Questions tagged [protein-interaction]

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61 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 ...
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1answer
94 views

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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38 views

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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9 views

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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60 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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19 views

Improved Vascular Stiffness due to Protein

I found this study that seems to claim that whey protein is better for your vascular health than casein protein: https://www.essentialnutrition.com.br/media/artigos/hiwhey/1.pdf Sure, it seems to be ...
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1answer
41 views

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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13 views

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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1answer
55 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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49 views

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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76 views

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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1answer
48 views

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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27 views

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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1answer
55 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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243 views

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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318 views

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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1answer
32 views

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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1answer
52 views

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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3answers
98 views

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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1answer
30 views

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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2answers
5k views

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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1answer
34 views

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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37 views

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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1answer
43 views

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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37 views

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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35 views

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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64 views

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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1answer
151 views

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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51 views

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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1answer
257 views

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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0answers
131 views

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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1answer
938 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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0answers
165 views

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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1answer
145 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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37 views

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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38 views

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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2answers
1k views

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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2answers
291 views

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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1answer
83 views

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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2answers
100 views

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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1answer
50 views

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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0answers
86 views

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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1answer
171 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 is ...
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1answer
393 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
723 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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1answer
78 views

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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2answers
580 views

Alternatives to His-tags

What are the alternatives to using a histidine-tag in detecting protein-protein interactions? Why would they be more beneficial than his-tags?
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104 views

What are the structural characteristics of a protein-protein interaction network

I am an researcher in computer science. I am interesting in the alignment problem of PPI networks of difference species. I know a PPI network is a graph in its nature. I want to know whether there are ...
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1answer
34 views

C-myc/anti-myc Ab Interaction with Fusion Proteins

I am going to prepare a c-myc fusion protein with the following configuration: (28-residue signal sequence)-(c-myc)-(GGSGGGSG Linker)-(Protein of Interest (POI)) POI is a transmembrane protein and ...
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1answer
319 views

How to find a Cancer PPI network data [closed]

I need a Protein Protein Interactions network of Cancer (any type - just I want a PPI of any type cancer), I search and see DIP PPI and .... How to specify that is Cancer PPI and how to get a PPI of ...