Hot answers tagged enzymes
14
According to "Resolution of distinct rotational substeps by submillisecond kinetic analysis of F1-ATPase" (Yasuda et al., Nature, 2001), ATPase rotates at 130 revolutions per second when saturated with ATP.
14
It seems that yes, it is possible to increase the tolerance for lactose over time, and it has to do with the adaptation of microbiota.
A simplistic explanation comes in the following article:
Hertzler SR, Savaiano DA. 1996. Colonic adaptation to daily lactose feeding in lactose maldigesters reduces lactose intolerance. The American journal of clinical ...
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 ...
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 ...
9
You can certainly get massive differences between EC50 and affinity. This is especially true for cell-based assays and membrane protein systems.
The reason why is because the appropriate time scales to achieve binding equilibrium (hrs for nM affinity, days for picomolar, feptomolar affinity according to back of the envelope calculations) may be and likely ...
8
The macromolecule concentration within E Coli is estimated to be around 0.3-0.4 g/ml [1]
The concentrations of your substrate in respect to your enzyme are generally fairly analogous to in vitro studies compared to in vivo studies. However, this is heavily based on the assumption that the diffusion constants for both molecules stay consistent. In many cases ...
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 ...
7
This is true of all protein binding as well as the special case of enzyme-substrate interaction:
Various proteins are more dynamic than others: some have only one or two overall conformations and are relatively implastic otherwise. An example would be a receptor tyrosine kinase like Kit (or CD117, or Mast Stem Cell Growth Factor Receptor, whatever you want ...
7
First of all we should distinguish between the physiological clotting factors that are parts of the normal clotting pathways, and those that might affect clotting pathways but are not observed under healthy conditions.
TPA (tissue plasminogen activation), PAI-1 (plasminogen activator inhibitor) and prothrombin are normal clotting factors that are essential ...
7
I think the KEGG pathway database may be of some use to you.
Link is here: http://www.genome.jp/kegg/pathway.html
This a database of manually drawn pathway maps, I have used the site myself and it is very useful in determining if your enzyme is in a pathway and where it lies in it. This is assuming though, your enzyme is in the database and has been ...
7
It is possible to search for enzymes or a series of enzymes that will take similar reactants to similar products.
ReBIT allows you to query enzymes by your molecular structures of interest using their SMILES code. Unfortunately, a quick search using coumarin didn't produce any results but searches for phenol and phenolate gave some hits.
If you're seeking ...
6
Composition of E. coli (dry weight): 55% protein, 20% RNA, 10% lipid, 15% other
Protein concentration is about 100 mg/ml or 3 mM. From the size of an E. coli cell, 1 nM is about 1 molecule/cell. This is ~1000 molecules/cell for HeLa cells.
Diffusion coefficient for an "average" protein: D ~ 5-15 microns^2/s, or ~10 ms to traverse an E. coli. For reference, ...
6
For a great visualization of the macromolecules inside the cell, check out David Goodsell's illustrations. He tries to reproduce the protein and DNA density within the cell to show how things might be in vivo. Really great stuff.
The answer is - its very concentrated. Compare the density of the cell to that of a typical crystallized protein, which is I ...
6
The protein referred to in the question is encoded by gene PNLIP, pancreatic lipase. From this annotation of the protein, I see that there is a signal peptide from amino acids 1 to 16. Thus, this signal peptide must be cleaved before the protein can be active in its digestion of emulsified triacylglyerides.
A paper describes the structural changes induced ...
5
Here are my thoughts on the topic.
Dairy good is not only milk, but also the following milk products: sour milk products (like yougurt, kefir, katik, buttermilk, etc.), cheese, etc. These products can contain less lactose than in the milk solids (due to fermentation during processing). It is also common for some of these products to contain living ...
5
This refers to the turnover number (a.k.a kcat or k2) of an enzyme and is usually calculated using Michaelis-Menten kinetics. Jump to the summary at the end if you want a simple answer. If you want a more thorough answer, consider the following chemical equation:
[E] + [S] ⇌ [ES] → [E] + [P]
This says that a certain concentration of enzyme mixed with a ...
5
Having done an inordinate number of rather mind-numbing A.S. practicals involving milk and enzymes the year before last, in my experience lactase always began breaking down the lactose immediately and converting a boiling tube worth of milk in less than 50 minutes at below room temperature.
To further allay your concerns, this website suggests that most ...
4
Both models are true depending on how you frame the mechanisms of catalysis. As mentioned by @Blues, proteins are highly dynamic. In that manner, a protein will adopt both the unbound active state shown in the induced fit model and the complementary shape shown in the lock and key model.
(apologies since this is the only figure that I could find to explain ...
4
Early histochemical work indicated that the internal surface of the lysosomal membrane has a glycocalyx - a layer of polysaccharide, presumed to have a protective role.
Neiss, W. F. (1984) A coat of glycoconjugates on the inner surface of the lysosomal membrane in the rat kidney. Histochemistry 80, 603–608
Subsequently it was found that major membrane ...
4
For recombinant Taq polymerase, industrial-scale production produces liters of highly concentrated enzyme in a single run. It comes in such small, dilute quantities when sold that only a few preps a year would be necessary to satisfy research lab demand.
I don't know the Thermus aquaticus protocol, but considering the achievements in yield for E. coli, and ...
3
There's a paper from 1973 describing a very simple protocol:
Wolf PL, Von der Muehll E, Praisler K. 1973. A test for bacterial alkaline phosphatase: use in rapid identification of Serratia organisms. Clinical chemistry 19: 1248–9.
3
I found this kit that appears to be compatible with biological samples. Rather than buying the kit you may also be able to imitate / modify their protocol to do the assay with your super natant.
3
Both are measures of carbon fixation rate.
RuBisCO activity specifically refers to the rate at which the enzyme RuBisCO fixes carbon to RuBP, and is measured by isolating the enzyme from tissue samples and, usually, using radiolabelled CO2 to measure how much carbon is fixed in a set amount of time in controlled conditions and with controlled supply of ...
3
Have you heard of something known as "Occam's Razor" ?
It says when you have multiple possible explanations/hypotheses then select the one which is simplest (i.e least number of assumptions)
Same with mathematical models. Chemical kinetics models usually assume first order unless there is some evidence against it. Similarly, for enzyme kinetics, as long ...
2
I'm just taking a stab, because my inorganic chemistry is rusty.
cyanate (CN-) is well known to bind to iron (it inhibits hemoglobin and causes anoxia), and it also forms a pretty strong complex with Zinc:
http://en.wikipedia.org/wiki/Zinc_cyanide
I would guess that in the case of the SOD that the other liganding amino acids and the pocket of the ...
2
This expands my comment on the question to an answer.
If an enzyme exhibits Michaelis-Menten kinetics, then it is valid to define a KM and this equates to the substrate concentration when reaction velocity is 0.5 * Vmax.
However, many enzymes do not exhibit Michaelis-Menten kinetics. One example is when the enzyme shows a co-operative response to ...
2
It is not typical to investigate spectral absorption of compounds that are not useful for light absorption qualities, such as the compounds you've listed. Enzymes in particular will have less information because of the changes in binding partners our physical conformation to be enzymatically active. If you think there should be known info then I would try ...
2
The first step after sequencing is finding probable genes. After that, genes and their proteins can be classified to belong to protein classes. This is the most what you can do with completely unknown genes. It's possible nowadays to predict the final structure using contact maps (if there is no homologous structure known) but this will still leave you ...
2
ELISA is Enzyme-Linked ImmunoSorbent Assay (capitalisation to point out source of acronym).
You can read about the various ways to do an ELISA here.
In your case this was probably an indirect ELISA. All ELISA techniques make use of the fact that proteins stick to plastic. In your case the protein components of the saliva, including the virus (the viral ...
2
I have found that caffeine is mostly metabolized over CYP1A2 (as we know), but also over CYP1A1, CYP2E1 and CYP3A4. The question is how much the individual can cope with this alternate pathways if he is a CYP1A2 poor metabolizer. [1]
Secondly I found in my pharmaceutics textbook that CYP2A1 activity determination is indicated due to undesirable side effects ...
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