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Questions tagged [protein-binding]

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

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How do you determine the structure of a molecular recognition feature (MoRF) after it binds to itself?

I have a protein that has a roughly 10 residue chain that registers at a MoRF in MoRFPred and MoRFchibi. I have the PDB files to correlate the known structure of the protein with the site of the MoRF; ...
vdg's user avatar
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1 vote
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How to elute the protein that is bound to biotinylated RNA immobilized with streptavidin?

I would like to test the proteins that bind to biotinylated-RNA by mass spectrometry , I was using Dynabeads™ MyOne™ Streptavidin C1 (invitrogen) coupled with biotinylated-RNA,than mix these beads up ...
Fino's user avatar
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3 votes
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Why am I getting a large horizontal band spreading across my native gel?

On every gel of this type that I've ran so far, I'm getting this large band interfering with my gel analysis no matter how much troubleshooting I've done. This is a Novex Wedgewell 6% Tris-Glycine Gel ...
novara's user avatar
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DnaA binding energy to E coli genome

I have been told that DnaA binds strongly to DnaA boxes on the E coli genome, but binds weakly to 8 out of 11 sites near ori. I want to know more quantitatively what strongly and weekly mean. Are ...
stochastic's user avatar
24 votes
3 answers
6k views

How do proteins 'know' where to go?

I've just found once again this famous animation I've been curious about for many years: https://youtu.be/WFCvkkDSfIU?t=213 Here's a screenshot from the animation: The green blobs (proteins, I ...
Vladislav's user avatar
  • 341
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0 answers
27 views

How much protein to add for complete binding

I have 7mg of a 74kDa protein $A$ bound to a column. I want to bind another protein $B$ which is 19kDa onto protein $A$ so that every protein $A$ is bound (or as close to 100% binding as possible). I ...
Ruochan Liu's user avatar
1 vote
1 answer
96 views

What are some experimental techniques to identify binding partners?

What experimental techniques can be used to identify binding partners for a given protein? I know that if you have some candidates that may bind to a given protein, then you can use techniques such as ...
Cactus's user avatar
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2 votes
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Comparison of different glassy matrices for protein immobilization at room temperature

I am completely new to protein biology experiments. I care about experiments where proteins are immobilized near a surface with the help of a glassy matrix or similar materials. I am looking for a ...
Ben's user avatar
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2 votes
1 answer
714 views

Is there are theoretical limit to the number of proteins possible and their respective structure?

I saw an article saying that DeepMinds AI has catatogued every protein known to science. I guess "known to science" and what is the theoretical limit is not exactly the same thing but the ...
Sedumjoy's user avatar
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How long is the typical peptide sequence recognized by a T-cell?

A naive T-cell recognizes either a certain sequence of amino-acids (even if that sequence occurs as a part of a longer sequence of amino-acids(*)), or a small set(**) thereof. Only T-cells that do ...
Jirka Hanika's user avatar
4 votes
1 answer
403 views

How does one derive a KD from an equilibrium titration experiment?

If I have an antibody A and a target B, and experimentally titrate the antibody against a single concentration of B, and then measure the % of B that is bound after the solutions reach equilibrium, I ...
Justin's user avatar
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T-Cell Receptor Receptor-Associated Immune Receptor Activation Motifs (ITAMs) Inconsistency

In reading the information associated with the cytoplasmic machinery of the T-Cell Receptor (TCR), the one tyrosine motif that is consistently mentioned is the receptor-associated immune receptor ...
Hawkeye's user avatar
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3 votes
1 answer
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What other sites do non-competitive inhibitors bind to apart from allosteric sites?

I learned competitive inhibition and non-competitive inhibition. My teacher told me that we should say that non-competitive inhibitors bind to somewhere on the enzyme apart from active sites. I ...
Bruce M's user avatar
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1 answer
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Can mrna spike protein block other proteins entering cells?

When vaccinated with pfizer a mrna is injected which eventually creates spike proteins. These will bind to cells. Now there is a rumour that when these spike protein binds to cells it can block other ...
Nuri Ensing's user avatar
5 votes
2 answers
926 views

Meaning of ‘motif’ in molecular biology

I would like to understand the meaning of the term motif as used in molecular biology. In an article in Nature Biotechnology, Patrik D’haeseleer states: Sequence motifs are short, recurring patterns ...
Manuela's user avatar
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4 votes
1 answer
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What is meant by “unique ligand” on the RCSB Protein Data Bank website?

I went to the https://www.rcsb.org/ site, and searched for some proteins. For each entry, “unique ligands” are listed. I understand a ligand is a molecule or ion that binds to a metal atom. I don’t ...
Harsh Dua's user avatar
6 votes
2 answers
514 views

Compatibility between spytag/spycatcher versions

Background SpyTag and SpyCatcher are peptides which can associate via a spontaneous amide bond. Because of this, they can be fused to proteins of interest as tags to cause the proteins to bind. There ...
Brad0440's user avatar
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Question about : RNA interference - small-interference RNA AND about Rab-protein in vesicles

First Question : RNA interference - small-interference RNA in the textbook -Essential cell biology By Bruce Alberts, Dennis Bray, Karen Hopkin this Figure is Shown my question is : if the foreign RNA ...
cisco_guy's user avatar
1 vote
1 answer
258 views

SPR TRIS or PBS buffer

Hey guys I want to ask why I can't get any binding interaction if I use TRIS-NaCl buffer for protein quantification using aptamer as its bioreceptor. But I can see the binding interaction if I use PBS ...
NexusRay's user avatar
1 vote
1 answer
71 views

Binding BSA to silver surface via large difference in isoelectric points of the two materials

I would like to bind BSA to a silver surface so that I can utilize plasmonic sensing to detect the BSA. There seems to be two methods of doing this: 1) to rely on electrostatic forces or 2) to form a ...
ngc1300's user avatar
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Measuring the protein content using UV Vis

The experiment is to determine the protein content of the solution. I followed the procedure of the Bradford assay but the reagent needed is unavailable and so we use an alternative by using cold pure ...
unknown0000's user avatar
-1 votes
1 answer
65 views

Is there an enzyme that functions without being associated with a complex?

I'm looking for an enzyme that does not function as part of a complex in its active state. Preferably it also is not part of a kinase or other kind of activating cascade as well though I would ...
Sarthak Garg's user avatar
0 votes
1 answer
312 views

What are " temporal kinetics"?

I am new to Biology and I am reading some papers about kinase proteins. I know what kinases do in the body. However, I found it hard to understand what are "kinetics". I googled this term ...
Adel's user avatar
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5 votes
2 answers
104 views

How do anticholinesterase pesticides kill nematodes?

Compounds that inhibit the enzyme acetylcholinesterase are commonly used as pesticides. In animals with centralized respiratory systems controlled by the nervous system, poisoning with an ...
user73910's user avatar
  • 409
0 votes
1 answer
56 views

SARS-CoV-2 proteome: is the SPIKE protein not an issue for a hospitalized patient?

I am performing molecular docking of ligands using the modeled proteome of SARS-Cov-2. My question is, after a patient is hospitalized, is the SPIKE protein not really an issue anymore, since its role ...
user avatar
2 votes
1 answer
131 views

Which proteins are part of the most different protein complexes?

Let n be the number of different protein complexes (as defined here) that a protein may be a stable part of for a considerable amount of time (and not only transiently). Which proteins have the ...
Hans-Peter Stricker's user avatar
1 vote
1 answer
61 views

What prevents mRNAs that are localized to a specific part of the cell from being translated before they reach their destination?

One of the methods of mRNA localization, for example, is random diffusion of mRNAs where the mRNA binding proteins are localized to a certain part of the cell. However, I was taught that the ribosome ...
Ben's user avatar
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1 vote
1 answer
74 views

Why does the structure for cellular retinol binding protein show interactions with cadmium ions?

A structure of cellular retinol binding protein (1CRB) contains two cadmium ions as ligands. Is Cd2+ a ligand of CRBP and, if so, is that interaction necessary for protein function or is the protein a ...
Eric Robinson's user avatar
0 votes
0 answers
438 views

Ligand-binding assays: IC50, EC50 and Kd

I am reviewing several MHC-peptide binding affinity predictors trained on IEDB data. Quantitative records for MHC class I allotypes come from a lot of different assays and, by extension, have ...
Eli Korvigo's user avatar
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0 votes
0 answers
55 views

What kind of bonds are there between a Transcription Factor and its DNA binding site?

I want to know what kind of bonds are there between a Transcription Factor and its DNA binding site when the complex is created. This information will be used to determine the method for a molecular ...
user avatar
9 votes
1 answer
466 views

What determines the direction in which motor proteins go?

I know that kinesin motor proteins move towards the positive (beta) end of the microtubule, while dyenin motor proteins move towards the negative (alpha) end of the microtubule. However, because the ...
F16Falcon's user avatar
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2 votes
2 answers
402 views

How do organophosphates actually work?

The common explanation as to what the primary mechanism of action for organophosphates (and carbamates) is is the inhibition of the enzyme acetylcholinesterase and resulting buildup of acetylcholine ...
user73910's user avatar
  • 409
2 votes
1 answer
93 views

How does the body detect irreversible binding to receptors?

I have read an article on Wikipedia about irreversible agonists and antagonists. These permanently bind to a target receptor on a cell. However, the receptor protein is then internalized and recycled ...
user73910's user avatar
  • 409
1 vote
1 answer
54 views

Where do the lysines come from during ubiquitination?

I know that Ub forms an isopeptide bond with lysine, but where do the lysine come from? Are they just always available for the Ub to find to during the ubiquitination process? Is there a free lysine ...
user3665690's user avatar
2 votes
1 answer
27 views

Can someone help me interpret these charts on fluorescent polarization?

I have to present an article about binding designed proteins to fentanyl for my biochem class; I understand everything except how to interpret these charts on fluorescence at the very top of Figure 2a:...
Wylona's user avatar
  • 21
1 vote
1 answer
41 views

Osmosis vs protein-binding in preserving foods through salting

I had assumed that the preservative function of covering foods with NaCl or brine was due to osmosis killing the microorganisms on the food by dehydration. However, I am now wondering to what extent ...
S. Fishman's user avatar
1 vote
0 answers
77 views

How does Ran GDP get from the cytoplasm back to the nucleus following nuclear import and export?

I understand that in Ran-dependent nuclear import Ran GTP binds importin in the nucleus, and after diffusing through the nuclear pore complex Ran GTP is hydrolyzed to Ran GDP and releases importin. ...
Ben's user avatar
  • 65
1 vote
1 answer
1k views

Can multiple antibodies bind the same antigen?

Given the size difference between small molecule antigens and antibodies is it ever possible for multiple antibodies to bind to the same antigen if they recognize different domains on that antigen? ...
Ike's user avatar
  • 49
2 votes
1 answer
121 views

How to characterize stability of a protein from Trp fluorescence vs [denaturant] curves?

A colleague of mine has taken Trp fluorescence measurements from a dimer in combination with various ligands, over a range of denaturant concentrations. The idea is that ligands which bind more ...
overdisperse's user avatar
1 vote
1 answer
4k views

What is the difference between Integrin to Cadherin?

My question is probably very basic but i couldnt get it in lecture and not from looking in the net. What is the difference between Integrin to Cadherin. By difference I am looking for say: ...
user135172's user avatar
1 vote
0 answers
28 views

Database of predicted protein-ligand binding/docking score

Is there a database of computationally determined "binding scores" across protein-ligand pairs in the PDB? My phrase "binding score" is deliberately generic, since any such score would be fine. In ...
user3658307's user avatar
4 votes
1 answer
2k views

Reversal of cross-linking in ChIP-seq

Chromatin immunoprecipitation (ChIP) is a type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell. A summary of the protocol for ...
Anu014's user avatar
  • 43
2 votes
0 answers
34 views

Smallest, specific RNA-binding protein - w/ sequence?

I'm looking to synthetically fuse an RNA-binding protein onto another protein, inside a viral vector which has a size-limit. I've considered some options, but I'm wondering what StackExchange will say....
Mike Flynn's user avatar
1 vote
0 answers
37 views

Dyes that won’t bind to dna

I am looking for a dye that won’t bind to DNA. I want to add dye to proteinase K to make is visible when adding to clear buffer liquid samples. I need it to not bind to the DNA so it will be removed ...
Lindsay's user avatar
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3 votes
1 answer
466 views

Could AI be applied to protein folding?

Two years later, there is a follow up question to the one asked here: How do we know if the folding@home project results are right? Since we are quite sure F@H is working right and following this ...
kreuzerkrieg's user avatar
10 votes
3 answers
1k views

What does a female mosquito need from blood?

I have come across many articles stating that female mosquitoes suck blood from vertebrate hosts to develop their eggs. Some also state that they need proteins, carbohydrates, iron etc., from human ...
RKK's user avatar
  • 630
5 votes
1 answer
102 views

Does cocaine bind competitively or non competitively to DAT?

I was just wondering whether cocaine, once reaching a synapse, binds to a DAT (Dopamine transporter) competitively or non competitively, or neither of them?
ModoUnreal's user avatar
0 votes
3 answers
166 views

Do different chiral centers on ligands cause different confirmational changes and effects in their target proteins?

Say pathogenic bacteriaA makes toxinA, which had D-amino acids instead of L-amino aids, does this difference in chirality cause a different conformational change in the receptor or enzyme, thus ...
Confusedbyeverything's user avatar
2 votes
0 answers
146 views

Protein/ligand affinity databases?

Is there any database that contain binding affinities reported in litterature for different proteins and ligands? I have checked uniprot already and it does not seem to included any binding affinity ...
Jeppe Nielsen's user avatar
1 vote
0 answers
52 views

Human Papillomavirus E7 (HR HPV16)

So there's a protein that binds to E7 viral protein, I want to remove a sub domain of the protein to see which exact domain the E7 binds to. What is the procedure for this? Edit: I believe the virus ...
Hoon's user avatar
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