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15

It has been well established that mRNA abundance serves as a poor proxy for protein abundance in most cases. This paper on yeast and this paper on cancer both establish this, although using older techniques (SAGE and microarrays, respectively), while this more recent review discusses the topic in light of more recent technologies (e.g. RNA-seq). Perhaps the ...


14

Phosphorylation can occur on specific amino acids only, what you have called phosporylation sites. These amino acids are Ser, Tyr, Asp, Thr and His. In theory any of these amino acids may be phosphorylated, but in reality it may not actually occur for a number of reasons. Some of these are because of the change in overall charge of the protein which can ...


13

IDPs are indeed attractive drug targets and there are ongoing efforts to develop drug molecules that block interactions between a disordered and a structured protein. According to this relatively recent paper, however, these efforts have not brought a drug on the market, yet. A few promising studies have shown drug-like molecules that inhibit ...


13

The formation of protein complexes or aggregates in aqueous buffers is determined by a number of factors: physical properties of the protein itself, pH, temperature, type and concentration of the used cosolvent (salt). Solutes are often roughly divided by type into chaotropes ('disorder-making'), which destabilise protein structures and kosmotropes ...


13

The protein is called rhodopsin and the bit that gets kinked up is called retinol. Normally when light hits it, it does trans to cis isomerization at the 11th carbon. 'kinks up' is a pretty apt way of describing it. I'm not familiar with the shipped down to the liver part, but I'm guessing that the photo reaction of the retinol with itself or the ...


12

It's just so much more convenient to have the enzymes ready without having to thaw them. The main reason you freeze enzymes is to keep them active, if you figure out a buffer that keeps them unfrozen without compromising activity, that is a huge increase in convenience. Not having to thaw the enzymes before use saves a lot of time, if you can manage to keep ...


12

The only difference between FPLC and HPLC is the amount of pressure the pumps apply to the column. FPLC columns have a maximum pressure of about of 3-4 MPa, whereas HPLC columns can withstand or require much higher pressures. As a general rule, HPLC columns won't work with old FPLC equipment; FPLC columns can go on HPLCs as long as the pressure can be ...


10

This paper published last year, address the answer for your question, about computational methods, they mention 3 principal algorithms for structural alignment of proteins: Structural alignment directly at the level of C atoms. The second class of algorithms first uses the SSEs (Secondary Structure Elements) to carry out an approximate alignment, and then ...


10

As nobody has answered this good question, I'll have a go. Firstly, let me state that I have little-or-no knowledge of heat-shock proteins. What follows are some general observations and thoughts. It would not be unusual for the same enzyme from different species to have different kinetic properties. For example, yeast and horse liver alcohol ...


10

Yes. All proteins actually begin to get synthesized on cytoplasmic ribosomes but if they are going to be used for extracellular purposes, they are tagged and whole ribosome is taken to ER where protein synthesis is completed. The proteins are exocytosed with help of Golgi body, the post office tagging and packaging organelle (the Golgi body packages these ...


9

One important thing is missing in the other answers: not only phosphorylation will happen only at selected aminoacids, but it will not happen at all of those. So, not all of the Ser/Thr/Tyr of a protein can be phosphorylated because they could be structurally unaccessible to protein kinase and because they need to be in a specific motif in order to be ...


9

I have been working on this problem for quite some time now and believe me getting specific binding is a real issue with IDRs. Also, since these regions dont form core structure of the protein, the residues are less conserved (more prone to mutations). So in case of evolving drug-resistance contributing proteins this become a bottleneck. I have done some ...


8

PDB is a good resource for answering such questions, since it will let you filter results by many additional parameters. To count and extract 3D structures of human proteins: Open Advanced search tab of the PDB website. Select Biology -> Source organism from the menu. Type Homo sapiens (human). You can reduce redundancy by checking Remove Similar ...


8

To address your list: a high quality 3D structure: this you can easily get from PDB, using the answers to the question you linked as starting point. However, it is become increasingly clear that intrinsically unstructured proteins also play important roles in the cell, and for these you won't get a good 3D structure. known activity in vivo / known ...


8

Image from wikipedia page on ATP synthase In brief, the addition and release of protons to the structure cause a conformational change that leads to another conformational change. This series of conformational changes occurs in such a way that it induces a rotational motion. The rotation of the central axel that extends through both hemispheres of ...


8

The answer is that common folds are discovered in sequences which are completely divergent where essentially no alignment can be found by conventional means. David Eisenberg's group created profiles based on alignments from known structures which were more sensitive to discovering whether a given protein sequence was related to a given structure, solving ...


8

You use a library of many yeast in which each expresses only one target, or 'prey' protein. Then you grow each yeast colony separately, for example in different wells. It's definitely not a high-throughput method if you do it the old-fashioned way, i.e. making your own yeast library, or if you do it with only a few targets. But these days you can buy ...


7

The term you are looking for is psychrophile or cryophile. There are examples of microbes adapted to very cold conditions in Bacteria, Archaea, and Eukarya. There are also fairly complex animals capable of surviving very low temperatures - Tardigrades, for example. There are multiple issues that organisms face in withstanding extremely low temperatures - ...


7

Ramachandran plots show the relationship between the phi and psi angles of a protein referring to dihedral angles between the N and the C-alpha and the C-alpha and the C-beta. As an aside, the omega angle between the C-beta and the N tends to be fixed due to pi-pi interactions. Dihedral Angles There are limits to possible distributions of phi and psi ...


7

Phosphorylation requires exposed serine, threonine, tyrosine, or histidine residues (in eukaryotes). This is because the transfer of phosphate groups to proteins is mediated by a class of proteins called kinases. Kinases can have broad or specific activity. This review ought to have most of the answers to your questions : ...


7

Essentially, yes, "proteins that we consume form new proteins that are different". The processes are each of them topics for themselves. In short, consumed proteins are digested by peptidases (enzymes) in the stomach, breaking them down into their consituent amino acids. These are absorbed in the gut and transported in the blood to all cells. These take up ...


7

Biopython and the other bio-programming languages typically have examples of how to do this kind of thing. For example here is some python code for calculating some of these: http://biopython.org/w/index.php?title=ProtParam&redirect=no Many of the propensity scales are in this database: http://www.genome.jp/aaindex/ And there are also biojava ...


7

Transmembrane proteins are inserted into the membrane in the ER in a rather complicated system, there is a whole chapter about translocation of proteins in "Molecular Biology of the Cell". The proteins are moved through an aqueous pore in the Sec61 complex, which explains how charged parts of a protein are moved across the membrane. The parts of a ...


7

ATryn is a human antithrombin produced in the milk of transgenic goats by GTC Biotherapeutics. It has FDA approval and I believe that it is available for prescription in the USA. Added later, after the emphasis of the question changed somewhat. Proteins produced in a mammalian system are more likely to have post-translational modifications that are much ...


6

I am not sure I understand your question. According to the article you mention the proteins in teardrops kill the bacteria which are invading the eye (e.g. also present in the teardrops): "Those jaws chew apart the walls of the bacteria that are trying to get into your eyes and infect them," EDIT: These proteins are enzymes called lysozymes. Those ...


6

if you are using NMR structures you might be making the mistake of using several superimposed structures - it would be nice to develop with x-ray structures at less than 2.0 A resolution for starters. Some of the models at low resolution can be sloppy, but submitted after 1994 or so will not have any center to center distances as that's when the x-ray ...


6

There are so many types of protein-protein interactions via various domains, such as SH2 binding (in RTK signaling), Pleckstrin Homology domain (involved in signaling) among others. This site gives a nice list: http://pawsonlab.mshri.on.ca/index.php?option=com_content&task=view&id=30&Itemid=63 Of course, protein-protein interactions rely on the ...


6

The storage of memories in cells is rarely thought of on the protein level of the cell. Cells are usually given a developmental state, but no memory. A cell may become a liver cell, cancerous, or diabetic, but this is not memory, but a physiological change in the cell which is usually not reversible to a previous state. For example cancer treatments are ...


6

That's quite a laundry list, and I doubt someone is going to sit down and give you hints for all of them. Note that some of the properties (like percent alpha helix) rely on prediction method (secondary structure prediction, in this case). "Net donated hydrogen bonds" sounds like it makes sense only for a given complex with a solved 3D structure. ...


6

These are are completely different concepts, which sometimes may be connected. A motif in biology is a mathematical model, typically of a sequence, which is predictive of which sequences to some defined group. For example, a DNA sequence motif can characterize the binding site of a transcription factor, i.e. which sequences tend to be bound by this factor. ...



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