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Computational Compound Protonation and Reaction Balancing

in MetaCyc and EcoCyc

Tomer AltmanBioinformatics Research Group

SRI International

taltman@ai.sri.com

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What is ‘Protonation’?

A ‘protocenter’ is typically a C, N, or O in a molecule, that might have a variable number of bound H as a function of pHMolecules that differ only by the state of their various protocenters are known as ‘protoisomers’

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Problem Motivation

MetaCyc and EcoCyc compounds were curated with no consistent pH in mind

Compound sources come from various sources, each of which might have its own favorite reference pH

Often, compound structures are not specified to this level

Makes the auto-generation of Flux Balance Analysis models more complicated

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Protonation of Compounds in MetaCyc

ChemAxon’s Marvin chemoinformatics softwareMajor microspecies plug-inUses a electronegativity partial charge PDE

approach (approximation method)Validated by exhaustive comparison with

published pKa data from the liturature (IUPAC “Dissociation Constants of Organic Bases in Aqueous Solution”)

Statistically-significant differences were sent to ChemAxon, which tweaked their software to improve their algorithm (Marvin >=5.1.2)

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Protonation of Compounds in MetaCyc

Compounds that can be protonated by Marvin (no coordination bonds), and that are not specified at a particular pH state (H2SO4), are evaluated

If protonation would change the compound structure, the change is saved, otherwise discarded (avoid history changes)

Use of Condor cluster for protonating >7000 compounds

Done for each release based on compounds with modified structures

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Reaction Balancing

All small molecule reactions in a PGDB are evaluated

Reactions that cannot be balanced for various reasons (classes, R-groups, etc.) are skipped

Reactions that can be balanced are grouped by the types of elements that are out of balance

Reactions only unbalanced by hydrogen are balanced by the addition or subtraction of proton moieties

Implemented as a stoichiometric vector calculation in Pathway Tools

Done for every release

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Balanced Reaction

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Future Work

Protonation of compounds with coordination bonds

Provide code that will allow users to protonate their own PGDBs

Extend auto-balancing code to cover more complicated conditions

Recast stoichiometric vector calculations to other applications, such as FBA analysis and stoichiometric consistency checks

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Further Reference

Please see the BioCyc Guide:http://biocyc.org/biocyc-guide.shtml#protonation

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Acknowledgements

•Ron Caspi•Ingrid Keseler•Markus Krummenacker•Anamika Kothari•Jeremy Zucker•Stanford University Organic Chemistry Library

MetaCyc.org EcoCyc.org