this class: regulation of protein activities (1) what is a protein activity?
DESCRIPTION
This class: Regulation of protein activities (1) What is a protein activity? (2) How to change the rate of a specific cellular activity? (3) Rapid vs slower change (4) Varying amount vs specific activity of a protein (5) Coordinating simultaneous changes in related proteins - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/1.jpg)
This class:
Regulation of protein activities
(1) What is a protein activity?(2) How to change the rate of a specific cellular activity?(3) Rapid vs slower change(4) Varying amount vs specific activity of a
protein(5) Coordinating simultaneous changes in
related proteins(6) How to achieve fine/differential regulation
![Page 2: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/2.jpg)
What is meant by a protein activity?
![Page 3: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/3.jpg)
Overall cellular activity vs specific activity
Specific activity of a protein = amount of event performed per unit time per molecule of that protein
Overall activity of a protein = amount of event per unit time per cell (or unit tissue mass)
![Page 4: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/4.jpg)
Regulation of protein function
How to change the rate of a protein’s overall cellular activity?
(1) Change specific activity of that protein(2) Change amount of that protein
![Page 5: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/5.jpg)
Important additional considerations:
(1) What rate of change is required?(2) Do activities of any other proteins need to be changed simultaneously?
![Page 6: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/6.jpg)
Post-translational regulation of protein function
• Affects existing proteins (does not ∆ amt, but ∆ specific activity)• Can be rapid• Can be short- or long-lived• Multiple proteins may be affected• Multiple modifications are possible within a protein
![Page 7: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/7.jpg)
Post-translational regulation
1. Reversible phosphorylation
the first example (historically): mobilization of glucose from glycogen
![Page 8: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/8.jpg)
Sugar stored in skeletal muscle and liverPolymer of glucoseThe enzyme glycogen phosphorylase releases individual subunits of glucose from the polymer
![Page 9: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/9.jpg)
Glycogen phosphorylase
![Page 10: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/10.jpg)
How to control glycogen phosphorylase so it catalyzes this reaction only when necessary?
![Page 11: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/11.jpg)
Glycogen phosphorylase - P
ATP
ADPPhosphorylasekinase
![Page 12: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/12.jpg)
Glycogen phosphorylase - P
Phosphoproteinphosphatase
![Page 13: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/13.jpg)
Protein phosphorylation: a ubiquitous strategy
ATP cleaved to ADP; the P released covalently attached to a protein
![Page 14: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/14.jpg)
Phosphorylation is often of just a single amino acid residue :
SerineTyrosineThreonine
![Page 15: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/15.jpg)
Reversible protein phosphorylation: a widespread regulatory strategy
![Page 16: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/16.jpg)
Post-translational regulation
2. Other chemical modifications of individual amino acids
- egs. reversible acetylation, hydroxylation
- Use of mass spectrometry to identify prosthetic groups:
![Page 17: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/17.jpg)
Post-translational regulation
3. Cleavage of an internal domain
![Page 18: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/18.jpg)
Post-translational regulation
3. Cleavage of internal domain
Pro-caspase-3 activated to caspase-3 to initiate apoptosis
![Page 19: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/19.jpg)
Post-translational regulation
4. Movement between subcellular compartments
![Page 20: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/20.jpg)
Post-translational regulation
4. Movement between subcellular compartments
![Page 21: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/21.jpg)
Post-translational regulation
5. Reversible association-dissociation
![Page 22: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/22.jpg)
Heat shock factor-1 (HSF-1)
![Page 23: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/23.jpg)
Post-translational regulation
6. Modification of immediate environment- eg. oxidation of cardiolipin causes
cytochrome c release
![Page 24: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/24.jpg)
• Post-translational modifications change specific activity of proteins
• Only change the absolute amount of proteins secondarily (because transcription factors may also be reversibly phosphorylated)
![Page 25: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/25.jpg)
Regulation by altering absolute amount of a protein
![Page 26: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/26.jpg)
Regulation by altering absolute amount of a protein
(1) change synthesis rate
(2) change degradation rate
![Page 27: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/27.jpg)
Steps on the road to protein synthesis
![Page 28: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/28.jpg)
http://vcell.ndsu.nodak.edu/animations/transcription/movie.htm
![Page 29: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/29.jpg)
Assembly of the basal transcriptional complex on DNA
![Page 30: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/30.jpg)
Various factors interact with transcriptional complex to alter gene
transcription rate
![Page 31: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/31.jpg)
![Page 32: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/32.jpg)
Affecting transcription rate
Some terminology:Regulatory elements on DNA (cis-acting):
Positive = enhancersNegative = silencers
Regulatory elements not on DNA (protein factors; trans-acting)
Positive = activatorsNegative = repressors
![Page 33: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/33.jpg)
Some definitions
• Transcription factor: interacts with basal transcriptional complex and DNA
• Co-transcriptional activator: interacts with transcription factors to activate or repress (eg. PGC-1)
![Page 34: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/34.jpg)
Hormones can activate gene transcription
![Page 35: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/35.jpg)
Hormones regulate transcription of broad suites of genes due to presence of response elements
![Page 36: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/36.jpg)
Example: thyroid hormone (thyroxine)
Stimulates metabolism and metabolic rate (many genes)
Hormones regulate transcription of broad suites of genes due to presence of response elements
![Page 37: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/37.jpg)
Thyroxine Response Elements (TREs)
Direct Repeat
AGGTCAnnnnAGGTCAInverted Repeat
TGACCCnnnnnnAGGTCAPalindrome
AGGTCATGACCT
![Page 38: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/38.jpg)
Half-Site Promiscuity modulates effect
Achieves finer control of transcriptional activationPerfect Palindrome (= `the ideal` TRE)
AGGTCATGACCT
Promiscuity = substitution of “non-essential” bases
CGGTCATGACCA
AGGTCATGACCC
* The greater the divergence of RE from the ideal, the less strongly it enhances gene transcription
![Page 39: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/39.jpg)
Linking hormone response elements (HREs) to modulate effect
HRE
HRE HRE HRE
![Page 40: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/40.jpg)
Hormone receptors that act as transcription factors tend to share a modular design
![Page 41: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/41.jpg)
Other ways?
Regulation by altering absolute amount of a protein
![Page 42: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/42.jpg)
Regulated degradation
Other ways?
Regulation by altering absolute amount of a protein
![Page 43: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/43.jpg)
Wide variability in cellular protein half-lives
![Page 44: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/44.jpg)
N-terminal amino acid
Protein half-life
Ala (A) 4.4 hour Cys (C) 1.2 hour Asp (D) 1.1 hour Glu (E) 1 hour Phe (F) 1.1 hour Gly (G) 30 hour His (H) 3.5 hour Ile (I) 20 hour Lys (K) 1.3 hour Leu (L) 5.5 hour Met (M) 30 hour Asn (N) 1.4 hour Pro (P) >20 hour Gln (Q) 0.8 hour Arg (R) 1 hour Ser (S) 1.9 hour Thr (T) 7.2 hour Val (V) 100 hour Trp (W) 2.8 hour Tyr (Y) 2.8 hour
Half-lives of cellular proteins vary widely, depending on:
• identity of N-terminal amino acid (table)
• damage
• specific chemical modifications (eg. ubiquitinylation)
![Page 45: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/45.jpg)
Regulated protein degradation via ubiquitinylation and proteosomal digestion
![Page 46: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/46.jpg)
A ubiquitous (pun intended) regulatory strategy
![Page 47: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/47.jpg)
Next week:
More of chapter 2- Receptors and signal transduction
![Page 48: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/48.jpg)
![Page 49: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/49.jpg)
![Page 50: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/50.jpg)
![Page 51: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/51.jpg)
![Page 52: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/52.jpg)
![Page 53: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/53.jpg)
![Page 54: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/54.jpg)
![Page 55: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/55.jpg)
![Page 56: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/56.jpg)
1. Relatively rapid adjustments in activity
![Page 57: This class: Regulation of protein activities (1) What is a protein activity?](https://reader035.vdocuments.mx/reader035/viewer/2022062400/5681597e550346895dc6bc59/html5/thumbnails/57.jpg)