Krasnoyarsk Scientific Center
Discussion
Started 8th Aug, 2021
Amino Acids sequence to form Protein
I'm coming from pure Computer Science background, my research is to utilize the amino acids to encode Network transactions. I'm thinking of using Amino Acids for the encoding then to use any of the pattern matching.
My main question here is whether if there is any rules between amino acids order when formulating protein sequence? Meaning for example can glycine (G) follow any amino acids like leucine (L)?
Also if you can provide Amino acids sequences for actual proteins, that would help.
Most recent answer
Formally, there are no constraints in combinations of AA in a protein sequence, at all. However, some combinations are rather frequent while others are very rare. This is a real way to study the point you are asking about. The problem is what frequency of a specific combination of two or several AAs one should consider to be a reference. A possible answer to this question comes from the method of invariant manifolds.
All replies (7)
Any amino acid can follow any other amino acid.
Protein sequences can be found in various databases, including here:
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Chungnam National University
Dear Thaer Hani,
There are just 20 amino acids that can be found in human proteins. The amino acid can be of any order directed by the genetic code. Sample proteins can be downloaded from the NCBI database using the FASTA format.
Best wishes,
Amal.
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MilliporeSigma
Hi Thaer Hani!
I do agree with others that amino acids can be in any sequence to make a protein. For structural integrity some amino acids might be favored than others. For example, Ala, Glu, Leu, and Met are mostly found in helices whereas, Gly, Tyr, Ser, and Pro are less likely to be there. But in general any amino acid sequence can be present in a protein.
Best of luck!
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Private Person
Just to add to the comments given by others, look up the keywords Ramachandran plot, helix and sheet propensity, hydropathy. Those are computer science concepts to analyse protein structures.
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Krasnoyarsk Scientific Center
A tentative answer STRONGLY depends on the meaning of the word "rule". So, what did you mean?
De Montfort University
Hi @michael,
My "Rule" word supposed to refer to "constraints" like constraint on consecutive Amino acids, or on repetitive occurrences of same amino acids, etc.
Krasnoyarsk Scientific Center
Formally, there are no constraints in combinations of AA in a protein sequence, at all. However, some combinations are rather frequent while others are very rare. This is a real way to study the point you are asking about. The problem is what frequency of a specific combination of two or several AAs one should consider to be a reference. A possible answer to this question comes from the method of invariant manifolds.
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