The fragment molecular orbital (FMO) method is recently attracting attention as a method of calculating the electronic state of macromolecular systems. To enhance the speed of the FMO method, it is necessary to apply an approximation in which SCF calculations are neglected for distant fragment (monomer) pairs (dimers) and instead the electrostatic interactions between the two monomers are calculated. This approximation is called the dimer-es approximation. The accuracy and speed brought by the dimer-es approximation depend on the minimum threshold distance between two atoms to apply the approximation. This threshold distance given in unit of van der Waals radii is named “Ldimer-es”. In this communication, we examined dependence of HF and MP2 electron correlation energy errors on “Ldimer-es”, and it is preferable to calculate FMO4-HF and FMO4-MP2 for calculation of FMO-HF and FMO-MP2 of side chain-split peptides with Ldimer-es=2.0.
Ryuzo Azuma, Sae Kishi, Greg Gutmann, Akihiko Konagaya
Here we present a novel technique that utilizes a supporting inorganic film for MD simulations of flat-shaped DNA origami structures in explicit solvent. The number of atoms is typically over 16 million including water molecules. By utilizing a GPU capable simulation engine, we have addressed conformational changes of a DNA origami structure under normal ionic strength and deionized water conditions up to the order of one nanosecond simulation time. Our results demonstrate that DNA origami configuration undergoes a continual growth in the absence of cations, while it is not the case for normal ionic strength. Statistical analysis of helix forms for these DNA origami structures reveals that not only cations but also water permittivity contributed to the maintenance of B-DNA helix form during the stretching motion. These results will provide key features in designing molecular robots as assembly of DNA origami structural components such as scaffolds, connectors and channels.
Doi Hideo, Okuwaki Koji, Naito Takamitsu, Saitou Sona, Mochizuki Yuji
We developed a portable code for dissipative particle dynamics (DPD) simulations. This Fortran program named CAMUS has a couple of notable features. One is the omission of constructing the so-called neighboring particles list, providing a sizable speed-up per step and also a near linear scaling of costs with respect to the number of particles. The other is an easy inclusion of additional specific (such as 1-3 and 1-5 Morse bonding) interactions which are crucial in describing protein structures. The formations of α-helix and β-sheet through DPD were then demonstrated. CAMUS is freely available at the GitHub site.
Sona Saitou, Jun Iijima, Mayu Fujimoto, Yuji Mochizuki, Koji Okuwaki, Hideo Doi, Yuto Komeiji
We have applied Google’s TensorFlow deep learning toolkit to recognize the visualized results of the fragment molecular orbital (FMO) calculations. Typical protein structures of α-helix and β-sheet provide some characteristic patterns in the two-dimensional map of inter-fragment interaction energy termed as IFIE-map (Kurisaki et al., Biophys. Chem. 130 (2007) 1). A thousand of IFIE-map images with labels depending on the existences of α-helix and β-sheet were prepared by employing 18 proteins and 3 non-protein systems and were subjected to training by TensorFlow. Finally, TensorFlow was fed with new data to test its ability to recognize the structural patterns. We found that the characteristic structures in test IFIE-map images were judged successfully. Thus the ability of pattern recognition of IFIE-map by TensorFlow was proven.
Curcumin can bind to tubulin and inhibit the formation of tubulin polymer, which contributes to the formation of microtubule. Binding sites of curcumin on the α- and β-tubulin heterodimer were predicted by a molecular docking study to ascertain probable causes for the observed anti-microtubule effects of curcumin. However, the specific interactions between curcumin and the tubulins have yet to be elucidated at an electronic level. We here investigated the binding properties between curcumin and α- or β-tubulin of Plasmodium falciparum, using ab initio fragment molecular orbital (FMO) calculations, in order to reveal the preferable binding sites of curcumin on these tubulins. The results were compared with those for some microtubule destabilizing drugs evaluated by the same method to confirm the efficiency of curcumin as an inhibitor to the tubulins. Our ab initio FMO calculations might provide useful information for proposing novel therapeutic agents with significant binding affinity to both the α- and β-tubulins.
The chirality of a compound affects its biochemical and pharmaceutical properties. It was found that the binding affinity between vitamin D receptor (VDR) and its ligand depends significantly on the chirality of the ligand. To elucidate the reason for this dependence, we here investigated the specific interactions between VDR and two types of ligands with different chirality, using ab initio fragment molecular orbital (FMO) calculations. The FMO results reveal that the part of ligand with different chirality interacts strongly with the imidazole ring of histidine side-chain in VDR, and that the binding affinity between VDR and the ligands depends on the protonation state of the histidine. This finding indicates the possibility that ligands with different chirality can assign the protonation state of VDR histidine residues existing near the ligand.
We are presently continuing to perform biomolecular chemical simulations for Burkholderia cepacia lipase (BCL) and Candida antarctica lipase typeB (CALB) to predict their enantioselectivity and reactivity toward various organic compounds. Here, we describe molecular dynamics (MD) and fragment molecular orbital (FMO) calculations on the complexes of CALB with primary and secondary alcohol esters. For esters with high enantioselectivity, the fast-reacting enantiomer of esters is located near the active site of CALB, whereas the slow-reacting enantiomer of esters moves away from the active site of CALB. On the other hand, for the esters with low enantioselectivity, we found that both (R)- and (S)-enantiomers of esters remain the active site of CALB. The FMO computations indicate that for the esters with high enantioselectivity, each fast-reacting enantiomer shows strong interactions with some particular amino acid residues, including Thr40, whereas for the esters with low enantioselectivity, both (R)- and (S)-enantiomers interact with identical amino acid residues including Thr40. It is predictable that Thr40 in CALB plays an important role in the chiral recognition of enantiomers through lipase-catalyzed biotransformations.
The fashionable but stereotypic thinking on the concept of the so-called “hydrophobic bond” has been examined in light of criticisms raised by many scientists: Hildebrand, Shinoda, Israelachvili, and so on. The author's comments are given on the harmful influence of the concept of “hydrophobic bond” in chemistry and biochemistry. In my opinion, this concept can be considered as a myth in modern science.