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Seel M, Ladik J. The tragicomedy of modern theoretical biology. ADVANCES IN QUANTUM CHEMISTRY 2020. [DOI: 10.1016/bs.aiq.2019.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Theoretical designing of the electronic structures and conduction properties of copolymers of donor–acceptor polymers: effect of multi-neighbour interaction. Chem Phys 2005. [DOI: 10.1016/j.chemphys.2004.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Bakhshi AK, Bhargava P. Ab initio study of the electronic structures and conduction properties of some donor-acceptor polymers and their copolymers. J Chem Phys 2003. [DOI: 10.1063/1.1626628] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Cizek J, Martinez A, Ladik J. A note on the mechanism of charge transport at different temperatures in aperiodic nucleotide base-stacks. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0166-1280(02)00748-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Some remarks about the electronic structure and transport properties of stacked systems. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0166-1280(01)00437-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Wang Q, Ye YJ, Chen F, Zhao H. The relationship between biological activity and the electronic structure and transfer of the whole acidic PLA2 molecule in ab initio level. Biophys Chem 1998; 75:129-39. [PMID: 9857481 DOI: 10.1016/s0301-4622(98)00200-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The electronic structure of the whole molecule of acidic phospholipase A2 (PLA2) from the venom of Agkistrodon halys pallas (A. halys pallas) has been calculated using the extended negative factor counting (ENFC) method in which dimers were calculated at the ab initio level using a minimal basis set, with simulation of the aqueous environment. Hopping conductivities were determined by the use of random walk theory. The results show that the frontier orbitals are mainly localized to residues which are involved in the biological activity of acidic PLA2. The C-terminal region might play some important role in biological activity because of its active electrons. The aromatic patch on the surface of the enzyme, together with two neighbouring acidic residues, has very active electrons that may be responsible for the inhibition of platelet aggregation. Trp30, which is involved in the interfacial recognition region, may transfer its electrons to the aggregated substrate. It is also concluded that the conductivity of the protein is caused mainly by holes transported through the valence band rather than electrons transferred in the conductive band. The a.c. conductivity of acidic PLA2 confirms that proteins, if doped, are amorphous conductors. Moreover, the a.c. conductivities of acidic PLA2 are approximately one order of magnitude higher than those of some other proteins. This suggests that the toxicity of acidic PLA2 may be related to its high a.c. conductivity.
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Affiliation(s)
- Q Wang
- Department of Protein Engineering, Chinese Academy of Sciences, Beijing, People's Republic of China
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Jiang Y, Ye YJ, Chen RS. Electronic energy levels and hopping conductivity of an entire molecule of hagfish insulin. Biophys Chem 1996; 59:95-105. [PMID: 8867330 DOI: 10.1016/0301-4622(95)00116-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The quantum-chemical calculation of an entire molecule of hagfish insulin was done by the ENFC method in which the matrix elements were calculated at the ab initio level using a minimal basis set with simulation of the aqueous solution environment. The ac conductivity for hagfish insulin was also calculated at the ab initio level by random walk theory. All the results were compared with those of pig insulin. It is shown that the reduction of HOMOs and LUMOs localized on the active sites of hagfish insulin agrees with the decrease in the biological reactivity of the insulin. The analysis of primary hopping events showed that a different sequence could influence the biological activity of insulin through the distribution of the hopping centers and the quantities of the hopping frequencies. The curve of the frequency versus ac conductivity of hagfish insulin shows that the different amino acid sequences of proteins influence the hopping conductivity. However, the electronic properties of native proteins are dominated by the three-dimensional conformations. Finally, the electronic mechanism of trans-membrane signal transforms by insulin and its receptor, which had been proposed by Ye and Ladik, was clearly described.
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Affiliation(s)
- Y Jiang
- Laboratory of Protein Engineering, Chinese Academy of Science, Beijing
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Némethy G, Bakhshi A, Paterlini G, Ladik J. On the level distribution of periodic and non-periodic collagen models. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/0166-1280(95)04136-t] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Luo Y, Liegener C, Ågren H. Size dependency of soft X-ray emission spectra. Calculations on finite polyenes and polyacetylene. Chem Phys Lett 1995. [DOI: 10.1016/0009-2614(94)01427-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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dos Santos DA, Quattrocchi C, Friend RH, Brédas JL. Electronic structure of polyparaphenylene vinylene copolymers: The relationship to light‐emitting characteristics. J Chem Phys 1994. [DOI: 10.1063/1.466421] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Ye YJ, Ladik J. Theory of hopping conductivity in pig insulin. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 48:5120-5126. [PMID: 10009026 DOI: 10.1103/physrevb.48.5120] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Matrix-block negative-factor-counting treatment of electron correlation in long alkane chains. Chem Phys Lett 1993. [DOI: 10.1016/0009-2614(93)87056-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Liegener CM. The treatment of electron correlation in aperiodic systems. IV. Exciton bands and double ionization potentials. Chem Phys 1991. [DOI: 10.1016/0301-0104(91)87142-i] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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dos Santos DA, Brédas JL. Influence of polymerization irregularities on the electronic properties of polythiophene. J Chem Phys 1991. [DOI: 10.1063/1.461527] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Lavarda F, dos Santos D, Galvão D, Laks B. On the disordered distribution of defects in transpolyacetylene. Chem Phys 1991. [DOI: 10.1016/0301-0104(91)87001-c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Effects of correlation and hydration on the electronic structure of aperiodic polypeptides. ACTA ACUST UNITED AC 1989. [DOI: 10.1016/0166-1280(89)85113-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Liegener CM. The treatment of electron correlation in aperiodic systems. I. Description of methods. Chem Phys 1989. [DOI: 10.1016/0301-0104(89)80197-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Abu-Eittah R, Obaid A, Basahl S, Diefallah E. Molecular Orbital Treatment of Some Amino Acids. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1988. [DOI: 10.1246/bcsj.61.2609] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Bakhshi AK, Ladik J, Seel M. Comparative study of the electronic structure and conduction properties of polypyrrole, polythiophene, and polyfuran and their copolymers. PHYSICAL REVIEW. B, CONDENSED MATTER 1987; 35:704-712. [PMID: 9941456 DOI: 10.1103/physrevb.35.704] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Zhang X, Hwang M, Gonis A, Freeman AJ. Numerical and analytic methods for the study of disordered alloy surfaces. PHYSICAL REVIEW. B, CONDENSED MATTER 1986; 34:5169-5176. [PMID: 9940343 DOI: 10.1103/physrevb.34.5169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Otto P, Bakhshi A, Ladik J, Seel M, Chin S. On the electronic structure and conduction properties of aperiodic DNA and proteins. III. The band structures of periodic polypeptides. Chem Phys 1986. [DOI: 10.1016/0301-0104(86)85044-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Ladik J, Seel M, Otto P, Bakhshi A. On the electronic structure and conduction properties of aperiodic DNA and proteins. I. Strategy and methods of investigations. Chem Phys 1986. [DOI: 10.1016/0301-0104(86)85042-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Hwang M, Podloucky R, Gonis A, Freeman AJ. Electronic densities of states of semi-infinite disordered chains: Comparisons of exact and analytic calculations. PHYSICAL REVIEW. B, CONDENSED MATTER 1986; 33:765-771. [PMID: 9938334 DOI: 10.1103/physrevb.33.765] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Gazdy B, Seel M, Ladik J. The role of self-consistency in quantum-mechanical studies of disordered quasi-one-dimensional systems. Chem Phys 1984. [DOI: 10.1016/0301-0104(84)85154-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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