Separable spectral and conformational channels in proteins: A quantum-like view of dual information encoding

Abstract

The aim of this paper is to test whether biological macromolecules carry information through two distinct, separable channels. The conformational channel (C-channel), governed by three-dimensional structure and the Coulomb potential, sets binding geometry, catalysis, and stability. The spectral channel (S-channel), the one-dimensional electron-ion interaction potential (EIIP) profile and its characteristic frequency fRRM, is proposed to mediate resonant molecular recognition. In quantum information biology, recognition - a protein selecting a partner among thousands of candidates - is modelled as a decision following quantum-probabilistic laws despite macroscopic physics. This requires the channels to form a bipartite system whose state space factorises as a tensor product HC⊗HS of separable degrees of freedom. Whether the channels are coupled, independent, or complementary is the empirical prerequisite tested here. We analyse 87,389 single-nucleotide missense substitutions across 222 non-redundant, full-length proteins (51-4684 residues, <40% pairwise identity, >40 functional families), classifying each as fRRM-silent or fRRM-disruptive over seven physicochemical metrics, with within-protein clustering handled explicitly (intraclass correlation, design effect, and a protein-level cluster bootstrap). We report two principal findings. First, across the full sample fRRM is essentially uncorrelated with every conformational determinant, namely Grant ham distance, hydropathy, molecular weight, and helix and sheet propensity (all |ρ|<0.1), establishing channel independence. Second, the silent-versus-disruptive contrast reproduces: disruptive substitutions are marginally more conformationally conservative on every metric, yet each difference, though statistically significant, is negligible in magnitude (|d|<0.2), a consistent but negligible-magnitude anti-correlated tendency, not a substantive coupling. The sequence-level state is therefore separable, a product state in HC⊗HS rather than an entanglement-like or complementary one, and this holds residue by residue (aspartate is the principal spectral hotspot, tryptophan is conserved structurally yet remains spectrally neutral). We interpret these results within the quantum-like framework: the protein is a dual-channel processor whose spectral "software" (frequency-domain recognition) can be updated independently of its conformational "hardware" (spatial binding), providing the separable substrate that quantum-like molecular decision-making requires.