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I'm learning about proteins and need to understand this concept. What makes this colourful ball of squiggles identifiable? Why is it a protein, and not any other biomolecule (like DNA for example)? What are the colours showing? What are the variations in the shape of the image?

Basically, the question is: What is this image trying to tell me about this protein?

I know this is a protein, but not why.

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    $\begingroup$ This question is unclear. Are you asking "What is this protein?" or "What about this structure makes it a protein?" $\endgroup$
    – James
    Commented Oct 13, 2016 at 5:39
  • $\begingroup$ DNA is a double helix. This, obviously, is not. $\endgroup$
    – MattDMo
    Commented Oct 13, 2016 at 13:00
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    $\begingroup$ I'm tempted also to say "experience" - for example, to me this is clearly a TIM barrel fold... $\endgroup$
    – gilleain
    Commented Oct 13, 2016 at 15:22
  • $\begingroup$ @MattDMo DNA was my added example. I think OP wanted to know something along the lines of: "How do people recognise this instantly as a protein rather than any other biomolecule?" $\endgroup$
    – James
    Commented Oct 14, 2016 at 4:11

2 Answers 2

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Shapes

This is a common way of illustrating a protein and is often called a "protein cartoon". There are other common ways of illustrating proteins.

This cartoon shows you where α helices are (spirals) and where β sheets are (arrows) which are important structural elements. The strings connecting those structural elements are flexible "loop" regions.

If you want to query this against other structures and see which protein it is, check out PhyreStorm. You'll need the PDB file, not just an image.

Colour

The colouring is also common. The N-terminus (the first amino acid) is coloured blue, and the colours go through the rainbow to red, the C-terminus (the last amino acid in the polypeptide chain).

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Even though this question has been answered (and the answer accepted), I want to add something regarding scientific language and convention.

Language in general is a means of communication which allows people to share ideas they have inside their minds. Scientific language is used for sharing scientific knowledge between people, and apart from verbal and written communication, it also uses drawings of all kinds to better illustrate complex ideas that are usually invisible to the naked eye (whether we are talking about molecules in chemistry, biological microsystems in biology, forces in physics, etc.).

The image in question represents the conventional way of portraying a protein structure, and this widely-accepted convention is characterized by certain colors and shapes, as stated in the above answer. I imagine that anyone seeing this kind of representation for the first time would not know immediately that this is a computer rendition of a protein, because no one knows what a single protein looks like before actually studying about it. But once you are told it is a representation of a protein, you accept it and "tag" it in your mind, so that next time you see it, you already know this is what a protein "should" look like.

And the more you study it, the more natural this language becomes for you.

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  • $\begingroup$ you're pointing something very important to understand to students of science - most of what we learn in classes is not actually the study of the subject, but rather the conventionally accepted languages and modes of representation used by the scientific community to talk about the subjects and convey information. $\endgroup$
    – Filipe Rocha
    Commented Mar 22, 2017 at 16:13

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