51 votes
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Does any molecule other than DNA have a double-helical structure?

A few examples: Starch A polymer of glucose that can form a double helix and functions primarily as energy storage in plants. [image source] f-Actin Filamentous actin forms a helical structure with ...
canadianer's user avatar
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21 votes
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Coronavirus capsid missing?

Does it really contain a capsid? Yes. Coronaviruses have a capsid, but it's not reminiscent of the polygonal (icosahedral) capsid depicted in the Research Gate picture you referenced. Icosahedral ...
MikeyC's user avatar
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19 votes
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How hard it is to determine a 3d structure of a protein?

Experimental protein structure determination is hard: the most common method is X-ray crystallography, which can be done in a few months if you are lucky and can take years if you're not. The problem ...
Nicolai's user avatar
  • 4,391
17 votes

Does any molecule other than DNA have a double-helical structure?

Yes, double-stranded RNA as found in some viruses.
Remi.b's user avatar
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14 votes

How hard it is to determine a 3d structure of a protein?

I'll address NMR for structure determination. It is the less common method, only ~10% of protein structures are determined this way, though it has e.g. advantages for nucleic acids and more than a ...
Mad Scientist's user avatar
13 votes

In which direction does ATP synthase rotate?

Short answer The direction of rotation depends on the viewing point of the observer and the reaction catalyzed by the ATP synthase. When synthesizing ATP, and viewed 'from the bottom' (observer faces ...
AliceD's user avatar
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12 votes

Does any molecule other than DNA have a double-helical structure?

The structural protein collagen consists of a triple helix of polypeptides. Whether this answers the question is arguable—you could say that the triple helix contains double helices. In any case, ...
WaterMolecule's user avatar
10 votes
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By just looking at an unlabeled picture, how do you know it is a protein?

Shapes This is a common way of illustrating a protein and is often called a "protein cartoon". There are other common ways of illustrating proteins. This cartoon shows you where α helices ...
James's user avatar
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7 votes
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Twist in the DNA double-helix

First, your description is accurate. The only pedantic critique I would make is that the technical term for nucleotides in DNA is deoxyribonucleotide. Second, I don't want to say that non-helical DNA ...
canadianer's user avatar
  • 17.7k
6 votes

What is the transmembrane 'Positive-Inside Rule' nowadays? Has the definition changed over time?

I think you have misunderstood the "inside" part of the "positive-inside rule". Perhaps because "inside" is indeed an imprecise term (but now it is history and cannot be changed ;) ). In order to ...
UbuntingBiochemist's user avatar
6 votes

Sheep vs. Furry animals

Fur, wool, and hair are all made of keratins. To the best of my knowledge wool and fur are separated arbitrarily, based on the properties of the fibres. This arbitrary division allows rabbits to ...
Michael_A's user avatar
  • 1,305
6 votes
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Are there functional examples of parallel DNA double helices?

Surprisingly, a parallel DNA duplex has been reported! In a paper, Tchurikov et al have reported the presence of parallel complementary DNA in the non-coding region of alcohol dehydrogenase gene as ...
another 'Homo sapien''s user avatar
6 votes
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Parallel DNA double-helices with Watson–Crick base-pairing: Why do they not occur?

“The only specific suggestions that I could find was because of the DNA replication process and…” No. The explanation can have nothing to do with DNA replication. If the structure does not exist, you ...
David's user avatar
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5 votes

Why does Thiamine pyrophosphate have phosphates?

The diphosphate* part of TPP does not serve any catalytic function but, rather, helps bind the coenzyme to the enzyme. In this respect it is similar to the non-nicotinamide portions of NAD/NADP (think,...
David's user avatar
  • 25.2k
5 votes

Can two protein secondary structures "overlap" in the PDB?

TLDR; Answer: You could consider this particular residue to belong to both structural elements, but it's a tricky call and depends on the method of secondary structure assignment. Ambiguous secondary ...
James's user avatar
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5 votes
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Is there a reason for the lack of full RTK structures?

Large proteins are challenging for NMR: the more amino acids, the more peaks one has to assign. Peak overlap is also more likely the more amino acids you have, making assignment difficult. Some NMR ...
Guillaume's user avatar
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4 votes
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DNA-DNA cross-linking with formaldehyde?

The fact that there is no inter-strand cross-linking between different double strands might be just because the cross-linker cannot bridge the distance between amines of different bases on different ...
aretaon's user avatar
  • 131
4 votes
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Why add hydrogens in molecular dynamics simulations?

The RCSB Protein Data Bank (PDB) presently has 137,917 structures deposited in it, of which less than 10% have been solved by nuclear magnetic resonance (NMR). Most techniques in structural biology ...
Stefan's user avatar
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3 votes
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Subset of Protein Crystal Structures (from PDB)

Richardsons' Lab has a top8000 list. See their paper from 2016. They also have top500 list, but it hasn't been updated for many years.
marcin's user avatar
  • 449
3 votes
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At what point, when connected, do DNA strands become a helix?

In general, a single stranded nucleic acid is helical in the absence of other secondary structure. The base stacking that drives helix formation does occur between adjacent bases in the same strand. ...
canadianer's user avatar
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3 votes

Twist in the DNA double-helix

One key point for someone coming to structural biology from another disciple is to understand the basic thermodynamics underlying the concept of ‘stable’ structure. This is described in an ...
David's user avatar
  • 25.2k
3 votes

Can protein structure be determined by X-Ray Diffraction in a single image?

Can protein structure be determined by X-Ray Diffraction in a single image? Yes. Using a technique called Laue diffraction, it is possible to obtain sufficient data from a single image to solve a ...
Karsten Theis's user avatar
3 votes

What are the benefits of elucidating the three-dimensional structure of a protein?

Why study protein structure? “What is the secret of life?’ I asked. ‘I forget,’ said Sandra. ‘Protein,’ the bartender declared. ‘They found something out about protein.‘ ‘Yeah,’ said Sandra, ‘that’s ...
David's user avatar
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3 votes
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Why does sequence of amino acids presented on the Catalytic Site Atlas from a given protein differs from the sequence on the RSCB Protein Data Bank

Crystallography results (pdb files) almost always contain a truncated sequence. Both ends of a protein are often flexible (even in a crystal) and don't result in enough data for a good fit. The ...
VonBeche's user avatar
  • 1,473
3 votes

Generating Cartesian coordinates of each atom in protein chain from the internal coordinates using python or some software

Have a look at Biopython There are specific questions about the specific internal coordinates on Bioinformatics forum i.e. : https://bioinformatics.stackexchange.com/questions/18849/help-using-...
pippo1980's user avatar
  • 131
3 votes
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If a protein has multiple globular domains with flexible peptide linkers in between, how do they fold?

Obviously, this must be considered on a case-by-case basis, so the original poster’s “easy test” is no such thing, relating to viral rather than cellular proteins, and only relevant for the individual ...
David's user avatar
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2 votes
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How to find PDB id of an amino acid sequence

One way of doing this is to run a protein BLAST search at NCBI in which you specify the Protein Data Bank as your database, as in the example shown below: The results will be all for proteins in the ...
David's user avatar
  • 25.2k
2 votes

How many residues can a reliable ab initio structural model contain?

Year on year reliable ab initio predictions are becoming more common for longer proteins. 400 residues is not an unfeasible length. Of course, loops still remain more of a challenge than helical and ...
James's user avatar
  • 11.3k
2 votes
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Generate mesh surface from protein structure

PyMOL and Chimera can do that, and both can be script-driven. The PyMOL wiki is full of examples, and probably already has some how-to that would get you started. Chimera also has a complete ...
Guillaume's user avatar
  • 715

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