4.2. The side chains of
amino acids as the physical operators
In this section in the presented tables all 20
amino acids of proteins will be considered as physical operators.
Practically nobody was able to show so far work of amino acids in a role of operators
of anti-connectivity experimentally. Therefore our pictures devoted to operators of anti-connectivity,
generally, are assumptions. However they take into account both
structural features of the given group of amino acids, and their sizes.
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OPERATORS OF
ANTI-CONNECTIVITY |
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Proline is the imino acid (nitrogen atom is in five-membered cycle)
and in principle cannot form a hydrogen bond with the
Oi-4=C. Occupies
the first line of block С. |
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Alanine has a very short side chain,
which can shield the nitrogen atom,
thereby preventing the formation of a
hydrogen bond with the Oi-4=C. Located
on the second line of the block
С. |
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Serine and threonine, as observed in the structures of the studied proteins, often forming a hydrogen bond with the Oi-3=C. In this case, a 4-link
cycle does not occur. They occupy the 3rd and 4th lines in the block С. |
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Leucine and valine
- are close analogues.
Methyl groups of side chains can block the bond NiH...Oi-4=C. They are in
1st and 2nd lines of block U. |
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Phenylalanine and isoleucine are
also analogues of
leucine and valine. Their side
chains may also block the
bond NiH...Oi-4=C.
They are located in 3 and 4th lines of
block U. |
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Methionine is a
sulfur-containing amino acid and
by its action is probably similar to isoleucine. Located in the fourth line
of the block U. |
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Thus, all amino acids located in blocks C
and U, in principle are capable to recreate opened conformation of the protein pentafragments and are suitable for performance of
functions of operators of anti-connectivity. |
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The group of the amino acids, capable to carry out
function of operators of connectivity, is presented on the basis of the
analysis of protein structures studied by X-ray analysis. Their existence is the
real fact. Pay attention, how in process of increase in length of the
side chain the slope of the hydrogen
bonds changes.
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OPERATORS OF CONNECTIVITY |
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Glycine has no side chain, and readily forms a 4-link cycle - Gly1. Because of easy mobility of HNi+1-C=O-group it often forms a
hydrogen bond Ni+1H...Oi-4=C, which works as an operator of
connectivity (Gly2). Located in block G. |
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The side chains of serine and threonine form hydrogen bonds with the Oi-4=C and may contribute to formation of
a 4-link cycle. Two
serine belong to the triplets of block G,, and threonine is in block C on
the border with the block G,. |
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Cysteine is a
sulfur-containing analog of serine. His side
chain can participate in the formation of a 4- link cycle. Located
in the third line of block G. |
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The side chains of aspartic acid and
asparagine are structurally similar. They form hydrogen bonds with the Oi-4=C Located
in block A. |
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The side chains of histidine and tryptophan contain heterocycles. Despite the rare occurrence,
both of them form hydrogen bonds
with the Oi-4=C. Located,
respectively, in blocks A and G. |
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Glutamic acid and glutamine are structural analogs of
aspartic acid and asparagine. They
are also often involved
in the formation of hydrogen bonds with the с Oi-4=C. Located in block A. |
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The side chains of arginine and lysine are
close both by the structural and physical properties. Despite the large size, form hydrogen bonds
with the Oi-4=C. Located,
respectively, in blocks of G and A. |
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Tyrosine has the longest side
chain. Analysis of over 300 protein structures did not reveal 4-link cycles with the simultaneous
formation of a hydrogen bond of its side chain to the main chain. It was usually found out, that in the formation
of a hydrogen bond of the side chain with Oi-4=C hydrogen bond NiH...Oi-4=C was broken. It is located in block A. |
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Thus, practically all the amino acids can apply for a role of operators of
connectivity, are in blocks G and A. |
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The result of our analysis of the side chains
of amino acids as physical operators summarized in section 4.3.
in section 4.3.
