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

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2
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0answers
55 views

Does antibody staining / immunolabeling block or inhibit protein function?

In dissociated live cells, does staining them with an antibody block the protein's function? I am sorting cells based on their expression of a few marker genes, and culturing them post-sort for ...
0
votes
0answers
18 views

Help with STRING database

How can I generate a graph on the STRING web server for physical interacting proteins only? I know we could extract the data and use Cytoscape to create a graph, but I would prefer to have a graph ...
2
votes
1answer
26 views

In protein-protein interactions what is the difference between a binding site and an interface?

I see binding site and interface used almost interchangeably in the literature, but I'm not sure if it is exactly the same thing or not - what is the difference?
2
votes
0answers
51 views

What effects would be caused by exposure to common life forms with opposite enantiomer biology? [closed]

Pretend a human had their body "reflected": heart on the wrong side, etc.; but also at the biochemical level: proteins, sugars, cells, DNA, everything. What would the effects be of that human's ...
6
votes
1answer
228 views

How many RNA-binding proteins can simultaneously bind on a single mRNA?

Typically, how many RNA-binding proteins can simultaneously bind to a single mRNA? Or said differently, how many "binding sites" does an mRNA have? What order of magnitude? I am interested in RNA ...
2
votes
1answer
68 views

How is protein cavity centre related to binding?

I am confused and I have the following questions: 1. What are (in the context of article below) protein cavity centres? 2. How are they related to binding? (Automated identification of protein-ligand ...
6
votes
1answer
51 views

Is there a formula for determining the % of ligand bound to a given receptor in a mixture with multiple ligands and receptors?

When a ligand and receptor interact with a given kd, one can easily determine % of ligand bound to the receptor when the kd, total concentration of ligand, and total concentration of receptor are ...
2
votes
1answer
47 views

Edman method to identify peptides with Phenylisothiocyanate (PTH)

We all know that in this method the PTH reacts with the first amino acid (aa) from the N-terminal to the peptide and separates from it giving PTH-aa so that we can know the amino acids sequence in the ...
6
votes
3answers
218 views

Proteins folding

Some of us are involved in the folding@home project, spending time, money and resources. I would like to know an answer to two main questions: how do we know we fold it right? I mean these models ...
12
votes
2answers
330 views

Do transcription factors bind to both strands of DNA?

Do transcription factors (or generally proteins) bind to only single strand of DNA or both strands? Since it can have non covalent bonds to both strands in theory. I would like to know the mechanism. ...
0
votes
0answers
18 views

How to get chemical structures in PDB format?

I am about to embark on the final step of a research project that involves molecular docking. Specifically, I am planning on docking an alpha(2,6)-linked sialic acid glycan to the influenza ...
2
votes
1answer
161 views

Proteins: Post translational modification

I am a physicist and trying to understand some protein chemistry for a small project. Basically, amino acids combine to form proteins and after forming the primary structure, some chemical ...
5
votes
2answers
153 views

What does units/mg mean for Streptavidin

I got streptavidin for surface reaction. The label says "biotin binding: 16 units/mg". What does units/mg mean? Does it mean "1 mg biotin can bind to 16 units ...
1
vote
2answers
70 views

Kinetic binding / unbinding constants of protein + mRNA ⇌ mRNP

I wish to find an order of magnitude for the binding/unbinding constants of mRNA and RNA-binding proteins. Suppose molecules A and B reversibly associate to give the complex C. Assuming the diffusion ...
4
votes
1answer
55 views

protein-binding sRNAs

I am actually a computational biologist, pardon me if my question description is a bit off-note, my curiosity is driving me on A bit of background and context: In bacteria, a regulatory protein ...
22
votes
1answer
380 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 ...
5
votes
1answer
86 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 ...
2
votes
1answer
81 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?
7
votes
1answer
587 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 ...
4
votes
1answer
33 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 ...
3
votes
1answer
88 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 ...
1
vote
1answer
21 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 ...
3
votes
1answer
47 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 ?
8
votes
0answers
536 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 ...
2
votes
1answer
91 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 ...
11
votes
2answers
83 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 ...
0
votes
1answer
41 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?
2
votes
1answer
76 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
373 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 ...
5
votes
1answer
3k 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 ...
1
vote
1answer
151 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 ...
6
votes
1answer
274 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 ...
3
votes
0answers
79 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 ...
6
votes
1answer
128 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 ...
3
votes
2answers
332 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 ...