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Hello,
I want to manipulate the binding rate of two proteins and essentially prevent them form binding to each other.
I understand there has to be an optimal environment for the proteins including pH and temperature.
I am just not sure how I could test this.
I figured I could use protein phosphorylation, so the proteins will no longer bind to each other.
But I can not figure out how to build an experiment around this.
Any suggestions?
Thank you
Protein interaction
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deleted-145947
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Protein interaction
Last edited by deleted-145947 on Tue Mar 25, 2014 9:37 am, edited 1 time in total.
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SciB
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Re: Protein interaction
Hi Devy,
Protein-protein interactions are at the heart of all biological processes. Enzymes recognize very specific substrates, signaling molecules recognize very specific receptors and transcription factors bind to very specific regions of DNA.
You are on the right track with phosphorylation, but it can work both ways. Some proteins bind only when phosphorylated and some do not bind when phosphorylated.
You need to decide on a hypothesis. You did not say WHY you want to interrupt binding and which protein interactions you might have in mind. In our lab we use specific peptides that bind to virus proteins and this binding prevents the virus from attacking cells. There are other scientists who are studying why the amyloid protein binds to itself to make the plaques that cause nerve damage in Alzheimer's disease. That would certainly be an important area to study. Preventing Alzheimer's would spare millions of people from a terrible wasting disease.
Cancer is another disease in which protein interactions are critical for tumor progression. We study a protein that binds to a receptor and causes certain types of cells to make new blood vessels that feed the growing tumor. We are researching ways to block this interaction in order to starve the cancer of its blood supply and kill it. There are some drugs that can block this interaction.
What are your ideas? I think it is great that you are interested in biochemistry since that was my major. Think about a question that you want to ask and do some online reading then get back to us with a proposal and we will steer you along into a great project.
Sybee
Protein-protein interactions are at the heart of all biological processes. Enzymes recognize very specific substrates, signaling molecules recognize very specific receptors and transcription factors bind to very specific regions of DNA.
You are on the right track with phosphorylation, but it can work both ways. Some proteins bind only when phosphorylated and some do not bind when phosphorylated.
You need to decide on a hypothesis. You did not say WHY you want to interrupt binding and which protein interactions you might have in mind. In our lab we use specific peptides that bind to virus proteins and this binding prevents the virus from attacking cells. There are other scientists who are studying why the amyloid protein binds to itself to make the plaques that cause nerve damage in Alzheimer's disease. That would certainly be an important area to study. Preventing Alzheimer's would spare millions of people from a terrible wasting disease.
Cancer is another disease in which protein interactions are critical for tumor progression. We study a protein that binds to a receptor and causes certain types of cells to make new blood vessels that feed the growing tumor. We are researching ways to block this interaction in order to starve the cancer of its blood supply and kill it. There are some drugs that can block this interaction.
What are your ideas? I think it is great that you are interested in biochemistry since that was my major. Think about a question that you want to ask and do some online reading then get back to us with a proposal and we will steer you along into a great project.
Sybee
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Re: Protein interaction
Hi Devyn,
This is a great idea! One way to test the interaction of proteins is to look at enzyme-substrate reactions. For example, there is a project in which you can investigate the action of the enzyme tyrosinase (which is responsible for the browning of food - apples, avocados, etc. - when cut, and also for creating melanin - dark pigmentation - in your skin). Tyrosinase creates a color-change reaction when combined with its substrate L-DOPA to form the pigment dopachrome. You can measure the extent of color change under different conditions: control, altered pH, etc.
If you are interested in this idea, go to this page [https://sites.google.com/site/sciencebr ... curriculum] and check out the Lab Prep materials listed under Enzyme-Substrate Reactions. You can try to do a similar project, or perhaps come up with your own idea based on this.
Please post again (in this same thread) if you have more questions.
Heather
This is a great idea! One way to test the interaction of proteins is to look at enzyme-substrate reactions. For example, there is a project in which you can investigate the action of the enzyme tyrosinase (which is responsible for the browning of food - apples, avocados, etc. - when cut, and also for creating melanin - dark pigmentation - in your skin). Tyrosinase creates a color-change reaction when combined with its substrate L-DOPA to form the pigment dopachrome. You can measure the extent of color change under different conditions: control, altered pH, etc.
If you are interested in this idea, go to this page [https://sites.google.com/site/sciencebr ... curriculum] and check out the Lab Prep materials listed under Enzyme-Substrate Reactions. You can try to do a similar project, or perhaps come up with your own idea based on this.
Please post again (in this same thread) if you have more questions.
Heather