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Preprint . 2026
License: CC BY
Data sources: Datacite
ZENODO
Preprint . 2026
License: CC BY
Data sources: Datacite
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Geometric Admission as Primitive: A Reframing of Translational Fidelity at the Ribosomal Decoding Center

Authors: Mohan, Deepak;

Geometric Admission as Primitive: A Reframing of Translational Fidelity at the Ribosomal Decoding Center

Abstract

This theoretical note proposes a reframing of the ribosomal A-site geometric invariant — the Watson–Crick geometry check performed by conserved 16S rRNA residues A1492, A1493, and G530 — from a fidelity-serving mechanism into an admission primitive: a local structural predicate whose satisfaction is necessary for progression to the next step in decoding, and whose outcome cannot be redefined by kinetic parameters acting in isolation. Under the dominant kinetic proofreading account (Hopfield, 1974; Ninio, 1975), the geometric check is one node in a rate network, subordinate to energy-driven rejection cycles. Under the conformational proofreading account (Savir and Tlusty, 2007–2013), geometry is the substrate of optimization toward maximal discrimination. This note proposes a third position: geometry sets the admissibility envelope within which kinetic proofreading operates, and translational fidelity is the residual error rate after that envelope has been applied — not a design target, but an emergent consequence. The note explicitly does not deny kinetic proofreading; it proposes a hierarchy in which geometric admissibility is more fundamental. The reframing is motivated by Demeshkina et al. (2012, Nature), who found identical 30S domain closure for both cognate and near-cognate tRNA — a result strongly congruent with a universal admission check rather than a tuned discriminator. The note generates four experimental predictions that distinguish the geometric admission account from kinetic-first interpretations, each with a stated falsifier: (1) geometry–kinetics decoupling via modified EF-Tu variants; (2) structured error distribution with overdispersion and geometry-class clustering, distinct from rate-driven error patterns; (3) correlated errors across a translation run arising from persistent conformational heterogeneity established at assembly; and (4) stop codon as geometric halt, with termination driven by a structurally distinct invariant satisfied by release factors rather than tRNA. Aminoglycoside antibiotics (streptomycin, paromomycin) are discussed as a natural experiment supporting the account: their primary action is geometric displacement of the monitoring bases, with kinetic changes as downstream consequences. This note is deposited as timestamped prior art to establish priority for the hypothesis, its operational definition, and its associated experimental predictions. It is intended as a foundation for a subsequent empirical program and for the development of a geometric invariant modulation framework for antibiotic and genetic disease therapy.

Keywords

translational fidelity, streptomycin, precision medicine, codon-anticodon recognition, ribosome heterogeneity, G530, theoretical biology, premature stop codon, A1493, A1492, error distribution, structural biology, 16S rRNA, conformational proofreading, nonsense mutation readthrough, geometric admissibility, aminoglycoside mechanism, biosolvency, tRNA selection, admission primitive, molecular recognition, Structural biology, A-site geometry, kinetic proofreading, Watson-Crick geometry, Ewing sarcoma, ribosomal decoding, single-molecule translation

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average
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