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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Relationship between TADs and supergenes
I need to investigate the architecture of supergenes. If someone is familiar with the topic (TADs and supergenes) could you please send me some links to articles covering this topic?
Already did ...
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Clustering collection of PDB files based on 3 dimensional structural similarity in python
I have generated a set of 3-dimensional structures of the peptide AGAGAG with different structures. Total number of PDB files are 300. I need to cluster the peptide structures based on their ...
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Can one use DSSP (secondary structure assignment) for short peptides of size 6, 10 and 18?
I have large number of PDB files of peptides of size 6, 10 and 18. I wanted to cluster the peptide structure based on the secondary structure. I used DSSP in mdtraj module in python to assign DSSP ...
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Aligning two PDB structures with different numbers of atoms
What options do I have to align two PDB-files of ribosomes but with different number of atoms? I need to do the alignment using selection "name CA or name P", because the ribosome has both ...
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How to fix outliers in Ramachandran plot using Coot
I have the following Ramachandran plot generated by Coot:
Notice that it has high outliers content (red dots). I want to manually drag those
red dots into some part of the region. Eventually, I ...
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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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Where is the location of cutin or cuticle in the plant leaf [closed]
Cutin's main role is to prevent the the plant leaf from water loss, cutin is thick in shape , but I need to know where is the location of it ,for example is it in the lower epidermis or in the upper ...
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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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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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Using BLAST for molecular replacement in structural biology
This is my first time trying to do molecular replacement to solve a protein structure. I am using the NCBI blastp program to find suitable search models. When choosing a search model, I understand ...
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Why does DNA synthesis require nucleoside triphosphates? [closed]
Writing the DNA sequence is done with nuclosides that have three phosphates attached to them, and two of these phosphate are thrown away back into "phosphate pool" of cell. What are main ...
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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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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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Do SILK fibres let light pass through it?
The reason given by Wikipedia for silk fibres being lustrous is that:
Silk fibres have triangular prism-like structure, which allows them to refract the incoming light at different angles.
By my ...
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What is the difference between a myofibril and a myoblast? (In skeletal muscle)
I read that a muscle fibre (myofiber) is formed when myoblasts fuse.
https://teaching.ncl.ac.uk/bms/wiki/index.php/Skeletal_muscle#:~:text=The%20multinucleate%20feature%20is%20established%20in%...
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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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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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Is mucus significantly affected by the presence of ions?
In mucus, there is besides water and the mucins (Proteins for mucus), there are Ions like $Ca^{2+},Na^{+}$, etc. I have read that These Ions can Control the mucus swelling, i.e. the volume that the ...
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Which proteins are most sensitive to electric fields?
Many Proteins have ionic charges that can attract each other (e.g. Formation of salt bridges) or repel each other. On the other Hand, Proteins are mostly immersed in water that screens most of the ...
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"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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What are the uses of Helical Wheel Projections in Structural Biology?
I have seen helical wheel projections used to illustrate amphipathic helices in proteins. Are there any other uses for these models?
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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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How do fatty acid and polyketide synthases handle the varying size of their substrates?
Polyketide synthesis involves six modules, each containing certain common constituent enzyme activities (KS, AT, KR) that are involved in extending the chain (see e.g. Dutta et al.(2014) ). The ...
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Is there a reason for the lack of full RTK structures?
Bocharov et al. (2013) write that
As there are no structures of full-length RTKs [receptor tyrosine kinases], we do not fully understand how different domains function together to mediate signal ...
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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: ...
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Automating figure-making with PyMOL [closed]
What I want to do
I have a list of almost 200 PDB entries that I need to visually inspect. Luckily, the thumbnail image displayed on the PDB website (examples with RCSB or PDBe for a well-known ...
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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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How does antibody structure relate to function? [closed]
I know that antibodies have 2 binding sites (as Y shape) so they can bind to 2 pathogens for agglutination. They have a hinge, heavy and light chains, constant and variable sections on these chains.
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What are the applications of predicting the structure of proteins?
Protein molecules are very important as they are used for catalyzing almost all the chemical reactions in the cell, regulation of gene activity and provide cellular structure.
However, in predicting ...
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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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Why add hydrogens in molecular dynamics simulations?
In my molecular dynamics lecture, our prof said, that we always have to add hydrogen atoms to titratable groups, before we start the force field simulations, and that it is especially important for ...
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Parallel DNA double-helices with Watson–Crick base-pairing: Why do they not occur? [duplicate]
I know that parallel DNA helices exist and are governed by Hoogsten base pairing, but why can’t they be possible with Watson-Crick pairing? In the diagram below, if we were to flip one of the strands ...
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Why does sequence of amino acids presented on the Catalytic Site Atlas from a given protein differs from the sequence on the RSCB Protein Data Bank
I wanted to compare the amino acid sequence of enzymes for this project I'm working on and need to compare them at their catalytic site. For that, I went to the Catalitic Site Atlas to get the ...
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What are the structural factors affect enzyme's Km?
Is there any rules (should not be exact), to estimate the kinetic changes in an enzyme if I did any mutation on it?
If I cannot estimate the new kinetic values, is it possible at least to clarify or ...
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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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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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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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What is meant by "complexity of carbon sources"?
My biology book states
"life on earth depends upon carbon based molecules, most of these food sources are also carbon based. Depending upon the complexity of these carbon sources, different ...
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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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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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What does "local folding" means in secondary structure?
I'm new to biology field, so I'm learning all kinds of biochemistry knowledge for a bioinformatics project. I've found a few definitions of secondary structure online. For example, I found this brief ...
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At what point, when connected, do DNA strands become a helix?
When synthesizing DNA strands and beginning to "connect" them, how quickly does it become a helix?
In this answer, canadianer says
The helical structure is more stable than the "straight" form (...
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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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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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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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Does the Plasma Membrane have a hydrophilic interior/exterior/contain vesicles? [closed]
I am very new to the study of biology, and have been unable to find information in other sources which could tell me whether the plasma membrane has the following traits:
has a hydrophilic interior
...
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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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Why we utilize dextro glucose and levo amino acids?
Our body only digest dextro(Right handed) glucose and levo(Left handed) proteins and can't digest Levo glucose and dextro proteins. Why?
Our body synthesis levo proteins. What is the reason?
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Sheep vs. Furry animals
Why can't we take the fur of a fox without killing or skinning it just like the sheep , what's the biological or chemical structure or even the trait which is on a sheep's body that separates wool ...
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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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