Questions tagged [protein-interaction]
The protein-interaction tag has no usage guidance.
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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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How does HIV assemble its capsid correctly?
HIV’s capsid is very unusual. The capsid is made of around 1200 identical CA proteins (p24). These CA proteins first assemble into either pentamers or hexamers, which assemble into a fullerene like ...
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Should Secondary Antibody Bind better through adsorption than using an EDC Linker?
Recently, I conducted an experiment to compare the use of EDC versus passive adsorption.
I attempted to immobilize goat anti-rabbit HRP secondary antibody to Carboxylated polystyrene beads via EDC ...
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What is the actual mechanism by which ApoA-1 Milano exhibits its phenotype?
ApoA-1Milano is a variant of the apolipoprotein A-I protein that was discovered by the University of Milan when sequencing the genome of those native to the village Limone sul Garda. The mutation has ...
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What is the "GTP activator protein" that activates GTP-cyclohydrolase-1?
From GTP-cyclohydrolase deficiency responsive to sapropterin and 5-HTP supplementation: relief of treatment-refractory depression and suicidal behaviour (BMJ Case Reports, 2011)
The metabolic profile ...
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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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Do RNA modification proteins bind to specific repeats on the RNA polymerase II CTD?
The C-terminal domain (CTD) of human RNA polymerase II has 52 repeats of a similar heptapeptide sequence.
Will the RNA modification proteins only bind to some repeats at specific locations on this (e....
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How does the order of the pairs of cross-links in DNA determine the arrangement of the amino acids?
Quoting Richard Feynman from Chapter 3 of his book Six Easy Pieces, when he talks about DNA:
Attached to each sugar along the line, and linking the two chains together, are certain parts of cross-...
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What are the interaction energies/chemical potential values for the cytoplasm - protein interactions within the cytoplasm?
I'm trying to simulate phase separation in a biological based system using a Cahn Hilliard model. I have 3 components, they are 2 theoretical enzymes and the cytoplasm. I have found plenty of sources ...
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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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Why bovine serum albumin is used in mass-spectroscopy and how to interpret such data?
In the paper Network organization of the huntingtin proteomic interactome in mammalian brain, there is a description of a mass spectroscopy experiment where Bovine Serum Albumin (BSA) is added to a ...
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Peak-calling in CLIP: What is the effect of RNA-concentration?
I hope it's ok to repost my question from 8 months ago from StackExchange:Bioinformatics, that is still in beta.
https://bioinformatics.stackexchange.com/questions/10730/peak-calling-in-clip-what-is-...
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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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If species are reproductively isolated, then how are interspecific hybridisations carried out?
during fertilisation there is compatibility test done so that both sperms and eggs are of same species. the zona pellucida of egg bears sperm specific receptor proteins(ZP3 receptor proteins) which ...
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How many proteins could participate in a complex
Disclaimer: I’m a computer science student with minimum knowledge of biology.
I’m working on an algorithm to cluster proteins in Protein-Protein-Interaction Networks to find protein-complexes. While ...
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Application of molecular dynamics simulation (or alternatives) for the full pathways of protein interactions?
If one would like to control the biological system (e.g. to treat disease or aging/senescence) then one should introduce the drugs in the system, that initiate complex protein interaction pathways ...
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Computational approaches for making hypotheses about the effects of genetic engineering? Experiment planning methods?
Let's assume that I am searching for gene editing candidates for curing human adiposis. Are there computational frameworks that can allow me to select the best candidate-genes for editing via some ...
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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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Where would vegetarians/vegans get a substitute of hemo/myoglobin from?
As far as I understand, there is a difference in the iron absorbed from meat than from other sources like grains and vegetables.
If this is the case, is it possible that not ingesting the hemoglobin ...
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Hydrophobic interactions in the helix-turn-helix
This slide states that the second helix works to stablize the configuration of the two helixes via hydrophobic interactions. What exactly is this hydrophobic interaction? In other words, what ...
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Fluorescent protein tags and colocalisation
We want study if 2 proteins A and B are co-located, for that we use 2 FTP(Fluorescent tag proteins) for each protein?and after the expirement these 2 FTP are co-located. Does that mean necessarily ...
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False positives in TAP - MS experiments
Is anyone aware of a website where they show common false positives often found when doing a TAP-MS experiment to find protein-protein interaction experiments?
Particularly the Acs1 protein (Acetyl-...
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Biological validation of computationally determined gene-gene interaction
How can a computationally determined three-way gene interaction be biologically validated? What kind of assays or tests must be performed using cell/tissue-based and/or mouse models to prove that the ...
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Will the interaction of two proteins vary across different tissues? [closed]
Suppose protein A and B is both abundant in tissue X an tissue Y. Will A and B interact in X but not interact in Y?
I guess A and B could be biomarkers of a certain disease, and in the pathological ...
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Is tyrosine hydrophobic or hydrophilic?
I’ve seen tyrosine classified as a hydrophobic amino acid due to its aromatic ring in some textbooks and as hydrophilic due to its hydroxyl group in other textbooks.
How does tyrosine actually ...
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Query regarding KEGG KGML pathway files
With respect to the the Wnt pathway in KEGG, the KGML file of this pathway has description of each interaction between a pair of genes. These interactions are designated in the form:
...
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How to interpret the relationships of PTMs from BioGRID's data
On BioGRID Database, PTMREL is a file that describes relationships of the PTMs (Post Translation Modification) tabulated in a PTMTAB file.
I have several issues with this file.
Foremost, I am not ...
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What are the types of interactions in biological network (protein networks)?
In the KGML files, the types of relations between genes or proteins are precisely activation, inhibition, expression, repression, indirect effect, state change, binding/association, dissociation, ...
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functionality of protein based on amino acid covalently linked to something
This question is directly taken off from "challenge question" as part of my bio-engineering class.
The functionality of any individual protein covalently linked to a device is dependent on the ...
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Get Network Out of proteins of interest
I have generated a list of Proteins using oncogeenes and suppressor genes of cancer.
I have 5827 mapping identifier for 3916 interactions using STRINGdb R package .
How do I build a network of 200k ...
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String-db locally downloaded
I need a ppi network of cancer and it should have 200k to 300k proteins (nodes)
As the web inteface don't allow more than 2000 ...
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Stringdb using R Bioconductor package
I need to retreive a large dataset from String-db.
I 'm newbie in R so even with the documentation , I could not get the dataset fron String
How do I do to retreive a network from String 2k to 3k ...
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Biogrid interaction protein network
I need a ppi network for cancer or Alzheimer .
I'm using BioGrid , In the search field I can specify the gene id only ,
I want to know how can I make an interaction network for one of the disease ? ...
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Where can I find large datasets of protein-interaction networks?
Where do I find large datasets of protein interaction networks for cancer or alzheimer diseases? So far, I found String but it is does not have enough proteins for my purposes. Are there such ...
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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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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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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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map list of proteins into an already built network
I have a built reliable network which can be downloaded from here
http://www.filedropper.com/mynetwork
This network is bulit using Cytoscape. Now I have a list of proteins IDs, for example
...
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How would one determine if an up regulation of one protein leads to an over expression of another?
Again, I'm new to biology and have a bunch of questions.
Does it depend on the proteins involved? OR are there basic co expression procedures one could implement to determine exactly how much one ...
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difference between motifs, domains, patterns, signatures and profiles
I can't get clear the difference between those terms, I see them a lot while browsing on Prosite, Pfam, Expasy e.t.c.
However, I can find documentation about them, but It still not clear what the ...
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How do prions transmit their conformation to other proteins?
I was reading about prions and many sources say something to this effect:
"Prions may propagate by transmitting their misfolded protein state: When a prion enters a healthy organism, it induces ...
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How are PPI networks constructed?
I am a CS graduate working in Computational Biology. While the theoretical aspects of both AP/MS (and the various types) and Y2h are quite clear to me, the actual technical aspect of building large-...
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Protein-protein interactions search
I used STRING db in order to find all the interactions of the precursor protein APP. What I specifically need is a confirmation (supported by some article and experiments in it). But significant ...
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How to predict Protein-Protein Interactions from a pair of gene symbols?
I have a list of pairs of gene symbols who interact (putatively) and would like to assign each pair a score (and record other details) based on the predicted Protein-Protein Interaction (PPI). The ...
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How to predict cancer-related proteins in Protein-Protein Interaction networks [closed]
Protein-Protein Interaction networks are known. It's an undirected graph. Each row of the networks is like this (Protein 2 - Protein 6), and It represents the interaction between Protein 2 and Protein ...
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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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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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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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Stabilizing forces between the protein sequences?
we know that Protein structures from secondary to Quaternary are maintained by noncovalent or weak interactions including electrostatic interactions,van der Waals forces & hydrogen bonding. What ...
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