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March 30, 20260 citationsOpen Access

The Funneled Void: Protein Folding as Péclet-Number Minimization and the Thermodynamic Resolution of the Levinthal Paradox

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AEAnthony W. Eckert

Key Points

  • The study aims to formalize the process of protein folding as a Péclet-number minimization and resolve the Levinthal paradox.
  • Formulated the protein folding as a Péclet-number minimization process
  • Utilized AlphaFold2's Evoformer to compute co-evolutionary weights
  • Conducted empirical tests across 35 proteins from prion, amyloid, and IDP classes
  • Achieved correlation ρ(Pe_agg, aggregation_propensity) > 0.85 across all tested proteins
  • Class 1 demonstrated perfect correlation ρ=1.000
  • Class 2 showed strong correlation ρ=0.909
  • Class 3 resulted in ρ=0.936
  • Pooled analysis yielded a correlation of ρ=0.972

Abstract

Formalizes protein folding as a Péclet-number minimization process. The Levinthal paradox (3¹00 conformational states) is resolved by showing the funneled energy landscape is the physical implementation of the prohibition-ritual pair: the funnel IS the constraint specification. AlphaFold2's Evoformer computes pair-residue coevolutionary weights equivalent to BG (native contact probability matrix), making it an implicit Pe minimizer. Empirical test: ρ (Peₐgg, aggregationₚropensity) > 0. 85 across 35 proteins in 3 classes (prion variants, amyloid-forming sequences, IDPs). Results: Class 1 ρ=1. 000, Class 2 ρ=0. 909, Class 3 ρ=0. 936, Pooled ρ=0. 972. Falsification test: rat IAPP (non-amyloidogenic) has Peₐgg < 0, human IAPP Peₐgg = 16. 0.

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Cite This Study

Anthony W. Eckert (2026) studied this question.

synapsesocial.com/papers/69c9c5c5f8fdd13afe0bdb7bhttps://doi.org/10.5281/zenodo.19299727
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