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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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?
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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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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?
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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 ...
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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 ...
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3answers
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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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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 ...
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2answers
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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 ...
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1answer
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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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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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Simple protein graphics software for stick models

Anybody know of a good free molecular graphics system that allows PDB file input? I prefer that it does not use Java. I also prefer that it is online, although I would consider recommended software ...
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1answer
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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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Does protein structure depend on phylogeny? [closed]

Proteins have two basic secondary structure forms - beta strand and alpha helix. Do these depend on the organism or do the two forms exist for every protein? For tertiary and quaternary structure: do ...