A parallelized integral-direct second-order M�ller?Plesset perturbation theory method with a fragment molecular orbital scheme

Mochizuki, Yuji; Nakano, Tatsuya; Koikegami, Shigeru; Tanimori, Souichirou; Abe, Y.; Nagashima, Umpei; Kitaura, Kazuo

doi:10.1007/s00214-004-0602-3

Cited by 173 publications

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“…[26][27][28] The FMO method was originally developed for the Hartree-Fock (HF) level of theory, but so far the second-order Møller-Plesset perturbation correction (MP2) has been introduced to include the electron correlation effect. [29][30][31] The polarizable continuum model (PCM) has been combined with FMO to incorporate the solvent effect in an implicit way. 32 FMO and related methods have been successfully applied to electronic structure calculations of several biological molecules.…”

Section: Introductionmentioning

confidence: 99%

Change in a protein's electronic structure induced by an explicit solvent: An ab initio fragment molecular orbital study of ubiquitin

et al. 2007

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The effect of solvation on the electronic structure of the ubiquitin protein was analyzed using the ab initio fragment molecular orbital (FMO) method. FMO calculations were performed for the protein in vacuo, and the protein was immersed in an explicit solvent shell as thick as 12 A at the HF or MP2 level by using the 6-31G* basis set. The protein's physical properties examined were the net charge, the dipole moment, the internal energy, and the solvent interaction energy. Comparison of the computational results revealed the following changes in the protein upon solvation. First, the positively charged amino acid residues on the protein surface drew electrons from the solvent, while the negatively charged ones transfer electrons to the solvent. Second, the dipole moment of the protein was enhanced as a result of the polarization. Third, the internal energy of the protein was destabilized, but the destabilization was more than compensated for by the generation of a favorable protein-solvent interaction. Finally, the energetic changes were elicited both by the electron correlation effect of the first solvent shell and by the electrostatic effect of more distant solvent molecules. These findings were consistent with the picture of the solvated protein being a polarizable molecule dissolved in a dielectric media.

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Section: Introductionmentioning

confidence: 99%

Change in a protein's electronic structure induced by an explicit solvent: An ab initio fragment molecular orbital study of ubiquitin

et al. 2007

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“…commercial version 17 of ABINIT-MP 11 at the MP2/6-31G level. 18 The IFIE, ∆E IJ , between fragments I and J was evaluated as ∆E IJ = E IJ -E I -E J -Tr (∆P IJ V IJ ), where E IJ is the dimer electronic energy for a fragment comprising the fragments I and J; E I and E J are monomer electronic energies for fragments I and J, respectively; and ∆P IJ and V IJ are the difference density matrix and environmental electrostatic potential 11 for the IJ dimer, respectively. During the calculation, the protein structure was divided into fragments per residue unit, except for the covalently bridged disulphide residues, Cys179 and Cys214, which were treated as a single S-S bond fragment.…”

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Fragment molecular orbital calculations reveal that the E200K mutation markedly alters local structural stability in the human prion protein

Hasegawa

Mohri

Yokoyama

2010

Prion

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“…yellow; non-matching residues, green; weak matching residues, light blue; strong matching residues, red; helix, blue; sheet and the binding sites (E H3 ) to estimate binding energies (ΔE) between the receptor and H3 by the following expression; ΔE=(E receptor +E H3 )−E complex . Ab initio FMO calculations were performed by using ABINIT-MP program [30][31][32][33][34][35][36][37][38][39]. Binding energies ΔE and the selected IFIEs of Neu5Acα(2-3 or 2-6)Gal with amino acid residues at the FMO-HF/STO-3G and FMO-MP2/6-31G levels are summarized in Tables 1, 2, 3, 4, and 5.…”

Section: Methodsmentioning

confidence: 99%

“…However, we just urgently request a simple and essential approach with a reasonable cost. Ab initio fragment molecular orbital (FMO) calculations [30][31][32][33][34][35][36][37][38][39] to evaluate the binding energies between HA and Neu5Acα(2-3/6)Gal receptors are one of the promising strategies.…”

Section: Introductionmentioning

confidence: 99%

Ab initio fragment molecular orbital studies of influenza virus hemagglutinin–sialosaccharide complexes toward chemical clarification about the virus host range determination

et al. 2008

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If we predict the host range of new or mutant influenza virus in advance, we are able to measure against pandemic human influenza immediately after the new virus emerges somewhere. Influenza viral hemagglutinin(HA)-sialoside receptor interaction is a target event for in silico chemical prediction studies about the virus host range determination. We theoretically studied avian and human influenza A virus HA H3 subtype complexed with avian or human type receptor Neu5Acα(2-3 or 2-6)Gal analogues by ab initio fragment molecular orbital (FMO) method at the second order Møller-Plesset (MP2)/6-31G level, which can evaluate correctly not only electrostatic interactions but also lipophilic interactions based on van der Waals dispersion force. Avian H3 bound to avian α2-3 11.4 kcal/mol stronger than to human α2-6 in the model complexes with taking account of intermolecular lipophilic interaction. A substitution at the position 226 between Gln (avian) and Leu(human) on influenza H3 HA1 has altered Glycoconj J (2008) its virus host range between avian and human. In the ab initio FMO studies, binding energy of avian Gln226Leu H3-human α2-6 was quite similar to that in the human H3-human α2-6 complex with amino acid sequence differences at nine positions in the models. This similarity indicates that avian Gln226Leu H3 virus can infect human with the same level as human H3 virus. Opposite mutation Leu226Gln in the human H3 gave the moderate binding energies to avian α2-3 with similarity to avian H3-α2-3 complex that supported our previous virus-sialoside binding assay. Ab initio FMO studies have revealed the relationship between influenza H3 virus host range and H3-α(2-3 or 2-6) receptors binding. Our theoretical approach may predict the infectious level of new viruses and point out some unknown dangerous mutation positions on HA in advance.

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A parallelized integral-direct second-order M�ller?Plesset perturbation theory method with a fragment molecular orbital scheme

Cited by 173 publications

References 0 publications

Change in a protein's electronic structure induced by an explicit solvent: An ab initio fragment molecular orbital study of ubiquitin

Change in a protein's electronic structure induced by an explicit solvent: An ab initio fragment molecular orbital study of ubiquitin

Fragment molecular orbital calculations reveal that the E200K mutation markedly alters local structural stability in the human prion protein

Ab initio fragment molecular orbital studies of influenza virus hemagglutinin–sialosaccharide complexes toward chemical clarification about the virus host range determination

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