Structural study of the recognition mechanism of tau antibody Tau2r3 with the key sequence (VQIINK) in tau aggregation.

One of the histopathological features of Alzheimer's disease (AD) is higher order neurofibrillary tangles formed by abnormally aggregated tau protein. The sequence 275VQIINK280 in the microtubule-binding domain of tau plays a key role in tau aggregation. Therefore, an aggregation inhibitor targeting the VQIINK region in tau may be an effective therapeutic agent for AD. We have previously shown that the Fab domain (Fab2r3) of a tau antibody that recognizes the VQIINK sequence can inhibit tau aggregation, and we have determined the tertiary structure of the Fab2r3-VQIINK complex. In this report, we determined the tertiary structure of apo Fab2r3 and analyzed differences in the structures of apo Fab2r3 and Fab2r3-VQIINK to examine the ligand recognition mechanism of Fab2r3. In comparison with the Fab2r3-VQIINK structure, there were large differences in the arrangement of the constant and variable domains in apo Fab2r3. Remarkable structural changes were especially observed in the H3 and L3 loop regions of the complementarity determining regions (CDRs) in apo Fab2r3 and the Fab2r3-VQIINK complex. These structural differences in CDRs suggest that formation of hydrophobic pockets suitable for the antigen is important for antigen recognition by tau antibodies.

Quantum mechanical tunnelling through the catalytic effects of A2451 ribosomal residue during a stepwise peptide bond formation.

The search for the mechanism of ribosomal peptide bond formation is still ongoing. Even though the actual mechanism of peptide bod formation is still unknown, the dominance of proton transfer in this reaction is known for certain. Therefore, it is vital to take the quantum mechanical effects on proton transfer reaction into consideration; the effects of which were neglected in all previous studies. In this study, we have taken such effects into consideration using a semi-classical approach to the overall reaction mechanism. The M06-2X density functional with the 6-31++G(d,p) basis set was used to calculate the energies of the critical points on the potential energy surface of the reaction mechanism, which are then used in transition state theory to calculate the classical reaction rate. The tunnelling contribution is then added to the classical part by calculating the transmission permeability and tunnelling constant of the reaction barrier, using the numerical integration over the Boltzmann distribution for the symmetrical Eckart potential. The results of this study, which accounts for quantum effects, indicates that the A2451 ribosomal residue induces proton tunnelling in a stepwise peptide bond formation.

Theoretical study on carbon-carbon short contact of ∼2.3 Å: intermediate state between nonbonding and σ-covalent bonding.

An unusual intermolecular carbon-carbon short contact, observed previously in the crystal structure of the copper complex of pyridoxal-5-phosphate- pyridoxamine-5-phospate Schiff base, was investigated from a standpoint of quantum chemistry by DFT calculations with plane wave basis sets. The DFT-optimized structure qualitatively reproduced the short contact (2.6-2.8 Å) of the intermolecular carbon-carbon pairs for the dimer of the copper complexes in the unit cell, compared to that (∼2.3 Å) of the X-ray diffraction data. By the occupied and unoccupied orbitals, the dimer showed the in-phase and out-of-phase interactions along the direction of the intermolecular distance. The dimer of the copper complexes was confirmed as the stable intermediate between nonbonding and σ-covalent bonding by the electronic energy curve along the distance of the monomers.

CH-π interaction in VQIVYK sequence elucidated by NMR spectroscopy is essential for PHF formation of tau.

One of the histopathological features of Alzheimer's disease (AD) is higher order neurofibrillary tangles formed by abnormally aggregated tau protein. Investigation of the mechanism of tau aggregation is important for the clarifying the cause of AD and the development of therapeutic drugs. The microtubule-binding domain, which consists of repeats of similar amino acids (R1-R4) is thought to form the core component of paired helical filament (PHF). The hexapeptide(306) VQIVYK(311) of R3 has been shown to take a key role of promoting tau aggregation and assumed that its CH-π interaction between the side chains of Ile308 and Tyr310 would contribute in stabilizing the filament. In this work, we investigated a short isoform of tau (4RTau), R3, VQIVYK peptide and their mutants by thioflavin S (ThS) fluorescence, and NMR measurements, and proved for the first time that this CH-π interaction stabilizes the filament at the atomic level. In addition, by molecular modeling, we revealed that this interaction further supports an extended amphipathic structure for molecular self-association during the process of PHF formation of tau protein. The present work indicates new approach that inhibits the CH-π interaction for developing a therapeutic agent for AD.

A model theoretical study on ligand exchange reactions of CooA.

Rr-CooA is a CO-sensor heme protein, where binding of CO with the heme group stimulates a transcriptional activator activity of CooA. In this process, the heme undergoes a series of ligand exchanges. In the ferric form, the heme has Cys75 and Pro2 as the axial ligands. In the reduced ferrous form, the heme has His77 instead of Cys75 as an axial ligand with Pro2. Only in the reduced form, CooA can bind CO that replaces Pro2. Model calculations are carried out to elucidate the ligand exchange reactions of CooA. The coordinated proline is found to be the neutral, protonated form. The ligand exchange of cysteine for histidine is reproduced by a relatively small model. This exchange would be mainly due to difference in stability of the non-bonding sulfur p-orbital in Cys75 between the ferric and ferrous states. The selectivity of gas molecules among CO, NO, and O2 in the proteins is explained by the relative stability of products for Rr-CooA. This is also the case for Ch-CooA, where the amino group of the N-terminus and a histidine are coordinated to the iron ion both in the ferric and ferrous states. The ability to bind the gas molecules is a little stronger in Rr-CooA than in Ch-CooA. In the ferric form of Rr-CooA, heme is deformed to a ruffled form whereas heme is planar in the ferrous form, which leads to a red-shifted Q-band in the former.

Analytical study of superaromaticity in cycloarenes and related coronoid hydrocarbons.

Recently synthesized septulene is a unique cycloarene molecule in that no macrocyclic conjugation circuits can be chosen from the π-system. This molecule has essentially no superaromatic stabilization energy (SSE) and can be viewed as an ideal nonsuperaromatic macrocycle. SSEs for kekulene and other cycloarenes are also very small. In these hydrocarbons, a macrocycle formed by fused benzene rings effectively suppresses not only the aromaticity inherent in macrocyclic (4n+2)-site conjugation circuits but also the antiaromaticity inherent in macrocyclic (4n±1)-site circuits. Comparative study of superaromaticity in multilayered coronoid hydrocarbons revealed that not only SSE but also the HOMO contribution to SSE is minimized in odd-layered coronoids.

A conserved motif within the flexible C-terminus of the translational regulator 4E-BP is required for tight binding to the mRNA cap-binding protein eIF4E.

Although the central α-helical Y(X)4LΦ motif (X, variable amino acid; Φ, hydrophobic amino acid) of the translational regulator 4E-BP [eIF (eukaryotic initiation factor) 4E-binding protein] is the core binding region for the mRNA cap-binding protein eIF4E, the functions of its N- and C-terminal flexible regions for interaction with eIF4E remain to be elucidated. To identify the role for the C-terminal region in such an interaction, the binding features of full-length and sequential C-terminal deletion mutants of 4E-BPn (n=1-3) subtypes were investigated by SPR (surface plasmon resonance) analysis and ITC (isothermal titration calorimetry). Consequently, the conserved PGVTS/T motif within the C-terminal region was shown to act as the second binding region and to play an important role in the tight binding to eIF4E. The 4E-BP subtypes increased the association constant with eIF4E by approximately 1000-fold in the presence of this conserved region compared with that in the absence of this region. The sequential deletion of this conserved region in 4E-BP1 showed that deletion of Val81 leads to a considerable decrease in the binding ability of 4E-BP. Molecular dynamics simulation suggested that the conserved PGVTS/T region functions as a kind of paste, adhering the root of both the eIF4E N-terminal and 4E-BP C-terminal flexible regions through a hydrophobic interaction, where valine is located at the crossing position of both flexible regions. It is concluded that the conserved PGVTS/T motif within the flexible C-terminus of 4E-BP plays an auxiliary, but indispensable, role in strengthening the binding of eIF4E to the core Y(X)4LΦ motif.

Photochemical dynamics of indolylmaleimide derivatives.

On-the-fly nonadiabatic ab initio molecular dynamics simulations have been carried out for three anionic species of indolylmaleimides (3-(1H-3-indolyl)-2,5-dihydro-1H-2,5-pyrroledione, IM) to clarify the mechanisms of photochemical reactions. The results are obtained for (i) a monovalent anion with a deprotonated indole NH group (IM(-)'), (ii) a monovalent anion with a deprotonated maleimide NH group (IM(-)'') and (iii) a divalent anion with doubly deprotonated indole and the maleimide NH groups (IM(2-)). Quantum chemical calculations are treated at the three state averaged complete-active space self-consistent field level for 6 electrons in 5 orbitals with the cc-pVDZ basis set (CAS (6, 5) SCF/cc-pVDZ). Molecular dynamics simulations are performed with electronically nonadiabatic transitions included using the Zhu-Nakamura version of the trajectory surface hopping (ZN-TSH) method. It is found that the nonadiabatic transitions occur accompanied by the stretching and shrinking motions of the N(7)-C(8) bond in the case of IM(-)' and the C(11)-N(12) bond in IM(2-) rather than the twisting motion of the dihedral angle. We also found that the ultrafast S(2)→ S(1) nonadiabatic transitions occur through the conical intersection (CoIn) right after photoexcitation to S(2) in IM(-)' and IM(2-). Furthermore, the S(1)→ S(0) nonadiabatic transitions are found to take place in IM(-)'. It is concluded that IM(2-) would mainly contribute to the photoemission, because the S(1)← S(0) and S(2)← S(0) transitions of IM(-)'' are dipole-forbidden transitions and, moreover, IM(2-) is found to be the only species to stay in the S(1) state without non-radiative decay.

Identification and function of the second eIF4E-binding region in N-terminal domain of eIF4G: comparison with eIF4E-binding protein.

The eukaryotic initiation factor 4E (eIF4E) serves as a master switch that controls mRNA translation through the promotive binding to eIF4G and the regulative binding with the endogenous inhibitor 4E-BP. Although the bindings of eIF4G and 4E-BP to eIF4E proceed through the common eIF4E recognition Y(X)(4)Lφ motif (X: variable, φ: hydrophobic) (first binding site), the relationship between their eIF4E binding mode and the functional difference is hardly known. Recently, we have clarified the existence and function of the second eIF4E binding site in 4E-BP. Surface plasmon resonance (SPR) analysis based on the sequential comparison between 4E-BP and eIF4GI clarified that eIF4G has the second binding site at the periphery of the (597)SDVVL(601) sequence and that it plays an auxiliary but indispensable function in stabilizing the binding of the first binding sequence (572)YDREFLL(578). The kinetic parameters of the interactions of the eIF4GI and 4E-BP2 fragment peptides with eIF4E showed that the association (ka) and dissociation (kd) rates of the former peptide are about three and two orders of magnitude lower than those of the latter peptide, respectively. This means that eIF4G has a potent resistive property for release from eIF4E, although its rate of binding to eIF4E is not as high as that of 4E-BP, that is, 4E-BP is apt to bind to and be released from eIF4E, as compared with eIF4G. Isothermal titration calorimetry (ITC) showed the opposite behavior between the second binding sites of eIF4GI and 4E-BP for the interaction with eIF4E. This clearly indicates the importance of the second binding region for the difference in function between eIF4G and 4E-BP for eIF4E translation.

Structural scaffold for eIF4E binding selectivity of 4E-BP isoforms: crystal structure of eIF4E binding region of 4E-BP2 and its comparison with that of 4E-BP1.

To clarify the higher eukaryotic initiation factor 4E (eIF4E) binding selectivity of 4E-binding protein 2 (4E-BP2) than of 4E-BP1, as determined by Trp fluorescence analysis, the crystal structure of the eIF4E binding region of 4E-BP2 in complex with m(7) GTP-bound human eIF4E has been determined by X-ray diffraction analysis and compared with that of 4E-BP1. The crystal structure revealed that the Pro47-Ser65 moiety of 4E-BP2 adopts a L-shaped conformation involving extended and α-helical structures and extends over the N-terminal loop and two different helix regions of eIF4E through hydrogen bonds, and electrostatic and hydrophobic interactions; these features were similarly observed for 4E-BP1. Although the pattern of the overall interaction of 4E-BP2 with eIF4E was similar to that of 4E-BP1, a notable difference was observed for the 60-63 sequence in relation to the conformation and binding selectivity of the 4E-BP isoform, i.e. Met-Glu-Cys-Arg for 4E-BP1 and Leu-Asp-Arg-Arg for 4E-BP2. In this paper, we report that the structural scaffold of the eIF4E binding preference for 4E-BP2 over 4E-BP1 is based on the stacking of the Arg63 planar side chain on the Trp73 indole ring of eIF4E and the construction of a compact hydrophobic space around the Trp73 indole ring by the Leu59-Leu60 sequence of 4E-BP2.

Electronic and magnetic characteristics of polycyclic aromatic hydrocarbons with factorizable Kekulé structure counts.

The Kekulé structure count (K) for some types of polycyclic aromatic hydrocarbons (PAHs), such as fluoranthene and perylene, can be factorized into the product of those for two or more aromatic subunits. The ring-current map for these PAHs placed in a perpendicular magnetic field exhibits a substantial localization on aromatic subunits. We found that such localization of π circulation is a characteristic of fairly small K-factorizable species in the neutral electronic state. Even in such a case, no single π molecular orbital (πMO) is associated with localized π circulation. Apparent localization of π circulation is caused by the superposition of currents induced by all occupied πMOs. π circulation is less localized in larger K-factorizable species.

Use of a genetic algorithm for multiobjective design optimization of the femoral stem of a cemented total hip arthroplasty.

There are many designs of the femoral stem of a cemented total hip arthroplasty, and mechanical failure of the stem is caused by several factors related to the cement, such as failure of the cement. Optimization of the shape of the stem, especially multiobjective optimization, is required to solve these design problems because a cement fracture is caused by multiple factors. The objective of this study was to determine a stem geometry considering multiple factors at the same time. A three-dimensional finite element model of the proximal femur was developed from a composite femur. A total of four objective functions--two objective functions, the largest maximum principal stress of proximal and distal sections in the cement mantle, for each of the two boundary conditions, walking and stair climbing--were used. The neighborhood cultivation genetic algorithm was introduced to minimize these objective functions. The results showed that the geometry that leads to a decrease in the proximal cement stress and the geometry that leads to a decrease in the distal cement stress were not the same. However, the results of the walking and the stair climbing conditions matched. Five dominant stem designs were considered to be the Pareto solution, and one design was identified as the "better design" for all objective functions. It was shown that multiobjective optimization using a genetic algorithm may be used for optimizing the shape of the femoral stem in order to avoid cement fracture.

Crystallization and preliminary X-ray crystallographic analysis of BxlA, an intracellular beta-D-xylosidase from Streptomyces thermoviolaceus OPC-520.

BxlA from Streptomyces thermoviolaceus OPC-520, together with the extracellular BxlE and the integral membrane proteins BxlF and BxlG, constitutes a xylanolytic system that participates in the intracellular transport of xylan-degradation products and the production of xylose. To elucidate the mechanism of the hydrolytic degradation of xylooligosaccharides to xylose at the atomic level, X-ray structural analysis of BxlA was attempted. The recombinant BxlA protein (molecular weight 82 kDa) was crystallized by the hanging-drop vapour-diffusion method at 289 K. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 142.2, b = 129.5, c = 101.4 A, beta = 119.8 degrees , and contained two molecules per asymmetric unit (V(M) = 2.47 A(3) Da(-1)). Diffraction data were collected to a resolution to 2.50 A and provided a data set with an overall R(merge) of 8.3%.

Unusually high aromaticity and diatropicity of bond-alternate benzene.

Enormous effort has been devoted to the elucidation of possible effects of bond-length alternation on the benzene pi-system. Benzene tends to stay highly aromatic and highly diatropic even if strong bond-length alternation is introduced artificially into the pi-system. Such peculiar aromatic and magnetic characters of benzene were justified consistently and unambiguously within a single theoretical framework. From all physically sound points of view, bond-alternate benzene is highly aromatic with a large aromatic stabilization energy. We confirmed that in the annulene family benzene is least sensitive in aromaticity to bond-length alternation.

Nonadiabatic ab initio dynamics of a model protonated Schiff base of 9-cis retinal.

The dynamics of the photoisomerization of a model protonated Schiff base of 9-cis retinal in isorhodopsin is investigated using nonadiabatic molecular dynamics simulation combined with ab initio quantum chemical calculations on-the-fly. The quantum chemical part is treated at the complete-active space self-consistent field level for six electrons in six active pi orbitals with the 6-31G basis set (CASSCF(6,6)/6-31G). The probabilities of nonadiabatic transitions between the S(1) ((1)pipi*) and S(0) states are estimated in light of the Zhu-Nakamura theory. The photoinduced cis-trans isomerization of 9-cis retinal proceeds slower than that of its 11-cis analogue and at a lower quantum yield, confirming experimental observations. An energetic barrier in the excited state impedes the elongation and twist of the C(9)=C(10) stretch and torsion coordinates, respectively, resulting in the trapping of trajectories before transition. Consequently, the isomerization takes longer time and the transition more often occurs at smaller twist angle of =C(8)-C(9)=C(10)-C(11)=, which leads to regeneration of the 9-cis reactant. Thus, neither the smaller twist observed in the X-ray crystal nor the slower movement of nuclei in the transition region would be the main reason for the longer reaction time and lower yield. A well-known space-saving asynchronous bicycle pedal or crankshaft photoisomerization mechanism is found to be operational in 9-cis retinal. The simulation in vacuo suggests that the excited-state barrier and the photoisomerization itself are intrinsic properties of the visual chromophore and not triggered mainly by the protein environment that surrounds the chromophore.

Crystal structure of the human tau PHF core domain VQIINK complexed with the Fab domain of monoclonal antibody Tau2r3.

Neurofibrillary tangles formed by abnormally aggregated tau protein are a histopathological feature of tauopathies. A tau aggregation inhibitor is a potential therapeutic agent for tauopathies. In this study, we prepared a monoclonal antibody for tau, monoclonal antibody to tau protein (Tau2r3), using as epitope the 272 GGKVQIINKKLD283 peptide in the microtubule-binding domain of tau, the key region mediating tau aggregation. We show that Tau2r3 clearly inhibits tau aggregation. To analyze the inhibition mechanism of Tau2r3, we solved the crystal structure of the Fab domain of Tau2r3 (Fab2r3) in complex with the VQIINK peptide. In the Fab2r3-VQIINK structure, the second and sixth polar residues and the fourth hydrophobic residue of VQIINK are crucial for binding to Fab2r3. The structural data for the Fab2r3-VQIINK complex could contribute to the design of new tau aggregation inhibitors.

Crystal structure and molecular dynamics simulation of ubiquitin-like domain of murine parkin.

Parkin is the gene product identified as the major cause of autosomal recessive juvenile Parkinsonism (AR-JP). Parkin, a ubiquitin ligase E3, contains a unique ubiquitin-like domain in its N-terminus designated Uld which is assumed to be a interaction domain with the Rpn 10 subunit of 26S proteasome. To elucidate the structural and functional role of Uld in parkin at the atomic level, the X-ray crystal structure of murine Uld was determined and a molecular dynamics simulation of wild Uld and its five mutants (K27N, R33Q, R42P, K48A and V56E) identified from AR-JP patients was performed. Murine Uld consists of two alpha helices [Ile23-Arg33 (alpha1) and Val56-Gln57 (alpha2)] and five beta strands [Met1-Phe7 (beta1), Tyr11-Asp18 (beta2), Leu41-Phe45 (beta3), Lys48-Pro51 (beta4) and Ser65-Arg72 (beta5)] and its overall structure is essentially the same as that of human ubiquitin with a 1.22 A rmsd for the backbone atoms of residues 1-76; however, the sequential identity and similarity between both molecules are 32% and 63%, respectively. This close resemblance is due to the core structure built by same hydrogen bond formations between and within the backbone chains of alpha1 and beta1/2/5 secondary structure elements and by nearly the same hydrophobic interactions formed between the nonpolar amino acids of their secondary structures. The side chain NetaH of Lys27 on the alpha1 helix was crucial to the stabilization of the spatial orientations of beta3 and beta4 strands, possible binding region with Rpn 10 subunit, through three hydrogen bonds. The MD simulations showed the K27N and R33Q mutations increase the structural fluctuation of these beta strands including the alpha1 helix. Reversely, the V56E mutant restricted the spatial flexibility at the periphery of the short alpha2 helix by the interactions between the polar atoms of Glu56 and Ser19 residues. However, a large fluctuation of beta4 strand with respect to beta5 strand was induced in the R42P mutant, because of the impossibility of forming paired hydrogen bonds of Pro for Arg42 in wild Uld. The X-ray structure showed that the side chains of Asp39, Gln40 and Arg42 at the N-terminal periphery of beta3 strand protrude from the molecular surface of Uld and participate in hydrogen bonds with the polar residues of neighboring Ulds. Thus, the MD simulation suggests that the mutation substitution of Pro for Arg42 not only causes the large fluctuation of beta3 strand in the Uld but also leads to the loss of the ability of Uld to trap the Rpn 10 subunit. In contrast, the MD simulation of K48A mutant showed little influence on the beta3-beta4 loop structure, but a large fluctuation of Lys48 side chain, suggesting the importance of flexibility of this side chain for the interaction with the Rpn 10 subunit. The present results would be important in elucidating the impaired proteasomal binding mechanism of parkin in AR-JP.

Detection of free monomeric silver(I) and gold(I) cyanides, AgCN and AuCN: microwave spectra and molecular structure.

The chemistry of the group 11 metal cyanide system has been of considerable interest because of the commercial importance of some of the complexes formed in this system. These metal cyanides contain one-dimensional linear -M-CN-M-CN-M- chains in the solid state; however, they have not been observed as free monomeric species. This Article reports the first detection of monomeric AgCN and AuCN in the gas phase by using rotational spectroscopy. The sputtering reaction of silver and/or gold sheets placed on a stainless steel cathode with CH3CN diluted in Ar resulted in the production of AgCN and AuCN spectra. Spectroscopic observation of the parent and several rare isotopic species allowed the determination of r(0), r(s), r(Iepsilon), r(m)(1), and r(m)(2) structures in the case of AgCN and r(0) and r(s) structures in the case of AuCN. All data indicate that these two species have a linear MCN geometry with a low-energy bending vibration.

Three-/four-repeat-dependent aggregation profile of tau microtubule-binding domain clarified by dynamic light scattering analysis.

The analysis of the self-assembly mechanism of the tau microtubule-binding domain (MBD) could provide the information needed to develop an effective method for the inhibition of the tau filament formation because of its core region that forms the filament. The MBD domain in the living body consists of similar three or four 31- to 32-residue repeats, namely 3RMBD (R134) and 4RMBD (R1234), respectively. The filament formation of the MBD has been mainly investigated by fluorescence spectroscopy utilizing the beta-sheet structure-binding signal sensor thioflavin. This method observes the aggregation indirectly, and provides no information on the time-dependent change in aggregation size or volume. Thus, to determine the structure necessary for initiating MBD self-association, the dynamic light scattering (DLS) method was applied to the analysis of the aggregations of 3RMBD, 4RMBD and their component single repeats and shown to be a powerful tool for directly analyzing filament formation. DLS analysis clearly showed that the building unit for initiating the aggregation is the intermolecular R3-R3 disulfide-bonded dimer for 3RMBD and the intramolecular R2-R3 disulfide-bonded monomer for 4RMBD, and their aggregation processes under physiological condition differ from each other, which has not been clearly revealed by the conventional fluorescence method. The repeat-number-dependent aggregation model of MBD, together with the function of each repeat, reported in this paper should help to devise a method of preventing tau PHF formation.

Nonadiabatic ab initio dynamics of two models of Schiff base retinal.

On-the-fly classical dynamics calculations combined with ab initio quantum chemical computations are carried out for two models of protonated Schiff base retinal in vacuo. The models are the 6pi system of 2-cis-penta-2,4-dieneimminium cation and the 12pi system in which two methyl groups are removed from the Schiff base of retinal. The CASSCF(6,6) level with the 6-31G basis set was employed for the quantum chemical part and the velocity Verlet algorism is utilized for time evolution of trajectories. The probabilities of nonadiabatic transition between the excited and ground state are estimated by the Zhu-Nakamura formulas. The 9-cis form product in addition to the all-trans one is generated in the present gas phase calculation for the 12pi model, despite the 9-cis generation being suppressed in protein. We have found that energy relaxation on the ground state occurs in two steps in the 12pi model. In the first step a metastable intermediate state is formed at approximately 100 fs after photoexcitation at the energy around 20-40 kcal/mol down from the excited potential energy surface, then it further relaxes to the energy around 60-80 kcal/mol from the excited surface, leading to the final state (second step). This relaxation pattern can be seen in all the three pathways to the all-trans, 9-cis, and (reverted) 11-cis form. Fourier transformation analysis reveals that the effective vibrational frequencies of the intermediate state are 1600-2000 cm(-1), which can be attributed to the conjugate CC bond frequencies in the electronic ground state. The two-step relaxation may be due to dynamical barriers. The two-step relaxation is not revealed in the smaller 6pi model. The crank-shaft motion of the C11C12 and C9C10 bonds is found in the isomerization, which indicates the motion is intrinsic in retinal, not due to the surrounding protein. The branching ratio is about 1:1:2 for the all-trans, 9-cis, and 11-cis form generation. The ratio is different from earlier works where Tully's fewest switching scheme was employed. The bond length and the dihedral angle at the transitions are also analyzed to investigate the transition mechanism.