Eli5 : protein folding problem


Eli5 : protein folding problem

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Since your question is so broad, here is the most correct answer; Hydrogen Bonding (attaction of hydrogen to electronegative portions of amino acids), Disulfide bridges (Some amino acids have a sulfur, these form bonds with other sulfurs on other amino acids), and Steric interaction (With the last 2, folds and bends exist, but some amino acids bond at angles meaning they naturally form an angle when they bond, and sometimes the superstructure prevents certain kinds of bonds)

Proteins are long (sometimes *really* long) chains of smaller building blocks. The building blocks are called amino acids. Because of all the potentially complicated chemistry between the building blocks (see /u/BrownBoi377 ‘s comment for details), the chain of amino acids folds up into a 3D shape depending on what amino acids you have in what order. The shape of the protein largely governs what it does, hence is really important.

The protein folding *problem* is calculating what shape the protein will end up being just based on knowing it’s “recipe” (how many amino acids, which ones, and in what order).

There’s 4 structures to how a protein folds itself, but I have to start with basic chemistry before I can get into that. Proteins are made up of amino acids, which all have a base structure that’s attached to what’s known as an R group, which is a placeholder for different chemical structures. This R group determines how the amino acid will react with its surroundings, and can be polar, nonpolar, or charged. Polar R groups have an affinity for water, while nonpolar R groups want to stay away from water. Charged R groups can donate or receive protons to other biological molecules to do other things.

Now to the 4 structures. Your DNA codes for proteins, and to start with, for the primary structure, we find just a list of amino acids in order. Think of a long, thin sheet of paper, and that’s the primary structure. This primary structure will quickly assort itself into a secondary structures. Those R groups start interacting with each other, and chemical interactions create what’s known as alpha-helices and beta-sheets. Once the protein contorts itself into secondary structure, tertiary structure can begin, which is when the protein assorts itself into its final structure. Once proteins are in their tertiary structure, they combine with other tertiary proteins to form quaternary structures, which are the full proteins. Going back to R groups for a moment, polar R groups tend to be on the outside of proteins, and nonpolar R groups are on the inside. Charged R groups can be anywhere on proteins. The shape and structure of a protein can determine how it reacts with different proteins around it, and problems in this protein sequence can have devastating effects.