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Experimental tests of the quantum property of protein folding

Liaofu Luo

Published Mar 17, 2016• 0 citations
Publisher

Abstract

Abstract Experimental tests on the quantum property of protein folding are discussed. It includes: the test of the instantaneousness of torsion transition through observation of protein structural change in a short time scale of microsecond; the test of non-Arrhenius temperature dependence of protein folding rate and other biomolecular conformational changes; and the search for the narrow spectral lines of the protein photo-folding.

DOI
10.1101/044230

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Abstract Experimental tests on the quantum property of protein folding are discussed. It includes: the test of the instantaneousness of torsion transition through observation of protein structural change in a short time scale of microsecond; the test of non-Arrhenius temperature dependence of protein folding rate and other biomolecular conformational changes; and the search for the narrow spectral lines of the protein photo-folding.
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.
The Levinthal paradox states that it would be impossible for a protein to reach its native conformation in a physically meaningful time by randomly searching over all possible conformations. So far, it has been widely assumed that this random conformational search does not occur in the folding process, for which various putative hypotheses have had to be employed in model studies. Here we show that the quantum approach, describing the folding process as a quantum walk on a definite graph, gives rise to a fast protein-folding time. In terms of the conventional lattice model describing protein conformation, we introduce a procedure to enumerate all possible structures and then determine the definite connection graphs. Evaluating the mean first-passage time, we find it is much shorter than that obtained via random searching, and the magnitude of the quantum approach is reasonably in agreement with the experimental result. Some further discussions of various characteristic average quantities are also made by comparing both cases of quantum walk and classical random walk.
The large-molecules conformational transitions problem (the 'protein folding problem') is an open issue of vivid current science research work of fundamental importance for a number of modern science disciplines as well as for nanotechnology. Here, we elaborate the recently proposed quantum-decoherence-based approach to the issue. First, we emphasize a need for detecting the elementary quantum mechanical processes (whose combinations may give a proper description of the realistic experimental situations) and then we design such a model. As distinct from the standard approach that deals with the conformation system, we investigate the optically induced transitions in the molecule electrons system that, in effect, may give rise to a conformation change in the molecule. Our conclusion is that such a model may describe the comparatively slow conformational transitions.
Protein folding has been one of the most difficult problems for over a half-century,The random thermal motions causing conformational changes that lead energetically downhill towards the native structure, a principle captured in funnel-shaped energy landscapes.Unfolded polypeptides have a wide range of possible conformations. The search problem becomes intractable for classical computers due to the exponential growth of potential conformations with chain length. So far, there is theoretical and experimental evidence that solving such optimization problems using Quantum Computing approaches such as Quantum Annealing, VQE, and QAOA has an advantage. Although Google's DeepMind-AlphaFold has accomplished much,But we can go even further with the quantum approach.Here we show how to predict structure of protein as well as RNA folding using the Variational Quantum Eigensolver with Conditional Value at Risk (CVaR) expectation values for the solution of the problem and for finding the minimum configuration energy and our task is to identify a protein's minimal energy structure. The protein's structure is optimized to reduce energy. Also making sure that all physical constraints are met and encoding the protein folding problem into a qubit operator.
In the traditional random-conformational-search model, various hypotheses with a series of meta-stable intermediate states were proposed to resolve the Levinthal paradox in protein-folding time. Here we introduce a quantum strategy to formulate protein folding as a quantum walk on a definite graph, which provides us a general framework without making hypotheses. Evaluating it by the mean of first passage time, we find that the folding time via our quantum approach is much shorter than the one obtained via classical random walks. This idea is expected to evoke more insights for future studies.
Protein folding has been one of the most difficult problems for over a half-century,Therandom thermal motions causing conformational changes that lead energeticallydownhill towards the native structure, a principle captured in funnel-shaped energylandscapes.Unfolded polypeptides have a wide range of possible conformations. Thesearch problem becomes intractable for classical computers due to the exponentialgrowth of potential conformations with chain length. So far, there is theoretical andexperimental evidence that solving such optimization problems using QuantumComputing approaches such as Quantum Annealing, VQE, and QAOA has anadvantage. Although Google's DeepMind-AlphaFold has accomplished much,But wecan go even further with the quantum approach.Here we show how to predict structureof protein as well as RNA folding using the Variational Quantum Eigensolver withConditional Value at Risk (CVaR) expectation values for the solution of the problem andfor finding the minimum configuration energy and our task is to identify a protein'sminimal energy structure. The protein's structure is optimized to reduce energy. Alsomaking sure that all physical constraints are met and encoding the protein foldingproblem into a qubit operator.