6

You were looking in the wrong spot. The PTM section you clicked on is for post-translational modification databases such as PhosphoSite. To get the actual modified residues, click on "PTM/Processsing" (sic) further up the page and then select "Modified Residue", and in your results table you'll get a list of all phosphorylations, glycosylations, acetylations,...


5

A similar question was already answered at How do Gram + bacteria use a proton gradient for F-type ATPase? . In those answers, there is a general belief that Gram negative bacteria do not have much control over their intermembrane space pH, because their outer membranes have many porins, such as OmpC, which allows free passage both ways for protons and other ...


3

I think I understand your question, and stumbled upon it because i was wondering the same thing while studying for my Microbio test. I know its a year late, but someday someone else might need this info...so here it is. To put it simply: there is a second pair of phosphates added to the two 3-carbon molecules cleaved from the preparatory stage before the 4 ...


3

You are correct, the 368 stands for the position of the amino acid in the protein's sequence - this particular serine is the 368th residue in the protein counting from the amino-terminal end.


3

I just want to add a slight clarifying point to the previous member's already great answer. Keep in mind that these 10 protons that are pumped into the intermembrane space by the end are per one molecule of NADH. So each molecule of NADH will result in 10 protons being transported into the intermembrane space (as previously stated). For each molecule of ...


3

It seems like the mistake is in complex III. Look at this image from here: It clearly shows the number of protons reduced in (and taken from) matrix and number of protons pumped into inter-membrane space. So the data becomes: Complex I: matrix: 2H+ reduced (from NADH + H+) + 2H+ pumped out IMS: 4H+ pumped in Complex II: matrix: 2H+ reduced (from ...


2

The numbering of the complexes in the respiratory chain is confusing, as it creates the impression that the chain is structured like Complex I $\rightarrow$ Complex II $\rightarrow$ Complex III $\rightarrow$ Complex IV ... but this is wrong. There are in fact several ways of feeding electrons into the respiratory chain. They all begin with one enzyme E ...


2

Don't be discouraged. At least in vitro, if there is ample chemical substrates (e.g. ATP) and protein A (i.e. kinase) remains active, the kinase will just keep phosphorylating its protein substrates (B alone or a mixture of B, C, D) until the substrates are depleted. Thus, all substrates will be phosphorylated eventually. The contrived Condition 1 may occur ...


2

First, I would like to clarify what is meant by "spontaneous". In chemistry, thermodynamically favorable reactions ($\Delta G < 0$) are indeed termed spontaneous because they will eventually occur, regardless of how slowly. But if transition states are unfavorable (high energy barrier), the reaction rate can be extremely slow --- millions of years in some ...


2

I know this is a two years old question... but I recently developed a web application which could be useful for you: Prot pi The Protein tool lets you simulate the mass spectrum of the intact protein, while the Peptide tool gives you the fragment ions of peptides. Modifications can easily attached to every site you want.


2

There's a very simple answer: scale. If a drug company wants to screen a million-compound library to find which ones inhibit the kinase activity of a certain target, they're not about to do a million IPs and a million Western blots. Instead, they'll use recombinant kinase and substrate peptides, with a variety of readout systems to choose from. Other ...


2

X-ray crystallography has been used to detect phosphorylated sites. The RCSB protein database currently contains 856 structures that have both a resolution below 3 angstroms and the keyword "phosphorylated" in their listing. It also appears to be possible to use NMR to study phosphorylated proteins. The situations where NMR/x-ray crystallography or ...


2

In principle X-ray crystallography or NMR could detect phosphorylation sites but they are much more complex and expensive techniques than mass spec. So for simply figuring out phosphorylation patterns in a protein is much easier using mass spec. Detailed reasons: For X-ray you need to crystallize the protein which is often very difficult/impossible and ...


1

I use PhosphoSitePlus too. I use it in combination with ELM as it finds linear motifs and generally gives a good generic candidate. The literature if not. Checking all close homologues sometimes pays off. Checking protein protein iteraction databases such as StringDB or IntAct may help too, but that gets very iffy —XL-MS (a smoking gun) is rare and does ...


1

Here are a couple Wikipedia articles that might help out: Critical period - Critical period: the idea that certain types of plasticity in the nervous system occur only at certain "critical" times. Long-term potentiation - LTP, talked a lot about in the paper you linked: it's a mechanism for strengthening of synaptic connections. Synaptic pruning - # ...


1

The concentration of a kinase is completely independent of the concentration of the substrate, and vice versa. In a typical kinase cascade (such as the Ras→Raf→MEK→Erk pathway), signal transduction is generally amplified with each successive step. A relative small population of one kinase (like Raf) phosphorylates orders of magnitude more of its substrates (...


1

There are many other sources of ADP in the cell: various proteins that use ATP as an energy source hydrolyze it to form ADP + phosphate, thereby extracting energy. This ADP can then be re-phosphorylated by glycolysis to form ATP again. If glycolysis did not produce a net yield of ATP it would be pointless, so it really should be unbalanced in this sense.


1

Have a look at PeptideMass, you can choose to use the "post-translational modifications" option that will output the masses of phosphorylated (among other modifications) peptides.


1

For peptides (bottom up) mMass accepts a sequence of interest and phosphorylated tyrosine can be specified as a modification after that. The program also performs in silico enzyme digests and in silico MS/MS fragmentation. There are other tools that attempt to accurately mimic the intensities of the various fragments that could be generated. The meaning ...


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