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Questions tagged [structural-biology]

For questions related to the molecular structure of biological macromolecules (especially proteins and nucleic acids), how they acquire the structures they have, and how alterations in their structures affect their function.

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28 votes
2 answers
14k views

Confusion about direction of dipole arrow in alpha-helices and other molecules

I understand that molecular dipoles are electric dipoles. And electric dipole moment vectors point from the negative to the positive charge. In class we learned to draw these special molecular dipole ...
Reto Höhener's user avatar
25 votes
1 answer
2k views

What software is used to generate the PDB molecule of the month images?

What software does the PDB use to generate these "cel-shaded" protein models with outlines around foreground atoms? (Leptin: May 2012 Molecule of the Month by David Goodsell)
Nick T's user avatar
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19 votes
2 answers
2k views

How large is the energy difference between keto- and enol-form of guanine and uracil?

The nucleobases in DNA and RNA are generally present in the keto-form, and not in the enol-form. As an interesting historical note, James Watson and Francis Crick did initially believe them to adopt ...
Mad Scientist's user avatar
17 votes
5 answers
11k views

Are there notable organic compunds which look very similar but have very different properties?

I've seen people arguing for some questionable "miracle cure-all" alternative medicines not scientifically, but by their own logic. A common claim is, that if a compound looks very similar to an ...
vsz's user avatar
  • 2,794
17 votes
2 answers
4k views

What makes heat resistant proteins heat resistant?

We were doing the chapter Biomolecules in class the other day, and a doubt popped up once we reached the section on proteins. We were taught that the stuff that keeps proteins together are: Ionic ...
paracetamol's user avatar
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16 votes
1 answer
3k views

What is Cβ (C-beta) deviation?

Molprobity and some other protein structure validation tools report a Cβ deviation statistic and offer plots for it (example below). Apparently if the Cβ is greater than 0.25 Å, some ...
Nick T's user avatar
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15 votes
1 answer
14k views

Why/how is blood red? (colours of hemoglobin)

Oxyhaemoglobin is red, deoxyhaemoglobin is bluish-purple, and carboxyhaemoglobin is a cherry red colour. Evidently in the porphyrin around the iron molecule in heme there is a conjugated $\pi$-system ...
James Harrison's user avatar
9 votes
4 answers
3k views

Does quantum mechanics play a role in protein folding?

Protein folding takes a very long time (relatively speaking) when thinking of quantum mechanical effect. However, for the initial micro-steps of folding, when an atom, or a configuration of atoms, can ...
yariv's user avatar
  • 101
9 votes
2 answers
526 views

Kolmogorov backward equations in active biological systems

I am trying to understand the following equations from a paper by Wang et al. [1, p. 5 at the SI]: Michaelis–Menten Representation of the Kinesin Cycle We assumed that there is a strong coupling ...
0x90's user avatar
  • 924
8 votes
1 answer
275 views

What chemical file formats are compatible with 3D printing?

I would like to print some molecules rather than building them using a kit. What file formats work?
bobthejoe's user avatar
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8 votes
1 answer
282 views

Why is it so difficult to create mock NMR spectra of macromolecules?

From what I understand, if you have a NMR spectra, you can determine the structure of a macromolecule but it is very difficult to determine what the NMR spectra of an expected structure would look ...
bobthejoe's user avatar
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8 votes
1 answer
304 views

How to dock aggregated structures comprised of "elementary" protein units like LEGO pieces?

There are proteins with intrinsic symmetries. For example: I was wondering how to use transformations such as: rotations, translation, replications to construct possible structures using 2 types of ...
0x90's user avatar
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7 votes
1 answer
549 views

What could these letters "S" in red circles mean in a biochemical diagram?

What could be the meaning of the red circles with letters S in them in the diagram below? I searched in the text but could not find. From "Role of TREK-1 in Health and Disease, Focus on the ...
CowperKettle's user avatar
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7 votes
1 answer
193 views

How can subtilisin still function without its catalytic triad?

I read chapter 9 in the book Biochemistry (5th edition), by Berg, Tymoczko, and Stryer (provided in the NCBI site here). It describes the mechanism of action of the chymotrypsin enzyme. The catalysis ...
Ynk's user avatar
  • 279
6 votes
1 answer
479 views

Which textbook is this image on protein tertiary structure from?

I am trying to find the original textbook image that is the inspiration for many schematic figures showing tertiary interactions (hydrogen bonding, ionic interactions, hydrophobic interactions, ...
Karsten's user avatar
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6 votes
1 answer
203 views

Biomolecular energy functions and entropy

From what I've been reading, it seems that entropy (rather than enthalpy) is the biggest driver of protein folding (especially the burying of hydrophobic residues). However, popular energy functions ...
Opt's user avatar
  • 163
6 votes
0 answers
167 views

How to model CRISPR/Cas9 binding and cleavage using a generalized Kittel's zipper model?

I am thinking about how to model the binding of a CRISPR/Cas9+guide-RNA complex to a double-stranded DNA that cause its cleavage. This post describes four steps at which a CRISPR/Cas9 system binds and ...
0x90's user avatar
  • 924
5 votes
2 answers
170 views

Obtain chemical insight from neural network results

I have recently read many papers where neural networks (NNs) are trained to predict chemical properties (starting from the structure of small chemical compounds) for compounds rather close to the ones ...
Open the way's user avatar
5 votes
1 answer
411 views

Is the structure of a crystalized protein the native one?

When one finds the 3D structure of a protein by crystalizing it and then making a X-ray experiment, how does one know that the geometrical configuration of the crystal is the same (or even close) to ...
user avatar
5 votes
1 answer
71 views

Does migraine medicine Topiramate work by supplanting Pyridoxal phosphate in enzymes?

I have seen it said that the precise mechanism of action of migraine medicine Topiramate is not known. But I certainly see a resemblance between that molecule and PLP (Pyridoxal phosphate, the ...
user240254's user avatar
5 votes
1 answer
98 views

What is the appropriate method to visualize electrostatic potentials?

Using a molecular viewer like PyMOL, I understand that its often incorrect to simply look at positive and negative residues and use those residues to calculate the charge density and instead, you ...
bobthejoe's user avatar
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5 votes
1 answer
228 views

Thermal stability of charged and uncharged alpha helices (the concept of alpha-helix capping)

I just learned that charged alpha helices are less thermally stable than uncharged ones. The only difference I see between them would be a larger dipole moment in the charged helix, but how would this ...
ste's user avatar
  • 662
4 votes
1 answer
110 views

How to determine the dimensions of a bixin molecule?

I need the dimension of a bixin molecule. I do not know where to look or how to calculate this information. I understand that this molecule has several rotational axes and conformation, so there is ...
Jose Enrique Calderon's user avatar
4 votes
1 answer
53 views

What are some of the more easily manipulated residues on an enzyme?

I am trying to attach a cross-linker to an enzyme and I am looking for candidates for reaction sites. I have several amino acids that are present on the surface of the enzyme (hydrophilic) but I am ...
user30150's user avatar
4 votes
1 answer
1k views

Determine if two molecule structures are the same molecule (perhaps in different conformations)?

I have two .pdb files describing two (small ligand) molecular structures. I need to determine if these two pdbs describe the same molecule, perhaps in different spatial conformations. Is there a ...
a06e's user avatar
  • 729
4 votes
2 answers
576 views

How to measure distance along solvent-accessible surface of protein complex in PDB file?

I am looking for a straightforward way to measure the distance between two active sites in a protein complex (PDB file). I need the distance along the solvent-accessible surface of the protein and not ...
user46680's user avatar
  • 313
4 votes
1 answer
135 views

How to connect proteins via disulfide bonds computationally?

I want to connect proteins together to form a dimer. As seen in the picture, the monomers come close to each other along the edge of the higher-order structure (forget about the sulfate there). How ...
ste's user avatar
  • 662
4 votes
1 answer
71 views

Is it possible to have an anhydrous solvent for virology, specifically in vitro phage assembly?

Typical protocols for lambda phage in vitro assembly call for you to dump all your viral components and buffer solutions into water. Water is a great solvent, drives extraction of energy from atp, and ...
edmund shelto's user avatar
3 votes
1 answer
977 views

Adding hydrogens to multiple pdb files using Openbabel GUI software [duplicate]

I am completely new to using OpenBabel software. I have about 9000 pdb files to which, I want to add hydrogens. It will be a very hectic task to open all of them 1 by 1 and then convert each of them....
Tapasvi Bhatt's user avatar
3 votes
2 answers
1k views

Why energy of some intermediates of glycolysis increases?

It is possible that I do not understand the concept of energy, but according to the diagram in my book, the energy between steps 4 and 5 and between 6 and 8 increases. How is this possible? Also, as ...
Wiktor Lippa's user avatar
3 votes
1 answer
288 views

Distance requirement for hydrogen bonding to occur

I am trying to understand the distance requirement for hydrogen bonding to occur (more specifically in the context of protein folding). There needs to be a donor and acceptor atom for bonding to occur....
Chris's user avatar
  • 73
3 votes
0 answers
2k views

Ester vs ether links: Why are archaeal cell membranes more resistant to high temperatures and acidity than bacterial and eukaryotic membranes?

The phospholipids composing the cell membranes of eukaryotes and bacteria contain ester links between the glicerol and the fatty acids. Archaeal membranes, instead, are composed of phospholipids ...
FriedHaggis's user avatar
3 votes
0 answers
109 views

Is DNA a base inside the cell?

DNA is deoxyribonucleic acid because it has phosphate groups in every one of it's nucleotides. However, in aqueous solutions protons will ionize, leaving phosphates alone as negative groups, i.e., ...
user avatar
2 votes
3 answers
1k views

Are crystallographic omit maps only used with molecular replacement?

(This is in the context of macromolecular X-ray crystallography.) From Lamb et al. 2015: Model bias is the result of how maps are calculated: because the phase estimates [of the structure factor] for ...
Dunois's user avatar
  • 161
2 votes
1 answer
482 views

Is a beta pleated parallel sheet always formed from more than one peptide?

I can conceptually grasp the beta pleated anti-parallel sheet by imagining a curved length of string i.e. one polypeptide, starting with the N- terminus on the left and ending with the C-terminus at ...
Naj's user avatar
  • 267
2 votes
2 answers
2k views

Why do chiral biological molecules only exist as one enantiomer? Does it have any advantage?

Why is it that chiral biological molecules are enantiomerically pure? The other enantiomer would have the same reactivity, and the only difference is their angle of rotation of plane polarized light. ...
Mr.HiggsBoson's user avatar
2 votes
2 answers
138 views

How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center?

So for example there is a paper by Ramakrishnan and Qasba which presents a model in a 3d stereo picture it has UDP-Gal, Glc, Mn++, a piece of the lactalbumin protein (?) and a piece of the lactose ...
Gunther Schadow's user avatar
2 votes
2 answers
480 views

Atomic coordinates for DNA bases as they appear in a B-form or A-form duplex

Where can I find atomic coordinates for guanosine / cytosine / thymine / adenine (either the ribonucleotide or deoxyribonucleotide bases) where the atoms are configured in the manner we would expect ...
Mhr's user avatar
  • 21
2 votes
0 answers
50 views

What do cannabinioids have in common structurally?

I'm looking at the wikipedia page for cannabinioids, and trying to find structural similarities between them. For plant based ones it's hard enough, the only similarity I could find seemed to be 6 ...
tox123's user avatar
  • 957
2 votes
0 answers
51 views

Why there are just two Ramachandran angles in protein structure for two peptide bonds?

I really want to understand why there are just two ramachandran angles to understand the structure of the protein and why not three or many ? Can someone suggest some reference and explain this ?
user135580's user avatar
1 vote
1 answer
82 views

Is it possible to identify the source of a protein hydrolysate [closed]

I have a powder which only declares to be "Protein Hydrolysate" Meaning that the all the protein has been broken down. We've tried to identify the source of the powder with DNA research. But no ...
Monthy's user avatar
  • 27
1 vote
1 answer
119 views

Preferred IUPAC name of Protoporphyrin IX

I was looking up protoporphyrin IX and was surprised to find that no two websites gave the same IUPAC name for the compound. Here are some examples: 3,3'-(7,12-Diethenyl-3,8,13,17-...
Caitie's user avatar
  • 11
1 vote
2 answers
297 views

What provides the energy allowing membrane proteins to facilitate diffusion across the membrane?

We know that facilitated diffusion requires no energy. But the transport proteins, when bind to a molecule from ECF (extra-cellular face) , the proteins rotate and deliver the molecule into ICF (...
user avatar
1 vote
1 answer
495 views

What exactly is peptone (tryptone?) and why does it not get precipitated?

According to Wikipedia Peptone (also called Tryptone) is a form of amino acid that has been treated by stomach acids. According to Google it also stays in solution when treated with acids or heat. Why ...
user97603's user avatar
1 vote
1 answer
287 views

Nomenclature of carbohydrates

In the chapter on Biomolecules in my book, the following points are given regarding carbohydrates. Numbering the C-chain with consecutive rank The C-atom present in the aldehyde group of aldoses and ...
MrAP's user avatar
  • 775
1 vote
1 answer
152 views

Can Isopropyl β-D-1-thiogalactopyranoside be degraded into either 1-deoxy-galactose or just galactose?

This may be a silly question, but is it feasible that Isopropyl β-D-1-thiogalactopyranoside (IPTG) when acted upon by a beta-galactosidase could produce 1-deoxy-galactose or just galactose? The ...
Jeppe Nielsen's user avatar
1 vote
1 answer
49 views

What happened to mesoporous materials for drug delivery?

A review on the topic can be found here: Wang, S. Ordered mesoporous materials for drug delivery. Microporous Mesoporous Mater. 2009, 117 (1–2), 1–9. DOI: 10.1016/j.micromeso.2008.07.002. So the 21st ...
Insaneinthemembrane's user avatar
1 vote
1 answer
44 views

When DNA degrades, does any chemical environment preserve sequence information?

Small bits of DNA information can be found in ancient remains. In analogy to old bones becoming mineralized, is there a chemical environment in which the nucleic acid sequence of the original strand ...
Whit3rd's user avatar
  • 468
1 vote
0 answers
19 views

Which position do retro aldol reactions occur in (comparing glucose and fructose)?

Regarding glycolysis, my text states: What is the biochemical rationale for the isomerization of glucose 6-phosphate to fructose 6-phosphate and its subsequent phosphorylation to form fructose 1,6-...
user143539's user avatar
1 vote
0 answers
223 views

Is Porphyrin Planar?

I have been looking at this diagram from quite some time, I know the 18 pi electron cycle that forms porphin(e) is definitely planar but what about the whole molecule?... The Nitrogen's act as a ...
Informal Limits Lad's user avatar