Questions tagged [structural-biology]

The study of the molecular structure of biological macromolecules and how that structure relates to their function.

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Why can polar molecules like water pass aquaporin better than unpolar like H2 or CO2

We learned in our lecutre, that aquaporin lets Water pass, but blocks Ions like H+ and unpolar molecules like CO2 and H2. The reasons for the Ion blocking are comprehensible, but I dont get, why less-...
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91 views

Reduce protein structure representation dimensionality.

In my lab we are trying to extract spatial features from protein structures. The software we develop makes use of CUDA for all heavy number-lifting, thus we are limited by the GPU's memory (12GB). ...
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345 views

Is the number of stamens always 9 for geranium?

We are studing in class the reproduction of plants. We start the lesson by observing some components of flowers, it was the Géranium. First of all we start counting the number of sepals , petals and ...
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1k views

How can the directionality of a protein structure be defined?

For a DNA molecule, you can define directionality using the convention of a 5'-3' direction on the Sense strand. However, using an N to C convention for a protein doesn't work since the ends may be on ...
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50 views

What is the biggest structure in nature for structural coloration?

I'm interested in the actual sizes behind structural coloration: I find it fascinating and I think it may have a couple very nice applications. The problem is I couldn't find anything but vague ...
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50 views

What protein(s) bind together the calcium carbonate tiles in abalone shell to give it strength?

The articles that I've been able to find on the structure of abalone shells mention that they consist of calcium carbonate plates connected by proteins, but don't name the proteins. These proteins are ...
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33 views

What is the structure of PduK in the Pdu BMC?

My lab is creating 1,2-propanediol utilization bacterial microcompartments (Pdu BMCs) with an operon containing genes for PduA, PduB, PduJ, PduK, PduN, PduU, and PduT. According to Mayer et al., all ...
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25 views

Database of predicted protein-ligand binding/docking score

Is there a database of computationally determined "binding scores" across protein-ligand pairs in the PDB? My phrase "binding score" is deliberately generic, since any such score would be fine. In ...
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638 views

How to find the radius of gyration for a protein?

While going through the paper titled "GEOMETRIC ANALYSIS OF THE CONFORMATIONAL FEATURES OF PROTEIN STRUCTURES" by Manish Dutt, it talked about finding the radius of gyration of each protein structure. ...
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48 views

Can I explain the kinetics of a ligand looking at the ligand-protein co-structure?

Can I explain the kinetics of a ligand binding to a target protein (association and dissociation rates) by looking at the protein-ligand co-structure? Editing my question after a few comments: I ...
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40 views

Differences in structural target for LPS detection by LAL and MD-2/TLR4

I remember there being a significant difference in the pathogen-associated molecular patterns (PAMPs) used for detection of lipopolysaccharide (LPS) by mammalian cells and the Limulus amoebocyte ...
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56 views

Visualizing secondary RNA structure binding to target

I am designing synthetic ribozymes, and need to see the secondary structure that arises from its flanking arms binding to a target mRNA. I've used Mfold as well as IDT's OligoAnalyzer (Hairpin), but ...
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35 views

Determine directionality of backbone from electron density map

I am given a polypeptide with three electron density maps at different resolutions; 1.85, 2.5 and 3.5Å. And from this I am to determine at which resolution you could be certain about the ...
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30 views

What is the structure of heterochromatin?

A short article about euchromatin and heterochromatin mentions that the structure of heterochromatin usually depicted in images "has never been visualized in vivo, and its existence is ...
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49 views

Generating Cartesian coordinates of each atom in protein chain from the internal coordinates using python or some software

I am trying to compute Cartesian coordinates of backbone atoms and side-chain atoms (C beta alone) for a given set of internal coordinates (bond lengths, bond angles and dihedral angles) I have ...
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38 views

"Straight" or "linear" helix

If an alpha helix is discontinued for a short while and then continues in a different direction, I prefer to call in "kinked". If the helix is simply uniformly following one direction, I prefer to ...
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69 views

What is the difference among biochemistry, molecular biology, molecular genetics and structural biology?

I have never heard of straigthforward definitions of these fields in my college lectures, and the Internet searches were not very helpful. However, from what I have learned at different subjects, this ...
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45 views

Normalise protein database domain-wise

Suppose we've collected a big (hundreds of thousands) library of different protein sequences with certain features. Then we want to use this data base to train a classifier. And for several ...
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140 views

Why is the macromolecular composition of a human cell seemingly hard to find?

I am trying to find a 3D rendering or list of molecules by volume in a cell (originally I was searching for human, but I'll take any at this point!). I understand the open-endedness of the question: ...