The study of the molecular structure of biological macromolecules and how that structure relates to their function.
Questions tagged [structural-biology]
119 questions
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Does any molecule other than DNA have a double-helical structure?
DNA is known to have a double-helical structure. Do any other molecules have this structure?
The Riddler
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What is the significance and method behind Ramachandran plots?
My PI showed a Ramachandran plot in class today with minimal explanation, but I'm interested in finding out more. I understand that the Ramachandran plot shows the relation between the omega phi and psi angleson either side of an amino acid…
Emmie MC
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16
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Can two protein secondary structures "overlap" in the PDB?
I have a technical question regarding the syntax in Protein Data Bank files. In the protein with PDB# 1AE9 (pdb file), there are two lines in the .pdb file:
HELIX 4 4 MET A 255 ILE A 265 1 11
SHEET 2…
Douglas S. Stones
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4 answers
What implications has the missing 2'-OH on the capability of DNA to form 3D structures?
The chemical difference between RNA and DNA is the missing 2'-hydroxyl group in the nucleotides that build DNA. The major effect of that change that I know of is the higher stability of DNA compared to RNA. But I'm wondering whether this difference…
Mad Scientist
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How can Valonia ventricosa cells get so big?
Valonia ventricosa are single-celled algae that range between one and few centimetres. In rare cases, they can reach sizes exceeding 5cm. They range from grass-green to dark green, and some are even a blackish colour.
Weirdly, a lot of the…
James
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15
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How do I get the current "camera position" in PyMol so I can reuse it in scripts?
I have a few protein models I want to take pictures of with various ligands bound. It would be nice if I could do it from the same "position", but the only way I can figure out to repeat the same view is with zoom resi. 64, 152, 150 or the like,…
Nick T
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15
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1 answer
Fibonacci sequence in nature, truth or just wishful thinking?
I'm reading a bit on the Fibonacci sequence in nature, be it the golden ratio or the golden spiral forming over and over again in biological structures, and then I came across this online article by Donald E. Simanek, refuting a lot of these…
Ben
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14
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4 answers
How many human proteins have a solved 3D structure?
I was wondering how many human proteins have a solved 3D structure. Is there a database with only human proteins? I looked at pdb but couldn't find a filter.
Gergana Vandova
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13
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Why does RNA adopt an A-form helix?
RNA is known to form an A-form helix, while DNA generally forms a B-form helix under physiological conditions.
From left to right: A-form DNA, B-form DNA, Z-form DNA. Image created by Richard Wheeler
The preference of RNA for the different…
Mad Scientist
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13
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4 answers
What are the benefits of elucidating the three-dimensional structure of a protein?
I have spent months as a student working on trying to form a tricky protein crystal. But I have never actually had explained to me why the structure will be useful. Once elucidated, what can we potentially learn from the structure in terms of…
James
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12
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What is the transmembrane 'Positive-Inside Rule' nowadays? Has the definition changed over time?
First definition.
Two publications by von Heijne in 1989 and 1992 coined the 'Positive-Inside rule' and showed it's practical value in topology prediction of transmembrane helices. It was clearly defined and evidenced that in bacteria the positively…
James
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11
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Coronavirus capsid missing?
According to several sources, Coronavirus is a helical virus, i.e. it should have a helical capsid. Although most sources did not labelled or pointed any kind of capsid. It was mysterious to watch diagrams of spherical envelops with no underneath…
Always Confused
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In which direction does ATP synthase rotate?
I heard about the rotation of ATP synthase in a biochemistry course. The professor said it will rotate counterclockwise. Is that true? If so, what mechanism defines its direction?
latra
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Can protein structure be determined by X-Ray Diffraction in a single image?
I'm reading about the use of x-ray crystallography to determine protein structure. According to my book, data is collected at 30-360 angles (dependent on the symmetry of the protein). An illustration is given with concentric rings labelled with…
Ultimate Gobblement
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How many human proteins are very well characterized?
Following up on How many human proteins have a solved 3D structure?,is there a list of very well characterized human proteins / protein complexes?
My criteria for "very well characterized" includes, at least:
a high quality 3D structure
known…
Thomas Ingalls
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