Hot answers tagged structural-biology
9
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 ...
8
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 ...
8
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 ...
8
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 ...
7
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 ...
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 ...
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 ...
5
ProDy works quite well, especially from within an existing Python script.
The following code takes an existing PDB file, performs some selection query on it, then saves it to another file.
import prody
def pdbsubset(inpdb, outpdb, selection):
with open(inpdb) as protf:
prot = prody.parsePDBStream(protf)
atoms = prot.select(selection)
...
5
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 ...
5
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 ...
5
You could try other visual differences, like make what you're interested in ball-and-stick, and everything else wireframe, like in this example:
.
.... Because, from: http://www.ysbl.york.ac.uk/~lohkamp/coot/doc/coot-python.html
procedure: hilight_binding_site (imol, centre_residue_spec,
hilight_colour, radius): hilight-colour is specified in degrees ...
4
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,\
...
4
I only know of one method, but here it is. You create a sphere the diameter of the VdW radius of water, and then 'roll' it along the surface. I know this as a Richards-Lee surface, wikipedia has another name for it.
This looks complicated, but its not. you move the probe sphere along the surface of the molecule in the XY plane until it just touches ...
4
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 ...
4
I don't know of any examples of this but I would say no doubt, that's quarternary structure. Quarternary isn't so much defined by the kind of interaction but much more the fact that it's between different polypeptides; all lower-level structures are within one polypeptide. (Wikipedia agrees.)
4
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 ...
3
Isoleucine only has one delta carbon, which we can just call CD. But it seems like some PDB files still name it CD1, and hence programs map CD1 to CD in this case. (E.g. see this tutorial where this practice is shown.)
3
If I understand the question correctly, you're thinking something along the lines of modular tertiary domains, but in a quaternary sense?
For a reversible interaction, heterotrimeric G proteins spring to mind. Once activated by a G protein coupled receptor (GPCR), the alpha subunit and the beta-gamma complex dissociate from the receptor and from each ...
3
I also had to do the same using Jmol, and I figured it out how to get a list of all the hbonds.
Step 1: Calculate the hbonds with or without RASMOL method. It's up to you, e.g.,
jmolScriptWait("select not hydrogen; set hbondsRasmol FALSE; calculate HBONDS")
Step 2: Only display the hbonds
jmolScriptWait("display connected(hbond)")
Step 3: Export the ...
3
I dont know about JMol, but this can be easily done with UCSF Chimera.
I loaded the 1a1x structure.
Then selected: Tools > Structure Analysis > FindHBond
I kept the default values and selected Write information to reply log
Then clicked OK
On the structure the H Bonds will be identified with a coloured line.
To view which is the donor and acceptor go ...
3
From your comments it doesn't seem like you are adverse to writing some custom scripts so one option would be to take advantage of the NCBI Structure database. You can filter it by organism and then download the results as a text file / XML. If you need access to the raw PDB data you could then download the PDB archive and examine the ones in your filtered ...
3
The answer lies entirely in the thermodynamic stability that is provided with having a 2'-OH. As mentioned by Aleksandra, RNA will adopt only the C3'-endo conformation whereas DNA adopts both the C2'-endo and C3'-endo. Effectively, this makes the DNA strand more flexible not RNA. In doing so, a single stranded DNA oligomer will be able to adopt more states.
...
3
Not by analysing a single protein. There is work with x-ray lasers.
You have to take a simultaneous image of millions of proteins and use that to get a structure. It's not quite prime time. People are also doing this with electron beams in electron microscopes.
These methods will reconstruct 3D models of the molecules, sometimes in states which ...
2
Not quite as ideal as I had hoped, but it works:
Get and install CCP4.
Obtain minimal CIF file from PDB or elsewhere. Save to some folder easy to get at with the console.
Launch console and cd to folder with the minimal definition.
Run libcheck by typing it and hitting return
If it complains it's not found, the CCP4 bin directory may not be in your ...
2
These two links go through the specifications required for the PDB format:
Link1: http://deposit.rcsb.org/adit/docs/pdb_atom_format.html
Link1 primarily goes through the specs. required if you say have a NMR file you would therefore require the MODEL statement. It also goes through other statements such as when to use TER and how each ATOM line should look ...
2
The RNA hairpin transcription terminator in prokaryotes is terminated by the GC rich hairpin followed by 4+ uracil bases as you describe it.
The original reference describing the hairpin, described the sequence requirements as being for the thermodynamic stability of the hairpin, but the protein nusA has also been found to stimulate termination.
You ...
2
I've always just gone with the name hetereodimer but there isn't any technical reason why it isn't a quaternary structure. As for an example, I work with antibody fragments or FAbs and cys-diabodies which are exactly that, two distinct polypeptides that are connected by a disulfide bond linkage.
These do have a significant amount of non-covalent ...
2
Try looking at structure homology databases - the sequences that they have no annotation for are likely the kind of sequences that you are seeking.
SUPERFAMILY has a comprehensive annotation across almost 2500 fully sequenced cellular genomes. this would be a good place to start ...
2
This is how I would do it:
Download the UniProt/SWISSPROT flat file for bacteria from here.
After decompressing the files, extract the E. coli protein IDs for which there is no PDB annotation in the file (I am giving you a command line that will work on *ix systems (Linux/Unix/OSX etc)):
zcat uniprot_sprot_bacteria.dat.gz | gawk ...
2
As far as I remember, Fibonacci patterns emerge in plants from hormone gradients. I.e. an apical meristem forms a leaf where the auxin concentration is highest, and already existing leafs lower auxin concentration, leading to some negative feedback.
See e.g.
http://www.sciencedirect.com/science/article/pii/S1360138507000581
or ...
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