Dear all, I have taken protein sequences of 5 different species and calculated the no. of individual amino acid and also calculated no. of individual atoms in that particular species. My aim is to study proteins at its atomic level. But to my surprise, all the species which is having different protein sequences show almost same C,H,N,S,O at its atomic level.
Any suggestions to proceed further.
1 answer
It is a fundamental insight of biochemistry that proteins and nucleic acid are large polymers which are build from a small set of monomers. The monomers are amino acids or nucleotides. The chemical structure of the monomers (number of atoms AND their connectivity/molecular geometry) are identical in all domains of life.
Please make yourself familiar with the basics of biochemistry:
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It could strictly be by chance (if the numbers are perfectly identical or close). You have not said anything about how many sequences/whole sequences/domains that went into this analysis. Since replacement AA's in homologous proteins are going to have constraints over structure/properties, this result may not be surprising.
I have selected the whole sequence which i found in ftp ncbi.
Are the sequences for a specific protein?
Yes. for eg. Human has 98130 protein sequences in ftp ncbi
I have not really understood your idea of
that you have referred to in many of your posts here.
I am skeptical that you are getting a similar number for atoms for proteins from 5 different species (not sure which five (besides human) and if they have protein complements that are in the same ball park. e.g. number of proteins, size/number of amino acids and their distribution etc).
What do you ultimately hope to propose/predict/achieve with this line of thought/work?
Sir, Proteins are nothing but amino acid, amino acid are made up of atoms. Instead of studying protein at amino acid level, i am studying one step down to atomic level. I made a program which will calculate the total no. of amino acid and also atoms. The four other species are plasmodium falciparum, schizosaccharomyces pombe, saccharomyces cerevisiae and rattus norvegicus and also danio rerio.