Elsevier

Physics of Life Reviews

Volume 8, Issue 3, October 2011, Pages 264-286
Physics of Life Reviews

Review
The theory of bio-energy transport in the protein molecules and its properties

https://doi.org/10.1016/j.plrev.2011.06.001Get rights and content

Abstract

The bio-energy transport is a basic problem in life science and related to many biological processes. Therefore to establish the mechanism of bio-energy transport and its theory have an important significance. Based on different properties of structure of α-helical protein molecules some theories of bio-energy transport along the molecular chains have been proposed and established, where the energy is released by hydrolysis of adenosine triphosphate (ATP). A brief survey of past researches on different models and theories of bio-energy, including Davydovʼs, Takenoʼs, Yomosaʼs, Brown et al.ʼs, Schweitzerʼs, Cruzeiro-Hanssonʼs, Fornerʼs and Pangʼs models were first stated in this paper. Subsequently we studied and reviewed mainly and systematically the properties, thermal stability and lifetimes of the carriers (solitons) transporting the bio-energy at physiological temperature 300 K in Pangʼs and Davydovʼs theories. From these investigations we know that the carrier (soliton) of bio-energy transport in the α-helical protein molecules in Pangʼs model has a higher binding energy, higher thermal stability and larger lifetime at 300 K relative to those of Davydovʼs model, in which the lifetime of the new soliton at 300 K is enough large and belongs to the order of 10−10 s or τ/τ0700. Thus we can conclude that the soliton in Pangʼs model is exactly the carrier of the bio-energy transport, Pangʼs theory is appropriate to α-helical protein molecules.

Highlights

► Investigating the properties of bio-energy released by ATP hydrolysis. ► Investigating the mechanism of bio-energy transport in protein molecules. ► Finding the solutions dynamic equation of bio-energy transport in protein molecules. ► Obtaining the properties of bio-energy transport in protein molecules. ► Giving the correctness of theory of bio-energy transport in protein molecules.

Introduction

What is life or life activity? In the light of biophysicistʼs view, the so-called life or life activity is just processes of mutual changes and coordination and unity for the bio-material, bio-energy and bio-information in the live systems. Their synthetic movements and cooperative changes are just total life activity. Therefore we can say that the bio-material is the foundation of life, the bio-energy is its center, the bio-information is the key of life activity, but the transformation and transfer of bio-information are always accompanied by the transport of bio-energy in living systems [1]. Thus, the bio-energy and its transport are a fundamental and important process in life activity. The bio-energies needed are mainly provided by that released in adenosine phosphate (ATP) hydrolysis in the living systems. Namely, an ATP molecule reacts with water, which results in the energy release of 0.43 eV under normal physiological conditions. The reaction can be represented byATP4+H2OADP3+HPO42+H++0.43 eV where ADP is the adenosine diphosphate. The bio-energies needed in biological processes in the bio-tissues come basically from this energy, namely, it is mainly used in these processes, for example, the muscle contraction, DNA duplication and the neuroelectric pulse transfer on the membranes of neurocytes as well as work of calcium pump and sodium pump. Therefore, there is always a process of bio-energy transport from the producing place to required organisms in the living systems. However, understanding of mechanism of the bio-energy transport in the living systems is a long standing problem which retains interesting up now. Plenty of the models of bio-energy transport were proposed, but most of them are not successful [1], [2], [3], [4]. In general, ATP molecules bind often to a specific site on the protein molecule, the energy supply for most protein activity and functions is provided by the ATP hydrolysis. Thus the transport of bio-energy released by ATP hydrolysis is always related to the protein molecules and their changes of conformation and configuration.

As it is known, the protein molecules are composed of more than twenty different kinds of individual building blocks called amino acids. Each amino acid is again constructed by an amino group (NH2), a carboxyl group (COOH), and a side group, or radical attached to an α carbon atom. The radical is what distinguishes one amino acid from another. Amino acids polymerize to form long chains of residues that constitute a protein molecule. When two amino acids join together, they release one water molecule and form a peptide bond. When the polypeptide chain has been formed, it can fold into a variety of complex three-dimensional conformations. Of particular are the three structural configurations that recur over and over in proteins: the α-helix, the β-sheet and globular conformation. In the α-helix the polypeptide chain is tightly coiled about its longitudinal axis. In the β-sheet the chain can be visualized as pleated strands of protein. The globular conformation is most complex since the chains are folded irregularly into a compact near-spherical shape. Part of the chain can often be in the α-helix or the β-sheet configuration [1], [4], [5].

Generally speaking, the energy can be converted to a particular vibrational excitation within a protein molecule. A likely recipient exchange is the amide-I vibration. Their vibration is primarily a stretch and contraction of the Cdouble bondO bond of the peptide groups. The amide-I vibration is also a prominent feature in infrared and Raman spectra of protein molecules. Experimental measurement shows that one of the fundamental frequencies of the amide-I vibration is about 0.205 eV. This energy is about half the energy released during the ATP hydrolysis. Moreover, it remains nearly constant from protein to protein, indicating that it is rather weakly coupled to other degrees of freedom. All these factors can lead to the assumption that the energy released by ATP hydrolysis might stay localized and stored in the amide-I vibration excitation. A biological role for vibrational excited states was first proposed by McClare in connection with a possible crisis in bio-energetics [6] (for more information about McClareʼs work see the article by Luca Turin, in this issue [7]). Then, as an alternative to electronic mechanisms, one can assume that the energy is stored as vibrational energy in the Cdouble bondO stretching model (amide-I) of polypeptide chains in the protein molecules. In view of the features of bio-energy some theoretical models of the bio-energy transport have been proposed subsequently. In this review paper we will survey these theoretical models as well as their properties and correctness.

Section snippets

Davydovʼs theory

It is well known that an inspection of the α-helix structure reveals three channels of hydrogen-bonded peptide groups approximately in the longitudinal direction with the sequence: …Hsingle bondNsingle bondCdouble bondO…Hsingle bondNsingle bondCdouble bondO…Hsingle bondNsingle bondCdouble bondO…Hsingle bondNsingle bondCdouble bondO…, where the dotted lines indicate the hydrogen bond, Davydov worked out this idea in the α-helix protein molecules, which is shown in Fig. 1, based on McClareʼs proposal for explaining the conformational changes responsible for muscle contraction [7], [8], where the trigger is the energy donating

The properties of carrier (soliton) of bio-energy transport in protein molecules

Although forms of the above equations of motion and corresponding solutions, Eqs. (6), (7), are quite similar to those of the Davydov soliton, the properties of the new soliton have very large differences from the latter because the parameter values in the equation of motion and its solutions Eqs. (6), (7), including R(t), GP, and μP, have obvious distinctions from that those of Davydov model. A straightforward result in Pangʼs model is to increase the nonlinear interaction energy, GP (GP=2GD[1+

Conclusion

As it is known, the bio-energy transport is a basic problem in life science and related to many biological processes. Therefore it is very necessary to establish the mechanism of bio-energy transport and its theory, where the energy is released by ATP hydrolysis. Scientists established different theories of bio-energy transport based on different descriptions of property of structure of α-helical protein molecules, for example, Davydovʼs, Takenoʼs, Yomosaʼs, Brown et al.ʼs, Schweitzerʼs,

Acknowledgements

Author would like to acknowledge the National Basic Research Program of China (“973” program) for the financial support (Grant No. 212011CB503701).

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