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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16
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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 ...
13
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2answers
439 views

Protein tertiary Structure formation

As we know that coils and loops are evolutionary variable regions where mutations,deletions, and insertions frequently occur. So does it mean that they don't have much role in the structure of protein?...
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1answer
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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?
9
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1answer
826 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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2answers
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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 ...
8
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1answer
617 views

What is peptide mapping?

After searching online for peptide mapping to my understanding it can be treated as the fingerprint of the protein. It is obtained at the end of several chemical processes and it helps to understand ...
6
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2answers
1k 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 bit of surface ...
6
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1answer
149 views

Has the protein composition (with identification) in honey and other honeybee byproducts been studied?

I am interested in studying honey and other honeybee byproducts. I have not been able to find sequence or structure records for any of the contents of honey. In particular, I want to study the ...
6
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3answers
2k views

Function of the alpha subunit in mitochondrial ATP-synthase?

Within the catalytic core of mitochondrial ATP-synthase there are two different types of subunits; $\alpha$ and $\beta$. From what I have read, the catalytic sites occur only in the $\beta$ subunit so ...
5
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4answers
269 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 ...
5
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1answer
633 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 ...
5
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1answer
122 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 ...
5
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2answers
336 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 ...
5
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1answer
1k views

Are there any primary structure sequences that strongly suggest b-sheet or alpha helix?

Is there a particular sequence of amino acids that we know will take on a beta-sheet or an alpha helix or is it essentially random?
5
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1answer
100 views

Resolution of X-ray crystallography

A structure determined by X-ray crystallography has a resolution of 1.5 Å. When I look at the coordinates, I find every backbone C-N distance is 1.32 Å.i.e. Accurately predicted. If resolution is not ...
5
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2answers
502 views

How to obtain a list of proteins sorted by the ~1400 unique protein folds?

The databases CATH and SCOP both have around 1400 unique protein folds recorded from analysis of the PDB. However, I do not see any method to access this particular data. A list of each of the 1400 ...
5
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1answer
354 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? ...
5
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1answer
136 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 ...
5
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1answer
951 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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5answers
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Are There Rules for How Proteins Are Formed?

Proteins are formed by stringing together different amino acids. Different amino acids have different properties (such as being attracted to or repelled by water, positively or negatively charged, ...
4
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2answers
696 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 ...
4
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2answers
205 views

Protein structure prediction from amino acids sequence

Information given at this resource https://predictioncenter.org/ is close to impossible to digest (as with everything in this field), so if anyone could tell me what is the accuracy we can predict ...
4
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1answer
5k views

What is an isolated beta bridge?

DSSP gives the letter B for a "residue in isolated β-bridge (single pair β-sheet hydrogen bond formation)", according to Wikipedias page for secondary structure (and various other proper sources). Can ...
4
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1answer
1k views

Why is ab initio protein secondary structure prediction less reliable than alternatives?

To predict secondary structure of proteins three types of Algorithms are used Ab initio, homology based and neural networks. Among these neural networks prove to be more accurate and give good results ...
4
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1answer
113 views

Proteins in water vs proteins in crystal

I am not very familiar with the experimental procedure of x-ray crystallography except that it involves the very delicate matter of producing crystal that contain proteins and then diffracting rays ...
4
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2answers
132 views

Why do large, aromatic residues prefer beta-pleated sheets?

I read in many journals that amino acids with branched and large aromatic R-groups have higher beta pleated sheet propensities. However, none really go in depth into the significance or reasoning ...
4
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1answer
78 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 ...
4
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2answers
576 views

Which server to use for volume and accessible surface area calculation of proteins

I want to find the accessible surface area and the volume of a protein, giving PDB file as the input for the protein. I used two servers, 3vee and Vadar. For the PDB id, 1LTM, the websites are giving ...
3
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2answers
406 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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2answers
126 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 ...
3
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1answer
148 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 ...
3
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3answers
123 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 ...
3
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1answer
413 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 ...
3
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1answer
3k views

Generate full dimer from monomer with C2 symmetry?

I downloaded a PDB file of a dimer, but it only contains the monomer, and it says that the dimer can be obtained from C2 symmetry. For an example see here: http://www.rcsb.org/pdb/explore/explore.do?...
3
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1answer
117 views

NMR spectroscopy detection methods for proteins

I've stumbled upon a table comparing the sensitivities of different detection methods in NMR spectroscopy: "Direct", "DEPT" and "Inverse", where "Inverse" seems to be the most sensitive. What exactly ...
3
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1answer
88 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 ...
3
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1answer
203 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 ...
3
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1answer
8k views

What is a “monomeric polypeptide”?

In the sentence: "Bacteriophage (viral) polymerases are typically monomeric polypeptides". I know that polypeptides are chains of amino acids monomers. But what is a "monomeric polypeptide" and what ...
3
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1answer
57 views

Interaction of charged triphosphates with the ATP binding region in proteins

DNA-histone interactions involve positively charged amino acid side chains groups neutralizing the negatively charged phosphate of the sugar-phosphate backbone. Is the same true for ATP binding sites ...
3
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1answer
62 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 ...
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 ...
3
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1answer
861 views

The meaning of the $\alpha$ helix and $\beta$ sheets in proteins [duplicate]

I asked this question to my Biology teacher and he, in collaboration with a Chemistry teacher, couldn't find the answer. My question is the following: "What does the $\alpha$ and $\beta$ represent in ...
3
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2answers
169 views

Protein Structure Parameters

I'm wondering about the minimal set of parameters necessary to define a protein's structure. My understanding is that the backbone geometry is defined by the phi and psi angles (torsion angles), and ...
3
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1answer
45 views

Using BLAST for molecular replacement in structural biology

This is my first time trying to do molecular replacement to solve a protein structure. I am using the NCBI blastp program to find suitable search models. When choosing a search model, I understand ...
3
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1answer
125 views

How do I retrieve electronic annotation from Uniprot and GO records that relates to molecular function?

I'm interested in the endonuclease activity of the G3BP1 gene, specifically the uniprot record Q13283. An external link guides me to UniprotKB-KW electronic annotation. How can I retrieve valuable ...
3
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1answer
133 views

Prediction of transmembrane beta barrels?

I studied that prediction of transmembrane alpha helices is more easy and accurate and also good algorithms are available for their prediction. But when we move towards prediction of transmembrane ...
3
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0answers
36 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, ...
3
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0answers
130 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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0answers
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?
3
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0answers
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 ...