Questions tagged [protein-structure]

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

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Putting labels of different sizes on one PyMOl Object [migrated]

I'm new to PyMol (and StackExchange!) and working on my first project. I have the structure of a protein as an object, called PolyA-M, and the idea is that the residues of it are shown as spheres of ...
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Types of bonds in protein chains?

I'm trying to understand possible bonds on the protein backbone. There are a lot of hydrogen bonds and sometimes disulphide bridges. Are both of these non-covalent bonds? I've read that we also have ...
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Gene therapy with disulfide-linked protein

Say I transduce a nucleic acid sequence that encodes a protein having at least one disulfide linkage. For simplicity, let’s assume that there are only two cysteines in the protein and the side chains ...
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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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Can 1.5 gigabytes encoded in the human genome really account for the complexity of a human being?

I read the human genome is 1.5 gigabytes in size. Thats actually not a lot; Photoshop probably takes more space. Mac OS takes 10+ gigabytes of space. Also, the genome is 1.5 gigabytes when counting ...
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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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Software to model and analyse protein–ligand interactions

I am currently trying to model a certain protein (Golgi Mannosidase II) and compare the induced fit of the inhibitor swainsonine. I would like to be able to analyse the distances between bonding ...
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Is the chitin in an insect's exoskeleton cross-linked?

This answer to the question How to clean and preserve a cicada's molted exoskeleton (exuvia)? states: The exuvia is made of cross-liked chitin, and will not decay. You don't need any special ...
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Can denatured GFP show fluorescence?

GFP ( green fluorescent protein) can show green fluorescence. And its fluorescence is due to the tri peptide chromophore which is given in below I was wondering, can we observe fluorescence, if we ...
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Why does it matter to predict protein structure?

And how do you predict it ? What is your input data (sequence of amino acids, temperature, pH, ...) ? Is there a "standardized" input that scientists agree on ? Moreover, I've read that knowing the ...
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Protein structure prediction using PSSM? Or not?

I have been studying protein structure prediction algorithms. A lot of recent work uses something called the PSSM, the position-specific scoring matrix. I think that what a PSSM does is to build a 2-...
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What is the relationship between Ca- and Na-ions and mucins and why?

According to Wikipedia https://en.wikipedia.org/wiki/Mucin#Secretion mucins (Proteins that form mucus) obtain viscoelastic properties by the Exchange of sodium and Calcium Ions. What is Happening ...
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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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Emergence of novel protein interactions by mutation of amino acids

Are there any examples of proteins that, without coming from a recent duplication event, underwent a mutation(s) that caused it to have a novel interaction with a new ligand, substrate, other protein ...
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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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Backbone hydrogen bonds between adjacent amino acids in a protein?

Is it possible for two adjacent amino acids in a peptide to form hydrogen bonds between the backbone NH and CO? Are there any examples of such situations in proteins and how common are they? If ...
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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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Difference between prions and amyloid proteins?

Amyloid and prions are misfolded proteins, but what, if any, is the difference between them? Is amyloid a type of prion with a fibrillar structure?
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Obtaining protein atomic co-ordinates from dihedral angles

https://en.wikipedia.org/wiki/Dihedral_angle#/media/File:Protein_backbone_PhiPsiOmega_drawing.svg I've been reading on Protein Amino Acid Sequences and their 3D structure. It seems that the 3D ...
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What are the different types of helices in protein secondary structures and how do they differ?

What are the different types of helices in protein secondary structures and how are they differentiated? In the DSSP docs, types of helices mentioned are: Alpha-Helix, Helix-3, and Helix-5. In the ...
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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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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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When does protein folding begin?

I had always assumed that protein folding is an independent activity that occurs after translation is complete. However, recently, I learned that intermolecular forces begin shaping the peptide bonds ...
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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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What is the length and number of the parts of a conformational epitope?

I am interested in the question whether exposure to protein A might create antibodies that also bind to protein B. I am wondering whether, if the antigen of protein A is a conformational epitope, it ...
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How similar do proteins have to be to trigger the same immune response?

The title really says it all. How precise or vague is the immunity we get from vaccination or from having encountered a germ before? Is it about protein parts that are recognised if they are ...
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Homology modelling of protein with two identical subunits in its quaternary structure

I am using homology modelling to assign the 3D structure of Torpedo acetylcholine receptor (Unwin 2004, 2bg9 in RCSB) to human muscle nAChR. The problem is, both Torpedo receptor, and human receptor ...
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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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Why are the first and last amino acids of an alpha helix not hydrogen bonded?

I am studying protein structures and in alpha helix I found out that one amino acid residue's carbonyl oxygen is linked to the nitrogen of amino group of 4 residues ahead.. However the first and last ...
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List of proteins by number of amino acids / chain length

Is there any protein database online where I could obtain a list of proteins ordered by the length of their chains / number of amino acids, starting from the shortest, as well as to see their amino ...
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What proportion of proteins require chaperone-assisted folding?

I am new to the field of biochemistry (I am a chemist, actually). I have long known the process of folding as the process that leads to the minimum energy conformation of a protein. Now, I am ...
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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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What is protein secondary structure?

Could someone please clarify what is protein secondary structure: https://en.wikipedia.org/wiki/Protein_secondary_structure I believe I understand the primary structure, I am not sure what's the ...
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In centrioles, what type of fibers connect the triplet microtubules?

In a centriole, each "arm" (a triplet microtubule) is attached from its A-tubule to the C-tubule of the adjacent arm. What is the type of fiber that connects each arm ("connecting fibrils" in the ...
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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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Program (on Mac) to show 3D protein structures?

I have an assignment for 6th grade biology. I have to look at a 3D structure of a protein and manipulate it so it only shows the AA I’m interested in currently. what I already did I already looked up ...
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How does chemical shift assignment from NMR spectroscopy is translated to three dimensional structure of protein?

I am currently involved in determination of protein structure using NMR spectroscopy. As part of structure determination I have finished the chemical shift assignment. The chemical shift information ...
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Is the ACh receptor more permeable to sodium ions?

The AChR is permeable to sodium and potassium ions only and has a reversal potential of 0mV. However the Nernst potentials for sodium and potassium ions is ~ +60mV and -88mV respectively. Taking a ...
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mRNA and Protein relation [closed]

A and B are two different proteins: 1- can they have same mrna 2- is it possible that the gene types which encoding the synthase are same ? my answer is yes to both . because after protein synthased ...
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Is protein folding symmetric with respect to reversing the sequence order?

Suppose that I have two proteins, protein A and protein B, and suppose that the sequence of amino acids of protein B is exactly the reverse of the sequence of protein A. For example (these are made-...
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Cold adaptation at sequence & structural level

When looking for cold adaptation in unicellular eukaryotes there is not much work found. Most of the time general sequence comparative sequence analysis between marine mesophile & psychrophile ...
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Do all transmembrane proteins contain channels or tunnels?

In my book, there is written something like this. The integral proteins pass into the lipid bilayer to different depths and establish hydrophobic bonds with lipid molecules. Some of the integral ...
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What is C-terminal tryptic peptide?

A biologist wrote to me: ... C- or N-terminus,... For example, a C-terminal tryptic peptide like AGWRGSDSHSR, would be... I don't have any idea what that is. When ...
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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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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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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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Can pymol show cartoon (secondary structure) for a pdb of multiple frames?

I am using pymol to visualise the secondary structure of protein using its cartoon representation. The ...
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Can VMD change its cartoon representation for secondary structure according to trajectories?

I am using VMD to visualise the secondary structure of protein. The trajectories are from my Gromacs simulation. Firstly I use ...
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Do non-functional (‘junk’) protein sequences exist?

For DNA one can distinguish between protein-coding DNA sequences, i.e. nucleic acid sequences inside DNA (vs. non-coding sequences) DNA sequences that do not code for proteins but are transcribed ...