Tohru Sugimoto

On the Models for Phytochrome Chromophore. IV

On the stereoisomers of bilitriene with no ionic structure in their π-systems, their wavelengths and oscillator strengths of absorption are calculated by the ZDO approximation of the LCAO-ASMO-SCF-CI theory of π-electrons. The interaction of the π-systems with a point-dipole is also investigated using the stationary perturbation theory for degenerate states. It is thus shown that a stereoisomer of bilitriene with no ionic structure in its π-system can explain the observed absorption spectrum of P r , and that an interaction between such stereoisomer and a point-dipole is further necessary to reproduce the observed spectrum of P fr . The photoisomerization of a terminal pyrrole ring is also concluded to be probable for the origin of P r -P fr conversion.

An electronic state of the chromophore, phycocyanobilin, and its interaction with the protein moiety in C-phycocyanin: protonation of the chromophore

Abstract An electronic state of phycocyanobilin (PCB, a derivative of an open tetrapyrrole) in C-phycocyanin, an antenna pigment-protein complex for photosynthesis, was estimated by including the effect of an electrostatic field of protein moieties and water molecules. We adapted our unique method for calculation of the resonance integral. The observed absorption wavelength and an oscillator strength were reproduced only when the PCB was assigned to the protonated form with a net charge of 1. This was rationalized by the negative charge of a specific aspartate residue which was equidistant from the two nitrogen atoms of two central pyrrole rings.

Picosecond dynamics of the glutamate receptor in response to agonist-induced vibrational excitation.

Conformational changes of proteins are dominated by the excitation and relaxation processes of their vibrational states. To elucidate the mechanism of receptor activation, the conformation dynamics of receptors must be analyzed in response to agonist‐induced vibrational excitation. In this study, we chose the bending vibrational mode of the guanidinium group of Arg485 of the glutamate receptor subunit GluR2 based on our previous studies, and we investigated picosecond dynamics of the glutamate receptor caused by the vibrational excitation of Arg485 via molecular dynamics simulations. The vibrational excitation energy in Arg485 in the ligand‐binding site initially flowed into Lys730, and then into the J‐helix at the subunit interface of the ligand‐binding domain. Consequently, the atomic displacement in the subunit interface around an intersubunit hydrogen bond was evoked in about 3 ps. This atomic displacement may perturb the subunit packing of the receptor, triggering receptor activation. Proteins 2004;54:000–000.

INTERPRETATION OF THE ‘DICHROIC ORIENTATION’ OF PHYTOCHROME

The dichroic orientation of phytochrome observed both in the phytochrome‐mediated phototropism in Adiantum protonemata and in the phytochrome‐mediated chloroplast movement in Mougeotia were analyzed in terms of the orientation of the transition moment associated with the long‐wavelength absorption band, assuming that phytochrome, associated with the plasma membrane, rotates around the normal to the membrane. The orientation of the long‐wavelength transition moment of the phytochrome chromophore was calculated using the zero‐differential overlap approximation of the molecular orbital theory for ir‐electrons. The results indicate that the orientation of the long‐wavelength transition moment mainly changes later than 2 ms after red light excitation of Pr, and that the different dichroic orientations of Pr and Pfr can be attributed to the change in the angle of the long‐wavelength transition moment of phytochrome with the plasma membrane from 18o to 72o during phototransformation.

Molecular dynamics simulations for glutamate-binding and cleft-closing processes of the ligand-binding domain of GluR2

The gating of ion channel of ionotropic glutamate receptors is controlled by the structural change of the ligand-binding domain of GluR2. We examined the roles of residues in the glutamate-binding and cleft-closing mechanisms by molecular dynamics (MD) simulations. A glutamate entered the cleft deeply within the order of nanoseconds and the cleft locked the glutamate completely at 15 ns in an MD run. TYR450 seemed to regulate the orientation of the glutamate upon binding by cation-π interaction. A semi-open state was identified in the free energy profile evaluated with the structures on the spontaneously glutamate-bound and cleft-closed pathway by the unbiased MD simulations for the first time to our knowledge. In the semi-open state, the two sub-domains were bridged by two hydrogen bonds of GLU705 in the sub-domain 2 with TYR732 in the sub-domain 1 and with the glutamate bound to the sub-domain 1 until the transition to the closed state.

A MODEL FOR THE MOLECULAR STRUCTURE AND ORIENTATION OF THE CHROMOPHORE IN A DIMERIC PHYTOCHROME MOLECULE

A model for the molecular structure and orientation of red‐light absorbing form of phytochrome (P,) chromophores in a dimeric molecular model of Pr is proposed. A chromophore model with probable molecular structures was generated to reproduce the absorption spectrum produced by its π‐electron conjugating system. The model has C5‐Z, syn, C10‐E, anti and C15‐Z, syn configurations and a protonation at a C‐ring nitrogen. Orientation of the chromophore model in the dimeric phytochrome molecular was analyzed by displaying the atoms of the chromophore, the coordinates of which were converted into those with respect to the molecular axes to the dimeric molecule, on a 3‐D graphic workstation. The conversions were performed by using the azimuthal angles between the Z axis of the dimeric molecule (axis of 2‐fold rotational symmetry) and the dipole moments of the electronic transition at the blue‐ (384 nm) and red‐ (667 nm) absorbing bands of the chromophore, which were calculated as 55.5° and 59.3°, respectively, based on linear dichroism of the oriented phytochrome molecules. The result demonstrates that the long axis of the P, chromophore lies almost parallel to the Y axis of the molecular model, and that the tetrapyrrolic chromophore is well contained within the flat chromophoric domain without protruding from it, a configuration that assures that the chromophore is protected against aqueous environments. The model may explain the rotation angle of the transition moment of the red‐absorbing band, induced by the phototransformation from Pr to Prr which we measured as smaller than that measured in nonoriented preparations by a photoselection technique. The model also suggests a molecular basis for the polarotropic response of phytochrome.

Quantum chemical study of ligand-receptor electrostatic interactions in molecular recognition of the glutamate receptor

Abstract To understand the mechanism of molecular recognition of glutamate receptors, we calculated the dipole moments, net charges, and electrostatic potentials of the agonists and antagonists of the glutamate receptors under aqueous conditions by the ab initio molecular orbital method at the HF/6-311++G(3df,2pd) level. All of the ligands had negative net charges at both termini and, consequently, formed negative electrostatic potentials at these termini. We further calculated the net charges and electrostatic potential of the S1S2 lobes of the glutamate receptor subunit GluR2 under aqueous conditions by the semiempirical PM3 molecular orbital method, and found that the ligand-binding cleft of the S1S2 lobes formed a primarily positive electrostatic potential. A strongly positive electrostatic potential was formed particularly around Arg485 in the S1 lobe. A negative electrostatic potential was observed only in a small region around Glu657 in the S2 lobe in the ligand-binding cleft. When a ligand approaches the ligand-binding cleft, it may proceed to Arg485 in the S1 lobe, due to both repulsion by the negative electrostatic potential of Glu657 as well as the attraction of the strongly positive electrostatic potential of Arg485 itself.

Models for the Change in Chromophore Structure of Allophycocyanin Corresponding to Its Observed Reversible Change in Absorbance

On the basis of the ZDO approximation of LCAO-ASMO-SCF-CI theory of π-electrons, the optical absorption of phycocyanobilin is calculated, by taking its interaction with a point-charge and a point-dipole into account. It is thus shown that the reversible change in absorbance of allophycocyanin from Anabaena cylindrica , which was observed by Murakami et al. , can be reproduced according to the following model: when allophycocyanin changes its tertiary structure due to the change in its physico-chemical environment, the terminal pyrrole ring D of one of the two phycocyanobilins in allophycocyanin rotates around the single and double bonds of its adjacent methyne bridge.

Theory of the 3-Methyl Lumiflavin in Solution

The optical absorption of 3-methyl lumiflavin in solution is examined within the framework of π-electron approximation, according to our previous formulation of LCAO-ASMO-SCF-CI calculation. It is thus found that the absorption spectrum of 3-methyl lumiflavin observed in benzene can be reproduced only when the screening of two-center Coulomb repulsion integrals is taken into account for all the pairs of atoms except bonded ones. It is also found that the absorption spectra observed in ethanol or water can be explained by the model interacting with (i) two point-dipoles or (ii) a point-dipole and a point-charge, although the model (ii) is higher in ground-state energy than the model (i) by amount of 3.64 or 5.24 eV in the case of ethanol or water, respectively.

An extended INDO-CI study on protonated retinal Schiff-base

The bond lengths, bond orders, electron densities and optical absorption of the ground state of retinal forming a protonated Schiff-base linkage with a lysine residue (PRSB-Lys) are calculated using the extended INDO-CI molecular orbital method, and the result is compared with the previous one obtained by the π-electron approximation. It is, thus, shown that the π-electron system of PRSB-Lys is appreciably polarized, and that the σ-π interaction in PRSB-Lys is too large to be neglected when a C-C bond in its polyene chain is twisted. It is also shown that the negative counter point-charge exerts influence on the π-electron distribution in a similar way to that shown by the π-electron approximation.