Questions tagged [protein-binding]

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

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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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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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227 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 ...
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48 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 ...
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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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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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1answer
29 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 ...
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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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457 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? ...
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1answer
84 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 ...
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2k 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: ...
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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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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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24 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....
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29 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 ...
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1answer
434 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 ...
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796 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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79 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?
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139 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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119 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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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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1answer
75 views

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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1answer
223 views

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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315 views

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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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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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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1answer
774 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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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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46 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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2answers
78 views

Fe in bacteria light-harvesting system Reaction Center

Is the Fe in the reaction center of bacteria light-harvesting system bounded or free atom?
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6k views

What is difference between High quality and low quality proteins [closed]

I have seen in news that some bodybuilder died of taking steroids; when I went through details I learned that "low quality proteins" contributed to their death. I have studied about linkages in ...
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63 views

Protein binds to DNA and just stays there, what will happen next?

If I hypothetically make an inactive version of Cas9 or ZFN (that will bind to the DNA but does not apply the cleavage reaction). What will happen after the protein bound to DNA? Will it be stuck in ...
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1answer
160 views

The meaning of the “Score” in ScanProsite

I'm doing some research about a proteïne which is sequenced, however Í'm not able to find any information about the score which ProSite scan shows after finding an possible domain profile. I have ...
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101 views

Pharmacological inhibition of Ras

I was reading this review and came by this: Direct pharmacologic inhibition of RAS has been a major challenge. Interference with the nucleotide-binding pocket of the protein seems to be far ...
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897 views

Are the arrows in this diagram of ATP synthase correct?

I have a question about this image below. Do you think that the pink arrow is actually going in the right direction? I would suggest a LTO sequence and not LOT, since it is in the T state that ADP + ...
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119 views

Rules of motif forming

I want to understand how a motif is present or not, can be deduced from a PDB file. Are there any rule of thumb for forming 3D motifs? Like a series of helices and sheets in some direction will lead ...
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101 views

How well can proteins discriminate between ATP and GTP? Can ATP act as a GTP mimetic?

GTP and ATP are similar structures with the adenosine and guanosine groups differing. Both are involved in a vast array of biological functions. However it has been shown that in certain cases, GTP ...
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135 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 ...
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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#...
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2answers
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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 ...
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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 ...
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1answer
84 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 ...
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1answer
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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 ...
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99 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,...
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1answer
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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 is ...
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1answer
316 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 ...
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1answer
669 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 ...
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How much nucleoside triphosphate is required to form one peptide bond 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, ...
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2answers
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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?