1. AH Biology: Unit 1 Protein Structure 3
Reversible Binding of Phosphate and Control of Conformation

2. Reversible binding of phosphate and control of conformation LOS
The additional or removal of phosphate from particular R groups can be used to cause reversible conformational changes in proteins. This is a common form of post-transitional modification.
This is how many cellular proteins such as enzymes and receptors are regulated.
Kinase is often responsible for phosphorylation of other proteins and phosphatase catalyses dephosphorylation.

3. Reversible binding of phosphate and control of conformation LOS 2
Some proteins (ATPases) use ATP for their phosphorylation.
Myosin has heads that act as crossbridges as they bind to actin. When ATP binds to myosin, the myosin head detaches from actin, swings forwards and rebinds.
The rebinding releases the ADP and a phosophate ion drags the myosin along the actin filament.

4. Think
What conditions are affected by the permanent activation of specific proteins?
What is the charge on a phosphate group?
What effect does phosphate have on protein?
How is ATP generated by a cell?
How is ATP used by a cell?
Think about these questions and answer them as you study this section on protein structure.

5. Kinase
Kinase is often responsible for the phosphorylation of other proteins through ATP.
The addition or removal of phosphate from particular R groups can be used to cause reversible conformational changes in proteins.
This is a covalent modification of the protein.
This is a common form of post-translational modification.
In this way the activity of many cellular proteins, such as enzymes and receptors, are regulated.

6. Kinase
A phosphate group is highly charged, altering the position of charged bonding in the three-dimensional structure of the protein and as a result causing a conformational change.

7. Kinase
Kinase animation 1
Kinase animation 2

8. Kinase Now read this article:
Knight JDR, Qian B, Baker D, Kothary R (2007) Conservation, Variability and the Modeling of Active Protein Kinases. PLoS ONE 2(10): e982. doi: /journal.pone
Use Proteomics Tutorial 1 and answer the targeted questions in relation to this article.

9. Phosphatase
Phosphatase catalyses dephosphorylation of other proteins by the hydrolysis of phosphate from the protein molecule.
This again changes the conformation of the protein as a result of charge interactions of the R groups in the protein.

10. Signal transduction
Extracellular hydrophilic signalling molecules are involved in the activation of extracellular receptor proteins that then interact with intracellular proteins through a series of kinases and phosphatases.
This cascade of phosphorylation and dephosphorylation quickly activates intracellular events.
Insulin and the blood sugar level are controlled in this way, as is cell death (apoptosis).
G-protein-coupled signal transduction
Cyclic AMP signalling

11. The letters represent kinase enzymes involved in controlling apoptosis and cell proliferation.
Hormones are the main signalling molecule involved in activating the process via transmembrane proteins.
Details, obviously, are not required for this course.
Kinase cascade

12. Sodium potassium pump
Some proteins (ATPases) use ATP for their phosphorylation.
The pump creates an electrochemical gradient across the cell membrane that can be used to provide energy for other processes, such as the transport of glucose.
The binding of ATP releases phosphate, which provides energy for the reaction and binds to the protein channel.
The binding of the phosphate changes the conformation of the protein so that it releases three Na+ to the extracellular space.
At the same time the affinity for K+ increases and as it does phosphate is released, changing the conformation again back to its original state and releasing two K+ to the intracellular space.
The affinity for Na+ is again increased in this state.
This creates a net gain of sodium ions in the extracellular space and potassium ions in the intracellular space.
This produces an electrochemical gradient and thus an energy source that can be used to power other reactions in the cell when coupled with a separate ion channel.
The glucose co-transporter is an example of this.

13. ATPases
Some proteins such as ATPases use ATP for their phosphorylation.
Sodium potassium pump animation
Glucose co-transporter animation

14. Mitochondria

15. Aerobic respiration

16. Skeletal/striated muscle and contraction using ATP
Striated muscle (skeletal muscle) is composed of muscle fibres, which are long multinucleated cells.
The following details are for not required for this course, but may be of interest to candidates:
Bone
Perimysium (connective tissue sheath surrounding a fascile)
Blood vessel
Muscle fibre
Fascile (a bundle of muscle fibres)
Endomysium (the connective tissue sheath around a muscle fibre)
Epimysium (the sheath of connective tissue surrounding a muscle)
Tendon

17. ATP and muscle contraction
A muscle contracts as the actin and myosin filaments slide past each other.
Myosin has heads act as cross bridges as they bind to actin at specific binding sites and allow the muscle to contract.
Sarcomere contraction animation

18. ATP and muscle contraction
When actin binds to myosin, the myosin head detaches from actin, swings forwards and rebinds. The rebinding releases the ADP and a phosphate ion drags the myosin along the actin filament.

19. Transmission electron microscope image: human striated muscle
Each muscle fibre contains longitudinal sections of parallel myofibrils.
Each myofibril has a striated (striped) appearance and is subdivided into sarcomeres.

20. Muscle contraction via ATPase
Breakdown of ATP and cross-bridge movement animation.
Actin and myosin animation
Actin and myosin animation: Harvard BioVisions in detail
Once the myosin binding site on the actin is free the myosin head can rebind. At this stage ADP and Pi are still attached to the myosin head from the previous contraction.
The rebinding releases the ADP and a phosphate ion, dragging the myosin head along the actin filament.
ATP then binds to the myosin head.
When ATP binds to myosin, the myosin head detaches from actin, swings forwards and rebinds to a new myosin binding site along the length of the actin.
ATP is converted to ADP and Pi, and the energy from this conversion is stored in the myosin head to power the transition.
This whole process repeats until the contraction ends, Ca2+ concentration decreases and the protein tropomyosin again blocks the myosin binding sites on the actin.

21. Reversible binding of phosphate and control of conformation LOS
The addition or removal of ________ from particular R groups can be used to cause _________ ________ changes in proteins. This is a common form of ____________ modification.
This is how many cellular proteins such as _______ and ________ are regulated.
_______ is often responsible for phosphorylation of other proteins and __________ catalyses dephosphorylation.

22. Reversible binding of phosphate and control of conformation LOS 2
Some proteins (_________) use ATP for their phosphorylation.
_______ has heads that act as crossbridges as they bind to _____. When ATP binds to myosin, the myosin _____ detaches from actin, swings forwards and rebinds.
The rebinding releases the _____ and a ________ ion drags the ______ along the _____ filament.

23. Reversible binding of phosphate and control of conformation
The addition or removal of phosphate from particular R groups can be used to cause reversible conformational changes in proteins. This is a common form of post-translational modification.
This is how many cellular proteins such as enzymes and receptors are regulated.
Kinase is often responsible for phosphorylation of other proteins and phosphatase catalyses dephosphorylation.

24. Reversible binding of phosphate and control of conformation
Some proteins (ATPases) use ATP for their phosphorylation.
Myosin has heads that act as crossbridges as they bind to actin. When ATP binds to myosin, the myosin head detaches from actin, swings forwards and rebinds.
The rebinding releases the ADP and a phosophate ion drags the myosin along the actin filament.

25. Think
What conditions are affected by the permanent activation of specific proteins?
What is the charge on a phosphate group?
What effect does phosphate have on protein?
How is ATP generated by a cell?
How is ATP used by a cell?
Think about these questions again and answer them as part of a discussion in class based on what you have learned in this section .