Hot answers tagged protein-binding
7
The techniques used to do this are ChIP-seq and ChIP-chip.
Basically, you
let the pathogen bind to the (highly replicated) DNA
cut up the DNA into little random pieces by sonication
enrich (“pull down”) the pathogen-bound DNA fragments by using a known antibody which binds to the pathogen
sequence the thus enriched DNA
map the sequenced fragments back to ...
4
This is the figure the question is about. On the right is the control experiment with GTP-γS, on the left without it:
The bands that are visible in both experiments are unspecific binding. If GTP-γS doesn't affect their presence, the mechanism by which they bind to the column can't be specific to the GTPase functionality.
The proteins the authors were ...
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.)
3
ChIP-exo does seem to be the "ChIP-seq killer." I've seen Dr. Pugh present it a few times, and the audience is pretty much always impressed.
One thing I'd do if I were of the "experimental bent" would be to add random degenerate barcodes in the library prep to control for potential PCR artifacts. I imagine that since the "peaks" in ChIP-exo seem to be quite ...
2
I've always just gone with the name hetereodimer but there isn't any technical reason why it isn't a quaternary structure. As for an example, I work with antibody fragments or FAbs and cys-diabodies which are exactly that, two distinct polypeptides that are connected by a disulfide bond linkage.
These do have a significant amount of non-covalent ...
2
A colleague of mine discovered the cipher that determines TAL effector DNA specificities, which is described in this short paper. These specificities were determined by observing TAL effectors bound to DNA and recording how often a given repeat-variable diresidue (RVD) would correspond to a given nucleotide (using a weight matrix).
Now that the ...
2
In prokaryotes the glucose transporter is always present in the cell membrane; in cells whose glucose uptake is insulin-regulated the transporter is only present in the plama membrane when hormone levels are high.
GLUT4 is the isulin-regulated glucose transporter found in muscle and adipose tissue. When insulin levels are low the GLUT4 protein is in the ...
2
Background binding in this case would be the extent to which two proteins associate together by chance.
A hypothetical example: you may have a mitochondrial protein import complex. Usually cases there is a specific peptide sequence the import complex binds to , but proteins without an import peptide sequence will occasionally be bound to the import ...
1
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866014/
In this work they find that formaldehyde crosslinking happens by formation of a methylol adduct (due to nucleophilic attack by N or S in case of proteins) in protein which then attacks the DNA or vice-versa.
The final crosslink is by a methylene bridge
Formaldehyde can react to amino groups in ...
1
Apparently poly(ethylene oxide) is a biologically interesting polymer, with minimal protein interactions.
The apparently means that I haven't tried it myself, but my polymer teacher told us so.
http://www.sigmaaldrich.com/materials-science/material-science-products.html?TablePage=20204110
http://en.wikipedia.org/wiki/Polyethylene_glycol
Nomenclature ...
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