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From Proteopedia
| This Sandbox is Reserved from January 19, 2016, through August 31, 2016 for use for Proteopedia Team Projects by the class Chemistry 423 Biochemistry for Chemists taught by Lynmarie K Thompson at University of Massachusetts Amherst, USA. This reservation includes Sandbox Reserved 425 through Sandbox Reserved 439. |
Contents |
LRRK2/Kinase Inhibitors
Introduction
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This is our scene for depicting protein chains from the N terminus to C terminus using rainbow coloring.
- Leucine rich repeat kinase 2 (LRRK2) is the key protein responsible for Parkinson’s disease. This disease is a disorder of the nervous system, which causes symptoms that affect a person’s movement. These symptoms may include tremors, rigid muscles, slowed movement, change of speech, and weakened balance.
- LRRK2 kinase inhibitors have been identified to be useful in the treatment of Parkinson’s disease. Due to the similarity in residues, the crystal structure of Tyk2 is being used to grasp a better comprehension of potential binding interactions of LRRK2.
- Other potential topics for discussion in the introduction would be the protein chains in the crystal structure Tyk2, the similarities between the crystal structures of LRRK2 and Tyk2, and what specifically LRRK2 kinase inhibitors would do to the symptoms of Parkinson’s disease
Overall Structure
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The Overall Structure of LRRK2 is shown in the window on the right and may be returned to by clicking .
The two chains, or units, that make up LRRK2 are essentially each TYK2 proteins, meaning LRRK2 is a dimer of TYK2. The Overall Structure of TYK2 is shown . The one major structural difference is that LRRK2 includes 2 Mg+ ions while Tyk2 does not.
- Building the LRRK2 Protein
There are 12 beta sheets that form the backbone of the protein. to add them. 6 sheets belong to Chain #1 and 6 sheets belong to Chain #2 . to differentiate each chain. They are organized into 4 groups of 3 sheets, where each group is adjacent to a group belonging to the opposite chain. This ordering increases the total protein stability by interweaving the two chains, but still allows for hinged movement.
LRRK2 additionally contains 10 alpha helices. The helices surround the beta sheets like a turtle’s shell, covering the beta sheets with the exception of one large side (belly) and the centers on the two long ends (head and tail). to add the alpha helices . to differentiate each chain.
Now we to complete the protein chain.
Now all that is left is to that are featured in the overall structure. There are 2 Guanosine Diphosphate compounds shown in ball and stick representation, along with 2 Magnesium ions, represented as spheres.
- Location of Hinge Structures
Each subunit of LRRK2 contains a single strand that connects the alpha helices to the beta sheets. These may act as hinges during binding interactions.
- Polar and Non-polar Groups
For LRRK2, when looking at the , you see that most residues are polar there are very few non-polar .
Conversely, the consist almost entirely of non-polar groups.
Binding Interactions
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LRRK2 contains binding sites for 6-[(2,5-dimethoxyphenyl)sulfanyl]-3-(1-methyl-1H-pyrazol-4-yl)[1,2,4]triazolo[4,3-b]pyridazine which we will refer to by its PDB code, 2YK.
The residues involved in binding interactions are listed below:
- LEU 903A
- VAL 911A
- GLY 1040A
- GLU 979A
- VAL 981A
These residues are highlighted in green and the ligand 2YK is shown in blue.
The scene below provides an alternative view of the binding interactions with the residues labelled in red with their corresponding number and the ligand, 2YK, labelled in blue.
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Additional Features
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LRRK2 is comprised of multiple domains:
- armadillo repeat (ARM)
- ankyrin repeat (ARK)
- leucine rich repeat (LRR)
- ras complex (ROC)
- C-terminal of ROC (COR)
- kinase
- WD40 repeat
The most well-known mutation, which occurs in the kinase domain, plays a role in Parkinson’s disease because it increases the kinase activity of LRRK2.
Mutations also occur in the ROC domain and play an indirect role in kinase activity.
Overview of Mechanism/Function
- GTP binding in the ROC domain regulates kinase activity
- Two PD associated residues, , stabilize the ROC dimer
- Mutations cause destabilization at these sites decreasing GTPase activity (and kinase activity)
Quiz Question 1
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The molecule shown is TYK2. Since the structure of TYK2 is almost identical to the structure of LRRK2, we will use it to simplify the concept of the .
The is the only segment that connects the (mainly) to the (mainly) . Various intramolecular interactions between the upper and lower segments help the protein maintain its tertiary structure. The strength of the interactions determines the rigidity of the hinge. If we were to add several cysteine molecules that were able to form disulfide bonds between the upper and lower segments without disrupting the active site, how would the kinase be affected? In your description, include whether the mutations would primarily affect Km or Vmax, how they would affect these kinetic parameters, and give a brief explanation of why.
Quiz Question 2
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For our second question I am going to present a green scene with the binding pocket shown and representation of the ligand shown. The green scene will show the details of the binding pocket including the secondary structures and the residues which make them up. I will then ask the student to think about the scene and give three ways in which they could modify the ligand which would make it a better competitive inhibitor.
See Also
- [2ZEJ]
- [Leucine-rich Repeat]
- [Crystal structure of a leucine-rich repeat protein]
- [Leucine-rich repeat-contain protein 4]
- [[1]]
Credits
Introduction - Megan Greiner
Overall Structure - Nick Barberio
Drug Binding Site - John Vetrano
Additional Features - Nicole Garvin
Quiz Question 1 - Charit Tippareddy
Quiz Question 2 - Peter Kelly
References
- ↑ Deng J, Lewis PA, Greggio E, Sluch E, Beilina A, Cookson MR. Structure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase. Proc Natl Acad Sci U S A. 2008 Feb 5;105(5):1499-504. Epub 2008 Jan 29. PMID:18230735
- ↑ Guo L, Gandhi PN, Wang W, Petersen RB, Wilson-Delfosse AL, Chen SG. The Parkinson's disease-associated protein, leucine-rich repeat kinase 2 (LRRK2), is an authentic GTPase that stimulates kinase activity. Exp Cell Res. 2007 Oct 1;313(16):3658-70. Epub 2007 Jul 19. PMID:17706965 doi:http://dx.doi.org/10.1016/j.yexcr.2007.07.007
- ↑ Li X, Tan YC, Poulose S, Olanow CW, Huang XY, Yue Z. Leucine-rich repeat kinase 2 (LRRK2)/PARK8 possesses GTPase activity that is altered in familial Parkinson's disease R1441C/G mutants. J Neurochem. 2007 Oct;103(1):238-47. Epub 2007 Jul 10. PMID:17623048 doi:http://dx.doi.org/10.1111/j.1471-4159.2007.04743.x
