51
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 ...
19
6405 proteins mapping to 5220 genes, according to Ensembl.
In Ensembl's BioMart, you can select the PDB ID as external reference. Export the results and count the unique proteins/genes that have a PDB ID.
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 ...
15
Yes, double-stranded RNA as found in some viruses.
14
Ramachandran plots show the relationship between the phi and psi angles of a protein referring to dihedral angles between the N and the C-alpha and the C-alpha and the C-beta. As an aside, the omega angle between the C-beta and the N tends to be fixed due to pi-pi interactions.
Dihedral Angles
There are limits to possible distributions of phi and psi ...
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
To make sure I'm not comparing apples and pears, my (attempt to) answer the question will be broken into two parts: comparison of single-stranded nucleic acids and double stranded ones.
Single stranded DNA and RNA
Both DNA and RNA can form single-stranded complex tertiary structures in which the secondary structure elements are associated through van der ...
12
PDB is a good resource for answering such questions, since it will let you filter results by many additional parameters. To count and extract 3D structures of human proteins:
Open Advanced search tab of the PDB website.
Select Biology -> Source organism from the menu.
Type Homo sapiens (human).
You can reduce redundancy by checking Remove Similar Sequences ...
12
The beta-form of DNA and the alpha-form of DNA are based on the pucker on the sugar ribose. As DNA doesn't have a 2'-OH, it can obtain both conformations.
RNA does not have this luxury. The steric clash of the 2-OH with the 3'-OH makes the B-form to be very unfavorable thus constraining the RNA to adopt the A-form. Incidentally this steric limitation is ...
12
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 ...
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.
11
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;...
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" regions.
If ...
9
You cannot solve a structure with a single frame, even with perfect diffraction.
The reason you need images over a large swath of angles is because the diffraction pattern is also in three dimensions, in the so-called "reciprocal space". At minimum, a 180° rotation of the crystal is needed to sweep the entire reciprocal space sphere with the plane of ...
9
To address your list:
a high quality 3D structure: this you can easily get from PDB, using the answers to the question you linked as starting point. However, it is become increasingly clear that intrinsically unstructured proteins also play important roles in the cell, and for these you won't get a good 3D structure.
known activity in vivo / known ...
9
Try to pass the matrix as a String containing 18 floats separated by commas, e.g. like
cmd.set_view ('''
0.590180993, 0.670941532, 0.448923886,\
-0.507570565, 0.740831316, -0.439937204,\
-0.627747774, 0.031782545, 0.777776182,\
0.000000000, 0.000000000, -417.497009277,\
0.741809845, 7.078243256, 16.473480225,\
...
7
With the program RasMol, you can select, as Mad Scientist explained it for PyMol, everything in a specific distance around an atom. RasMol can be run from command line, using a script (with the -script option under UNIX).
7
I looked for relevant publications at Web of Science using 'structur* AND cyclodextrin' in the Title field. For the period 2011-2012 there were 56 hits including:
Racz et al (2012) Structure of the inclusion complex of beta-cyclodextrin with lipoic acid from laboratory powder diffraction data. Acta Crystallographica Section B 68: 164-170
Ali et al (...
7
Short answer:
The term fiber axis is not in reference to the DNA model, it comes from the experiments that Watson and Crick used to guess their model. The fiber axis is basically the dimension along the length of the DNA strand.
Longer:
Watson and Crick created their model of DNA based on the esoteric experiment called X-ray fiber diffraction. To ...
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
Parallel DNA helix can exist and this has been observed experimentally. However these structures are stabilized by Hoogsteen type base pairing [1,2] and not the usual Watson-Crick type pairing because the parallel conformation does not allow the latter (See the figure below).
This elongates the hydrogen bonds and also causes a loss of one hydrogen bond ...
7
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.
...
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 ...
7
“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 ...
6
This is not my field so I'm risking a wrong/incomplete answer here, but I'd say that the critical difference is the almost complete occurrence of double-stranded DNA that precludes the formation of the tertiary structures in single-stranded RNA, rather than the 2'OH difference. In fact, and following the link you posted, the authors even comment in the ...
6
Hi sorry i missed this one - not too hard for "biology"
If you look at a protein crystal (or any crystal really) in an x-ray beam, it scatters lots of spots (diffraction reflections). If you look at a picture of crystalline diffraction, at larger angles from the center of the x-ray beam, the reflections get weaker and weaker and basically just stop, if the ...
6
Crystallography requires the collection of many measurements (could be a few thousand to even millions depending on the size of the molecule and complexity of the crystal (technically speaking, the size of the crystal's unit cell is a major determining factor for the size of the data set). I'm not going to assume this is a small molecule crystal like a salt ...
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 ...
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