Questions tagged [protein-structure]

The 3-dimensional organisation of amino acids in a protein, specifically including the secondary, tertiary and quaternary structures.

41 questions with no upvoted or accepted answers
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Are all organelle lumens a reducing environment like the cytosol, or nonreducing like the extracellular space and the ER lumen?

I am interested to know if cysteine can form disulphide bridges in proteins within organelles. Typically cysteine will not form disulphide bonds in the reducing environment of the cytosol, but will in ...
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37 views

Estimating diffusion constant of a protein based on number of amino acids

Is there a way to estimate the diffusion constant of a protein based on the number of amino acids it is comprised of. I know that the shape of the protein has an influence on the diffusion constant, ...
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132 views

Are there any enzymes without aromatic amino acids?

I'd like to try a new spectroscopic technique to study enzymatic reactions (which reaction doesn't especially matter, something simple and with fast kinetics like catalase would do fine - I'm just ...
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73 views

Proteins folds: relation to splicing and post-translational modification?

Is the secondary structure pattern of protein folds related in any way to alternative splicing and post-translational modification?
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69 views

α-β Interfaces of Hemoglobin

I am trying to learn the interactions that hold the hemoglobin tetramer together, and the conformational changes induced at various allosteric sites. So far, what I know is this: The tetramer can ...
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90 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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298 views

Determine secondary structure (per residue pair) from a protein contact map

Given a protein map contact map (which for this particular case is a matrix of all Ca-Ca atoms in protein 1a3a that are less than 8 Angstroms): Question: For each ...
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36 views

To which SCOP Class corresponds the following secondary structure?

I need to classify this protein into one of the SCOP class (all $\alpha$, all $\beta$, $\alpha +\beta$, $\alpha/\beta$, or small protein). I'm having difficulties understanding the difference ...
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104 views

When can helices form coiled-coils?

The other day, my teacher suggested we find out whether a chain of the following amino acid sequence would be able to form a coiled-coil: N-KIAEVRAQYEDVANKVRLIVE-C ...
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29 views

Differentiating molecules based on peptide sequence? How to annotate?

I want to differentiate between classical class I and non classical class I MHC molecules in a model organism using well conserved structural features within classical MHC I molecules (eg intradomain ...
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38 views

Why did the protein structure prediction accuracy in terms of GDT-TS decrease from 2008 (CASP 8) to 2014 (CASP 11)?

I read on https://doi.org/10.1038/d41586-020-03348-4: Why did the protein structure prediction accuracy in terms of GDT-TS (Global Distance Test — Total Score) decrease from 2008 (CASP 8) to 2014 (...
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30 views

Any kind of online “molecular modeling playground”?

I'm wondering if anyone has ever made a tool to try out new molecular modeling/simulation algorithms, where the tool itself handles the "boring" tasks of loading PDB files, building chains ...
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31 views

What are good techniques for determining direct maps of proteins?

I am looking for which techniques to explore to determine electron density maps (or Fourier maps) for a protein (possibly using an assumed model). In particular, I want to avoid techniques that ...
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21 views

What is the native structure of amyloid-beta protein under physiological conditions?

The amyloid-beta protein forms cross-beta structured fibrils. But under normal physiological conditions what is their predominant secondary structure. Is it alpha-helix, random coil or beta-sheet?
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21 views

Where can I find and download HMMTOP training set?

I would like to perform redundancy reduction for my test set for membrane topology prediction. I checked the 1998 paper and website of the HMMTOP server but haven't found any download links for the ...
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56 views

Quantify Protein Denaturation with Change in Solubility

I plan to run a lab which compares the impacts of ethanol and methanol, in varying concentrations, on the denaturation of whey protein. Change in water solubility is a good indicator of the degree ...
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23 views

Do the centrioles in the centrosome differ in their angle to one another?

The centrioles in the centrosome are often shown at an orthogonal angle, does this arrangement differ between samples, as in, does the daughter centriole show up in different sides of the mother ...
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805 views

Are microtubules in centrioles helical, like they are when in isolation?

Microtubules tend to be of a helical structure, do microtubules in centrioles also have a helical structure? The centriole is composed of nine circularly arranged triplet microtubules, one complete ...
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94 views

How a biologist attempts to explain the structure of the ribosomal proteins?

I have a Computer Science background and a minimal biology knowledge. This is the question I am asked to answer in one of the biology courses: What would be the structure of ribosomal proteins when ...
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18 views

Why glycosylation of a protein increases its non-specific binding properties?

This doubt arose while reading this website: https://www.thermofisher.com/cn/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-...
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30 views

Predict if a given protein can pass through the intestine

Assume that i have a 3d-protein structure in a PDB file on a computer. Is there any bioinformatic method to predict if that protein can pass through the intestine or not?
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13 views

BLAST protein sequences from 2 different bacterial species

I am interested in finding a consensus sequence of a protein found in e.coli, in Pseudomonas aeruginosa. I am using pseudomonas.com to BLAST p the amino acid sequence of the protein that i have found ...
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103 views

What is the upper limit of number of SNP based mutation in any protein?

I want to know if there is any upper limit of, how many point mutation a protein can have because of disease or nsSNPs? The general studies only focus mostly on a single or double site mutation of any ...
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28 views

Depositing/publishing protein structure simulations

Just wondering if anyone has any information on what the general consensus on publishing/depositing online protein structure simulations is? I've been doing a fair bit of work to characterise the '...
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3k views

Effect of pH on protein solubilty and denaturation

I'm a little bit confused about the influence of pH on proteins. Increasing or lowering the ph will give the protein a net positive or net negative charge, respectively. However a lower pH or higher ...
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620 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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107 views

How can I perform a 1:1 sequence-structure alignment for a pdb template dimer and homologous dimer sequence?

I have: 1. A PDB dimer protein structure template of a real solved protein. 2. An unsolved, but highly homologous dimer protein (>90% sequence identity.) How can I use MODELLER to make a theoretical ...
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125 views

How does RCSB determine the origin of the Cartesian coordinate system utilized in all PDB files

When perusing through the text version of a PDB file, I noticed in records that begin with "ATOM," there are x, y, and z coordinates for these atoms. How is the origin of each molecule's Cartesian ...
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501 views

What is the most stable globular protein?

What is the most thermodynamically stable globular protein? I am looking for a small (ideally less than 50kDa) soluble globular protein motif which folds easily/reliably and is known to be extremely ...
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36 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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72 views

Which condition is most likely to cause a buildup of materials in the lysosome?

Stated below, I must answer a question related to lysosomes. I am unsure of the answer, and have explained my reasoning after the question. Lysosomes contain hydrolytic enzymes that derive from the ...
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23 views

What programs account for structural alignment of different parts of distant homologs which have significant structural differences?

If there is a need to align structurally different parts of distant homologs, which program one should use? Since distant homologs often have significant structural changes, does that means the ...
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36 views

What is a Protein contact map, and how do I read one?

Protein contact maps are symmetrical and look great, but how does one read one? I tried to underside the following source: 'Understanding contact patterns of protein structures from protein contact ...
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23 views

How to build SEG in your personal environment?

I'm trying to implement SEG (Wootton & Federhen,1993) in my MATLAB and Python environment. From this oriinal article I cannot figure out what I need to build my script. Are there any related ...
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39 views

Why does insertion of transmembrane domains occur in the rough ER?

To elaborate on that question, why in the secretory pathway does the insertion of transmembrane domains into the membrane occur in the rough ER as the protein is translated and threaded across the ER ...
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73 views

conversion of distance matrices to pdb/coordinates

I am currently facing two transformational issues. Suppose I am given a protein's residue sequence and calpha distance matrix; is there a way to generate the 3d coordinates of the protein's residues ...
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14 views

TBX3 Protein structure and function

Is it possible for an anti-cancer monoclonal antibody to target the two repressor domains in the N and C terminal of the TBX3 protein ?
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131 views

Western blot extrange band

I performed a WB using plasma rats and monkeys samples with anti ubiquitin K-48 antibody. In every sample the antibody binds something and it appears a specific band that seems to be 71kDa. When I ...
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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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1answer
71 views

Is α-keratin a fully functional protein?

Is α-keratin before it coils with another polypeptide, makes chains, and build intermediate filaments a fully functional protein? I mean, is the single monomer of α-keratin a protein or does it have ...
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Maximum subarray problem for genomic sequence analysis

Genomic sequence analysis employs maximum subarray algorithms to identify important biological segments of protein sequences. These problems include conserved segments, GC-rich regions, tandem repeats,...