Questions tagged [protein-interaction]

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6
votes
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 ...
6
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1answer
262 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 ...
5
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2answers
258 views

Help with STRING database data

I'm working with data downloaded from STRING database (string-db.org) for protein-protein interactions. My idea is to compare the topology of connections of the same protein on different organisms. ...
4
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1answer
130 views

protein-binding sRNAs

I am actually a computational biologist, pardon me if my question description is a bit off-note, my curiosity is driving me on A bit of background and context: In bacteria, a regulatory protein ...
3
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1answer
81 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 ...
3
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3answers
99 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 ...
3
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1answer
3k views

What is the significance in an alpha-helix being right-handed or left-handed?

Why is that often when alpha-helices are discussed, it is also mentioned their direction - right-handed (clockwise) or left-handed (anti-clockwise)? I have heard that left-handed alpha-helices are ...
3
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1answer
97 views

I2D vs STRING for protein-protein interactions

Can someone clearly explain me the differences between STRING and I2D(Interlogous interaction database) ? What does each database do best ? Which database is better for what kinds of studies etc ?
3
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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 ...
3
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0answers
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 ...
2
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2answers
171 views

Are multi-chain proteins synthesized as one biological unit?

Are multi-chain proteins (especially homo/hetero-dimers) synthesized together as one overall unit or are they separate monomers which bind together at some point after synthesis, and are there any ...
2
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2answers
90 views

Determining the appropriate bioconjugate

I'm thinking of crosslinking two proteins. The crystallographic nature of the interaction and the binding motif for each molecule is know. The paper says the intermolecular contacts (over 50; van der ...
2
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1answer
1k views

Why are VAL, MET and ALA substitutions commonly used for protein behaviour and function studies?

I have seen that amino acids are commonly replaced with VAL, MET or ALA to study the effects of these specific substitutions. Why are these specific amino acids used in particular, what are the ...
2
votes
1answer
118 views

In protein-protein interactions what is the difference between a binding site and an interface?

I see binding site and interface used almost interchangeably in the literature, but I'm not sure if it is exactly the same thing or not - what is the difference?
2
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1answer
56 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 ...
2
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1answer
734 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 ...
2
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1answer
81 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 ...
2
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1answer
31 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 ...
2
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1answer
173 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 ...
2
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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 ...
2
votes
2answers
321 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 ...
2
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0answers
21 views

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 ...
2
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0answers
41 views

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 ...
2
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0answers
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 ...
2
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0answers
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 ...
2
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0answers
166 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. ...
2
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2answers
103 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 ...
2
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0answers
87 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 ...
2
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0answers
38 views

Interaction study of oligomeric proteins

I'm dealing with two different protein(say, protein_a and protein_b) which stays in an interacting-oligomeric form in biological system. I have so far successfully been able to purify both the ...
2
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0answers
45 views

What is the protein with the highest affinity to lactose?

I was wondering: What is the protein with the highest affinity to lactose? Are there some databases with values for affinity?
1
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1answer
53 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 ...
1
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2answers
616 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?
1
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1answer
63 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 ...
1
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1answer
101 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....
1
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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: ...
1
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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 ...
1
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1answer
64 views

How is Glycophorin A and straphylococcal related to Escherichia coli and what does readily purified mean in this context?

I am reviewing the paper "Glycophorin A Dimerization Is Driven by Specific Interactions between Transmembrane Alpha-Helices." There is a statement in the abstract which I don't understand: "The ...
1
vote
1answer
870 views

What are the differences between HPRD and BIOGRID databases?

What are the differences between HPRD and BIOGRID protein-protein interactions databases? What are their purposes? Why do we need two different databases? How is data collected into each one? How ...
1
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1answer
54 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-...
1
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1answer
44 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, ...
1
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1answer
957 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 ...
1
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1answer
153 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 ...
1
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1answer
716 views

Why are low throughput methods more trustable for protein interaction?

I read that protein interactions found using high throughput methods are less trustable than those found using low throughput methods. For example, searching for interaction of BRCA2 on BioGRID, I ...
1
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0answers
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 ...
1
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0answers
14 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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0answers
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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0answers
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 ? ...
1
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0answers
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 ...
1
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1answer
408 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 ...
1
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0answers
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 ...