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the addition of a phosphoryl group to a molecule

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What's the difference between using basal and insulin cells in a protein kinase assay?

I performed a protein kinase assay in which I tried to phosphorylate the SNARE protein syntaxin 16 in vitro. However the protocol I was given told me to carry out the assay twice, once using Basal ...
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1answer
4k views

What is exactly a phosphoester bond? [closed]

I've spent some hours trying to understand what exactly is a phosphoester bond, but I'm still confused and at this point I just want to throw myself out of the window. I've already read that post ...
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145 views

Protein phosphorylation in the cytoplasm. Typical time scale?

Is there a typical protein phosphorylation rate in the cell cytoplasm under physiological conditions, or at least an upper-bound? Suppose a protein $A$ is being phosphorylated into $A^*$ with the ...
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Does mammalian target of rapamycin (mTOR) resets over period of de-training?

I know this isn't probably a strictly biological question. But I don't know where else I can ask this. In litterature I'm struggling finding references or studies that investigate this particular ...
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1answer
33 views

Why the total phosphorylation of certain neuronal proteins decrease during development?

Looking at the effects of RIM1a which is a protein involved in neurotransmitter release. Any ideas as to why its total phosphorylation decreases as the rats develop? Many thanks Image; https://i....
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1answer
42 views

Can the concentration of a kinase be used to identify its substrate?

I'm currently working on a dataset were I'm trying to identify substrates of an kinase in silico, I have a dataset which contains the concentrations every 0h 2h,4h,6h,8h,10h,24h for a lot of proteins ...
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1answer
18 views

What for a Kinase Assay? [closed]

I am wondering why to use a kinase assay, since we can extract the proteins from cells and then do a Western with the specific antibodies we want to use.
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25 views

Kinases that are ATP-sensitive at physiological conditions?

Phosphorylation is an ATP-dependent process performed by kinases. At physiological conditions it is generally assumed that ATP concentration is high enough so that ATP is not a limiting factor. ...
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85 views

How well can proteins discriminate between ATP and GTP? Can ATP act as a GTP mimetic?

GTP and ATP are similar structures with the adenosine and guanosine groups differing. Both are involved in a vast array of biological functions. However it has been shown that in certain cases, GTP ...
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2answers
146 views

Techniques for detecting phosphorylation sites in proteins?

I would like to know how phosphorylated sites in proteins are detected in practice. I read some papers where the authors were talking about mass spectrometry techniques. But my question is that why ...
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4answers
2k views

Where do the four ADPs come from in the second stage of glycolysis?

In the first stage of glycolysis, the two molecules of ATP are broken down into 2 ADPs + 2 Pi through hydrolysis, then in the second stage of glycolysis they are phosphorilazed to obtain 2 ATPs. How ...
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3answers
94 views

How to generate simulated mass-spectrometry data for phosphorylated proteins?

I am trying to generate simulated MS data (Top-down and Bottom-up) for phosphorylated protein such as platelet-derived growth factor receptor (PDGFR-B). There are 10 tyrosine sites which are ...
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2answers
13k views

How many protons are pumped out per pair of electrons from NADH in oxidative phosphorylation?

I have searched the web and found that 10 protons are suppose to get pumped out during the electron cycle, but i'm a bit confused. I'm trying to count, for every complex(1/3/4), the number of protons ...
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2answers
776 views

Why does oxidative phosphorylation require complexes 2 and 3?

I am learning about oxidative phosphorylation in cellular respiration now and do not understand the roles of complexes 2 and 3 in the process. Specifically, my textbook says that 2 and 3 pump H+ out ...
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1answer
52 views

Phosphorylation capacity of an enzyme [closed]

Let's think ProteinA can phosphorylate proteinB, proteinC and proteinD. Condition1: All proteins are expressed and proteinA phosphorylates proteinB, proteinC and proteinD. Condition2: Only proteinA ...
4
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1answer
1k views

Phosphorylation-Dephosphorylation : ATP-driven VS spontaneous

Is protein dephosphorylation most commonly spontaneous (without need of ATP)? I came across some papers that mention it, as well as the opposite case (ATP-driven), but I can't figure out which is ...
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0answers
23 views

Would it be possible to regulate proper phosphorylation so the UPR wouldn't initiate a reactionary cell death in important cells?

In studying the correlation of folded versus unfolded proteins and their impact on neuro-degeneration, it looks like improper phosphorylation in the chaperones (at least, in part) causes the mis-...
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1answer
141 views

What information can Uniprot give me about phosphorylated forms of proteins?

I have a list of proteins formatted like this: ...
5
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1answer
1k views

Is oxidative phosphorylation less efficient in gram positive bacteria?

Gram negative bacteria perform oxidative phosphorylation in their periplasmic regions, between the inner and outer membrane where a proton gradient is maintained and used by the ATP synthase to make ...
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0answers
40 views

Phosphorylation alters structure: Specific Example?

Why does phosphorylation activate an enzyme? A common answer to this question is that the introduced phosphate group "alters the structure" of the enzyme. Can somebody point out a specific example ...
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1answer
346 views

What does the term 'modified residue position' in phosphorylation mean?

Does it mean the position of the amino acid in the protein sequence, or something else? For example, I came across the phrase "S 368 phosphoryation" where S is the modified residue and 368 is the ...