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YChromatic
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Is it true that an amino acid tends to substitute another if they share similar properties ?
Thanks
Thanks
Andy Resnick said:I'd be interested in hearing from an expert on this- my understanding is that a mutation that exchanges (say) a hydrophobic group for another (like leucine for valine) doesn't change the protein function much. Switching a lysine for cysteine *does* impair function considerably.
That is, my understanding is that amino acid substitutions range from benign to advserse based on the hydrophobicity- is that the only criterion? Cysteine also engages in disulfide bonds... like I said, I'd be interested in hearing from an expert.
nobahar said:As a kind of addendum. How far along generally are folding algorithms, are there any good mathematical theories to predict protein folding. I would be very suprised if you couldn't predict folding.
nobahar said:But there are some proteins that have to be folded in certain environments, or 'assissted' in folding (such as the use of chaperones). I have never understood why it is necessary.
nobahar said:Surely when you transfer the protein to another environment (presumably one in which it would not have folded correctly, hence the need for chaperones) wouldn't it's shape alter? Or is it such features as disulfide bridges that help preserve the shape? Since hydrophobic/philic interactions, and ionic interactions, are subject to change based on the environment much more than covalent bonds are.
nobahar said:But since sometimes 'assistance' is required, that means that either predicting shape is going to be based on probabilities or the protein is fairly rigid and retains it shape under some degree of environmantal pressure to change.
nobahar said:As a kind of addendum. How far along generally are folding algorithms, are there any good mathematical theories to predict protein folding. I would be very suprised if you couldn't predict folding.
But there are some proteins that have to be folded in certain environments, or 'assissted' in folding (such as the use of chaperones). I have never understood why it is necessary. Surely when you transfer the protein to another environment (presumably one in which it would not have folded correctly, hence the need for chaperones) wouldn't it's shape alter? Or is it such features as disulfide bridges that help preserve the shape? Since hydrophobic/philic interactions, and ionic interactions, are subject to change based on the environment much more than covalent bonds are. But since sometimes 'assistance' is required, that means that either predicting shape is going to be based on probabilities or the protein is fairly rigid and retains it shape under some degree of environmantal pressure to change.
An amino acid is a type of organic compound that serves as the building blocks of proteins. They contain both an amino group (-NH2) and a carboxyl group (-COOH) attached to a central carbon atom, along with a unique side chain that gives each amino acid its specific properties.
There are 20 commonly occurring amino acids that are used to build proteins in living organisms. These include essential amino acids that must be obtained from the diet and non-essential amino acids that can be produced by the body.
Essential amino acids are those that cannot be produced by the body and must be obtained through the diet. Non-essential amino acids, on the other hand, can be synthesized by the body from other amino acids and do not need to be consumed through food.
Amino acids play a crucial role in many biological processes, including protein synthesis, enzyme production, and hormone regulation. They also contribute to the structure and function of tissues, organs, and cells in the body.
Amino acids can be classified based on their side chain properties. There are four main categories: nonpolar, polar, acidic, and basic. Nonpolar amino acids have hydrophobic side chains, polar amino acids have hydrophilic side chains, acidic amino acids have a negative charge, and basic amino acids have a positive charge.