Questions tagged [protein-folding]

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

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1answer
149 views

Protein folding, extra dimensions and bio-mathematics [closed]

One metaphor that I have found to explain how proteins fold so quickly to a native shape is that of the blind golfer. I have made a video to illustrate this metaphor. This shows how the shape of a ...
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1answer
734 views

What causes a polypeptide to fold into an Alpha helix over a Beta pleated sheet

I know how they fold, but what causes some polypeptide chains to preferably fold into Alpha-helix rather than Beta-sheets (or vice-versa). What force makes it fold into one conformation over the other?...
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1answer
108 views

How to calculate the number of folds present in a protein [closed]

Suppose I have number of PDB files of proteins. How can I get the number of folds present in these proteins? Is the fold count derivable from the PDB files? If so, how?
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61 views

Are there proteins with multiple motifs?

Does each protein adopt a single specific structural motif (zinc finger for example) or are there any proteins with multiple motifs along the chain?
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269 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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307 views

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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163 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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31 views

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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114 views

How do I identify the protein with the highest Disulfide bond density? i.e protein with highest ratio of Disulphide bonds per Peptide bond? [closed]

I want to list all proteins in the protein database and list them by the ratio of number of disulphide bonds per peptide bond. I am not particular about the reliability of identification of ...
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65 views

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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2answers
198 views

How to use swiss-mod to predict the secondary structure and 3D structure of a protein?

I'm trying to predict the protein secondary and 3-D structure for the sequence [Q1NN20] and need some help getting the ball rolling. I'm getting confused with how and when to use Jpred, swiss-mod, ...
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224 views

What are the different types of helices in protein secondary structures and how do they differ?

What are the different types of helices in protein secondary structures and how are they differentiated? In the DSSP docs, types of helices mentioned are: Alpha-Helix, Helix-3, and Helix-5. In the ...
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145 views

Statistical Analysis of Protein Folding Problem [closed]

I’m new to the field of protein folding. I’ve been searching and came across some books for predicting structures (Introduction to Protein Structure Prediction: Methods and Algorithms). Does anyone ...
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1answer
359 views

Transmembrane protein: does signal peptide always form a loop?

So I have read a few times that b. SP probably forms loop not arrow. Loop enters channel (translocon) in membrane. SP loop is probably what opens (gates) the channel on the cytoplasmic side. ...
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1answer
2k views

Why denatured proteins can't fold back in their native form

I was wondering why a denatured protein isn't able to fold back into it's native form again. Because a polypeptide before it's folded has a enthalphy and entropy drive to do so. What does the ...
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1answer
125 views

Can exhaustive algorithms produce MSAs that are suitable for 3D structure modelling?

While predicting 3D structure of a protein through homology modelling, the most important step is Multiple Sequence Alignment of template sequences with the target protein whose 3D model is to be ...
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49 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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73 views

What is the subcellular location of synthesis of non-essential amino-acids?

What is location of non-essential amino acids synthesis in a cell? Is it some specific organelle? And what is the gene driver behind this? I thought the whole point of DNA is coding for how to ...
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1answer
257 views

Building a PDB file from amino acid sequence of non-folded structure

I am interested in experimenting with folding simulations and algorithms for arbitrary sequences. I'm wondering if there is an easy way to convert an amino acid sequence into a PDB file for further ...
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1answer
1k views

Relation of conformational entropy and protein folding

I'm trying to figure out the relation between conformational entropy and protein folding. I read the following in Lehninger, Principles of Biochemistry (6th edition): Most of the net change in ...
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1answer
618 views

Which is the correct statement on proteins?

I need help with one of the questions on my biochemistry assignment Choose the correct statement on proteins: a) proteins are folded by alpha-helix b) proteins can preserve their function even if ...
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48 views

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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1answer
83 views

Is protein folding symmetric with respect to reversing the sequence order?

Suppose that I have two proteins, protein A and protein B, and suppose that the sequence of amino acids of protein B is exactly the reverse of the sequence of protein A. For example (these are made-...
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36 views

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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805 views

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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576 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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454 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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1answer
177 views

What are the key differences in giant and large unilamellar vesicle preparation processes?

I have to study my peptide's folding on membrane mimetic (model membrane) by circular dichroism spectra. Now I'm looking for suitable methods for preparation of vesicles: LUV, SUV, GUV- large, small ...
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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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1answer
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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200 views

A question regarding evolution

I'm not a biologist so bear with me. I know that the DNA molecule carries extremely large amounts of information. If the process of evolution is driven by completely random process .I think about it ...
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1answer
127 views

Calculating fraction of protein unfolded from spectroscopy data

This is a question from a homework pset of previous year. We are given the absorbance at 222nm of both a wild type and mutant protein at different temperatures. We are then asked to calculate various ...
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63 views

What does 'kinetically accessible' mean in protein folding?

The hydrophobic collapse model discusses this term in the energetics section. What does this actually mean?
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67 views

Function of ER in reviewing mutated proteins

At least in the case of Cystic Fibrosis it happens that a mutant protein (which could actually function!) is held in the ER because the ER detects it as misfolded. Does this happen in every type of ...
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568 views

Given an amino acid sequence, how to determine the structure (helix, beta sheet etc)? [duplicate]

Assume there's a short sequence of an amino acids. MAKMGSKKKAGHGGKEKLENMGE I am using molecular structuring softwares to look at secondary structure. But it's ...
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111 views

Biological significance of correlation between the radius of gyration and number of layers of convex hull of protein structure

While going through the paper titled "GEOMETRIC ANALYSIS OF THE CONFORMATIONAL FEATURES OF PROTEIN STRUCTURES" by Manish Dutt, I came to know that there is a correlation between the radius of gyration ...
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39 views

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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131 views

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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1answer
391 views

Using Jpred to predict secondary structure

I'm trying to use Jpred to predict secondary structure for a protein sequence. When I run J-pred, I get a bunch of hits from PDB. I've also noticed these 'hits' are the same name as the templates i ...
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1answer
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 ...

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