Questions tagged [protein-folding]

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

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23 views

Dipeptide approximations for making Ramachandran plot [on hold]

How did Ramachandran arrived at his plot? Did he consider only the nearest neighbor amino acids and their steric clashes? In general all those interactions in protein are electrostatic in nature which ...
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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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Why does it matter to predict protein structure?

And how do you predict it ? What is your input data (sequence of amino acids, temperature, pH, ...) ? Is there a "standardized" input that scientists agree on ? Moreover, I've read that knowing the ...
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60 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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Backbone hydrogen bonds between adjacent amino acids in a protein?

Is it possible for two adjacent amino acids in a peptide to form hydrogen bonds between the backbone NH and CO? Are there any examples of such situations in proteins and how common are they? If ...
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Difference between prions and amyloid proteins?

Amyloid and prions are misfolded proteins, but what, if any, is the difference between them? Is amyloid a type of prion with a fibrillar structure?
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Do chaperone proteins misfold?

If molecular chaperone proteins assist in the folding process of other proteins and misfolded proteins, can chaperone themselves misfold since they are also proteins? What would happen if chaperones ...
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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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49 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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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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When does protein folding begin?

I had always assumed that protein folding is an independent activity that occurs after translation is complete. However, recently, I learned that intermolecular forces begin shaping the peptide bonds ...
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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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chaperone protein names

I am studying chaperon proteins DnaK, DnaJ etc. This question sounds trivial but I would like to know what the acronym stands for. I have looked on google/google scholar. My best guess is that the ...
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81 views

What proportion of proteins require chaperone-assisted folding?

I am new to the field of biochemistry (I am a chemist, actually). I have long known the process of folding as the process that leads to the minimum energy conformation of a protein. Now, I am ...
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68 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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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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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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What are the applications of predicting the structure of proteins?

Protein molecules are very important as they are used for catalyzing almost all the chemical reactions in the cell, regulation of gene activity and provide cellular structure. However, in predicting ...
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Could AI be applied to protein folding?

Two years later, there is a follow up question to the one asked here: How do we know if the folding@home project results are right? Since we are quite sure F@H is working right and following this ...
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375 views

Are proteins a different shape in space?

Is the shape of a protein affected by gravity? In space, will the shape of a protein be different to what it is on Earth? If the structure and shape is in fact affected, then would it be enough of a ...
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198 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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537 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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Why are proteins in the insoluble form when they are in frozen water?

Why would lowering the temperature of water change the intermolecular forces so much that proteins once soluble in water, become insoluble? I know freezing can create a crystal lattice, but I don't ...
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445 views

What characteristics of the protein folding process ensure that the energy landscape is a funnel?

The folding funnel hypothesis states that the energy landscape that proteins observe when they fold is funnel shaped with a single global optima. This ensures that no matter what sequence of folds the ...
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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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92 views

Can a bacterium survive without GroEL protein?

In prokaryotes, GroEL protein (together with GroES) is required for protein folding. Question: Can a bacterium survive without GroEL protein?
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What is protein folding and how is it relevant to disease?

I am trying to understand what is protein folding and how it could help cure some diseases. When reading articles about it, it looks like the goal is to find perfect folds for proteins because some ...
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274 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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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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The meaning of the $\alpha$ helix and $\beta$ sheets in proteins [duplicate]

I asked this question to my Biology teacher and he, in collaboration with a Chemistry teacher, couldn't find the answer. My question is the following: "What does the $\alpha$ and $\beta$ represent in ...
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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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511 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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Can estimating the likelihood of protein sequences adopting functional enzyme folds show life is too complex for evolutionary timescales?

An acquaintance provided me with this article1. I can't understand for sure what it is about. My acquaintance said that it proves that time for generation of even the simplest proteins is on a ...
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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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Mechanism of Myosin Head Bending in Cross Bridge Cycle Power Stroke Phase

What is the mechanism of bending of myosin head during the power stroke of the cross-bridge cycle of the muscle contraction? Does this have anything to do with the protein's 3-D structure i.e. folding ...
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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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Thermodynamics of spontaneous protein folding: role of enthalpy changes

I'm trying to get clear why protein folding occurs spontaneously. $$\ce\Delta G=\Delta H-T\Delta S$$ According to thermodynamics the ΔG should be negative for a process to occur spontaneously. When ...
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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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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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Are there any primary structure sequences that strongly suggest b-sheet or alpha helix?

Is there a particular sequence of amino acids that we know will take on a beta-sheet or an alpha helix or is it essentially random?
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Proteins in water vs proteins in crystal

I am not very familiar with the experimental procedure of x-ray crystallography except that it involves the very delicate matter of producing crystal that contain proteins and then diffracting rays ...
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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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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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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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Why is statistical mechanics relevant to RNA and protein folding?

This is a very naive question. As far as I understand the folding of a molecule is governed by the electromagnetic forces between its atoms and also between its atoms and the atoms in the surrounding ...
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154 views

Structure of proteins

Regarding the secondary structure of proteins, I know that there are 3 main types. The beta sheet formation is made up of beta strands stabilized by hydrogen bonds to form an anti parallel or a ...
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437 views

How to obtain a list of proteins sorted by the ~1400 unique protein folds?

The databases CATH and SCOP both have around 1400 unique protein folds recorded from analysis of the PDB. However, I do not see any method to access this particular data. A list of each of the 1400 ...
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355 views

Protein tertiary Structure formation

As we know that coils and loops are evolutionary variable regions where mutations,deletions, and insertions frequently occur. So does it mean that they don't have much role in the structure of protein?...
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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 ...