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Questions tagged [protein-folding]

The process in which a protein folds into a three-dimensional shape to achieve proper functioning.

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Determine secondary structure (per residue pair) from a protein contact map

Given a protein map contact map (which for this particular case is a matrix of all Ca-Ca atoms in protein 1a3a that are less than 8 Angstroms): Question: For each ...
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Experimental techniques to measure protein-protein and protein-ligand structure and dynamics

We would like to compare our simulation results with experimentation. When one wants to follow experimentally the dynamics (and possibly structure) of protein-protein or protein-ligand docking (...
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What is Genome Folding?

Why does genome folding have such great interest? For protein folding I could say that's important because protein's functionality closely depends on its folded state, since it affects its ...
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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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Incremental denaturation of protein mixtures

When a protein solution is heated above the denaturation temperature, it seems that denaturation does not happen at the time the temperature is reached, but it takes some time. I assumed that ...
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Protein Design - Target Structure Specification

I'm curious about how protein structures are defined in general, but in particular, I'm wondering how a target structure can be specified without knowing the amino acid sequence. For example, in ...
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Quantify Protein Denaturation with Change in Solubility

I plan to run a lab which compares the impacts of ethanol and methanol, in varying concentrations, on the denaturation of whey protein. Change in water solubility is a good indicator of the degree ...
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How can I render a protein non-functional to avoid problem during expression?

We're expressing a protein in a model organism for crystallization, however it seems the protein has some toxic effect on the cells. Is there something we can do to make it non-functional during ...
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Is the signal peptide always cleaved during protein synthesis in the ER?

My university supervisor said that the signal sequence is always cleaved, however my text book differs. What I gather from my text book (though it isn't very clearly stated so i'm not sure) is that: ...
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580 views

How to find the radius of gyration for a protein?

While going through the paper titled "GEOMETRIC ANALYSIS OF THE CONFORMATIONAL FEATURES OF PROTEIN STRUCTURES" by Manish Dutt, it talked about finding the radius of gyration of each protein structure. ...
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455 views

What is the most stable globular protein?

What is the most thermodynamically stable globular protein? I am looking for a small (ideally less than 50kDa) soluble globular protein motif which folds easily/reliably and is known to be extremely ...
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65 views

His Tag location in gene circuit

I am part of an undergraduate research group and we are trying to produce a protease in an E.coli gene circuit. We are not sure where to place the His tag in our circuit. The sequence is ...OmpA(gene)-...
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42 views

Which chemokines are being produced by melanocytes?

I am looking into Vitiligo it's an autoimmune disease that results in apoptosis of melanocytes due to misfolded protein accumulation. It also dramatically increases breast cancer rates (600 times) ...
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Are there well studied examples of ERAD-mediated membrane insertion, especially from viruses?

Membrane insertion of transmembrane proteins typically requires highly hydrophobic alpha helixes at the N-terminus, N-terminal signal peptides, tail anchors, or a combination of the three. Byun, H., ...
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Western blot extrange band

I performed a WB using plasma rats and monkeys samples with anti ubiquitin K-48 antibody. In every sample the antibody binds something and it appears a specific band that seems to be 71kDa. When I ...
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74 views

What causes the complementary copy of an RNA molecule to separate?

I have recently read an article which explains that, in the RNA World hypothesis, an RNA molecule gets 'scanned' by nucleic acid, catalysed by a different specifically-folded RNA molecule, to arrange ...