10
votes
Accepted
What makes heat resistant proteins heat resistant?
Szilágyi and Závodszky published an article in the journal Structure which analyses a number of different structural parameters of proteins of moderately thermophilic ($45~\mathrm{^\circ C} < \...
- 68.7k
10
votes
Accepted
What could these letters "S" in red circles mean in a biochemical diagram?
It almost certainly refers to the amino acid (residue) serine. The numbers (300, 333, 351) refer to the residue numbers. The COOH at the end signifies the C-terminus of the protein (subunit).
The ...
- 71.9k
7
votes
Accepted
Kolmogorov backward equations in active biological systems
UPDATED: I wrote a first answer assuming that $t>0$ which got close to what's in the paper, but not quite the same. Thanks go to Karsten Theis for pointing out that $t<0$ in these "backward ...
- 10.4k
7
votes
Accepted
How to determine the dimensions of a bixin molecule?
There is a paper on bolaamphiphiles (1) where it is stated that measured surface area corresponding to the area of a bixin molecule lying on the water surface with most methyl groups pointing outside ...
- 38.5k
6
votes
Accepted
Adding hydrogens to multiple pdb files using Openbabel GUI software
If you got an installation of openbabel's GUI, you equally have an installation of openbabel for the terminal (e.g., in Linuxes) / command line cmd.exe (in Windows)....
- 31.2k
4
votes
Accepted
Why do chiral biological molecules only exist as one enantiomer? Does it have any advantage?
Are all the biochemicals that our body uses enantiomerically pure or are racemic mixtures too?
Many molecules exist in both forms in nature. One fun example are the enantiomeric terpenoids R-(–)-...
- 42.3k
4
votes
Accepted
Is a beta pleated parallel sheet always formed from more than one peptide?
While it is true that some antiparallel beta sheets have neighboring strands that are adjacent in primary sequence, other cases do exist. As for parallel beta sheets, the polypeptide chain between ...
- 42.3k
4
votes
Are crystallographic omit maps only used with molecular replacement?
Experimental phasing and molecular replacement provide initial phases used to start model building. Later on (refinement, validation) phases are calculated from the model.
If the phases are what ...
- 416
4
votes
Accepted
Are crystallographic omit maps only used with molecular replacement?
[OP] ...if we don't have the phases (say for a part of a model), it just wouldn't get built even if we have the amplitudes for that part, right? Or is it that in this case (of omitting a part), there ...
- 42.3k
4
votes
Accepted
Which textbook is this image on protein tertiary structure from?
The illustration is likely taken from a later edition of Baum's Introduction to organic and biological chemistry.
The first edition [1, p. 292] presents nearly identical illustration under a different ...
- 38.5k
4
votes
Accepted
Does migraine medicine Topiramate work by supplanting Pyridoxal phosphate in enzymes?
Background
Topiramate (TPM) is an anticonvulsive and antimigraine drug that helps prevent or reduce the frequency of epileptic seizures and that is used as a prophylaxis of migraine. (Shank and ...
- 1,379
3
votes
Accepted
Distance requirement for hydrogen bonding to occur
You will probably find all this information in biochemistry textbook. To give you an idea in proteins, typically; alpha helices H..O distance is 2.06 Angstrom, and N..O, 2.99. In beta sheets (parallel)...
- 31.4k
3
votes
What ratio of bicarb to sugarcane juice with a pH level of 4.5-5.5 to neutralize pH level?
You need to know which acids are present in the sample, or determine the required amount experimentally.
Without any knowledge of the pKa values of the acid or acids present, there could be very ...
- 42.3k
3
votes
How do cells form a solid structure?
So how are the cells are arranged to form a solid structure a solid body?
Plant cells have cell walls, are filled with liquid, and have strong cell-cell adhesion. This gives a fairly rigid structure ...
- 42.3k
3
votes
How to dock aggregated structures comprised of "elementary" protein units like LEGO pieces?
Try DNA origami instead
While protein assemblies are well known, rationally using proteins to assemble larger supramolecular structures is still a difficult problem:
Predicting protein folding is ...
- 28k
3
votes
Accepted
Biomolecular energy functions and entropy
I am sure that a more definitive answer could be provided by someone more familiar with the field, but here are a couple of observations.
First, I think it is a bit of an exaggeration to say that ...
- 13.2k
3
votes
Why energy of some intermediates of glycolysis increases?
Step 1:
Phosphorylation activates glucose for the following reactions in the pathway. However, the formation
of such a phosphoester is thermodynamically unfavourable and requires
energy input to ...
- 5,164
3
votes
What is the chemical formula for snake venom?
The wikipedia article of snake venom clearly defines the composition of snake venom. To prevent being a wall of text, I arranged them in points and bolded the chemicals.
Proteins constitute 90-...
- 26.8k
3
votes
What are some of the more easily manipulated residues on an enzyme?
I'm assuming the OP concerns chemical means of modifying residues. Multiple protein residues other than Lysine may be labeled with an adduct. Here are some examples:
Histidine residues may be labeled ...
- 1,379
3
votes
Are crystallographic omit maps only used with molecular replacement?
The following doesn't fit into a comments box.
From the perspective of small molecule crystallography (say, ShelX), once you solved your model completely or completely enough to engage refining, you ...
- 31.2k
3
votes
Accepted
How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center?
The relevant PDB file is probably 1j8x because it contains both the carbohydrate and the nucleotide shown bound in the active site in the image the OP provided.
You could use Jmol, e.g. at https://...
- 42.3k
2
votes
Thermal stability of charged and uncharged alpha helices (the concept of alpha-helix capping)
This might relate to the concept of 'capping' alpha-helices, where the placement of beneficial charges at either end of a helix is shown to increase the overall stability of the protein. See the ...
- 928
2
votes
What is the chemical formula for snake venom?
Snake Venom is a mixture of chemical compounds. It certainly doesn't have "a chemical formula". Your question is similar to one asking "What is the color of a car?" Just like cars come in a wide range ...
- 906
2
votes
How to measure distance along solvent-accessible surface of protein complex in PDB file?
I would use linear distances between a suitable amount of fixed points as an approximation. You cannot measure exact distances along a rough surface, as the distance will vary depending on minimum ...
- 405
2
votes
Kolmogorov backward equations in active biological systems
First passage problems
This is a first passage problem, asking when a system reaches a certain final state for the first time . If you were to use a simulation to explore this, you would erase parts ...
- 42.3k
2
votes
How can subtilisin still function without its catalytic triad?
If the substrate still binds to the protein, other parts of the mechanism are still in place. Specifically, the main chain amide groups that help to stabilize the tetrahedral intermediate are still ...
- 42.3k
2
votes
What makes heat resistant proteins heat resistant?
To be frank, thermostable proteins are stable because they as you state contain a huge amount of stabilizing interactions. [notice my dry humor]
You state that the presence of large and complex ...
- 405
2
votes
Preferred IUPAC name of Protoporphyrin IX
I think both EPA and ChemSpider names are acceptable. However, I don't agree with dihydroporphyrin part in PubChem name. This is because the Gold Book gives following framework for porphyrin nucleus:
...
- 42.1k
2
votes
Accepted
Difference between Protoporphyrin and Porphyrin?
From here:
Protoporphyrin is a derivative of porphyrin. The key difference between porphyrin and protoporphyrin is that porphyrin is a group of aromatic chemicals which has four modified pyrrole ...
- 26.8k
Only top scored, non community-wiki answers of a minimum length are eligible