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The answer to this question emerges from an examination of the structure of tyrosine — or, more strictly, the tyrosyl residue, which is how it exists in proteins, the concern of the question: It has both hydrophobic and hydrophilic features and can exhibit both behaviours depending on the circumstances. The ring is aromatic and hydrophobic, but the ...


8

There is a bunch of decent protein-protein interaction databases: Biocarta, BioGrid, DIP, InnateDB, IntAct, MINT, PPID. Some of them aren't available now, but you can download datasets from the Expression2Kinases download page because they are integrated into X2K pipeline as part of Genes2Networks analysis. If you need more proteins, you can submit your list ...


4

A protein-protein interaction (PPI) binding site is a type of interface. If it has been established that the interface is a PPI binding site, then the terms can from that point forward be used interchangeably. But the word "interface" is very generic and does not have any specific scientific meaning so the nature of the interface must be defined or else the ...


4

Are multi-chain proteins synthesized as one biological unit? Sometimes yes but mostly not. Some proteins are synthesized as one long polypeptide pre-protein which is cleaved by some proteases to yield multiple chains. After cleavage the intramolecular interactions become inter-molecular or inter-chain interactions. Insulin is a good example of this (See ...


4

Substituting a single amino acid and checking the effect this has on a protein is a method to determine what this specific amino acid does in the protein. For example, substituting an amino acid that is part of the catalytic core would almost always make the protein non-functional. Alanine scanning is a technique that methodically replaces amino acids in a ...


4

Tyrosine (Tyr or Y, 4-hydroxyphenilalanin) is usually reffered as polar amino acid because its hydroxyl groupe (polar is rather hydrophilic), but there is a catch with the benzen ring and stacking pi-pi interactions. So many authors just put this aa in the "middle". But the other parth of your question is much more complicated. First of all you need to ...


4

Temporal kinetics does not refer to the kinetics of kinase phosphorylation reactions and, since it is not standard terminology, you likely wouldn’t find its meaning in any textbook. The authors of the paper quoted in the question use the phrase temporal kinetics to describe the phosphorylation state of a proteome-wide selection of kinase substrates (ie ...


3

What you need to do is compare the relative amounts of the protein in the insoluble (pellet) fraction to the soluble (supernatant) one. This way you can determine how soluble the RMAS has become through the effect of the indicated compound. DTT breaks disulfide bonds, but does nothing else to solublize the protein, so it's all in the pellet, with none ...


3

Proteins often undergo conformational changes. The activation energy required to undergo a conformational change in a protein with only covalent interactions would be much higher compared to that of a protein with weaker bonding forces. An example of a conformational change seen in enzymes is the change in conformation during allosteric regulation, in which ...


3

There are general guidelines for cross-linking protein-protein interactions, but specific parameters (i.e. cross-linker sub-types, spacer length, linker concentration, reaction pH and temperature) are often determined experimentally. Common protein cross-linkers target reactive functional groups that are more likely found on the surface of the protein than ...


3

The process of downregulating a receptor by internalizing and degrading it in response to (sometimes prolonged) activation or (sometimes prolonged) failure to activate is what pharmacologists call desensitization (in either context). You can read about this generally in Goodman and Gilman's Pharmacological Basis of Therapeutics, Chapter 3, under the ...


3

MD is used for studying structural changes. Simulation of biochemical pathways involves the kinetics (you are not really looking at how enzyme structure changes when it binds to substrate). You can certainly pool all the modelling strategies together to make a hybrid multiscale model. There are many people who work on such kind of modelling approaches. You ...


3

Acetylcholinesterase. Chosen because the esterase seems like a low energy reaction so it wouldn't need energetic co-factors. https://en.wikipedia.org/wiki/Acetylcholinesterase Not sure if I should do a new answer or not.


3

Yes, it was solved in the early 1960s, starting about 1961. See Wikipedia's Genetic Code - History, and perhaps "Establishing the Triplet Nature of the Genetic Code".


2

Basically, they engineered a vector which, when transfected to E. coli, produces transcripts of -and thus proteins to- a fusion gene which produces these transmembrane α helices conjugated to the staphylococcal nuclease. In other words, the E. coli are just factories for producing proteins: Expression, Extraction, and Purification of SN/GpA - For high ...


2

If protein 1 contains a glutamate near the binding site with protein 2 and is close enough to the lysine on protein 2, it may be possible to link the glutamate to the lysine through EDC coupling. EDC is 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide, which reacts with carboxyl groups to form an "active ester". This ester is highly reactive with primary ...


2

The sRNA mediated regulation in bacteria operates via diverse mechanisms. This case of sRNA competing with a mRNA for a protein is a passive kind of regulation. This might be good for finetuning but may not be very efficient. It is much better to actively regulate a mRNA by direct binding. Also, it will work only if the concerned protein is in limiting ...


2

I just looked and it seems I2D use the PPI from 5 organisms to predict interactions in those organisms, which have not yet been experimentally demonstrated, so its interolog PPI prediction tool by design (http://genomebiology.com/content/pdf/gb-2007-8-5-r95.pdf), where as STRING can be used to see what proteins are known to interact with a given protein, and ...


2

Interactions denote protein-protein interactions, which means physical association between proteins. By nature, these networks/graphs are undirected. Replication interactions (actually a not very good term) denote gene regulatory interactions that affect HIV replication. These sets also include the regulatory effects of HIV genes on host genes (and hence ...


2

This depends on the technology you're using for the interaction detection. Surface Plasmon Resonance and Isothermal Titration Calorimetry (and others) don't require tagged proteins of any kind. Though it doesn't hurt either one. If you're looking purely at chromotography, any tag that will stably capture. I commonly see GST, FLAG, and MBP in order of ...


2

Some experimental and modelling observations suggests, folding energy for right handed in more favorable. You can find more detailed answer to this question here.


2

This may or may not be possible, depending on what proteins you are considering. Generating a PDB file means predicting the structure of the protein. There are no methods for predicting protein folding accurately from plain sequence data, so you will need some experimental data on the structure of your proteins. If your proteins have not been structure ...


2

This question is waaaay too broad, but I'll give some short and simplified answers to the hypothetical you asked at the end. First, let's reformulate your example a little bit: How does the ribosome move along a strand of RNA? How would it do it? By hydrolyzing GTP and somehow coupling the free energy associated with that reaction to forward motion. Keep ...


2

Short Answer In a nutshell, there are two major differences: Species range: BioGRID integrates multiple species' protein-protein interaction (PPI) data, whereas HPRD focuses mainly on Human data. Functionality: HPRD has some GUI tools that can interact directly with it's database (e.g. BLAST - for searching proteins and their binding partners via sequence ...


2

See the manual: PPrel, in each of these, means protein-protein interaction, so we want to approach these by thinking about what the protein products of these genes can do with eachother. For the first and second example, the subtype(s) give more information about the interaction. They aren't necessarily mutually exclusive. For example, phosphorylation can ...


2

Your example of an interaction mediated by a scaffold protein is certainly one way of controlling protein interactions. This doesn't just happen in different tissues either, it is also used to fine-control the interaction of certain proteins within one cell, the most notable example for this are the kinases in the MAP pathway (see for example this paper). ...


2

I suspect that what you are asking for is years in the future yet. Bear in mind that the use of CRISPR-CAS9 is just entering clinical trials for a very few, well studied diseases. Almost all the work with CRISPR-CAS9 is still limited to model organisms and tissue cultures. Are you referring to Adiposis Dolorosa? Apparently the cause is not actually known ...


2

The problem with coming into bioinformatics from a non-biological background is all too apparent in your question, and very real. You are dealing with a category of object called a protein complex, you suspect that it will be reasonable to exclude a proportion of them, but as you don’t really know what they are (other than at a basic level) you don’t ...


2

Their LC-MS-MS data was only semi-quantitative as gathered, meaning they could compare relative levels of one protein to another in the same sample, but not necessarily between different samples with a high degree of confidence. So, they spiked known amounts of BSA, an extremely well-characterized protein frequently used in the lab, into their samples and ...


2

In attempting to answer questions about protein structure, the first port of call (which one might expect the questioner to have also visited) is the Protein Data Bank — the global repository of such structures. There one can search for RNA Polymerase II CTD, look for complexes with other proteins, find recent publications in which they are reported, and ...


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