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

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23
votes
1answer
474 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 ...
13
votes
2answers
872 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. ...
11
votes
2answers
86 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 ...
8
votes
0answers
606 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 ...
7
votes
1answer
268 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 ...
7
votes
1answer
614 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 ...
6
votes
3answers
269 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 ...
6
votes
1answer
362 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 ...
6
votes
1answer
328 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 ...
6
votes
1answer
131 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 substitution....
5
votes
2answers
419 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 SA"?...
5
votes
1answer
134 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 ...
5
votes
1answer
6k 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
1answer
85 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 ...
4
votes
1answer
55 views

What was Protein G named after?

Protein G (the bacterial antibody binding protein) is often used to pulldown antibodies, for example in chromatin immunoprecipitation (ChIP) experiments. However, I was unable to find a site ...
4
votes
1answer
37 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
2answers
402 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
150 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 mg/...
3
votes
1answer
124 views

Does urea at different concentrations (5 or 0.5M) have different effects on proteins?

The problem is to explain why each additive gives rise to the distribution of the protein (RMAS) as shown in the Western blow below: In each case, the homogenates were subjected to high-speed ...
3
votes
1answer
58 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 ?
3
votes
1answer
248 views

What is the significance in an alpha-helix being right-handed or left-handed?

Why is that often when alpha-helices are discussed, it is also mentioned their direction - right-handed (clockwise) or left-handed (anti-clockwise)? I have heard that left-handed alpha-helices are ...
3
votes
0answers
20 views

Phase Transitions of Purified Proteins

Why do solutions of purified protein condense into droplet phases? I'm trying to understand the protein phase transitions. Here is the article http://www.cell.com/cell/fulltext/S0092-8674(12)00634-4#...
3
votes
0answers
34 views

Minichromosome maintenance protein structure and function

I am having difficulty answering three homework questions which relate directly to Chong et al. (2000). Questions The authors have determined that MtMCM is able to bind both ssDNA and dsDNA (see ...
3
votes
0answers
87 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
130 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
2answers
60 views

Are multi-chain proteins synthesized as one biological unit?

Are multi-chain proteins (especially homo/hetero-dimers) synthesized together as one overall unit or are they separate monomers which bind together at some point after synthesis, and are there any ...
2
votes
1answer
49 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
1answer
114 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 ...
2
votes
1answer
276 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 ...
2
votes
1answer
52 views

How do proteins perform their function [closed]

I have asked a question on physics stackexchange, but was redirected here. I copy the entire question word for word. The original is here. Let's, for example, take a ribosome. It is an enzyme that ...
2
votes
1answer
77 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
542 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
2answers
73 views

How important is non-binding site of protein?

Just a curious question: What will happen if i remove most protein sequence that encoded for non-binding site of Restriction Enzyme to make a new enzyme, can the new restriction enzyme still work?
2
votes
1answer
75 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 ...
2
votes
1answer
83 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?
2
votes
0answers
38 views

Structure of proteins

Regarding the secondary structure of proteins, I know that there are 3 main types. The beta sheet formation is made up of beta strands stabilized by hydrogen bonds to form an anti parallel or a ...
2
votes
1answer
53 views

What is the P in LogP? [closed]

How does this value actually get calculated? Logarithms are usually written as log(base 10) of x So what is the 'P' equivalent of 'base 10'? I know it stands for octanol/water, but what does that ...
2
votes
0answers
27 views

How to determine suitable Cysteine mutations?

In the lab, I'd like to generate a dimer of a protein via disulfide bonds. The interface between the two looks as follows: Now, in the interface, there isn't any cystein I could use to dimerize the ...
2
votes
0answers
17 views

Interaction study of oligomeric proteins

I'm dealing with two different protein(say, protein_a and protein_b) which stays in an interacting-oligomeric form in biological system. I have so far successfully been able to purify both the ...
2
votes
0answers
55 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 ...
2
votes
0answers
106 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 ...
1
vote
1answer
31 views

How to induce a steady increase in cyctoplasmic [Ca2+] in HEK293T cells? And is there any simple marker/method to confirm it?

We are trying to find out whether increase or decrease of cytoplasmic calcium concentration affects the interaction of two proteins, using co-IP in HEK293T cells as a readout. In different forums and ...
1
vote
2answers
116 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 ...
1
vote
1answer
24 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
181 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 ...
1
vote
2answers
64 views

What makes DNA sequences most different/recognizable from a biological perspective? [duplicate]

We can pretty easily quantify the amount difference between two different strings/sequences of characters. For example, if we take the words trebuchet and trebucket, we can say they have a Levenshtein ...
1
vote
1answer
35 views

A question involving immunoprecipitation to identify interacting proteins?

Using recombinant Flag-tagged Dcr-2 and His-tagged protein X, pull-down assays were performed to determine whether protein X and Dcr-2 interact directly. The recombinant proteins (either alone or in ...
1
vote
1answer
18 views

Binding kinetics of 6xHis-Tag

For the planning of an experiment I would like to know the binding kinetics (kon and koff) of a 6x-His-tag to a Ni-NTA surface. I know they should differ due to surface quality and position of the ...
1
vote
0answers
34 views

Assays to determine competitive binding versus non-competitive

I'm looking for both simple and complex assays or technologies than can be used to determine if two competing molecules are competitive or noncompetitive. I figure xray crystallography is a clear one,...
1
vote
2answers
867 views

How much ATP is consumed during protein synthesis?

I'm trying to find out how many molecules of nucleoside triphosphates (ATP, GTP, UTP and/or CTP) it takes to release enough energy to link two amino acid monomers together with a peptide bond, ...