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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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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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1answer
67 views

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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1answer
58 views

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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1answer
149 views

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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1answer
33 views

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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1answer
49 views

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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2answers
82 views

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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1answer
62 views

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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1answer
65 views

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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1answer
27 views

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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1answer
59 views

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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1answer
43 views

is a-keratin a fully functional protein?

is a-keratin before it coils with another polypeptide, makes chains, and build intermediate fillaments a fully functioal protein? I mean, is the single monomer of a-keratin a protein or it has to ...
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2answers
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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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2answers
117 views

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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1answer
79 views

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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2answers
90 views

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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1answer
75 views

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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352 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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164 views

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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1answer
111 views

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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2answers
75 views

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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1answer
67 views

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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2answers
363 views

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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69 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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0answers
76 views

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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3answers
109 views

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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1answer
254 views

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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2answers
354 views

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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1answer
92 views

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 ...
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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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1answer
364 views

Are proteins a different shape in space?

Is the shape of a protein affected by gravity? In space, will the shape of a protein be different to what it is on Earth? If the structure and shape is in fact affected, then would it be enough of a ...
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1answer
178 views

Building a PDB file from amino acid sequence of non-folded structure

I am interested in experimenting with folding simulations and algorithms for arbitrary sequences. I'm wondering if there is an easy way to convert an amino acid sequence into a PDB file for further ...
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2answers
1k views

Where on an amino acid does it attach to the protein backbone? [closed]

I've been trying to find conclusive information regarding where within an amino acid (AA) it attaches to the protein backbone (PBB). I know that, coming off of the PBB, the AA side chain is connected ...
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31 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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511 views

Given an amino acid sequence, how to determine the structure (helix, beta sheet etc)? [duplicate]

Assume there's a short sequence of an amino acids. MAKMGSKKKAGHGGKEKLENMGE I am using molecular structuring softwares to look at secondary structure. But it's ...
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2answers
2k views

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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1answer
318 views

How to identify a coiled coil from the amino acid sequence?

I was wondering, when we have an amino acid sequence, is it enough to check whether the positions a-d correspond to hydrophobic amino acids in order to say whether it can form a coiled coil structure? ...
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3answers
2k views

Is prion a term used to describe the normal form of the protein as well as the disease causing form?

I've been reading my textbook and it refers to prions as a normal protein with a helpful function but it can turn into a disease causing form. However, I look in my other textbook and it refers to the ...
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57 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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2answers
972 views

Denaturation of protein

Exposure of native protein to heat leads to partial denaturation of the protein due to breaking of- a. S-S bonds b. H-bonds c. Hydrophobic interactions d. Peptide bonds After a ...
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2answers
533 views

Should there be separate Ramachandran plots for an amino acid in different contexts?

I understand the nomenclature of the phi and the psi angles of the alpha-Carbon atoms in protein stucture, but I am confused by the Ramachandran plot. Each alpha-Carbon atom (magenta) makes two ...
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95 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 ...