50
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 two strands of polymerized g-actin. This is a structural component of the cytoskeleton.
[image source]
Coiled Coil
Protein motif with a helical structure ...
21
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 capsids form a sort of shell around the viral genome, where helical capsids actually bind the viral nucleic acids, holding them in a more rigid shape.
Is it ...
19
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 with X-ray crystallography is that you need good protein crystals, and in most cases, proteins don't crystallize very well, so it takes a lot of time (and a lot ...
17
Yes, double-stranded RNA as found in some viruses.
15
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 organism possesses a large central vacuole which is multilobular in structure (lobules radiating from a central spheroid region).
The entire cell contains ...
14
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 third of those was solved by NMR. Take any numbers here as very rough estimates, there are a lot of factors that influence the difficulty and cost.
For NMR, the ...
13
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 the intermembrane space looking into the mitochondrial matrix) it rotates clockwise.
Background
ATP synthase is a membrane bound enzyme with two large subunits;...
12
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, depending on what prompted your question, I thought it might be an interesting structure to consider.
10
Protein structures, which can be obtained from protein crystals or from concentrated solutions of pure protein via NMR, are arguably the primary source of knowledge that we have about how genes perform their function on the molecular level.
I've added a link to RCSB.org above - they write up a story on an important protein structure monthly(?) - its a ...
10
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 are (spirals) and where β sheets are (arrows) which are important structural elements. The strings connecting those structural elements are flexible "loop&...
9
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 for the Watson-Crick (WC) type base pairing. In parallel conformation, the bases can form Hoogsteen (HS) and reverse Watson-Crick (RWC) type base pairing (see ...
7
There is indeed a repulsive force between the phosphates in the DNA backbone. (The pK of the phosphate is very low so it will be ionised at all physiologically-relevant pH.) This is why DNA behaves like a stiff rod over short distances. However cations in solution will help to shield some of this repulsion. This is why DNA melting temperature decreases as ...
7
Short answer:
The term fiber axis is not in reference to the DNA model, it comes from the experiments that Watson and Crick referenced to guess their model (performed by Rosalind Franklin). The fiber axis is the direction along the DNA strand.
Longer:
Watson and Crick created their model of DNA based on the esoteric experiment called X-ray fiber ...
7
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 never occurs since the structure of any macromolecule is dynamic, but I am specifically avoiding exceptions to the rule to avoid confusing the issue.
The ...
6
In many cases they are available. One of the establishing principles of the Protein Data Bank (PDB) was to store not only the models (atomic positions and identities) of macromolecules and proteins, but also the originating X-ray data, more recently in structure factors.
If the question is 'why are they giving only the structure factors and not the ...
6
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 understand it a bit better it helps to think about the topology of the membrane. During synthesis most membrane proteins (ignoring peroxisomal and mitochondrial ...
6
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 have fur but selective breeding has produced angora rabbits, which have wool. The opposite should be possible, with time you could breed a sheep that has fur.
...
6
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 well as between two Drosophila DNA sequences. The region, which is ~40 bp long, has 76% bases in same polarity along with complementarity. However, its presence ...
6
“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 can’t replicate it, if it does, Nature will evolve a mechanism. (The related SE question, mentioned by @Gilleain, asked whether it could still replicate if it ...
5
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 or aniosotropic B-factor (that models atom fluctuations).
A '1D' SMILES is not a physical 1-dimensional representation, and can be converted to a graph (...
5
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 relevant property is what they call "opening".
From the biochemistry textbook by Berg:
To explain in words, if the glycosidic bonds (which attach the nucleic base ...
5
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 action of unwinding DNA for transcription or replication introduces positive supercoils ahead of the polymerase and negative supercoils behind it.
Additionally, ...
5
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 they are different in molecular weight). Chains are products of translation (and some modifications such as clipping and/or other PTMs etc) and they assemble to ...
5
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 structure allocation comes up fairly often. Whilst obviously, not many people will be able to use this protein specifically, the below approach could be useful ...
5
You can use "as" to switch to a particular style (http://pymolwiki.org/index.php/As
):
as cartooon, 11AS and chain a
You can also hide everything, to remove all representations (http://pymolwiki.org/index.php/Hide):
hide every, 11AS and not (n. ca+c+n and resi 5-10)
I'm a fairly expert user of PyMOL and I've never seen an API exposed which will show ...
5
I always wondered this myself, but the structure of a protein can end up being quite important for a number of reasons. Most relate to the fact that protein function often depends on specific domains, and while a protein may have multiple functional domains it is important for all domains to be properly aligned and constructed in three-dimensional space. ...
5
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 interactions with biological systems. A quick search of the Dictionary of Drugs database gave 6845 compounds with optical rotation >0 (dextro-compounds) and 8406 ...
5
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 (click the S at the bottom right).
Highlight all the "residues" from the chains X and Y (these chains contain each strand of your DNA) in the sequence ...
5
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, why the P?), and represents a general theme, rather than a unique instance.
A pertinent paper that I found from an internet search unfortunately requires ...
4
I think you've got the list of good predictions from the Bragg, Perutz, and Kendrick paper. And the 310 helix was not really right either - it did turn out to show up occasionally in protein structures though.
At the time all of these secondary structure elements were well evidenced from noncrystalline diffraction data and small molecule crystal ...
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