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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Can the knowledge about torsion angles alone be sufficient for specifying secondary structures of protein?
I have read that Ramachandran plots are used to identify secondary structures of proteins. Also, alpha helices and beta strands cluster around specific regions of the plot which gives us the ...
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1answer
39 views
Glucose 6-phosphate dehydrogenase: reaction mechanism
I have searched the internet for the reaction mechanism of G6PD but couldn't find it, so I am asking whether anyone here knows its mechanism and whether they could recommend some sources that give ...
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1answer
45 views
Why does the structure for cellular retinol binding protein show interactions with cadmium ions?
A structure of cellular retinol binding protein (1CRB) contains two cadmium ions as ligands. Is Cd2+ a ligand of CRBP and, if so, is that interaction necessary for protein function or is the protein a ...
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0answers
29 views
Is it scientifically feasible to compare two samples of different sizes, while values in each sample are average numbers?
I want to compare result from my protein docking experiments to various protein structures of the same protein.
I have two samples and in Sample 1, I have ...
2
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1answer
51 views
Formation of disulfide bonds in protein expressed after transduction
Say I transduce a nucleic acid sequence using a viral vector that encodes a protein having at least one disulfide linkage. For simplicity, let’s assume that there are only two cysteines in the protein ...
2
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0answers
28 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, ...
2
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2answers
116 views
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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0answers
19 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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2answers
54 views
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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1answer
33 views
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 ...
3
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1answer
53 views
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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3answers
116 views
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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37 views
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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0answers
10 views
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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0answers
39 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 ...
3
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1answer
73 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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0answers
17 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 ...
5
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1answer
81 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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0answers
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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1answer
417 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
41 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 ...
1
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1answer
168 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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0answers
47 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 ...
3
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0answers
96 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 ...
3
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2answers
101 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 ...
2
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1answer
72 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
67 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 ...
0
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1answer
36 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 ...
0
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1answer
62 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 ...
0
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1answer
68 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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2answers
124 views
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 ...
5
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2answers
166 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 ...
2
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1answer
86 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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0answers
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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2answers
107 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
196 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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0answers
483 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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4answers
209 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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1answer
19 views
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 ...
3
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1answer
130 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 ...
1
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1answer
78 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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0answers
23 views
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 ...
2
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1answer
172 views
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 ...
3
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2answers
385 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 ...
3
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0answers
70 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
82 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.
...
3
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3answers
117 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
362 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 ...
