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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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?
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18 votes
1 answer
19k views

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 ...
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17 votes
1 answer
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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 ...
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16 votes
4 answers
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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 ...
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16 votes
2 answers
427 views

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: ...
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15 votes
1 answer
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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 ...
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15 votes
1 answer
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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 ...
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14 votes
4 answers
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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.
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13 votes
4 answers
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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 ...
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13 votes
1 answer
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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 ...
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12 votes
1 answer
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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 ...
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11 votes
1 answer
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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 ...
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11 votes
1 answer
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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?
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10 votes
4 answers
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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 ...
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8 votes
2 answers
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How hard it is to determine a 3d structure of a protein?

I seeing tens of thousands of PDB files on the internet. I really want to determine a 3D structure of my protein of interest. I've heard that 3D structure determination is a complex, expensive, and ...
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8 votes
2 answers
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How can I pare down a PDB file in Python to only include specific residues?

I'm trying to make a script that will take a MTZ file (reflections), convert it into a CCP4 map, then pare that map down to only encompass a desired area to cut down on the size of my PyMol session ...
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8 votes
2 answers
613 views

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,...
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8 votes
1 answer
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Are original x-ray diffraction data available

Is it customary for investigators to publish the original x-ray diffraction data used in macromolecular structural determination? If not, why not; and if so, is there an online database where these ...
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8 votes
1 answer
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How does one calculate the resolution of a crystal structure?

Considering that I have a diffraction pattern of a crystal, how would I calculate the resolution of a structure in Angstroms? How does that value differ from the information that I would get from the ...
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8 votes
2 answers
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Solution based measurement of Solvent-Accessible Surface Area of macromolecules

The Solvent-Accessible Surface Area (SASA) is a valuable metric for looking at protein folding and protein-protein interactions. However, this measurement is typically done by calculating the SASA ...
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8 votes
0 answers
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Rosetta ab initio prediction and protein-protein interaction fitness help [closed]

I have designed several proteins which I predict have interactions with another protein using the sequence based Conjoint Triad Method. I would like to know which ones structurally are predicted to ...
7 votes
1 answer
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What is the fibre axis in the Watson and Crick paper?

I was reading Watson and Crick’s original article on DNA structure in Nature 171, 737–738 (1953). The accompanying diagram (shown below) has something called the “fibre axis” going through the DNA. ...
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7 votes
1 answer
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Why does Thiamine pyrophosphate have phosphates?

The reactions that Thiamine Pyrophosphate(TPP) catalyses are associated with the thiazolium ring. Why is pyrophosphate a part of the structure of TPP then? What benefit do the additional phosphates ...
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7 votes
2 answers
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Why is the DNA helix anti-parallel? [duplicate]

Why is it that DNA strands are running in anti-parallel fashion? Given the chemical base-pairing, they could have been parallel just as well.
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7 votes
1 answer
757 views

DNA-DNA cross-linking with formaldehyde?

The 3C (chromosome conformation capture) technology for studying chromatin 3D organization starts by a cross-linking step using formaldehyde to find segments of DNA interacting. In my understanding ...
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7 votes
1 answer
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How does the Endoplasmic Reticulum scale with Cell Volume in Epithelial Cells?

I am working on a mathematical model of a biological tissue (drosophila pupal notum; an epithelial tissue) where the tissue is built up from cells all described by the same cellular-model. The tissue ...
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7 votes
1 answer
108 views

Which factors besides the thermodynamic stability are important for the hairpin in intrinsic transcription termination?

Intrinsic termination (rho-independent) relies on a stable hairpin with a subsequent uridine repeat. The common explanation on how these sequences cause the termination of the transcription are based ...
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7 votes
1 answer
231 views

RMSD during conformational transition in proteins

When I was investigating the differences between protein structures obtained by X-ray crystallography and NMR spectroscopy, I found the paper [1] compairing structures of several proteins resolved ...
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6 votes
2 answers
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Twist in the DNA double-helix

DNA, has a deoxyribose sugar — phosphate backbone with the purine and pyrimidine bases, adenine, cytosine, thymine, and guanine connected to the deoxyribose sugar. (The base–sugar molecules are ...
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6 votes
2 answers
211 views

Are there functional examples of parallel DNA double helices?

The anti-parallel structure of the DNA double helix is well studied, but I am curious if there are any examples of parallel DNA double helices. There are reports of synthetic such structures; see this ...
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6 votes
1 answer
355 views

Are quaternary protein monomers unique to a particular protein complex?

I know that quaternary protein structures are formed exclusively via non-covalent bonds. My biochemistry professor discussed a viral capsid that is essentially one quaternary structure with 240 ...
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6 votes
1 answer
166 views

How do I prepare a PDB for submission to the Protein Data Bank?

I have a couple structures that are nearly ready to be deposited in the PDB. Out of curiosity, I ran them through the ADIT's precheck tool and they failed with one error after another, as I lacked ...
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5 votes
2 answers
744 views

By just looking at an unlabeled picture, how do you know it is a protein?

I'm learning about proteins and need to understand this concept. What makes this colourful ball of squiggles identifiable? Why is it a protein, and not any other biomolecule (like DNA for example)? ...
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5 votes
1 answer
1k views

Stability of helical strands of DNA?

The DNA molecules contain phosphate groups involved in $3'\rightarrow 5'$phosphodiester linkages. These groups, in the bonded state with deoxyribose, contain 1 negative charges ($\ce{3'-PO4^{-}-5'}$). ...
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5 votes
1 answer
212 views

Structures of cyclodextrin complexed with small ligands

For some structural study I am looking for cyclodextrin strucutures (in 3D format such as pdb, mol2, etc) complexed with small molecule ligands, such as cholesterol and even smaller. Right now I could ...
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5 votes
1 answer
381 views

How would one describe the R-factor in crystallography?

Yes, there is the wikipedia definition, but how would one explain this concept to a non structural biologist?
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5 votes
1 answer
164 views

Which of Perutz et al's protein structures other than 3₁₀ helix were correct?

In 1950, Bragg, Kendrew and Perutz published "Polypeptide chain configurations in crystalline proteins" (open access) and were famously 'proved wrong' by Pauling, Corey and Branson the following year, ...
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5 votes
1 answer
161 views

Tryptophan side-chain structure, how should it be orientated?

I would like some clarification on whether it matters where the NH and double bond are placed in these two structures of tryptophan (W) that I drew. I marked the right side as correct and the left ...
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5 votes
1 answer
185 views

Generate mesh surface from protein structure

What tools are most widely used for generating a mesh surface of a protein from an x-ray crystallographic structure (from the PDB)? Pros and cons would be appreciated. I'd prefer the output to be a ...
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5 votes
1 answer
86 views

How many residues can a reliable ab initio structural model contain?

A recent question on ab initio that I answered involved touching on the limitations of ab initio modelling. A review from 2009 put forward that typically only in the order of 100-110 residues could be ...
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5 votes
1 answer
723 views

How do you turn a minimal CIF description into a complete one?

I have a CIF file that I downloaded from the PDB, but if I try to use it in Coot, it complains that it is not a complete CIF definition. This page provides a batch script that I may be able to tease ...
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5 votes
1 answer
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Isotropy of sarcomere bands in skeletal muscle cells

As seen under a polarization microscope, the A-Band in skeletal muscle fibres is so named because it is anisotropic in its refractive index which is a characteristic of orderly crystalline structure. ...
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5 votes
1 answer
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What is the distance between the 3' 18s rRNA (the Kozak consensus sequence) and the A-site of eukaryotic ribosomes during protein translation?

Reposted from Quora The Kozak sequence is shown to be important in translation initiation, and the A-site is the anti-codon recognition site. If the distance is not known, how could I find out what ...
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4 votes
1 answer
353 views

Simplified molecular-input line-entry system

This may be a bit abrupt/vague question, but I didn't know how to proceed the search to get the answer. What are the properties of a 3D biomolecule which gets ignored when a 3D biomolecule is ...
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4 votes
1 answer
215 views

Topology of closed circular DNA

Why are covalently closed circular plasmid DNAs naturally found in an underwound state ? Is it because this makes it easier for the DNA replication machinery to access and unwind DNA ? Or is it ...
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4 votes
1 answer
105 views

Questions regarding a particular paper

With respect to the following paper: Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study I have a few questions: in page 2,...
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  • 2,185
4 votes
1 answer
112 views

Parse PDB using DSR-PDB Library

I'm trying to parse ATOM section of a PDB file. I'm using the dsr-pdb library for this purpose. I've encountered a problem. This library interprets CD1 atom of ILE ...
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4 votes
1 answer
85 views

Subset of Protein Crystal Structures (from PDB)

Is there a well-accepted subset of the Protein Data Bank set of protein structures that: Has only "high quality" structures (may be differing metrics of this; e.g. resolution, size, or structural ...
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4 votes
2 answers
756 views

Which server to use for volume and accessible surface area calculation of proteins

I want to find the accessible surface area and the volume of a protein, giving PDB file as the input for the protein. I used two servers, 3vee and Vadar. For the PDB id, 1LTM, the websites are giving ...
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4 votes
1 answer
199 views

How to recognize a conserved motifs of the protein

I would like ensure that my reasoning is correct. Assuming that I know the aminoacids sequence of the protein of interest. I can't say anything about the structure looking only at the aminoacids ...
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