Kaori Ueno-Noto

A theoretical study of the physicochemical mechanisms associated with DNA recognition modulation in artificial zinc-finger proteins.

The DNA-binding ability of the zinc-finger (ZF) protein and the modulation of its affinity to DNA through amino acid mutations were theoretically investigated. Classical molecular dynamics and energy decomposition analysis based on large-scale ab initio fragment molecular orbital calculations were used to obtain the DNA binding affinities of wild-type and three mutant ZFs. Calculated binding free energies qualitatively well explained the DNA binding affinity modulation experimentally observed by Dhanasekaran et al. [Dhanasekaran, M.; et al., Biochemistry 2007, 46, 7506-7513]. It had been considered that only the α-helix domain in the ZF plays an important role in DNA recognition; however, our results clearly show that the N-terminal regions, BR1 and BR2, also play important roles in DNA recognition.

Affinity of HIV-1 antibody 2G12 with monosaccharides: a theoretical study based on explicit and implicit water models.

In order to develop potential ligands to HIV-1 antibody 2G12 toward HIV-1 vaccine, binding mechanisms of the antibody 2G12 with the glycan ligand of D-mannose and D-fructose were theoretically examined. D-Fructose, whose molecular structure is slightly different from D-mannose, has experimentally shown to have stronger binding affinity to the antibody than that of D-mannose. To clarify the nature of D-fructoses higher binding affinity over D-mannose, we studied interaction between the monosaccharides and the antibody using ab initio fragment molecular orbital (FMO) method considering solvation effect as implicit model (FMO-PCM) as well as explicit water model. The calculated binding free energies of the glycans were qualitatively well consistent with the experimentally reported order of their affinities with the antibody 2G12. In addition, the FMO-PCM calculation elucidated the advantages of D-fructose over D-mannose in the solvation energy as well as the entropic contribution term obtained by MD simulations. The effects of explicit water molecules observed in the X-ray crystal structure were also scrutinized by means of FMO methods. Significant pair interaction energies among D-fructose, amino acids, and water molecules were uncovered, which indicated contributions from the water molecules to the strong binding ability of D-fructose to the antibody 2G12. These FMO calculation results of explicit water model as well as implicit water model indicated that the strong binding of D-fructose over D-mannose was due to the solvation effects on the D-fructose interaction energy.

Novel sulfated gangliosides, high-affinity ligands for neural siglecs, inhibit NADase activity of leukocyte cell surface antigen CD38.

Three kinds of novel sulfated gangliosides structurally related to the Chol-1 (alpha-series) ganglioside GQ1balpha were synthesized. These sulfated gangliosides were potent inhibitors of NADase activity of leukocyte cell surface antigen CD38. Among the synthetic gangliosides, GSC-338 (II(3)III(6)-disulfate of iso-GM1b) was surprisingly found to be the most potent structure in both the NADase inhibition and MAG-binding activity. The present study indicates that the sulfated gangliosides are useful to study the recognition of the internal tandem sialic acid residues alpha2-3-linked to Gal(II(3)) as well as the siglec-dependent recognition including a terminal sialic acid residue.

Water molecules inside protein structure affect binding of monosaccharides with HIV-1 antibody 2G12.

Water molecules inside biomolecules constitute integral parts of their structure and participate in the functions of the proteins. Some of the X‐ray crystallographic data are insufficient for analyzing a series of ligand–protein complexes in the same condition. We theoretically investigated antibody binding abilities of saccharide ligands and the effects of the inner water molecules of ligand–antibody complexes. Classical molecular dynamics and quantum chemical simulations using a model with possible water molecules inside the protein were performed with saccharide ligands and Human Immunodeficiency Virus 1 neutralizing antibody 2G12 complexes to estimate how inner water molecules of the protein affect the dynamics of the complexes as well as the ligand–antibody interaction. Our results indicate the fact that d‐fructoses strong affinity to the antibody was partly due to the good retentiveness of solvent water molecules of the ligand and its stability of the ligands conformation and relative position in the active site.

CHEMICAL DESCRIPTION OF THE INTERACTION BETWEEN GLYCAN LIGAND AND SIGLEC-7 USING AB INITIO FMO METHOD AND CLASSICAL MD SIMULATION

We clarified in detail the theoretical features of the interaction between the glycan ligand containing α(2,8)-disialyl residue and a lectin called Siglec (sialic acid Ig-like binding lectin)-7 by ab initio fragment molecular orbital (FMO) calculations and classical molecular dynamics (MD) simulations. By comparing the ligand–Siglec-7 interaction of the wild-type Siglec-7 and those of mutant-Siglec-7s, we herein describe protein–glycan interactions thoroughly, and provide fundamentals to elucidate ligand-recognition mechanism. The experimentally observed decrease in ligand binding produced by mutagenesis at residues in non-active site was explained with MD simulations; both Trp85 and Trp74 residues are fundamental in structural stability of the Siglec-7, which is involved in the binding of the glycan ligand. The interaction energies obtained by the FMO method were consistent with the experimental ligand-binding results. The glycan ligand preferentially interacted with Siglec-7 via sialic acid residues. The stabilization by the dispersion interaction between the neutral parts of the ligand was also considerable in the binding.

A comparative computational study of matrix-peptide interactions in MALDI mass spectrometry: the interaction of four tripeptides with the MALDI matrices 2,5-dihyroxybenzoic acid, α-cyano-4-hydroxy-cinnamic acid and 3,5-dihyroxybenzoic acid

The mechanisms of matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) has been investigated by focusing on the interaction between MALDI matrices and several tripeptides. 2,5-dihyroxybenzoic acid, α-cyano-4-hydroxy-cinnamic acid and 3,5-dihyroxybenzoic acid were studied as MALDI matrices interacting with four tripeptide sequences taken from bovine insulin: glutamic acid-arginine-glycine, glutamine-histidine-leucine, serine-histidine-leucine and threonine-proline-lysine. Molecular dynamics/simulated annealing calculations followed by geometrical refinement via density functional theory reveal a variety of matrix/peptide interactions. Most matrix-tripeptide clusters are bound through the side chains of the amino acids. In all clusters, the ionization potential (IP) of the matrix bound to the tripeptide is reduced relative to that of the free matrix. The origin of this IP lowering is discussed. In many cases, ionization of the cluster resulted in spontaneous proton transfer between the matrix and the tripeptide. The exothermicity of the spontaneous proton transfer reaction is considerably greater for the 2,5-DHB and HCCA clusters than for the 3,5-DHB clusters. This is of significance because the former two matrices are known to be very effective matrices for the MALDI process, while 3,5-DHB, although structurally similar to the others, is completely nonfunctional as a MALDI matrix.

Computational Studies of Gas-Phase Ca3P2 and Ca6P4

The electronic and molecular structures of Ca3P2 and Ca6P4 are investigated using high-level ab initio methods. The lowest energy structure for Ca3P2 is found to be a Jahn-Teller distorted triplet. An excited-state singlet is found with various post HF methods; however, DFT incorrectly predicts a closed shell singlet to be the ground state. For the Ca6P4 system, both DFT and ab initio methods give consistent relative energies. The computational results demonstrate that the energetics are very sensitive to the size of the Ca basis set. Enhancing the Ca basis sets with additional s and p valence functions significantly affects the calculated energies.

Recognition of tandem sialic acid residues by CD38: A theoretical study

The electronic structures of gangliosides are described using semiempirical and ab inito molecular orbital theories as well as the density functional theory to clarify the causative factors of the differences in inhibitory effects and to elucidate the recognition mechanisms of the enzyme. Our results suggest that CD38 is likely to recognize the two phosphate groups in NAD and the two carboxyl groups in tandem sialic acid residues of gangliosides. The recognition mechanisms of the substrate are proposed based on the good correlation found between the orbital energy of the highest occupied molecular orbital of the gangliosides and the degree of the inhibitory effect.

Substrate recognition by enzymes: a theoretical study

We previously reported that a series of gangliosides inhibited the activity of an enzyme NAD glycohydrolase (CD38), and that those with tandem sialic acid residues in the sugar chain had great inhibitory effect. We describe the results of computer simulations on three-dimensional and electronic structures of gangliosides to clarify the causative factors of difference in the inhibitory effect and the recognition mechanisms of the enzyme. We found that dipole moments and HOMO were correlated with inhibitory effect by conformational analyses and molecular orbital (MO) calculations. CD38 is likely to recognize the two carboxyl groups in tandem sialic acid residues of gangliosides, as well as the phosphate groups in NAD. A strong correlation was found between the orbital energies of HOMO by MO calculations and the extent of the inhibitory effect. Salvation effects were also considered to interpret the substrate recognition mechanisms in the biological system, which supported the above results.