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

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19 views

Why are the hydrogen bonds between the backbones not straight down in a parallel B-sheet?

I am not sure why the hydrogen bond patterns in a parallel beta sheet are not straight down and why they are offset by about ~0.5 Angstroms. Is there any significance to this difference?
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1answer
40 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
12 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
55 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 ...
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17 views

Proline flexibility

I was reading about the role of proline-rich domains in proteins. There seem to be two schools of thought. One is that proline has 2 degrees of freedom instead of 4, making it more rigid. This makes ...
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1answer
76 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
61 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
19 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
57 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
26 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
52 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
94 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
12 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
votes
1answer
28 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
66 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
vote
1answer
46 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
13 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 ...
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0answers
16 views

Looking for references on protein activity prediction

My colleagues have measured Kcat for 29 mutants of a certain enzyme and they've studied the possible impact of those mutations on the protein's physicochemical properties through computational models. ...
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0answers
15 views

Which among the seven secretion systems in gram-negative bacteria are pathogenic?

Among the 7 secretion systems of a gram-negative bacteria, do all the systems secrete pathogenic proteins that harm the host into which the protein is secreted? Or is it the type 3, type 4 and type 6 ...
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2answers
325 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
60 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
33 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. ...
2
votes
3answers
89 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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0answers
48 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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1answer
101 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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votes
2answers
201 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 ...
3
votes
1answer
77 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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0answers
13 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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1answer
325 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
100 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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votes
2answers
902 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 ...
2
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0answers
30 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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0answers
203 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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votes
2answers
1k 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 ...
5
votes
1answer
199 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
1k 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 ...
4
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0answers
41 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 ...
6
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2answers
756 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
388 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 ...
5
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1answer
68 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 ...
3
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1answer
34 views

What would be the difference if I use the Web server instead of dedicated server for protein modeling and docking?

We know that software tools like I-tasser etc have a web server and a standalone option too. Is there any difference to protein C-scores or efficiency or accuracy if you do it on standalone instead of ...
2
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2answers
62 views

Predict if a given protein is recognized by antibodies

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 is recognized by all known antibodies of human and cause an immune ...
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0answers
28 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?
2
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2answers
57 views

Bonding in the primary structure of a protein [closed]

My textbook says: The amino group of an amino acid reacts with the carbonyl group of another amino acid at the end of a polypeptide chain. This condensation reaction forms a peptide bond. ... The ...
4
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1answer
465 views

Why do membrane proteins at lower temperatures contain more alpha helices than beta sheets?

Why do organisms found at low temperatures have membrane proteins with a higher percentage of alpha helices compare to beta sheets?
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1answer
460 views

How can I calculate alpha helix content from molar ellipticity?

How can I calculate the alpha helix content (i.e. percent) in a protein from a given molar ellipticity of 222 nm, without using any software. I have tried the Greenfield-Fasman equation, but the ...
11
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1answer
2k views

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?
1
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1answer
95 views

What difference do trans and cis configurations of amide groups bring to the polypeptide chain?

Hi I was just wondering whether there would be any difference to the structure of the polypeptide chain, or any changes to a proteins characteristics, if it has more amide groups with a cis or trans ...
4
votes
1answer
66 views

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 ...
2
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0answers
63 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 ...