Note No. 21 from the series "Cosmobiology of Mirny". Memory in the network: position, not mass. Proteomic positions of enzyme-loop carriers according to PaxDb 5.0

Note No. 20 [5] showed that the SABIO-RK database stores the constants of slow (hysteretic) memory of enzymes under neutral names, without containing a term for the phenomenon itself. This work adds a second dimension: the proteomic position of the loop carriers. Using integrated PaxDb 5.0 datasets (human liver, coverage 81%, n=15,891; rat liver, coverage 36%, n=7,972), it is shown that the loop carriers — DHFR (6.28 ppm, rank 4587) and TYMS (0.78 ppm, rank 8065) — lie in the far tail of the distribution, occupying fractions of a percent of the proteome mass, while their neighbors in the folate cycle, SHMT1 (1368 ppm) and MTHFD1 (1049 ppm), are in the top one percent. The cycle runs at full power, while its slow link is vanishingly rare: a rare carrier with long memory sets the temporal dynamics of the network. Memory in the network is held not by mass but by position.

Authors

Publication Details

Journal
Zenodo (CERN European Organization for Nuclear Research)
Published
2026-11-09
DOI
https://doi.org/10.5281/zenodo.24083271
Primary Topic
Bioinformatics and Genomic Networks
Type
preprint
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preprint

Note No. 21 from the series "Cosmobiology of Mirny". Memory in the network: position, not mass. Proteomic positions of enzyme-loop carriers according to PaxDb 5.0

Borodin Oleg BORODIN O.A.
Zenodo (CERN European Organization for Nuclear Research)
Bioinformatics and Genomic Networks
preprint

Note No. 21 from the series "Cosmobiology of Mirny". Memory in the network: position, not mass. Proteomic positions of enzyme-loop carriers according to PaxDb 5.0

Borodin Oleg BORODIN O.A.
preprint en

Abstract

Note No. 20 [5] showed that the SABIO-RK database stores the constants of slow (hysteretic) memory of enzymes under neutral names, without containing a term for the phenomenon itself. This work adds a second dimension: the proteomic position of the loop carriers. Using integrated PaxDb 5.0 datasets (human liver, coverage 81%, n=15,891; rat liver, coverage 36%, n=7,972), it is shown that the loop carriers — DHFR (6.28 ppm, rank 4587) and TYMS (0.78 ppm, rank 8065) — lie in the far tail of the distribution, occupying fractions of a percent of the proteome mass, while their neighbors in the folate cycle, SHMT1 (1368 ppm) and MTHFD1 (1049 ppm), are in the top one percent. The cycle runs at full power, while its slow link is vanishingly rare: a rare carrier with long memory sets the temporal dynamics of the network. Memory in the network is held not by mass but by position.

Zenodo (CERN European Organization for Nuclear Research)
Bioinformatics and Genomic Networks
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