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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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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 ...
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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 ...
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Why does the structure of haemoglobin change when the ferrous ion changes to ferric ion?

It is said that $\ce{Fe^2+}$ can bind oxygen while $\ce{Fe^3+}$ cannot. Why is that so? $\ce{Fe^3+}$ has an extra electron, it could bind more easily to the oxygen. And how and why does the structure ...
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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 ...
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1answer
281 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 ...
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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 ...
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0answers
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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 ?
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1answer
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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 ...
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1answer
155 views

How to measure a distance along the surface of a protein in a PDB

I would like to measure the distance between two active sites in a protein complex (pdb), but I do not find a straightforward way to do it. To be more precise I need the distance along the surface ...
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0answers
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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., ...
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2answers
418 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 ...
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What is the chemical formula for snake venom?

I haven't been able to get this question answered through the internet so far, so I was looking for a more professional angle in which this question can be answered.
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1answer
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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 ...
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0answers
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Comparing magnesium ion sensitivity in ribosomes to sensitivity in double-stranded DNA

I was doing some reading on this, and $\ce{Mg^2+}$ has a much greater sensitivity to ribosomes than to dsDNA (double-stranded DNA). It seems the best answer I can think of it that $\ce{Mg^2+}$ ...
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1answer
36 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 ...
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2answers
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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 ...
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1answer
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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 ...
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4answers
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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 ...
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1answer
528 views

Chondroitin Sulfate (greater volume in solution than in crystal form)

I've read in a textbook on biophysics that chondroitin sulfate occupies a greater volume in a solution than in crystalline form. Why is that? Is it because of hydrogen bonds in solution that the ...
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0answers
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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 ...
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1answer
7k 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 ...
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1answer
25 views

Does mechanotransduction of cells play a role in the biocompatibility of titanium?

What exactly is mechanotransduction? The definition seems to vary from source to source. Some indicate that mechanotransduction is the underlying principle where cells pull on the surface they grow on ...
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1answer
116 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 ...
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1answer
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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 ...
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1answer
282 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 ...
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2answers
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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 ...
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0answers
41 views

What are side chain order parameters?

I was reading an article: We first compared experimental (S 2 exp) and computed (S 2 calc) side-chain order parameters using the simplest approximation of side-chain conformational variability, ...
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1answer
75 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 ...
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0answers
108 views

Why are non-polar hydrogens neglected in computational protein-drug binding studies?

Why are (non-polar) hydrogen atoms generally neglected in a protein-ligand (or drug) binding energy calculation? They do have charge and mass. Doesn't that affect the free energy calculation? The ...
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2answers
353 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 ...
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0answers
51 views

Modelling planar ring molecules and their evolutions [duplicate]

This is the next step of my previous question. I am trying to simulate a circular chain (ring) of molecules which are planar (two dimensional). What I do is take a planar unknot and embed it into a ...
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1answer
60 views

Modelling planar molecules and their evolutions

I am trying to simulate a chain of molecules which are planar. Can anyone please give me an example of the molecular chain which can stay as planar with it's minimum energy state is planar. A ...
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1answer
41 views

What conditions to use to crystallise Equine Myoglobin?

What are the crystallisation conditions for Equine Myoglobin? I've tried repeating some from the PDB but no success.
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2answers
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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 ...
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1answer
60 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 ...
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5answers
5k 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 ...
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249 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?
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191 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 ...
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1answer
2k 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 ...
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1answer
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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)
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2answers
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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 ...