Hot answers tagged proteins
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 ...
9
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 ...
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 ...
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 ...
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
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 ...
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
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 ...
5
The group of Andrei Lupas studies this. He argues that the vast majority of folds arose only once, so that proteins that share a fold are homologous, even if their sequences have diverged. See for example this paper: "Evolutionary Relationships of Microbial Aromatic Prenyltransferases" where they show that there are subtle sequence similarities between two ...
5
Sarkar et al.(2007) Proline cis-trans Isomerization Controls Autoinhibition of a Signaling Protein. Molecular Cell 25, 413–426 (DOI 10.1016/j.molcel.2007.01.004), available here.
The authors report on the interactions between two SH3 domains of the Crk adaptor protein. Basically they find that the linker which tethers these two domains contains a ...
4
According to their website New England Biolabs use a version of the approach pioneered by Wayne Barnes, as described in:
Kermekchiev, M.B., Tzekov, A and Barnes, W.M. (2003) Nucl. Acids Res. 31, 6139–6147
This is basically an assay for the mutation rate in a PCR-amplified lacZ (β-galactosidase) gene, assayed by transforming E. coli, plating on the ...
4
This study in E.coli is useful in setting out some additional issues at play here, in a system where post-translational modifications are basically a non-issue. The authors see clearly a correlation between mRNA and Protein levels (Fig. 3C) and theorize that differences translation rate and protein turnover are responsible for differences in protein level ...
4
You can easly calculate the absorbance from Beer's Law
A = εlc
Here you can get the values for Extinction coefficient by sequence at http://web.expasy.org/cgi-bin/protparam/protparam1?P02769@25-607@
So for your example 0.001 g/L 3 g/L with this R code, you can get the absorbance values for each concentration.
> PM <- 66432.9 #g/mol
> c <- ...
4
Those that come up from a Google search ("predict DNA binding from protein domain tool") seem pretty well suited to your question.
BindN
DNAbinder
Depending on your computational/statistical know-how you might also find these papers relevant
Huang et al, Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of ...
4
I don't know of any examples of this but I would say no doubt, that's quarternary structure. Quarternary isn't so much defined by the kind of interaction but much more the fact that it's between different polypeptides; all lower-level structures are within one polypeptide. (Wikipedia agrees.)
4
The figure of 350 - 600 Units per mg refers to the specific activity of the enzyme.
The Unit is International Unit or IU and is usually defined as that amount of enzyme that will catalyze the transformation of 1 micromole of substrate (or product) per min, under defined assay conditions (such as pH, temperature, substrate concentration, presence of Mg++, ...
4
From the page linked from your link:
Unit Definition
One unit will convert 1.0 μmole of phospho(enol)pyruvate to pyruvate
per min at pH 7.6 at 37 °C.
So, the unit is defined by activity, and there is no way to know how many molecules or milligrams of protein are included
4
That's a good question, and honestly, the nomenclature for genes and their coded proteins is somewhat abused in scientific literature. For example, when referring to microbes (like E. coli), gene names are all lowercase (eg, lacZ). The problem of protein names is compounded when the protein name is (often) an abbreviation.
With respect to myc, it can refer ...
4
There is a useful set of links to nomenclature guidelines for all of the main genetic systems at this Wikipedia page. Personally, I think that the Saccharomyces cerevisiae system works best: it manages to cover dominant and recessive alleles of a gene, the name of the protein, how to refer to a related phenotype, and the use of a parallel convention for the ...
4
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. ...
3
A simple answer, you ingest daily dietary protein, then your body hydrolyze the proteins, to get all the building blocks for other proteins (amino acids).
Also, from diet you can get essential amino acids that cannot be synthesized de novo by the organism, this is more economically than amino acid synthesis.
3
The protein in question from Arabidopsis has this UniProt entry. In the comments you read: The N-terminus of the protein extends into the stroma where it is involved with adhesion of granal membranes and post-translational modifications; both are believed to mediate the distribution of excitation energy between photosystems I and II. As known PTMs we have ...
3
Protein interactions occur mostly (if not all) through residues that are on the "surface" and exposed to the milieu in which they exist, be it cytoplasmic or extracellular. So, a naive thought would be to guess that a greater surface area means a greater swathe of exposed regions and probable interacting parts. One protein can bind many others, even ...
3
I also had to do the same using Jmol, and I figured it out how to get a list of all the hbonds.
Step 1: Calculate the hbonds with or without RASMOL method. It's up to you, e.g.,
jmolScriptWait("select not hydrogen; set hbondsRasmol FALSE; calculate HBONDS")
Step 2: Only display the hbonds
jmolScriptWait("display connected(hbond)")
Step 3: Export the ...
3
I dont know about JMol, but this can be easily done with UCSF Chimera.
I loaded the 1a1x structure.
Then selected: Tools > Structure Analysis > FindHBond
I kept the default values and selected Write information to reply log
Then clicked OK
On the structure the H Bonds will be identified with a coloured line.
To view which is the donor and acceptor go ...
3
The way to check for steric clashing between any two atoms, backbone or otherwise, is to compute their Euclidean distance. If a and b represent two atoms (with a_x being the X coordinate of atom a and so forth), you can calculate their Euclidean distance as follows.
d(a, b) = sqrt( (a_x - b_x)^2 + (a_y - b_y)^2 + (a_z - b_z)^2) )
So essentially the ...
3
How about EWS-FLI1 and other oncofusion proteins?
One could argue that cancer progression is as close to viewing "evolution in real time" (as you say) as possible.
3
Yes, there are cases where one gene has become two. Or, at least, where multiple functions carried out by a single protein, the product of one gene, are carried out by distinct proteins, the products of different genes, in another species.
One case I have personally worked with is the bacterial SelB protein. It is essential for selenoprotein biosynthesis ...
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