49

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

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 ...


16

Yes, double-stranded RNA as found in some viruses.


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 ...


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

Yes, nucleosomes are completely unwound. Histone chaperones such as FACT (for H2A/H2B) and ASF1, CAF-1, HIRA, Nucleophosmin etc (for H3/H4), associate with RNA Pol II and handle the displaced nucleosomes. As you surmised, the histone octamer complex is disassembled, into the H3/H4 tetramer and two H2A/H2B dimers. Right behind the elongating Pol II, the ...


8

I think the picture will help you. In fact, to determine which kind of rearrangement for the chromosomal, we need to define an "orientation". However, this orientation is not fixed. It is a definition compared with the two chromosomes before and after the rearrangement. As the picture shows, the duplicated sequence after rearrangement should be in the same ...


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

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 ...


6

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.gov/data-specification I am correct in saying that the numbers in the 'element' array are corresponding to Atomic Numbers? Yes, 1 is hydrogen, 6 is carbon, ...


5

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 DNA is called the linking number (Lk). Assume that one DNA strand is the edge of an imaginary surface and count the number of times that the other DNA strand ...


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

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 because it intercalates between the base-pairs in the double helix. Although other weak chemical interactions stabilize this binding, much of it is through base ...


4

There doesn't seem to be a 3D structure of Osteopontin available, and after looking a bit at the literature about this protein I'm not really surprised. Osteopontin is hypothesized to assume an elongated and flexible structure (Sodek et al., 2000). Flexible proteins are very hard to impossible to crystallize, typically the flexible parts are either removed ...


4

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 pointing towards the C-terminus). The thin wires are regions with no regular structure. There are also two small green spiral ribbons in the foreground left ...


3

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 relevant measurement related to nucleotides, but it's specifically the distance between consecutive bases in a standard B-form DNA helix - that is, what's the ...


3

First of all: Honey is not a byproduct of bees - it's their main and most important product which stores energy for the bee hive for the time when no flowers are available. Honey itself consists (according to the USDA database) to about 99.5% of water and sugars (82.5% sugars, 17% water). The sugars are mostly fructose and glucose, but also some other mono- ...


3

3D structure. Use the PDB to identify structures that are similar to the one you have found (you can use BLAST to search the PDB). A 30% match or above is usually acceptable, and multiple alignments are of course useful at lower match scores. If structures exist that are similar enough, you can use homology modelling to generate a 3D structure (this is what ...


3

I'm resurecting an old question, but I've heard this question from a few young bioinformaticians and had a couple more points to consider about compressing PDB files. The first is that many PDB files (including all PDBs hosted on the PDB site) have some 300-400 lines of meta data at the top of the file. This accounts for about 10-20% of the total file size....


3

There is a model of an adult, male, real human brain here: http://brainder.org/download/brain-for-blender/ It can be imported into Blender or any other 3D application that can read Wavefront OBJ or Stanford PLY formats.


3

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. Note, however, that such structures are dynamic and dependent on properties such as temperature and salt concentration. You can see an example of a single-...


3

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 introductory chapter of Berg et al. online. Although it is strictly necessary to consider the entropy of the total system, in many cases the most important factor is the (...


3

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 ‘Go’. I conducted a search of this type myself: http://www.rcsb.org/pdb/results/results.do?tabtoshow=Current&qrid=91CA3A5F Which returned 4384 structures ...


2

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 documentation.


2

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 answer. Safaee N, Noronha AM, Rodionov D, Kozlov G, Wilds CJ, Sheldrick GM, Gehring K. 2013. Structure of the Parallel Duplex of Poly(A) RNA: Evaluation of a 50 ...


2

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 itself. From the diagram on the right, Writhe= - 6, you'll find 6 times the DNA crosses itself making 7 loops. [In negative writhe the upper stand moves from ...


2

http://www.turbosquid.com/3d-models/max-human-brain/580672 That one is only 30 which really isn't bad for a model. You will have trouble finding an anatomically correct model for free. I am curious, is the male brain that much different from the female brain? And do you want just the brain or a whole head with the skeleton and other anatomical features? ...


2

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 Format). The format uses MessagePack for serialization and does custom compression, achieving ~ 5x advantage over mmCIF gzipped files. Currently the whole PDB ...


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