Questions tagged [phosphorylation]

the addition of a phosphoryl group to a molecule

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Does it make sense to calculate the phospho protein (serine) : phospho protein (threonine) of the same protein in western blot?

I want to indirectly measure the nuclear accumulation of DARPP protein through phosphorylation. Their nuclear transport is controlled by phosphorylation of Threonine 34 and Serine 97 residues. S97 is ...
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Is plastoquinone not an electron carrier?

In my book, under the topic chemiosmotic hypothesis, it is given that proton gradient is created by accumulation of protons in the lumen of thylakoids. One of the ways by which the gradient is created ...
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Does the ribosome have protein kinase activity?

The ribosome synthesizes proteins by translating the mRNA. The nascent peptide needs to go through the nascent polypeptide exit tunnel in the large ribosomal sub-unit before it reaches the cytosol ...
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How to get a list of kinases that phosphorylated a particular protein?

I am analysing the protein SF2 (also named as SRSF1). In the database, it is shown that this protein is often phosphorylated at the 189th tyrosine residue. I want to know which proteins could have ...
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Akt phosphorylation at Thr308 and Ser473

I am studying Akt signaling pathway. I know that phosphorylation at both T308 and S473 is prerequisite for full activation of Akt but wonder if phosphorylation/de-phosphorylation of one of them is ...
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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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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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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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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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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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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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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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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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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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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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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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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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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 ...
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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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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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What information can Uniprot give me about phosphorylated forms of proteins?

I have a list of proteins formatted like this: ...
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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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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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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 ...
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