Fragment molecular orbital method: application to polypeptides

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

“…8,9 The ab initio fragment molecular orbital (FMO) method is a promising all-electron quantum chemical procedure for estimating the molecular interactions within biomolecules. 10,11 This method has been used to quantify the inter-and intramolecular interactions in various proteins and nucleic acids-interactions that contribute to the binding affinities and structural stabilities of these molecules. [12][13][14][15] Very recently, this method has been successfully used to reveal the intermolecular interactions between PrP and an anti-prion drug.…”

“…In the case of covalently adjoining secondary structure element pairs, molecular interaction energy ∆E cov between the N-terminal and C-terminal residues in the adjoining elements was added to ∆E Pair . This was simply evaluated from the IFIE between further cleaved side chain fragments or between a side chain group and a conventional fragment of corresponding pairs, in which the residues, except for glycine and threonine, were further divided into two fragments-main and side chain portions-by cutting the bond-detached atoms 10,11 at the C β atom of serine, asparagine, aspartic acid, histidine, tyrosine and valine; at C γ for glutamine and glutamic acid; and at C δ for arginine and lysine. For valine, the interaction energy was evaluated as the sum of the IFIEs for two fragmented methyl groups.…”

“…This study was supported by a Grantin-Aid from the BSE and other Prion Disease Control Projects of the Ministry of Agriculture, Forestry and Fisheries, Japan. 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.…”

“…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.…”

Density-fragment interaction approach for quantum-mechanical/molecular-mechanical calculations with application to the excited states of a Mg2+-sensitive dye

“…[34][35][36][37][38][39][40][41][42][43][44][45] There are also several approximate fragment approaches. 6,8,12,[46][47][48][49][50][51][52][53] In this paper, we propose a density-fragment interaction ͑DFI͒ approach for large-scale calculations based on a meanfield treatment of the electronic interaction between the fragments. In addition, the DFI scheme is combined with the QM/MM method, which we call the DFI-QM/MM method.…”