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Materials science forum

Biopolymer Chain Folding and Biomolecular Recognition: A Quantum Decoherence Theory Approach

Dejan I. Raković, M. Dugić, M.B. Plavšić

Published Sep 15, 2005• 10 citations
Publisher

Abstract

In this paper we describe the biopolymer chain folding problem in the framework of the so-called quantum decoherence theory. As we propose a rather qualitative scenario yet bearing generality, it seems this provides promising basis for the solution-in-principle of the (semi) classically hard kinetic problem of biopolymer chain folding from coiled to native conformation in highly selective ligand proteins/target-receptors biomolecular recognition processes, implying underlying macroscopic quantum nonlocality on the level of biological cell.

DOI
10.4028/www.scientific.net/msf.494.513

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In this paper we describe the biopolymer chain folding problem in the framework of the so-called quantum decoherence theory. As we propose a rather qualitative scenario yet bearing generality, it seems this provides promising basis for the solution-in-principle of the (semi) classically hard kinetic problem of biopolymer chain folding from coiled to native conformation in highly selective ligand proteins/target-receptors biomolecular recognition processes, implying underlying macroscopic quantum nonlocality on the level of biological cell.
Our recently proposed quantum approach to biomolecular recognition processes is hereby additionally supported by biomolecular Resonant Recognition Model and by quantum-chemical theory of biomolecular non-radiative resonant transitions. Previously developed general quantumdecoherence framework for biopolymer conformational changes in very selective ligandproteins/ target-receptors key/lock biomolecular recognition processes (with electron-conformational coupling, giving rise to dynamical modification of many-electron energy-state hypersurface of the cellular quantum-ensemble ligand-proteins/target-receptors biomolecular macroscopic quantum system, with revealed possibility to consider cellular biomolecular recognition as a Hopfield-like quantum-holographic associative neural network) is further extended from nonlocal macroscopicquantum level of biological cell to nonlocal macroscopic-quantum level of biological organism, based on long-range coherent microwave excitations (as supported by macroscopic quantum-like microwave resonance therapy of the acupuncture system) - which might be of fundamental importance in understanding of underlying macroscopic quantum (quantum-holographic Hopfieldlike) control mechanisms of embryogenesis/ontogenesis and morphogenesis, and their backward influence on the expression of genes.
In the context of the macroscopic quantum phenomena of the second kind, we hereby seek for a solution-in-principle of the long standing problem of the polymer folding, which was considered by Levinthal as (semi)classically intractable. To illuminate it, we applied quantum-chemical and quantum decoherence approaches to conformational transitions. Our analyses imply the existence of novel macroscopic quantum biomolecular phenomena, with biomolecular chain folding in an open environment considered as a subtle interplay between energy and conformation eigenstates of this biomolecule, governed by quantum-chemical and quantum decoherence laws. On the other hand, within an open biological cell, a system of all identical (noninteracting and dynamically noncoupled) biomolecular proteins might be considered as corresponding spatial quantum ensemble of these identical biomolecular processors, providing spatially distributed quantum solution to a single corresponding biomolecular chain folding, whose density of conformational states might be represented as Hopfield-like quantum-holographic associative neural network too (providing an equivalent global quantum-informational alternative to standard molecular-biology local biochemical approach in biomolecules and cells and higher hierarchical levels of organism, as well).
Two unresolved issues of the (semi)classically addressed problems in molecular biophysics are unreasonably long time necessary for the change of biopolymer conformations and long-range directedness of selective biomolecular recognition processes - implying their essential quantum origin. In this paper several possible quantum approaches to biomolecular recognition are considered: Theory of Non-Radiative Resonant Structural Transitions, Model of Quantum Decoherence, and Resonant Recognition Model. These approaches might be of fundamental importance in understanding underlying macroscopic quantum-holographic Hopfield-like control mechanisms of morphogenesis, and their backward influence on the expression of genes, with significant potential psychosomatic implications.
The conformational change of biological macromolecule is investigated from the point of quantum transition. A quantum theory on protein folding is proposed. Compared with other dynamical variables such as mobile electrons, chemical bonds and stretching-bending vibrations the molecular torsion has the lowest energy and can be looked as the slow variable of the system. Simultaneously, from the multi-minima property of torsion potential the local conformational states are well defined. Following the idea that the slow variables slave the fast ones and using the nonadiabaticity operator method we deduce the Hamiltonian describing conformational change. It is proved that the influence of fast variables on the macromolecule can fully be taken into account through a phase transformation of slow variable wave function. Starting from the conformation- transition Hamiltonian the nonradiative matrix element is calculated in two important cases: A, only electrons are fast variables and the electronic state does not change in the transition process; B, fast variables are not limited to electrons but the perturbation approximation can be used. Then, the general formulas for protein folding rate are deduced. The analytical form of the formula is utilized to study the temperature dependence of protein folding rate and the curious non-Arrhenius temperature relation is interpreted. The decoherence time of quantum torsion state is estimated and the quantum coherence degree of torsional angles in the protein folding is studied by using temperature dependence data. The proposed folding rate formula gives a unifying approach for the study of a large class problems of biological conformational change.