Questions relating to the binding of proteins to each other and other molecules.

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15
votes
0answers
166 views

Phagemid display

If I'm using a bacteriophage for phage display and I'm trying to avoid avidity effects by using a helper phage what would be the best way to maintain a large library size while keeping everything ...
11
votes
2answers
77 views

determining genome-wide exogenous binding of pathogens to host genome?

I've read this paper where they specifically modify a region in the rice genome to ablate the binding site of a pathogen, Xanthomonas oryzae, and disrupt the hijacking of a gene network in the rice ...
7
votes
1answer
511 views

ChIP-seq vs ChIP-exo

I'm currently investigating ChIP-seq vs. ChIP-exo for finding binding sites. As far as I can tell, ChIP-exo seems to be better in every way than ChIP-seq... but then again, I'm not strong in this ...
7
votes
0answers
356 views

Rosetta ab initio prediction and protein-protein interaction fitness help [closed]

I have designed several proteins which I predict have interactions with another protein using the sequence based Conjoint Triad Method. I would like to know which ones structurally are predicted to ...
6
votes
1answer
115 views

Ideal low-protein binding membranes

I'm looking through the literature on the topic. It seems like hydrophilic PVDF membranes are ideal for low-protein binding but it also sounds like Regenerated Cellulose is an appropriate ...
5
votes
1answer
179 views

Does GTP-γS (GTP gamma S) bind all GTP-binding proteins?

I've just read an article Rab10 GTPase regulates ER dynamics and morphology - Nature Cell Biology 15, 169–178 (2013) doi:10.1038/ncb2647. In this paper, to identify Rab proteins in ER, first they ...
4
votes
1answer
23 views

Telomerase in tetrahymena

In this amazing video, at 26:03 we see this image We now know that the telomerase contains a sequence complementary to the telomere sequence and so is able to do what it is capable of doing in this ...
4
votes
1answer
682 views

How does formaldehyde cause protein-DNA crosslinking?

How does formaldehyde cause protein-DNA crosslinking? I would guess it's because the strongly polar water molecule interacts strongly with polar residues on a protein-DNA complex, and adding a less ...
4
votes
0answers
34 views

Selective Androgen Receptor Agonist

I'm looking for an inducer that strongly activates the androgen receptor, but not the glucocorticoid receptor that is not DEA regulated. I know that SARMS (Selective Androgen Receptor Modulators) are ...
3
votes
2answers
218 views

Two subunits connected by only one disulfide bridge: quaternary structure?

I've always simply assumed quaternary structure to be characterized by non-covalent interactions such as hydrogen bonding, van der Waals interactions and whatnot. However, if two distinct polypeptides ...
3
votes
1answer
20 views

Function of heparin and dextran sulfate for removing proteins

From this article : The reaction was terminated and the histones, and most nonhistones, were removed by adding the nuclease-treated chromosomes to a solution containing dextran sulfate (2 ...
3
votes
0answers
56 views

Experimental techniques to measure protein-protein and protein-ligand structure and dynamics

We would like to compare our simulation results with experimentation. When one wants to follow experimentally the dynamics (and possibly structure) of protein-protein or protein-ligand docking ...
2
votes
1answer
46 views

How to identify active protein in a complex mixture?

I am trying to figure out how to identify which protein in a complex mixture is producing a certain effect. There is an assay for the effect, so anything (a fraction of the mixture) can be tested ...
2
votes
1answer
26 views

What stops telomerase?

The telomerase is an enzyme that adds telomeres. What stops the telomerase from adding too many telomere sequences ? What's the regulating mechanism ?
2
votes
1answer
71 views

How to bind antibodies to study their properties?

I want to experimentally look at the behavior of antibodies. To do so, I need to be able to bind these antibodies to a substrate. Does anybody know of a good substrate to use that antibodies bind to? ...
2
votes
1answer
150 views

How is transport of glucose into prokaryotic cells different from transport into eukaryotic cells?

I was reading page 92 of Fundamentals of Microbiology, 4th edition, which states In facilitated diffusion, the substance (glucose, for example) to be transported combines with a plasma membrane ...
2
votes
1answer
75 views

What type of distribution should binding affinities fit?

I've been averaging Ki values from the PDSP Ki Database, and I can't help but to wonder: how I can determine p values for the binding affinities, so I can exclude anomalies in the data if need be?
1
vote
1answer
16 views

2 types of telomerases?

As telomerase works by adding new nucleotides complementary to the RNA it contains, it cannot work for the complementary strand. Say telomerase X has RNA complementary to the 5' to 3' strand it ...
1
vote
1answer
65 views

What is background binding?

I'm reading a journal article about mitochondrial protein import and it mentions that one of the mutant proteins tested showed background binding with another protein. What the heck is background ...
0
votes
1answer
35 views

DAT1 dopamine and cocaine binding

I've searched the internet for several minutes and I've looked at DAT but I'm having trouble finding the DAT binding location. Where (and to which aa) does dopamine and cocaine bind to hDAT1?