Questions tagged [protein-binding]

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

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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 ...
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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 ...
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4 votes
1 answer
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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 ...
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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 ...
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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 ...
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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 ...
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5 votes
2 answers
329 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 ...
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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 ...
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6 votes
2 answers
344 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 ...
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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 ...
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1 vote
1 answer
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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 ...
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1 answer
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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 ...
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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 ...
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-1 votes
1 answer
62 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 ...
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0 votes
1 answer
193 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 ...
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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 ...
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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 ...
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1 vote
1 answer
115 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 ...
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1 vote
1 answer
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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 ...
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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 ...
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0 answers
164 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 ...
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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 ...
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9 votes
1 answer
280 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 ...
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2 votes
2 answers
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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 ...
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1 answer
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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 ...
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1 answer
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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 ...
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2 votes
1 answer
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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:...
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1 answer
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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 ...
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1 vote
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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. ...
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1 answer
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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? ...
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2 votes
1 answer
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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 ...
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1 vote
1 answer
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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: ...
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1 vote
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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 ...
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4 votes
1 answer
1k 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 ...
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2 votes
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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....
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1 vote
0 answers
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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 ...
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3 votes
1 answer
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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 ...
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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 ...
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5 votes
1 answer
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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?
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3 answers
156 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 ...
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2 votes
0 answers
132 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 ...
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1 vote
0 answers
50 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 ...
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3 votes
1 answer
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Is Sda a protein, or is it a protein domain of DnaA?

I initially thought that a domain was a specific part of a protein, with it given tertiary structure, to which a given molecule is able to bind. (I think I recall phrases such as "the haem binding ...
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2 votes
1 answer
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Are Raf, MEK, and ERK MAP kinases?

I am trying to make sense of this diagram. Can Ras activate RAF or MAPKKK, or is RAF a MAPKKK, making MEK a MAPKK, and ERK a MAPK?
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1 answer
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Signaling pathways with Receptor Tyrosine Kinase clarification

This question is regarding signaling pathways with RTKs, Receptor Tyrosine Kinase. The picture posted has one thing wrong with it and I am supposed to figure out what that is. What I have come up ...
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0 votes
1 answer
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Rosetta - What score does RosettaDock use for I_sc?

I want to get a score using Rosetta for how well a protein binds to a ligand. I understand RosettaDock has a score called I_sc which will give me a number to indicate that. I found documentation in ...
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7 votes
1 answer
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For Penicillin Binding Proteins, why is the enzyme-peptide complex less stable than the enzyme-β-lactam complex?

I'm trying to figure this out. I cannot find any publications that go into good detail about the chemistry of PBP inhibition by β-lactam antibiotics. PBPs cross-link adjacent pentapeptides to form ...
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1 vote
1 answer
1k views

What's the difference between physical (direct) and functional (indirect) protein interaction?

I read that the Protein-Protein interactions one can consider are generally of two types, namely physical and functional, but I cannot get the difference between the two. I was just thinking that if ...
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2 votes
0 answers
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How to quantify the "stability" of a protein complex?

From experiment we've identified a subset of known mammalian protein complexes as interesting (approximately 50 CORUM complexes). We'd like to do an enrichment-style analysis to know more about them. ...
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0 votes
1 answer
51 views

Computational engineering of protein binding pocket

I have an X-ray structure of an enzyme with reported activity to a small molecule. This activity is rather low since it is not the native substrate. I can run molecular modeling simulations (e.g. ...
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