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Cytidine deaminase is known as an important enzyme responsible for the hydrolytic deamination of cytidine, which is applied as a key step to the conversion of the precursor of the cancer drug to an active form in the living body. Cytidine with water is efficiently converted to uridine with ammonia in the cleft of cytidine deaminase. In this work, the(More)
We developed and implemented the ONIOM-molecular dynamics (MD) method for biochemical applications. The implementation allows the characterization of the functions of the real enzymes taking account of their thermal motion. In this method, the direct MD is performed by calculating the ONIOM energy and gradients of the system on the fly. We describe the(More)
Structural data of protein-DNA complex show redundancy and flexibility in base-amino acid interactions. To understand the origin of the specificity in protein-DNA recognition, we calculated the interaction free energy, enthalpy, entropy, and minimum energy maps for AT-Asn, GC-Asn, AT-Ser, and GC-Ser by means of a set of ab initio force field with extensive(More)
We applied the ONIOM-molecular dynamics (MD) method to the hydrolytic deamination of cytidine by cytidine deaminase, which is an essential step of the activation process of the anticancer drug inside the human body. The direct MD simulations were performed for the realistic model of cytidine deaminase by calculating the energy and its gradient by the ab(More)
Hydrogen-bonding (HB) patterns correspond to topologically distinct isomers of a water cluster and can be expressed by digraphs. We make use of the HB pattern to divide the configuration space of a water cluster ((H2O)n, n = 3-8) at a finite temperature. Each configuration of a water cluster generated in Monte Carlo (MC) simulation is classified into an HB(More)
A critical role is traditionally assigned to transition states (TSs) and minimum energy pathways, or intrinsic reaction coordinates (IRCs), in interpreting organic reactivity. Such an interpretation, however, ignores vibrational and kinetic energy effects of finite temperature. Recently it has been shown that reactions do not necessarily follow the(More)
The conformation of cyclolinopeptide A [c-(Pro-Pro-Phe-Phe-Leu-Ile-Ile-Leu-Val)], a naturally occurring peptide with remarkable cytoprotective activity, has been investigated by means of molecular dynamics simulations in various molecular environments. Structural and dynamical properties have been analyzed and compared with those experimentally determined.(More)
Exchange of guest molecules into capsule shaped host molecules is the most fundamental process in host-guest chemistry. Several examples of quantitative measurements of guest exchange rates have been reported. However, there have been no reports on the activation energies of these processes. A molecule known as cavitand-porphyrin (H2CP) has been reported to(More)
Thin films of chiral porphyrin J-aggregates have been studied by vibrationally and electronically doubly resonant sum frequency generation (SFG) spectroscopy. It was revealed that the chiral supramolecular structures of porphyrin aggregates in solutions were retained in the thin film samples, and their chirality was determined by using chiral vibrational(More)