Difference between revisions of "20.109(S21):Module 3"
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'''Lecturer:''' [https://be.mit.edu/directory/alan-p-jasanoff Prof. Alan Jasanoff]<br> | '''Lecturer:''' [https://be.mit.edu/directory/alan-p-jasanoff Prof. Alan Jasanoff]<br> | ||
'''Instructors:''' [http://be.mit.edu/directory/noreen-lyell Dr. Noreen Lyell], [http://be.mit.edu/directory/leslie-mcclain Dr. Leslie McClain], and [http://be.mit.edu/directory/becky-meyer Dr. Becky Meyer]<br> | '''Instructors:''' [http://be.mit.edu/directory/noreen-lyell Dr. Noreen Lyell], [http://be.mit.edu/directory/leslie-mcclain Dr. Leslie McClain], and [http://be.mit.edu/directory/becky-meyer Dr. Becky Meyer]<br> | ||
− | '''TAs:''' Jeff Hsaio and | + | '''TAs:''' Jeff Hsaio and Caleb Perez<br> |
==Overview== | ==Overview== | ||
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<font color = #0d368e>'''Research goal: Perform site-directed mutagenesis to alter the properties of a protein-based fluorescent sensor'''</font color> | <font color = #0d368e>'''Research goal: Perform site-directed mutagenesis to alter the properties of a protein-based fluorescent sensor'''</font color> | ||
− | [[Image:Sp21 M3 overview | + | [[Image:Sp21 M3 overview v4.png|center|750px|thumb|Image generated using BioRender.]] |
<br style="clear:both" /> | <br style="clear:both" /> | ||
==Lab links: day by day== | ==Lab links: day by day== | ||
− | M3D1: [[20.109(S21):M3D1 |Review | + | M3D1: [[20.109(S21):M3D1 |Review IPC literature and examine structural characteristics]] <br> |
− | M3D2: [[20.109(S21):M3D2 | | + | M3D2: [[20.109(S21):M3D2 |Identify IPC mutations]] <br> |
− | M3D3: [[20.109(S21):M3D3 | + | M3D3: [[20.109(S21):M3D3 |Evaluate effect of mutations on IPC variants ]] <br> |
− | + | M3D4: [[20.109(S21):M3D4 |Design new IPC variant ]] <br> | |
− | + | ||
==Assignments== | ==Assignments== | ||
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==References== | ==References== | ||
+ | Resources for calmodulin and IPC: | ||
*[http://pubmed.ncbi.nlm.nih.gov/10884684/ Calmodulin: a prototypical calcium sensor]. ''Trends in Cellular Biology.'' 10:322-328. | *[http://pubmed.ncbi.nlm.nih.gov/10884684/ Calmodulin: a prototypical calcium sensor]. ''Trends in Cellular Biology.'' 10:322-328. | ||
*[http://pubmed.ncbi.nlm.nih.gov/11248055/ Circularly permuted green fluorescent proteins engineered to sense Ca<sup>2+</sup>]. ''Proceedings of the National Academy of Sciences.'' 98:3197-3202. | *[http://pubmed.ncbi.nlm.nih.gov/11248055/ Circularly permuted green fluorescent proteins engineered to sense Ca<sup>2+</sup>]. ''Proceedings of the National Academy of Sciences.'' 98:3197-3202. | ||
Line 43: | Line 43: | ||
Reviews for calcium signaling: | Reviews for calcium signaling: | ||
*[http://pubmed.ncbi.nlm.nih.gov/18083096/ Calcium signaling]. ''Cell.'' 131:1047-1058. | *[http://pubmed.ncbi.nlm.nih.gov/18083096/ Calcium signaling]. ''Cell.'' 131:1047-1058. | ||
− | *[ | + | *[http://pubmed.ncbi.nlm.nih.gov/11830654/ Calcium signaling: a tale for all seasons]. ''Proceedings of the National Academy of Sciences.'' 99:1115-1122. |
==Notes for teaching faculty== | ==Notes for teaching faculty== | ||
[[20.109(S21): Prep notes for M3| Prep notes for M3]] | [[20.109(S21): Prep notes for M3| Prep notes for M3]] |
Latest revision as of 19:44, 21 April 2021
Contents
Module 3
Lecturer: Prof. Alan Jasanoff
Instructors: Dr. Noreen Lyell, Dr. Leslie McClain, and Dr. Becky Meyer
TAs: Jeff Hsaio and Caleb Perez
Overview
The process of scientific inquiry encompasses much more than the collection and interpretation of data. A key part of the process is designing experiments that address a hypothesis based on the collection of new information, new materials, or new technologies. In this, any design is subject to continued revision. You might redesign an experiment or tool based on your own research, or you might consult the vast body of scientific literature for other perspectives. During this module, you will analyze data collected by previous 109 students and use the information to design a new version of inverse pericam (IPC), which is a protein-based fluorescent sensor that responds to calcium levels.
Calcium is involved in many signal transduction cascades, which regulate everything from immune cell activation to muscle contraction, from adhesion to apoptosis. Intracellular calcium (Ca2+) is normally maintained at ~100 nM, orders of magnitude less than the ~mM concentration outside the cell. ATPase pumps act to keep the basal concentration of cytoplasmic calcium low. Often calcium acts as a secondary messenger, in that it relays a message from the cell surface to its cytoplasm. For example, a particular ligand may bind a cell surface receptor, causing a flood of calcium ions to be released from the intracellular compartments in which they are usually sequestered. These free ions in turn may promote phosphorylation or other downstream signaling.
The proteins that bind calcium do so with a great variety of affinities, and have roles ranging from sequestration to sensing. Some calcium responses may have long-term effects, particularly in the case of transcription factors that can bind calcium. Calmodulin works as a calcium sensor by undergoing a conformational change upon calcium binding. Your goal in this module is to study previously generated mutants of calmodulin (in the context of IPC). These mutants were generated in an attempt to alter the affinity and / or cooperativity of the resulting protein for calcium. You will assess the success of these mutations in altering the activity of IPC and then propose a new mutation that improves upon the previous results.
Research goal: Perform site-directed mutagenesis to alter the properties of a protein-based fluorescent sensor
Lab links: day by day
M3D1: Review IPC literature and examine structural characteristics
M3D2: Identify IPC mutations
M3D3: Evaluate effect of mutations on IPC variants
M3D4: Design new IPC variant
Assignments
Research proposal presentation
Mini-report
References
Resources for calmodulin and IPC:
- Calmodulin: a prototypical calcium sensor. Trends in Cellular Biology. 10:322-328.
- Circularly permuted green fluorescent proteins engineered to sense Ca2+. Proceedings of the National Academy of Sciences. 98:3197-3202.
Reviews for calcium signaling:
- Calcium signaling. Cell. 131:1047-1058.
- Calcium signaling: a tale for all seasons. Proceedings of the National Academy of Sciences. 99:1115-1122.