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 ...
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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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15 votes
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How can Valonia ventricosa cells get so big?

Ventricaria ventricosa (previously called Valonia ventricosa) is not exactly a single cell. It has a coenocytic structure with multiple nuclei and chloroplasts. As Jasand Pruski correctly guessed the ...
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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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9 votes
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Why is the DNA helix anti-parallel?

Parallel nucleic acid double strand is possible but it is not as stable as the antiparallel form (Szabat and Kierzek, 2017). This is because the nucleobases are not aligned in a way that is conducive ...
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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

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 ...
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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 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 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 ...
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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

Topology of closed circular DNA

DNA is not always negatively supercoiled naturally. It is important to keep in mind that different regions of topologically constrained DNA can have different supercoiling values. For example, the ...
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5 votes
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how do they identify different protein chains?

Chains are individual polypeptides that make up a multimeric protein complex. I'm curious as to how they are first found and what causes them? SDS-PAGE will resolve all the different chains (if ...
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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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Why do the major and minor groove exist in DNA?

Pitch is not a great word for this, as its meaning is ambiguous. It's hard to find a universal nomenclature for DNA geometry, but see the "Base pair geometry" section of this wikipedia page. The ...
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5 votes
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Simplified molecular-input line-entry system

A 3D model of a (bio)moelcule represents a physical 3-dimensions. For an experimental structure, each atom has a 3D coordinate (x, y, z) and, if determined by crystallography, an additional isotropic ...
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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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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 ...
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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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4 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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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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Questions regarding a particular paper

501 denotes 501st residue in the corresponding PDB entry — 1BDG. See here A single protein can have multiple cavities (see here) and the multiple entries denote centres of different cavities.
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3 votes
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About molecules and their shape

All molecules have a 3D shape. This is referred to as it's conformation. Most molecules have certain degrees of flexibility. For example, single bonds usually allow free rotation, while double bonds ...
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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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