51
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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 ...
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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 ...
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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 ...
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17
votes
Does any molecule other than DNA have a double-helical structure?
Yes, double-stranded RNA as found in some viruses.
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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 ...
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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 ...
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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, ...
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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 ...
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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 ...
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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 ...
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6
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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 ...
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 ...
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6
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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 ...
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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,...
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5
votes
How to perform a DNA structural alignment in pymol
Aligning in PyMol
PDB ID 1h9t contains a structure of both a DNA and a protein. It starts as one object.
Before we perform an alignment, we need to separate your DNA from the protein.
Show sequence (...
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5
votes
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Do drugs' levo isomers have a better interaction with the receptors in our body than dextro isomers?
This is purely coincidental. The term levo simply means the direction that the pure enantiomer of the compound rotates plane polarized light at a specific wavelength and has no direct bearing on the ...
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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 ...
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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 ...
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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 ...
- 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 ...
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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.
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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. ...
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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 ...
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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 ...
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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 ...
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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 ...
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3
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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-...
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2
votes
Accepted
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 ...
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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 ...
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