protein Folding Flashcards
What is a Protein in its stable conformation (folded)?
Native State
What are denatured proteins?
Loss of enough 3D structure to cause functional loss
What can cause denaturing of proteins?
•Heat
•Denaturing chemicals (urea, guanidine)
Denatured proteins do not have to be….
Completely void of structure/structural elements
Denaturation of proteins is a cooperative event meaning?
Loss of local structure in a protein destabilizes other regions of the protein
What are the ways to denature a protein?
•Heat
•Denaturant
•pH
•Organic Solvents
What does protein denaturation break?
Non-covalent interactions
In Protein denaturation, covalent interactions are not…
Broken
Protein denaturation can be….
A reversible process
What is it when denatured proteins form a precipitate?
Protein Aggregation
Protein Aggregation most of the time is a…
Irreversible process
Aggregation occurs in a….
Nonspecific manner
What is Proteostasis?
The steady-state complement of proteins that enable life of a cell
What is the defined definition of Proteostasis?
Is the coordinate function of pathways involved in Protein synthesis and function, Protein refolding of unfolded or partially folded proteins and Protein sequestration, targeting and degradation
Misfolded or unfolded proteins can form aggregates. What does this mean for the protein?
•Lead to a loss of function of the protein
•Aggregates can oligomerize
Common diseases that occur because of misfolded or unfolded proteins
•Sickle Cell
•Alzheimer’s
•Spongiform encephalitis
Is Proteostasis pathways, steps exist in both
A forward and reverse directions
In Proteostasis pathways, Proper folding may require
•Chaperones. Which may “rescue” misfolded proteins which may be degraded by Proteasome
What is NC?
Nascent chain. It’s the emerging polypeptide chain from the ribosome
In a PCR reaction, the temperature can be high enough to cause….
DNA strand separation but NOT denature the polymerase
Primary Amino Acid Sequence Determines…
The tertiary structure of a protein
Denatured protein that refolds is
Renatured. This occurs with the removal of denaturing conditions
Complexity of folding often correlates to
The size of a protein
What does the narrowing of the funnel represent? (thermodynamics)
Decreases in conformational repertoire that a protein needs to sample
What do minor peaks and valleys represent? (Thermodynamics)
Changes in free energy along the path to folded to state
What do Minor Valleys represent? (Thermodynamics)
Semi-stable intermediate structures and/or partially folded intermediates
What does “N” represent?
The Native state. The protein is now at its lowest free energy state
How do Chaperones assist in protein folding?
•Binding to and protecting regions of protein that are intrinsically disordered
•Protect misfolded proteins and assist in the refolding process
•Facilitate correct protein pathways
What are the Two Major Classes of Protein Chaperones?
•Heat Shock Proteins (Hsp-70 family)
•Chaperonins
Heat Shock Proteins
Are most abundant in cells that are stressed due to elevated heat (inflammation)
How to Heat Shock Proteins work?
•Bind to exposed hydrophobic regions of a polypeptide (prevents nonspecific protein aggregation
•May bind to an intrinsically disordered protein to prevent degradation or keep it disordered for a functional reason
Chaperone Assisted Protein folding
Can be a cycling event in which a protein released from HSP-70/HSP-40 complex has a chance to correctly fold. If not, may be bound to HSP-70 again
Chaperonins
Large protein complexes in which protein folding occurs within the chamber and protects proteins from aggregation (In bacteria called the GroEl/GroES system)
Protein Disulfide isomerase (PDI)
Allows for the formation of correct disulfide bonds between Cys amino acids; disulfide shuffling.
Where is PDI localized?
Several compartments of the cell; endoplasmic reticulum
Peptide propyl cis-trans isomerase (PPI)
Conversion of cis-proline to trans-proline
Insulin therapy in the treatment of diabetes
Long-acting/basal insulin injected under skin which adds 2 Arg amino acids to human insulin and shifts the isoelectric point to 6.8 which causes the injected insulin to precipitate under the skin and leads to a slow release by dissolving
How does MODY-maturation onset of diabetes occur?
Maturation of the Phe to Ser in human insulin. A misfolded protein “gets stuck” in the endoplasmic reticulum and cannot fold into its proper native conformation. Accumulation of the serine mutant insulin causes ER stress and leads to cell death.
Death of pancreatic b-cells=
Type 1 Diabetes
Amyloidosis
Secretion of a normally soluble protein in a misfolded state that becomes insoluble and forms an amyloid fiber
Amyloids have very specific arrangements in their
Tertiary structure
Mechanism of Amyloidosis
Secretion of the misfolded protein, self association between the misfolded regions and b sheets. Oligomerization of these misfolded proteins leads to the formation of a fibril. Large deposits leads to plaques
Neurogenerative diseases related to Amyloidosis
•Parkinson’s
•Alzheimer’s
What are the three ways of determining a protein structure?
•X-ray crystallography
•Nuclear Magnetic Resonance
•Electron Microscopy/ cryo-EM
Crystallography
Requires a protein or complex be easily purified and soluble at high concentrations. Size limitations depend on this and proteins will associate in a very particular manner creating a lattice
Protein crystals are subjected to
X-rays to obtain a diffraction pattern. The electron density map snd the structure can be determined
Pros of Crystallography
•Very high resolution data (Water molecules, h-bonds) and gives a Static picture of the protein/complex (snapshot)
Cons of Crystallography
•Will not work with intrinsically disordered proteins (or proteins with large regions of disorder
•Conditions that will allow a protein to crystallize may not reflect a biologically relevant form
Nuclear Magnetic Resonance (NMR)
Requires a protein be easily purified and soluble at high concentrations and used a strong magnetic field. Measured distances between atoms in a protein. Ramachandran plot is useful in structure determination
NMR structure determination
Can calculate distances and angles in the peptide backbone and R-groups. This information is then used to generate a structure of a protein. Repeated to ensure correctness
NMR pros
•Structural determination in solution
•Able to measure dynamics of a protein/complex
•More confidence that structure reflects function
NMR cons
•Concentrations of proteins can be lower for X-ray
•Size limitations of NMR (35 KDa)
•Required isotope labeling of your protein
•Protein has to be stable in solution for extended periods of time
Cryo-Electron Microscopy
•Useful for very large protein/complexes
•Receptor-ligand interaction interfaces
•Still requires purification of your protein/complex of interest
Motif
Recognizable folding pattern involving two or more elements
Domain
A segment of the polypeptide chain that is independently stable. They will retain structure if separated and typically retain functions as well
Protein and protein families can be arranged by
The presence of motifs. Generally these proteins have similar functions. Conserved motifs across species
