Why does it matter to predict protein structure? - Biology Stack Exchange
Protein structure predictions, need advice/help
Does Protein structural analysis have a future?
3D protein Structure Prediction
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How do you want to predict function and binding partners without knowing how your protein looks like? The sequence itself contains only limited information. Similar sequences might fold into similar structures with similar functions. These motifs can be used to transfer your knowledge from one protein to another, which might have similar e.g. binding abilities. But the motif might be nonfunctional in the second protein, because it is hidden in an inaccessible part of the protein due to its folding structure.
Interactions between proteins are weak compared to intramolecular bonds and dynamic. Different amino acid side chains have different characteristics (like polarity, hydrophobia etc.) which make specific interactions possible. Specific amino acids have to be accessible and while they might be far apart in the sequence, the folding of the protein brings them close together in its final shape.
Even small modifications like phosphorylation can alter the structural conformation significantly and e.g. change the enzymatic activity. Therefore, for analyzing protein function, finding binding partners or designing binding compounds (drug development), we need to know its three-dimensional structure. With the structure you can simulate binding affinity/dynamics. Scientists also try to resolve the protein structure in its different states to clearly see the differences.
Keep in mind that complex diseases can be caused by a single mutation, which exchanges only a single amino acid in the sequence but can have severe implications for protein function. Knowing the structure, the position of the amino acid and how the change affects the characteristics of the protein domain (e.g. charge), we can fully understand what's happening on the molecular level.
Since it is far from trivial to analyze the structure of a protein, predictions bridge the gap for functional predictions until the molecular structure of the protein has been reconstructed. But only with atomic resolution you will be able to properly identify interactions.
The question of how to do structural prediction might be beyond the scope of this answer. Pubmed lists around 400 papers each year on this topic. Depending on the amount of information you have about the protein or its family members (proteins with very similar sequences), you can use other known structures to predict an unknown structure:
https://medium.com/@HeleneOMICtools/a-guide-for-protein-structure-prediction-methods-and-software-916a2f718cfe
There are several reasons why understanding protein structure is useful; the most obvious is that drugs that interfere with a specific protein can be deliberately designed based on the protein structure.
Today, even though there is still quite a bit of fine-tuning necessary to perfect the process, structure-based drug design is an integral part of most industrial drug discovery programs [4] and is the major subject of research for many academic laboratories. ... The process of structure-based drug design is an iterative one ... Additional cycles include synthesis of the optimized lead, structure determination of the new target:lead complex, and further optimization of the lead compound. After several cycles of the drug design process, the optimized compounds usually show marked improvement in binding and, often, specificity for the target.
--The Process of Structure-Based Drug Design