SURF 2023: Membrane Proteins - Revision history

Dajohnso: /* Research overview */

2022-12-21T06:27:42Z

Research overview

← Older revision		Revision as of 06:27, 21 December 2022
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	The 10–12-week project will be split into three stages The first stage will involve screening a selection of membrane proteins for ability to integrate within the membrane and carry out predicted functions. Ideally, this stage will be completed within 4 weeks and a library of characterized parts will be documents for use in the next stage. The second stage would involve coupling the project to a parallel project designed by another SURF team. 2 weeks are suggested to redesign genetic parts for compatibility and couple the projects. The third and final stage carries the coupled project through characterization and elaboration resulting in system designed from parts and capable of a predetermined goal. One arm of the campaign is laid out below:		The 10–12-week project will be split into three stages The first stage will involve screening a selection of membrane proteins for ability to integrate within the membrane and carry out predicted functions. Ideally, this stage will be completed within 4 weeks and a library of characterized parts will be documents for use in the next stage. The second stage would involve coupling the project to a parallel project designed by another SURF team. 2 weeks are suggested to redesign genetic parts for compatibility and couple the projects. The third and final stage carries the coupled project through characterization and elaboration resulting in system designed from parts and capable of a predetermined goal. One arm of the campaign is laid out below:
	* Viral infection of a synthetic cell. Synthetic cells maintain the capability to transcribe and translate genetic components but remain largely featureless on their membrane surface. Successful integration of cognate proteins to known viruses may enable viruses to engage synthetic cells and deliver viral payloads[[https://www.mdpi.com/1422-0067/23/20/12146#B53-ijms-23-12146 4]]. A project in this realm would consider minimum requirements for viral binding and delivery of payload. It would also necessitate a quantitative detection method for payload identification. Additionally, it may capitalize on the delivery of a genetic payload to enable the synthetic cell to expand its capabilities.		* Viral infection of a synthetic cell. Synthetic cells maintain the capability to transcribe and translate genetic components but remain largely featureless on their membrane surface. Successful integration of cognate proteins to known viruses may enable viruses to engage synthetic cells and deliver viral payloads[[https://www.mdpi.com/1422-0067/23/20/12146#B53-ijms-23-12146 4]]. A project in this realm would consider minimum requirements for viral binding and delivery of payload. It would also necessitate a quantitative detection method for payload identification. Additionally, it may capitalize on the delivery of a genetic payload to enable the synthetic cell to expand its capabilities.

			Preferred Skills: <br/>
			Minimum one biology course with lab <br/>
			General Python language experience to analyze results <br/>
			Recombinant protein expression


	'''References:'''		'''References:'''

Dajohnso at 03:04, 21 December 2022

2022-12-21T03:04:32Z

← Older revision		Revision as of 03:04, 21 December 2022
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	* Co-mentors: Alex Johnson		* Co-mentors: Alex Johnson

	[[Image:integrated-membrane.png\|right\|100px\|frame\|Integration of a membrane protein for extracellular interaction.]]		[[Image:integrated-membrane.png\|right\|100px\|frame\|Integration of a membrane protein for extracellular interaction. Membrane proteins allow extracellular interactions through: viral targeting of cognate proteins, decoration of cell surface with a variety of external proteins, and identification and possibly import of environmental chemical species.]]
	== Introduction ==		== Introduction ==
	This SURF project aims to characterize membrane integrated protein expression in synthetic cells and leverage the results through design of a system to interact with the extracellular space. Taking synthetic biology out of the test tube and integrating it into our everyday life requires questioning the way in which cells interact with the world around them. Membrane integrated proteins provide a wide range of extracellular engagement such as information transmission and surface recognition and binding. Up to 200 species of proteins are found in the typical bacterial membrane and comprise 70% of the membrane mass [[https://bionumbers.hms.harvard.edu/bionumber.aspx?id=106255 1]]. Traditional microbes, even those well characterized such as E. coli, make interrogating membrane proteins difficult. A ~~current approach is~~ the use of synthetic cells, non-living encapsulates of cell-free solutions encased within lipid vesicles~~. A recent method was published which guides implementation of~~ membrane ~~proteins in synthetic cell systems~~[[https://link.springer.com/protocol/10.1007/978-1-0716-1998-8_16 2]].		This SURF project aims to characterize membrane integrated protein expression in synthetic cells and leverage the results through design of a system to interact with the extracellular space. Taking synthetic biology out of the test tube and integrating it into our everyday life requires questioning the way in which cells interact with the world around them. Membrane integrated proteins provide a wide range of extracellular engagement such as information transmission and surface recognition and binding [[https://royalsocietypublishing.org/doi/10.1098/rstb.2015.0023 1]]. Up to 200 species of proteins are found in the typical bacterial membrane and comprise 70% of the membrane mass [[https://bionumbers.hms.harvard.edu/bionumber.aspx?id=106255 2]]. Traditional microbes, even those well characterized such as E. coli, make interrogating membrane proteins difficult. A recently published protocol suggest the use of synthetic cells, non-living encapsulates of cell-free solutions encased within lipid vesicles, to examine isolated membrane protein activity [[https://link.springer.com/protocol/10.1007/978-1-0716-1998-8_16 3]].

	== Research overview ==		== Research overview ==

	The 10–12-week project will be split into three stages The first stage will involve screening a selection of membrane proteins for ability to integrate within the membrane and carry out predicted functions. Ideally, this stage will be completed within 4 weeks and a library of characterized parts will be documents for use in the next stage. The second stage would involve coupling the project to a parallel project designed by another SURF team. 2 weeks are suggested to redesign genetic parts for compatibility and couple the projects. The third and final stage carries the coupled project through characterization and elaboration resulting in system designed from parts and capable of a predetermined goal. ~~An example~~ of a campaign is laid out below:		The 10–12-week project will be split into three stages The first stage will involve screening a selection of membrane proteins for ability to integrate within the membrane and carry out predicted functions. Ideally, this stage will be completed within 4 weeks and a library of characterized parts will be documents for use in the next stage. The second stage would involve coupling the project to a parallel project designed by another SURF team. 2 weeks are suggested to redesign genetic parts for compatibility and couple the projects. The third and final stage carries the coupled project through characterization and elaboration resulting in system designed from parts and capable of a predetermined goal. One arm of the campaign is laid out below:
	* Viral infection of a synthetic cell. Synthetic cells maintain the capability to transcribe and translate genetic components but remain largely featureless on their membrane surface. Successful integration of cognate proteins to known viruses may enable viruses to engage synthetic cells and deliver viral payloads. A project in this realm would consider minimum requirements for viral binding and delivery of payload. It would also necessitate a quantitative detection method for payload identification. Additionally, it may capitalize on the delivery of a genetic payload to enable the synthetic cell to expand its capabilities.		* Viral infection of a synthetic cell. Synthetic cells maintain the capability to transcribe and translate genetic components but remain largely featureless on their membrane surface. Successful integration of cognate proteins to known viruses may enable viruses to engage synthetic cells and deliver viral payloads[[https://www.mdpi.com/1422-0067/23/20/12146#B53-ijms-23-12146 4]]. A project in this realm would consider minimum requirements for viral binding and delivery of payload. It would also necessitate a quantitative detection method for payload identification. Additionally, it may capitalize on the delivery of a genetic payload to enable the synthetic cell to expand its capabilities.

	'''References:'''		'''References:'''
			# Rollauer, S.E., Sooreshjani, M.A., Noinaj, N. and Buchanan, S.K. (2015). Outer membrane protein biogenesis in Gram-negative bacteria. Philosophical Transactions of the Royal Society B: Biological Sciences [https://doi.org/10.1098/rstb.2015.0023 https://doi.org/10.1098/rstb.2015.0023]
	# BioNumbers ID [https://bionumbers.hms.harvard.edu/bionumber.aspx?id=106255 106255], "Fraction of cell membrane that is made of proteins by mass"		# BioNumbers ID [https://bionumbers.hms.harvard.edu/bionumber.aspx?id=106255 106255], "Fraction of cell membrane that is made of proteins by mass"
	# Jacobs, M.L., Kamat, N.P. (2022). Cell-Free Membrane Protein Expression into Hybrid Lipid/Polymer Vesicles. In: Karim, A.S., Jewett, M.C. (eds) Cell-Free Gene Expression. Methods in Molecular Biology, vol 2433. Humana, New York, NY. [https://doi.org/10.1007/978-1-0716-1998-8_16 https://doi.org/10.1007/978-1-0716-1998-8_16]		# Jacobs, M.L., Kamat, N.P. (2022). Cell-Free Membrane Protein Expression into Hybrid Lipid/Polymer Vesicles. In: Karim, A.S., Jewett, M.C. (eds) Cell-Free Gene Expression. Methods in Molecular Biology, vol 2433. Humana, New York, NY. [https://doi.org/10.1007/978-1-0716-1998-8_16 https://doi.org/10.1007/978-1-0716-1998-8_16]
			# Taslem Mourosi, J.; Awe, A.; Guo, W.; Batra, H.; Ganesh, H.; Wu, X.; Zhu, J. Understanding Bacteriophage Tail Fiber Interaction with Host Surface Receptor: The Key “Blueprint” for Reprogramming Phage Host Range. Int. J. Mol. Sci. 2022, 23, 12146. [https://doi.org/10.3390/ijms232012146 https://doi.org/10.3390/ijms232012146]

Dajohnso: Created page with "'''2023 SURF project description''' * Mentor: Richard Murray * Co-mentors: Alex Johnson Integration of a membrane protein for extracellular interaction. == Introduction == This SURF project aims to characterize membrane integrated protein expression in synthetic cells and leverage the results through design of a system to interact with the extracellular space. Taking synthetic biology out of the test tube..."

2022-12-16T23:33:18Z

Created page with "'''2023 SURF project description''' * Mentor: Richard Murray * Co-mentors: Alex Johnson right|100px|frame|Integration of a membrane protein for extracellular interaction. == Introduction == This SURF project aims to characterize membrane integrated protein expression in synthetic cells and leverage the results through design of a system to interact with the extracellular space. Taking synthetic biology out of the test tube..."

New page

'''[[SURF 2023|2023 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentors: Alex Johnson

[[Image:integrated-membrane.png|right|100px|frame|Integration of a membrane protein for extracellular interaction.]]
== Introduction ==
This SURF project aims to characterize membrane integrated protein expression in synthetic cells and leverage the results through design of a system to interact with the extracellular space. Taking synthetic biology out of the test tube and integrating it into our everyday life requires questioning the way in which cells interact with the world around them. Membrane integrated proteins provide a wide range of extracellular engagement such as information transmission and surface recognition and binding. Up to 200 species of proteins are found in the typical bacterial membrane and comprise 70% of the membrane mass [[https://bionumbers.hms.harvard.edu/bionumber.aspx?id=106255 1]]. Traditional microbes, even those well characterized such as E. coli, make interrogating membrane proteins difficult. A current approach is the use of synthetic cells, non-living encapsulates of cell-free solutions encased within lipid vesicles. A recent method was published which guides implementation of membrane proteins in synthetic cell systems[[https://link.springer.com/protocol/10.1007/978-1-0716-1998-8_16 2]].

== Research overview ==

The 10–12-week project will be split into three stages The first stage will involve screening a selection of membrane proteins for ability to integrate within the membrane and carry out predicted functions. Ideally, this stage will be completed within 4 weeks and a library of characterized parts will be documents for use in the next stage. The second stage would involve coupling the project to a parallel project designed by another SURF team. 2 weeks are suggested to redesign genetic parts for compatibility and couple the projects. The third and final stage carries the coupled project through characterization and elaboration resulting in system designed from parts and capable of a predetermined goal. An example of a campaign is laid out below:
* Viral infection of a synthetic cell. Synthetic cells maintain the capability to transcribe and translate genetic components but remain largely featureless on their membrane surface. Successful integration of cognate proteins to known viruses may enable viruses to engage synthetic cells and deliver viral payloads. A project in this realm would consider minimum requirements for viral binding and delivery of payload. It would also necessitate a quantitative detection method for payload identification. Additionally, it may capitalize on the delivery of a genetic payload to enable the synthetic cell to expand its capabilities.

'''References:'''
# BioNumbers ID [https://bionumbers.hms.harvard.edu/bionumber.aspx?id=106255 106255], "Fraction of cell membrane that is made of proteins by mass"
# Jacobs, M.L., Kamat, N.P. (2022). Cell-Free Membrane Protein Expression into Hybrid Lipid/Polymer Vesicles. In: Karim, A.S., Jewett, M.C. (eds) Cell-Free Gene Expression. Methods in Molecular Biology, vol 2433. Humana, New York, NY. [https://doi.org/10.1007/978-1-0716-1998-8_16 https://doi.org/10.1007/978-1-0716-1998-8_16]