Proteins and Enzymes

ID #2332

Are there Van Der Waals interaction in both 3rd and fourth structure of protein folding? Is primary structure influenced by its side chain?


Van Der Waals interactions occur because as two atoms come near each other, they generally have a peripheral contact with each other. The contact in a Van Der Waals interaction is non-specific to the type of atoms interacting (ie it's not a specific interaction like a positive and negative charge interacting). So, both tertiary and quaternary structure have van der waals interactions. 
Primary structure is just the amino acid sequence in a linear chain. If you only have primary structure in a protein, then the protein is fully denatured. At that stage, the R groups are separated from each other or any backbone atoms, so they are interacting with the surrounding solvent only. So, you wouldn't say the primary structure is influenced by side chains, because there is no folding occurring at the primary structure stage. 

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