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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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
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
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
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6 votes
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How to interpret this PubChem record of L-Alanine

The PubChem format description is not that easy to find: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/asn_spec/pcsubstance.asn.html And the ASN file linked here: https://pubchemdocs.ncbi.nlm.nih....
Ashafix's user avatar
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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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6 votes
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DNA topology Linking number vs twist?

This article (DNA Topology: Fundamentals by Mirkin SM) probably defines and describes linking number better than I ever could: The fundamental topological parameter of a covalently closed circular ...
canadianer's user avatar
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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
5 votes
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Why do the calicheamicins bind to DNA at the minor, rather than the major, groove?

Accommodation in the major or minor groove I am not in a position to generalize about all drugs that bind to the major groove of DNA, but at least one well-known example, actinomycin D, does so ...
David's user avatar
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4 votes

What are the differences in ultrastructure of cilia and flagella?

Eukaryotic cilia and flagella are identical in ultrastructure. The only reason for two different terms for the same thing is historical usage. Traditionally, 'cilia' has been used for shorter, more ...
Adhish's user avatar
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4 votes
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Meaning of arrows in 3D representation of proteins

The flat arrows are a cartoon representation of β-strands (one type of regular hydrogen-bonded secondary structure). The direction of the arrow is the direction of the amino acid sequence (arrow head ...
David's user avatar
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3 votes

What is the actual size of a nucleotide?

If you want experimental papers, we should be precise about what we're measuring. "The dimension of a nucleotide" is rather imprecise, as a nucleotide is a rather oblong, knobbly thing. 0.34 nm is a ...
R.M.'s user avatar
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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. ...
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
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3 votes
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How many proteins on PDB have unknown function?

The article cited in the question indicates that the authors searched the PDB with the term “unknown function”. There is nothing special about this — you just type in the standard search field and hit ...
David's user avatar
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2 votes
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Programs/software used to create illustrations and scientific paper ready figures

Stick with „vector graphic design“ applications. They enable you to open .pdfs and move around individual elements and resize them to your needs without losing resolution. Biorender. It has a lot of ...
markur's user avatar
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2 votes

Compressing structural information in PDB files

I know the question is old, but for the record: the RCSB PDB is currently working on a project to compress the PDB structural data with a new file format, called MMTF (MacroMolecular Transmission ...
Jose Duarte's user avatar
2 votes

DNA topology Linking number vs twist?

For ds DNA Twist is the number of times a ss DNA turns around another ss DNA in a helix, i.e. simply the number of turns in the ds DNA helix. Writhe is the number of time a ds DNA wraps around ...
Tyto alba's user avatar
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2 votes
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Coordinates of amino acids in a protein sequence

If what you are after are the structural co-ordinates of particular amino acids crystalized individually (i.e. considered as small molecules independently of any role in proteins), then you should ...
David's user avatar
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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
2 votes

Are there functional examples of parallel DNA double helices?

All articles I found discussing parallel helices are purely speculative with regards to biological significance; but, they are still interesting. Here are some that I found, in addition to the other ...
canadianer's user avatar
  • 17.7k
2 votes
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Can pymol show cartoon (secondary structure) for a pdb of multiple frames?

It seems that if no HELIX record is present in the PDB, PyMol attempts to assign secondary structure itself. For whatever reason, it does not do this if multiple <...
canadianer's user avatar
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1 vote
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Please explain this notation MW around 9 MDa

The molecular weight of PDH enzyme is approximately 9$\times$10$^6$ gm/mol The Dalton (or atomic mass unit (amu) ) is a unit of mass defined as 1/12 weight of carbon-12 atom in ground state. 1 Da =...
fireball.1's user avatar
1 vote

3D models of adult male brain in the Blender software? Any open-sourced version for research?

I think all models are too generic out there. Radiological models you can find in imaios.com's e-Anatomy where the Premium access gives you some RTG, CT and MRI videos which you can combine to form ...
Léo Léopold Hertz 준영's user avatar

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