integrate curations #418

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1. edkerk commented on Sep 24, 2026

   

   edkerk

   on Sep 24, 2026

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   Checked against the current develop, three changes from modifyModel.m still apply to the general model:

   1. MAR08514 (L-lactate:ferricytochrome-c oxidoreductase, GPR CYB5D1) should be deprecated. This is a yeast enzyme (CYB2, EC 1.1.2.3) with no clear human equivalent, and it moves electrons from cytosolic lactate directly to mitochondrial cytochrome c, bypassing complexes I and III.
   2. MAR03859 (D-lactate:ferricytochrome-c oxidoreductase, LDHD) should be reviewed. LDHD is mitochondrial, but D-lactate, pyruvate and H+ are placed in the cytosol.
   3. MAR05113 (alanine cytosol → mitochondria) should be reversible. It is the only mitochondrial alanine transport, so alanine made by mitochondrial GPT2 cannot leave.

   fixNADHDirectionality.m addresses a problem that is still present: with all exchanges closed, the model converts NADH to NADPH for free, in the cytosol (e.g. MAR04316 + MAR02779) and in the mitochondria (e.g. MAR03802 + MAR03804). The HMR 2.00 list does not close this on its own, and five of its reactions would be blocked entirely. This will be handled as part of #1083.
2. edkerk

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   on Sep 25, 2026
3. edkerk

   added a commit that references this issue on Sep 27, 2026

   fix: apply remaining modifyModel.m curations from #418 (#1093)

   ...

   3de9e43
4. edkerk

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   fixed in developMerged into develop, will be in the next releaseMerged into develop, will be in the next release

   and removed

   wipA pull request for this issue is openA pull request for this issue is open

   on Sep 27, 2026
5. edkerk commented on Sep 28, 2026

   

   edkerk

   on Sep 28, 2026

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   Follow-up to #1093, in #1105 (open): The LDHD reaction MAR03859 keeps cytochrome c as acceptor, now supported by direct human data (PMID:38413804). The mitochondrial L-LDH MAR04280 is kept, with corrected references and a note that mitochondrial LDH is contested (two previous references did not support it). Details and evidence are in the comment on #1093.
6. edkerk

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   and removed

   wipA pull request for this issue is openA pull request for this issue is open

   on Sep 28, 2026
7. edkerk

   added this to the 2.1.0 milestone on Sep 28, 2026
8. edkerk commented on Oct 5, 2026

   

   edkerk

   on Oct 5, 2026

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   Fixed in Human 2.1.0.
9. edkerk

   closed this as completedon Oct 5, 2026
10. edkerk

    removed

    fixed in developMerged into develop, will be in the next releaseMerged into develop, will be in the next release

    on Oct 14, 2026