Protein structure drawing method

In summary, this method of drawing proteins, RNA and genes is called a "secondary structure diagram".
  • #1
John37309
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Protein structure drawing method

I want to know the proper name given to this particular method of drawing proteins, RNA and Genes. I have two examples;

If you look at the Wikipedia page for tRNA, they show the Tertiary structure of tRNA like this;

220px-TRNA-Phe_yeast_1ehz.png


http://en.wikipedia.org/wiki/Transfer_RNA

But they also show this particular type of secondary tRNA structure;

220px-TRNA-Phe_yeast_en.svg.png


I personally describe this method as flattening out the structure so we can see the exact amino acid sequence more clearly. Wikipedia describes this structure for tRNA as the "Secondary cloverleaf structure". But they only say that because tRNA looks like a three leaf clover when you flatten it out like that. Other proteins and stuff take on very different patterns when you flatten them out!

The same flattening method is used here for the Gene HAR1F;
http://en.wikipedia.org/wiki/HAR1F

I want to know what is the proper name given to this flattening method of drawing proteins, amino acids and genes?

John.
 
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  • #2
I don't know if there's a specific name, but it'd call it a secondary structure diagram. These types of images are meant to represent the secondary structure (e.g. the base pairing for RNAs or the alpha-helices/beta-sheets for proteins), but do not accurately represent the tertiary structure (the overall 3D folding) of the molecules.
 
  • #3
Thanks Ygggdrasil,
So your not aware of any specific name given to this particular drawing method other than just "secondary structure" or maybe "flattened secondary structure" or maybe "2D secondary structure".

OK, Thank you,
John.
 
  • #4
For nucleic acids (especially RNA), I've heard them referred to as stem-loop diagrams.

For proteins, it's usually just "secondary structure diagram" in my experience.
 
  • #5
Thanks Mike,
Yes, that seems to be the case here. People just seem to be referring to these drawings as secondary structure.

These drawings are beautiful, they have an hypnotic effect on my mind. Some of them become very large and very complex. But the more complex they get, the more beautiful they look. The look like street maps for living things! stunning! Shockingly beautiful! It reminds me of the London underground maps :)

16S rRNA Secondary Structure

rrna.gif


John.
 
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1. What is the purpose of protein structure drawing?

The purpose of protein structure drawing is to visually represent the three-dimensional structure of a protein in a two-dimensional format. This allows scientists to better understand the shape, function, and interactions of proteins, which are essential molecules for many biological processes.

2. What are the different methods for drawing protein structures?

There are several methods for drawing protein structures, including hand-drawing, computer-based modeling, and using specialized software such as PyMOL or UCSF Chimera. Each method has its own advantages and limitations, and the choice of method often depends on the specific research goals and available resources.

3. What are the main components of a protein structure drawing?

A protein structure drawing typically includes the backbone of the protein, which consists of a chain of amino acids connected by peptide bonds. It also includes the side chains, or R-groups, which determine the unique properties and functions of each amino acid. Additionally, the drawing may show any secondary or tertiary structures, such as alpha helices or beta sheets, and any bound ligands or cofactors.

4. How accurate and reliable are protein structure drawings?

The accuracy and reliability of protein structure drawings depend on the method used to create them. Hand-drawn structures may be less accurate compared to computer-generated ones, but they can still provide valuable insights. Computer-based models and software-generated structures can be very accurate, but their reliability is dependent on the quality of the data and algorithms used.

5. Can protein structure drawings be used to predict protein function?

While protein structure drawings can provide important information about a protein's structure, they cannot definitively predict its function. Protein function is determined by many factors, including its structure, sequence, and environment. However, protein structure drawings can provide clues and hypotheses about a protein's potential function, and can be further investigated through experimental methods.

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