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2
votes
2answers
38 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 ...
0
votes
0answers
14 views

Could bioluminescence be controlled by acetylcholine?

In a more extended question, I was thinking if there would be a way to control the brightness of bioluminescence by muscle stressing. Obviously skin and muscles are different tissues, but still I ...
2
votes
0answers
57 views

RAGE Oligomerization and Signalling Mechanism

I am looking to understand the mechanism of how the advanced glycation end products, s100 proteins and B-amyloids interact through oligomerization with the RAGE molecule (AGE receptor). I would also ...
0
votes
1answer
25 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 ...
2
votes
1answer
54 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 ...
1
vote
1answer
25 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 ...
2
votes
0answers
42 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
votes
1answer
51 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 ...
1
vote
1answer
33 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 ...
3
votes
1answer
107 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 ...
1
vote
1answer
42 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 ...
1
vote
2answers
58 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
vote
0answers
24 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 ...
0
votes
0answers
20 views

Will a metalloenzyme bind to its substrate in the absence of its metal ion cofactor?

A metalloenzyme is an enzyme using a specific metal ion as its cofactor. Their activity is dependent on this metal ion. For example, the T4 DNA ligase requires Mg2+ to ligate DNA strands; The ...
0
votes
0answers
17 views

How can I add metal ions in protein model with desired ligand?

I am working on docking study of different antibiotics. I want to check metal effect on the docking site or any active site in protein. So how can I add it with ligand? any docking tools are available ...
0
votes
1answer
18 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 ...
1
vote
1answer
105 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 ...
3
votes
1answer
216 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 ...
2
votes
2answers
59 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
votes
1answer
81 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 ...
1
vote
1answer
31 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 ...
2
votes
0answers
17 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 ...
0
votes
1answer
47 views

What tools can help me determine if a plant homologous protein interacts with an ncRNA in the same way?

First post here, so bare with me if I violate any etiquette or formatting rules. Let's say I've got a protein in humans. When it interacts with an ncRNA found in humans, it does something that I'm ...
2
votes
2answers
48 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 ...
0
votes
1answer
36 views

What is the difference between options protein and replication in the NCBI database?

After checking the NCBI help page, I am still unclear about the difference between protein and replication interactions for HIV. ...
2
votes
1answer
45 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?
5
votes
2answers
112 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. ...
2
votes
0answers
22 views

protein with 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 ? Thanks in advance
4
votes
1answer
83 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
votes
1answer
53 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 ?
1
vote
1answer
240 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
vote
1answer
421 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 ...