Jmol/Visualizing large molecules: Difference between revisions
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The frequency-in-protein weighted average molecular weight of an amino acid is 110<ref>Average molecular weight of an amino acid is about 138. When the average is weighted according to the occurrences of amino acids in proteins, it is about 128. Subtracting 18 for the weight of water removed when a peptide bond is formed, the average is 110. This is explained in [http://books.google.com/books?id=5Ek9J4p3NfkC&pg=PA84&lpg=PA84&dq=average+amino+acid+molecular+weight&source=bl&ots=ZxHCOzsnjL&sig=we53bW4b7kLuy53LL2BHNDd8CwU&hl=en&sa=X&ei=SD81UdatGo6B0AHy8oHwDQ&ved=0CFEQ6AEwBA#v=onepage&q=average%20amino%20acid%20molecular%20weight&f=false Lehninger Principles of Biochemistry].</ref>. Half of the atoms in protein are hydrogen, and the other half are mostly carbon (12), with some oxygen (16) and nitrogen (14). So if we take 13 as the average weight of a non-hydrogen atom, and average that with 1 for the other 50% of the atoms (hydrogen), we get (13 + 1)/2 = 7 as the approximate molecular weight of the average atom in protein. 110/7 is about 16 atoms for the average amino acid in protein. But half of those are hydrogen, missing from most PDB files. So the number of non-hydrogen atoms in the average amino acid is about 8. | The frequency-in-protein weighted average molecular weight of an amino acid is 110<ref>Average molecular weight of an amino acid is about 138. When the average is weighted according to the occurrences of amino acids in proteins, it is about 128. Subtracting 18 for the weight of water removed when a peptide bond is formed, the average is 110. This is explained in [http://books.google.com/books?id=5Ek9J4p3NfkC&pg=PA84&lpg=PA84&dq=average+amino+acid+molecular+weight&source=bl&ots=ZxHCOzsnjL&sig=we53bW4b7kLuy53LL2BHNDd8CwU&hl=en&sa=X&ei=SD81UdatGo6B0AHy8oHwDQ&ved=0CFEQ6AEwBA#v=onepage&q=average%20amino%20acid%20molecular%20weight&f=false Lehninger Principles of Biochemistry].</ref>. Half of the atoms in protein are hydrogen, and the other half are mostly carbon (12), with some oxygen (16) and nitrogen (14). So if we take 13 as the average weight of a non-hydrogen atom, and average that with 1 for the other 50% of the atoms (hydrogen), we get (13 + 1)/2 = 7 as the approximate molecular weight of the average atom in protein. 110/7 is about 16 atoms for the average amino acid in protein. But half of those are hydrogen, missing from most PDB files. So the number of non-hydrogen atoms in the average amino acid is about 8. | ||
</blockquote> | </blockquote> | ||
Since the maximum number of atoms in a single PDB file is 99,999 (see above), dividing by 8 non-hydrogen atoms per amino acid gives a maximum of about 12,500 amino acids in a PDB file (containing nothing but protein and no hydrogen atoms). In fact, longer chains can be represented if only the alpha-carbon atoms are present in the PDB file. | Since the maximum number of atoms in a single PDB file is 99,999 (see above), dividing by 8 non-hydrogen atoms per amino acid gives a '''maximum of about 12,500 amino acids in a single PDB file''' (containing nothing but protein and no hydrogen atoms). In fact, longer chains can be represented if only the alpha-carbon atoms are present in the PDB file. | ||
The PDB files containing the longest chains are listed at [[Believe It or Not!]]. | The PDB files containing the longest chains are listed at [[Believe It or Not!]]. | ||
