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Soltaninejad H, Sadeghan AA, Hosseinkhani S, Asadollahi MA, Hosseini M, Ganjali MR. Application of intercalating molecules in detection of methylated DNA in the presence of silver ions. Methods Appl Fluoresc 2019; 7:035005. [DOI: 10.1088/2050-6120/ab025b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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2
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Spyrakis F, Cozzini P, Eugene Kellogg G. Applying Computational Scoring Functions to Assess Biomolecular Interactions in Food Science: Applications to the Estrogen Receptors. NUCLEAR RECEPTOR RESEARCH 2016. [DOI: 10.11131/2016/101202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Francesca Spyrakis
- University of Parma, Department of Food Science, Molecular Modelling Laboratory, Parma, Italy
| | - Pietro Cozzini
- University of Parma, Department of Food Science, Molecular Modelling Laboratory, Parma, Italy
| | - Glen Eugene Kellogg
- Virginia Commonwealth University, Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development Richmond, Virginia, USA
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3
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Acosta-Silva C, Branchadell V, Bertran J, Oliva A. Mutual relationship between stacking and hydrogen bonding in DNA. Theoretical study of guanine-cytosine, guanine-5-methylcytosine, and their dimers. J Phys Chem B 2010; 114:10217-27. [PMID: 20684646 DOI: 10.1021/jp103850h] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The mutual relationship between stacking and hydrogen-bonding and the possible influence of stacking in the different behavior of cytosine (C) and 5-methylcytosine (C') in DNA have been studied through complete DFT optimization of different structures of G-C and G-C' dimers (i.e., G-C/C-G and G-C'/C'-G), using four different functionals. Our results show that stacking leads to an increase of the O(6)...H-N(4) hydrogen bond length and to a simultaneous decrease of the N(2)-H...O(2) one, in such a way that both lengths approach each other and, in some cases, an inversion occurs. These results suggest that stacking can be a factor to explain the disparity between theory and experiment on the relative strength of the two lateral hydrogen bonds. Regarding the difference between cytosine and 5-methylcytosine, we have shown that methylation enhances the stacking interactions, mainly due to the increase of polarizability. Methylation also favors the existence of slid structures which can produce local distortions of DNA.
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Affiliation(s)
- Carles Acosta-Silva
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193 Spain
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Adnan N, Buck DP, Evison BJ, Cutts SM, Phillips DR, Collins JG. DNA binding by pixantrone. Org Biomol Chem 2010; 8:5359-66. [PMID: 20865205 DOI: 10.1039/c0ob00295j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding of the anticancer drug pixantrone (6,9-bis[(2-aminoethyl)amino]benzo[g]isoquinoline-5,10-dione dimaleate) to the octanucleotide duplexes d(ACGATCGT)(2) and the corresponding C-5 methylated cytosine ((5Me)C) analogue d(A(5Me)CGAT(5Me)CGT)(2) has been studied by NMR spectroscopy and molecular modelling. The large upfield shifts observed for the resonances from the aromatic protons of pixantrone upon addition to either d(ACGATCGT)(2) or the corresponding (5Me)C analogue is consistent with the drug binding the octanucleotides by intercalation. The selective reduction in the sequential NOEs between the C(2)-G(3) and C(6)-G(7) nucleotides in NOESY spectra of either octanucleotide with added pixantrone confirms the intercalative binding mechanism. Strong NOEs from the side-chain ethylene protons of pixantrone to the H5 protons and the 5-CH(3) protons of the C(2) and C(6) residues of d(ACGATCGT)(2) and d(A(5Me)CGAT(5Me)CGT)(2), respectively, indicate that pixantrone predominantly intercalates from the DNA major groove at the 5'-CG and 5'-(5Me)CG sites. Simple molecular models based on the conclusions from the NMR experiments indicated that the (5Me)C groups do not represent a steric barrier to intercalation from the major groove. However, the observation of weak NOEs from the ethylene protons of pixantrone to a variety of minor groove protons from either octanucleotide suggests that the drug can also associate in the minor groove.
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Affiliation(s)
- Najia Adnan
- School of Physical, Environmental and Mathematical Sciences University College, University of New South Wales, Australian Defence Force Academy, Northcott Drive, Campbell, ACT 2600, Australia
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Abstract
We review the effect of sequence on the structure of left-handed Z-DNA in single crystals. The various substituent groups that define a nucleotide base as guanine, cytosine,thymine, or adenine affect both the DNA conformation and the organization of solvent around the duplex. These are discussed in terms of their effect on the ability of sequences to adopt the unusual Z-DNA structure. In addition, the experimental and theoretical methods used to treat DNA hydration are discussed as they relate to the stability of Z-DNA . Finally, we argue that Z-DNA , as defined by the crystal conformation, is sufficient in itself to account for the physical properties of left-handed conformations observed in polymers and in genomic sequences
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Affiliation(s)
- P S Ho
- Department of Biochemistry and Biophysics Oregon State University, ALSB 2011, Corvallis, OR, USA
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6
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Gomzi V. DFT study of sulfur centred radicals formed in 5-methylcytosine hemihydrate crystal doped with 5-methyl-2-thiocytosine. Mol Phys 2008. [DOI: 10.1080/00268970802238312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Kastenholz MA, Schwartz TU, Hünenberger PH. The transition between the B and Z conformations of DNA investigated by targeted molecular dynamics simulations with explicit solvation. Biophys J 2006; 91:2976-90. [PMID: 16998239 PMCID: PMC1578494 DOI: 10.1529/biophysj.106.083667] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The transition between the B and Z conformations of double-helical deoxyribonucleic acid (DNA) belongs to the most complex and elusive conformational changes occurring in biomolecules. Since the accidental discovery of the left-handed Z-DNA form in the late 1970s, research on this DNA morphology has been engaged in resolving questions relative to its stability, occurrence, and function in biological processes. While the occurrence of Z-DNA in vivo is now widely recognized and the major factors influencing its thermodynamical stability are largely understood, the intricate conformational changes that take place during the B-to-Z transition are still unknown at the atomic level. In this article, we report simulations of this transition for the 3'-(CGCGCG)-5' hexamer duplex using targeted molecular dynamics with the GROMOS96 force field in explicit water under different ionic-strength conditions. The results suggest that for this oligomer length and sequence, the transition mechanism involves: 1), a stretched intermediate conformation, which provides a simple solution to the important sterical constraints involved in this transition; 2), the transient disruption of Watson-Crick hydrogen-bond pairing, partly compensated energetically by an increase in the number of solute-solvent hydrogen bonds; and 3), an asynchronous flipping of the bases compatible with a zipperlike progression mechanism.
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Affiliation(s)
- Mika A Kastenholz
- Laboratorium für Physikalische Chemie, ETH Hönggerberg, HCI, Zürich, Switzerland
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9
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Abascal * JLF, Gil Montoro JC. Computer simulation of the thermodynamics of the B → Z-DNA transition: effect of the ionic size and charge. Mol Phys 2004. [DOI: 10.1080/00268970412331292704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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10
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Kellogg GE, Fornabaio M, Spyrakis F, Lodola A, Cozzini P, Mozzarelli A, Abraham DJ. Getting it right: modeling of pH, solvent and “nearly” everything else in virtual screening of biological targets. J Mol Graph Model 2004; 22:479-86. [PMID: 15182807 DOI: 10.1016/j.jmgm.2004.03.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2004] [Indexed: 10/26/2022]
Abstract
"Getting it right" refers to the careful modeling of all elements in the living system, i.e. biological macromolecules, ligands and water molecules. In addition, careful attention should be paid to the protonation state of ionizable functional groups on the ligands and residues at the active site. Computational technology based on the empirical HINT program is described to: (1) calculate free energy scores for ligand binding; (2) include the implicit and explicit effects of water in and around the ligand binding site; and (3) incorporate the effects of global and local pH in molecular models. This last point argues for the simultaneous consideration of a number of molecular models, each with different protonation profiles. Data from recent studies of protein-ligand systems (trypsin, thrombin, neuraminidase, HIV-1 protease and others) are used to illustrate the concepts in the paper. Also discussed are experimental factors related to accurate free energy predictions with this and other computational technologies.
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Affiliation(s)
- Glen E Kellogg
- Department of Medicinal Chemistry, School of Pharmacy, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298-0540, USA.
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11
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Abstract
In this review we summarize recent progress in our understanding of the structure of aqueous interfaces emerging from molecular level computer simulations. It is emphasized that the presence of the interface induces specific structural effects which, in turn, influence a wide variety of phenomena occurring near the phase boundaries. At the liquid-vapor interface, the most probable orientations of a water molecule is such that its dipole moment lies parallel to the interface, one O-H bond points toward the vapor and the other O-H bond is directed toward the liquid. The orientational distributions are broad and slightly asymmetric, resulting in an excess dipole moment pointing toward the liquid. These structural preferences persist at interfaces between water and nonpolar liquids, indicating that the interactions between the two liquids in contact are weak. It was found that liquid-liquid interfaces are locally sharp but broadened by capillary waves. One consequence of anisotropic orientations of interfacial water molecules is asymmetric interactions, with respect to the sign of the charge, of ions with the water surface. It was found that even very close to the surface ions retain their hydration shells. New features of aqueous interfaces have been revealed in studies of water-membrane and water-monolayer systems. In particular, water molecules are strongly oriented by the polar head groups of the amphiphilic phase, and they penetrate the hydrophilic head-group region, but not the hydrophobic core. At infinite dilution near interfaces, amphiphilic molecules exhibit behavior different from that in the gas phase or in bulk water. This result sheds new light on the nature of hydrophobic effect in the interfacial regions. The presence of interfaces was also shown to affect both equilibrium and dynamic components of rates of chemical reactions. Applications of continuum models to interfacial problems have been, so far, unsuccessful. This, again, underscores the importance of molecular-level information about interfaces.
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Affiliation(s)
- A Pohorille
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143, USA
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12
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Sambrano J, de Souza A, Queralt J, Oliva M, Andrés J. Density functional study of the 5-methylcytosine tautomers. Chem Phys 2001. [DOI: 10.1016/s0301-0104(00)00402-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Sponer J, Gabb HA, Leszczynski J, Hobza P. Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study. Biophys J 1997; 73:76-87. [PMID: 9199773 PMCID: PMC1180910 DOI: 10.1016/s0006-3495(97)78049-4] [Citation(s) in RCA: 168] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Base-stacking interactions in canonical and crystal B-DNA and in Z-DNA steps are studied using the ab initio quantum-chemical method with inclusion of electron correlation. The stacking energies in canonical B-DNA base-pair steps vary from -9.5 kcal/mol (GG) to -13.2 kcal/mol (GC). The many-body nonadditivity term, although rather small in absolute value, influences the sequence dependence of stacking energy. The base-stacking energies calculated for CGC and a hypothetical TAT sequence in Z-configuration are similar to those in B-DNA. Comparison with older quantum-chemical studies shows that they do not provide even a qualitatively correct description of base stacking. We also evaluate the base-(deoxy)ribose stacking geometry that occurs in Z-DNA and in nucleotides linked by 2',5'-phosphodiester bonds. Although the molecular orbital analysis does not rule out the charge-transfer n-pi* interaction of the sugar 04' with the aromatic base, the base-sugar contact is stabilized by dispersion energy similar to that of stacked bases. The stabilization amounts to almost 4 kcal/mol and is thus comparable to that afforded by normal base-base stacking. This enhancement of the total stacking interaction could contribute to the propensity of short d(CG)n sequences to adopt the Z-conformation.
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Affiliation(s)
- J Sponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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14
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Gil Montoro JC, Abascal JLF. The free energy difference between simple models of B- and Z-DNA: Computer simulation and theoretical predictions. J Chem Phys 1997. [DOI: 10.1063/1.473827] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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15
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Pearlman DA. Free energy derivatives: A new method for probing the convergence problem in free energy calculations. J Comput Chem 1994. [DOI: 10.1002/jcc.540150112] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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Miyamoto S, Kollman PA. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches. Proteins 1993; 16:226-45. [PMID: 8346190 DOI: 10.1002/prot.340160303] [Citation(s) in RCA: 198] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We present calculations of the absolute and relative binding free energies of complexation of streptavidin with biotin and its analogs by means of a thermodynamic free energy perturbation method implemented with molecular dynamics. Using the recently solved crystal structure of the streptavidin-biotin complex, biotin was mutated into a dummy molecule as well as thiobiotin and iminobiotin both in the protein and in solution. The calculated absolute binding free energy was dependent on the simulation model used. Encouragingly, the "best models" provided a reasonable semiquantitative reproduction (-20 to -22 kcal/mol) of the experimental free energy (-18.3 kcal/mol). Furthermore, the calculated results give clear insights into the binding nature of the protein-ligand complex, showing that the van der Waals energy dominates the electrostatic and hydrogen bonding energies in the binding of biotin by streptavidin. Specifically, the mutation of biotin into a dummy molecule in solution has a delta G (van der Waals) approximately -4 kcal/mol, due to the cancellation of dispersion and repulsion "cavity" effects. On the other hand, in the protein, a very small free energy price must be paid to create a cavity since one already exists and the mutation of biotin into a dummy molecule has a delta G (van der Waals) approximately 15 kcal/mol. These results are also consistent with the interpretation that the entropy increase to be expected from hydrophobic interactions from desolvation of biotin is counterbalanced by a decrease in entropy accompanying the formation of buried hydrogen bonds, which have been derived from the apparently conflicting experimental data. They provide an alternative interpretation of the reason for the extremely high affinity of the biotin-streptavidin interaction than that recently proposed by Weber et al. (J. Am. Chem. Soc. 114:3197, 1992). In the case of the relative binding free energies, the calculated values of 3.8 +/- 0.6 and 7.2 +/- 0.6 kcal/mol compare well with the experimental values of 3.6 and 6.2 kcal/mol for the perturbation of biotin to thiobiotin and iminobiotin, respectively in the related protein avidin. The calculations indicate that desolvation of the ligand is important in understanding the relative affinity of the ligands with the protein. The above successful simulations suggest that the molecular dynamics/free energy perturbation method is useful for understanding the energetic features affecting the binding between proteins and ligands, since it is generally difficult to determine these factors unambiguously by experiment.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- S Miyamoto
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143
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Chen YZ, Prohofsky EW. Differences in melting behavior between homopolymers and copolymers of DNA: Role of nonbonded forces for GC and the role of the hydration spine and premelting transition for AT. Biopolymers 1993. [DOI: 10.1002/bip.360330508] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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18
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Affiliation(s)
- W Zacharias
- Department of Biochemistry, School of Medicine, University of Alabama, Birmingham 35294-0005
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19
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Miyamoto S, Kollman PA. Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem 1992. [DOI: 10.1002/jcc.540130805] [Citation(s) in RCA: 5114] [Impact Index Per Article: 159.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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20
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Abstract
Molecular dynamics simulations have been undertaken for a B-form dodecanucleotide duplex in solution with and without an intercalated proflavine molecule between the central C.G base pairs. The introduction of this simple intercalator affects both the conformational features and dynamic properties of the oligonucleotide double helix. Changes are seen in the rms atomic fluctuations and anisotropy of phosphate, sugar and base atoms. The backbone conformation is slightly changed on average and more sugars adopt the C3' endo conformation in the simulation of the complex compared with the simulation of the oligonucleotide alone. Both major and minor grooves becomes wider on average with the addition of the intercalating drug. Flanking A.T base pairs on both sides of the intercalation site have undergone an increase in flexibility, with the base pairs, especially at the 5' side, having the N1...N3 hydrogen bonds being broken.
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Affiliation(s)
- P Herzyk
- Cancer Research Campaign Biomolecular Structure Unit, Institute of Cancer Research, Sutton, Surrey, UK
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22
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Wunz TP. Nucleoside free energy perturbation calculations: Mutation of purine-to-pyrimidine and pyrimidine-to-purine nucleosides. J Comput Chem 1992. [DOI: 10.1002/jcc.540130517] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Beglov DB, Lipanov AA. Charge grouping approaches to calculation of electrostatic forces in molecular dynamics of macromolecules. J Biomol Struct Dyn 1991; 9:205-14. [PMID: 1741958 DOI: 10.1080/07391102.1991.10507907] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Calculation of long-range electrostatic interactions is the most time-consuming step in theoretical simulation of the structure and dynamics of macromolecules. In practice very short cutoff distances are used, which may distort the behavior of the model system. We describe two accurate approaches to calculation of electrostatic forces based on hierarchical grouping of charges into cubes. The first is similar to the O(NlogN) algorithm developed by Barnes, J. and Hut, P., Nature (London) 324, 446-449 (1986), for simulation of a gravitational motion of N bodies. The second approach we formulate for a system with periodic boundary conditions in the nearest image approximation. The calculation of electrostatic interactions and a charge grouping procedure are faster than O(N2). The average inaccuracy in the force introduced by the grouping does not exceed 1%. We describe a small modification of the same approach which makes it suitable for long strongly charged polymers as well. This accurate approach to calculation of electrostatic interactions is illustrated with an example of the dynamics of ions near DNA. Quick equilibration of the ionic distribution is observed during molecular dynamics simulation if electrostatic forces are properly calculated, while the behavior and distribution of ions are less realistic when the conventional cutoff distances are used.
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Affiliation(s)
- D B Beglov
- Institute of Molecular Genetics, U.S.S.R. Academy of Sciences, Moscow
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