Spectral tuning of photoactive yellow protein

We report a theoretical study on the optical properties of a small, water-soluble photosensory receptor, photoactive yellow protein (PYP). A hierarchical ab initio molecular orbital calculation accurately evaluated the optical absorption maximum of the wild-type, as well as the lambda(max) values of 12 mutants. Electronic excitation of the chromophore directly affects the electronic state of nearby atoms in the protein environment. This effect is explicitly considered in the present study. Furthermore, the spectral tuning mechanism of PYP was investigated at the atomic level. The static disorder of a protein molecule is intimately related to the complex nature of its energy landscape. By using molecular dynamics simulation and quantum mechanical structure optimization, we obtained multiple minimum energy conformations of PYP. The statistical distribution of electronic excitation energies of these minima was compared with the hole-burning experiment (Masciangioli, T. [2000] Photochem. Photobiol. 72, 639), a direct observation of the distribution of excitation energies.     

Electronic structure of the PYP chromophore in its native protein environment

We report on supermolecular ab initio calculations which clarify the role of the local amino acid environment in determining the unique electronic structure properties of the photoactive yellow protein (PYP) chromophore. The extensive ab initio calculations, at the level of the CC2 and EOM-CCSD methods, allow us to explicitly address how the interactions between the deprotonated p-coumaric thio-methyl ester (pCTM-) chromophore and the surrounding amino acids act together to create a specifically stabilized pCTM- species. Particularly noteworthy is the role of the Arg52 amino acid in stabilizing the chromophore against autoionization, and the role of the Tyr42 and Glu46 amino acids in determining the hydrogen-bonding properties that carry the dominant energetic effects.     

Role of hydrogen-bond network in energy storage of bacteriorhodopsin's light-driven proton pump revealed by ab initio normal-mode analysis

Vibrational modes of the hydrogen-bond network in the binding site of bacteriorhodopsin (bR), a protein in halobacteria functioning as a light-driven proton pump, were investigated by an ab initio quantum mechanical/molecular mechanical (QM/MM) method. Normal-mode analysis calculations for O-D and N-D stretching modes of internal water molecules and the Schiff base of the retinal chromophore in the early intermediate state, K, reproduced well experimentally observed vibrational spectra. Supported by agreement with observed spectra, the QM/MM calculation suggests that weakened hydrogen bonds upon photoisomerization of the chromophore are an important means of energy storage in bR.     

Ab initio excited-state dynamics of the photoactive yellow protein chromophore

The photoisomerization mechanism of the neutral form of the photoactive yellow protein (PYP) chromophore is investigated using ab initio quantum chemistry and first-principles nonadiabatic molecular dynamics (ab initio multiple spawning or AIMS). We identify the nature of the two lowest-lying excited states, characterize the short-time behavior of molecules excited directly to S2, and explain the origin of the experimentally observed wavelength-dependent photoisomerization quantum yield.     

Quantum mechanical map for protein-ligand binding with application to beta-trypsin/benzamidine complex

We report full ab initio Hartree-Fock calculation to compute quantum mechanical interaction energies for beta-trypsin/benzamidine binding complex. In this study, the full quantum mechanical ab initio energy calculation for the entire protein complex with 3238 atoms is made possible by using a recently developed MFCC (molecular fractionation with conjugate caps) approach in which the protein molecule is decomposed into amino acid-based fragments that are properly capped. The present MFCC ab initio calculation enables us to obtain an "interaction spectrum" that provides detailed quantitative information on protein-ligand binding at the amino acid levels. These detailed information on individual residue-ligand interaction gives a quantitative molecular insight into our understanding of protein-ligand binding and provides a guidance to rational design of potential inhibitors of protein targets.     

烷基自由基β位裂解反应类反应势垒与速率常数的精确计算

提出反应类等键方法并用于高温燃烧机理中一类重要反应——烷基自由基β位裂解反应的反应势垒和速率常数的精确校正计算. 通过10种不同从头算水平对类反应中5个代表反应的反应势垒的计算发现, 用反应类等键反应方法和直接从头算方法获得的5 个代表反应的反应势垒最大绝对偏差的平均值分别为5.32 和16.16 kJ·mol^-1, 表明反应类等键反应方法计算的反应势垒对不同水平从头算方法的依赖性小, 可在较低从头算水平计算得到精确的反应势垒, 解决大分子体系反应势垒的精确计算问题. 此外应用反应类等键反应方法在BHandHLYP/cc-pVDZ 从头算水平计算了3 个代表反应的速率常数, 并与文献报道的实验值进行了比较, 其在500-2000 K温度区间内计算速率常数与实验速率常数中较大值与较小值的比值k_max/k_min的平均值为1.67, 最大值也仅有2.49. 表明应用反应类等键反应方法在较低从头算水平即可对同类反应的速率常数进行精确计算.最后在BHandHLYP/cc-pVDZ从头算水平用反应类等键反应方法计算了13个烷基自由基β位裂解反应的速率常数.     

Complete-active-space self-consistent-field/Amber parameterization of the Lys296–retinal–Glu113 rhodopsin chromophore-counterion system

A special hybrid quantum mechanics/molecular mechanics forcefield is defined, parameterized and validated for studying the photoisomerization path of the retinal chromophore in the rhodopsin protein. It couples a multireference ab initio Hamiltonian (CASSCF and second-order multireference many-body perturbation theory using a CASSCF reference) to describe the chromophore while the rest of the protein is approximated with the Amber forcefield. The frontier has been carefully parameterized in order to reproduce full quantum mechanics torsional energy profiles, for both the ground state and the first excited state. It is also shown that replacing the chromophore counterion with point charges is a valid approximation. This result is interpreted in terms of a cancellation effect for which a possible explanation is given.     

Photoinduced isomerization of the photoactive yellow protein (PYP) chromophore: interplay of two torsions, a HOOP mode and hydrogen bonding

We report on a detailed theoretical analysis, based on extensive ab initio calculations at the CC2 level, of the S(1) potential energy surface (PES) of the photoactive yellow protein (PYP) chromophore. The chromophore's photoisomerization pathway is shown to be fairly complex, involving an intimate coupling between single-bond and double-bond torsions. Furthermore, these torsional modes are shown to couple to a third coordinate of hydrogen out-of-plane (HOOP) type whose role in the isomerization is here identified for the first time. In addition, it is demonstrated that hydrogen bonding at the phenolate moiety of the chromophore can hinder the single-bond torsion and thus facilitates double-bond isomerization. These results suggest that the interplay between intramolecular factors and H-bonding determines the isomerization in native PYP.     

Structural and spectroscopical study of glutamic acid in the nonzwitterionic form

The molecular structure of glutamic acid in the non-zwitterionic form has been optimized by using the semiempirical MNDO and AMI methods and an ab initio calculation at the 4–31G level. The results were compared with previous reported data for other amino acids. The ab initio optimized structure was used as the starting point for a further force field calculation, and vibrational frequencies and theoretical assignments were thus obtained. In order to compare these results with experiments, the FT-IR spectrum of glutamic acid in an argon matrix was recorded and the measured frequencies were successfully compared with theoretical values, which were previously scaled by using a set of scaling factors.     

On the conformation of the propranolol molecule

The structure of the propranolol molecule has been optimized within the AM1 and PM3 semiempirical framework followed by ab initio HF/6-31G^* refinement. On each calculation level the conformational space was sampled to search for the lowest-energy conformer(s) from among a few hundreds of conformers at the semiempirical step and next from among a few dozens of conformers at the ab initio level. Finally, five stable conformers were found; each stabilized by one or two of the three possible hydrogen bonds. The geometrical and electronic parameters were established and found to differ only slightly in the structures with the hydrogen bond either present or not.     

Theoretical study on isotope and temperature effect in hydronium ion using ab initio path integral simulation

We have applied the ab initio path integral molecular dynamics simulation to study hydronium ion and its isotopes, which are the simplest systems for hydrated proton and deuteron. In this simulation, all the rotational and vibrational degrees of freedom are treated fully quantum mechanically, while the potential energies of the respective atomic configurations are calculated "on the fly" using ab initio quantum chemical approach. With the careful treatment of the ab initio electronic structure calculation by relevant choices in electron correlation level and basis set, this scheme is theoretically quite rigorous except for Born-Oppenheimer approximation. This accurate calculation allows a close insight into the structural shifts for the isotopes of hydronium ion by taking account of both quantum mechanical and thermal effects. In fact, the calculation is shown to be successful to quantitatively extract the geometrical isotope effect with respect to the Walden inversion. It is also shown that this leads to the isotope effect on the electronic structure as well as the thermochemical properties.     

Insight into the common mechanism of the chromophore formation in the red fluorescent proteins: the elusive blue intermediate revealed

Understanding the chromophore maturation process in fluorescent proteins is important for the design of proteins with improved properties. Here, we present the results of electronic structure calculations identifying the nature of a blue intermediate, a key species in the process of the red chromophore formation in DsRed, TagRFP, fluorescent timers, and PAmCherry. The chromophore of the blue intermediate has a structure in which the π-system of the imidazole ring is extended by the acylimine bond, which can be represented by the model N-[(5-hydroxy-1H-imidazole-2yl)methylidene]acetamide (HIMA) compound. Ab initio and QM/MM calculations of the isolated model and protein-bound (mTagBFP) chromophores identify the anionic form of HIMA as the only structure that has absorption that is consistent with the experiment and is stable in the protein binding pocket. The anion and zwitterion are the only protonation forms of HIMA whose absorption (421 and 414 nm, or 2.95 and 3.00 eV) matches the experimental spectrum of the blue form in DsRed (the absorption maximum is 408 nm or 3.04 eV) and mTagBFP (400 nm or 3.10 eV). The QM/MM optimization of the protein-bound anionic form results in a structure that is close to the X-ray one, whereas the zwitterionic chromophore is unstable in the protein binding pocket and undergoes prompt proton transfer. The computed excitation energy of the protein-bound anionic form of the mTagBFP-like chromophore (3.04 eV) agrees with the experimental absorption spectrum of the protein. The DsRed-like chromophore formation in red fluorescent proteins is revisited on the basis of ab initio results and verified by directed mutagenesis revealing a key role of the amino acid residue 70, which is the second after the chromophore tripeptide, in the formation process.     

Probing the rhodopsin cavity with reduced retinal models at the CASPT2//CASSCF/AMBER level of theory

We show that the ab initio CASPT2//CASSCF strategy previously used to investigate the ground and excited states of the chromophore of the vision receptor rhodopsin (Rh) in vacuo can be successfully implemented in a QM/MM scheme allowing for CASPT2//CASSCF/AMBER geometry optimization and excited state property evaluation in proteins. Two receptor models (Rh-1 and Rh-2) incorporating different reduced chromophores are investigated. It is shown that Rh-2 features a chromophore equilibrium structure with the correct helicity and a lambdamax that is only 52 nm blue-shifted from the observed value. This result should open the way to a qualitatively correct ab initio QM/MM modeling of the early excited state transient species involved in the vision process.     

Modeling the absorption spectrum of tryptophan in proteins

We have applied time-dependent density functional theory (TDDFT) to study the valence pi-pi* excited states of the tryptophan chromophore in the environment of the proteins barnase and human serum albumin. The chromophore is represented by indole. Due to the approximate nature of TDDFT, in the gas phase the calculated vertical transition energies to the 1L valence states are reordered with respect to experiment. The 1L(a) state responds more than the 1L(b) state to the local environment, described fully at the TDDFT level, and to bulk environment, described by a set of point charges. Nevertheless, the vertical transitions are readily identified. For human serum albumin, our calculations predict distinct spectral characteristics between structures with different tryptophan side chain torsion angles. The computational tractability of TDDFT relative to more accurate ab initio methods allows a large part of the surrounding protein environment (up to 100 atoms) to be explicitly included in the TDDFT calculations.     

The Importance of Charge Transfer between the Retinal Chromophore and the Protein Environment in Bacteriorhodopsin: A Theoretical Analysis on Reduced and Oxidized Chromophores

Abstract— The importance of charge transfer(CT) between the retinal chromophore and the protein environment in the ground state of bacteriorhodopsin(BR) has been verified by using ab initio and semiempirical molecular orbital methods. We hypothesize that the chromophore is stabilized in BR by highest occupied molecular orbital-lowest unoccupied molecular orbital(HOMO-LUMO) interaction with the protein environment. If sufficient charge is transferred between two sites due to the strong HOMO-LUMO interaction, the chromophore might be treated as a one-electron reduced species(when it behaves as an electron acceptor), or as a one-electron oxidized one (when it acts as an electron donor).In both optimized geometries, the -conjugated systems exhibit a drastic decrease in bond alternation. To estimate the rotational barrier for thermal isomerization between the al-trans and the 13,15-dicis form, the potential energy curve around these two bonds was computed. The first -_* transition energy was also calculated for an inspection of the opsin shift. The barrier height and the transition energy became much lower as a result of the chromophore reduction. The site selectivity in photo- and thermal isomerization and the opsin shift in BR can be well explained by considering CT from the protein environment to the chromophore.     

Comparison of AM1 and PM3 semiempirical to ab initio methods in the study of Diels-Alder reactions of butadiene and cyclopentadiene with cyanoethylenes

Assuming a concerted synchronous mechanism with one transition state of the Diels-Alder reactions, the structures of the transition states and the activation energies for the reactions of butadiene and cyclopentadiene with cyanoethylenes were calculated by AM1 and PM3 semiempirical methods. The structural parameters were compared with those obtained by high level Gaussian calculations, whereas the activation energies were compared both with the ab initio calculations and those obtained experimentally. The structural properties calculated with PM3 methods are in general in better agreement with the ab initio calculations. The low level ab initio calculations are in many cases worse than the semiempirical methods. All predicted activation energies with both semiempirical methods are up to 300% higher than the experimental values. The predicted reactivity is also opposite to the experimental data. Only the very high level Gaussian calculations are in good correlation with experimental results. The predicted selectivity of the reaction is also opposite to the experimental facts. Two explanations are offered for this discrepancy: AM1 and PM3 methods cannot handle the calculation of the concerted Diels-Alder transition states and are not recommended to be used for that purpose, or this Diels-Alder reaction is not concerted but is stepwise.     

Achieving fast convergence of ab initio free energy perturbation calculations with the adaptive force-matching method

This paper studies the possibility of improving the convergence of ab initio free energy perturbation (FEP) calculations by developing customized force fields with the adaptive force-matching (AFM) method. The ab initio FEP method relies on a molecular mechanics (MM) potential to sample configuration space. If the Boltzmann weight of the MM sampling is close to that of the ab initio method, the efficiency of ab initio FEP will be optimal. The difference in the Boltzmann weights can be quantified by the relative energy difference distribution (REDD). The force field developed through AFM significantly improves the REDD when compared with standard MM models, thus improving the convergence of the ab initio FEP calculation. The static dielectric constant ε_s of ice-Ih was studied with PW-91 through ab initio FEP. With a customized force field developed through AFM, we were able to converge ε_s to 80 ± 4 with 3,600 configurations. A similar ab initio FEP calculation with the TIP4P model would require 220 times more configurations to achieve the same accuracy. Our study indicates that the PW-91 functional underestimates ice-Ih ε_s by about 20%.     

Anharmonic vibrational calculations modeling the raman spectra of intermediates in the photoactive yellow protein (PYP) photocycle

The role of anharmonic effects in the vibrational spectroscopy of the dark state and two major chromophore intermediates of the photoactive yellow protein (PYP) photocycle is examined via ab initio vibrational self-consistent field (VSCF) calculations and time-resolved resonance Raman spectroscopy. For the first time, anharmonicity is considered explicitly in calculating the vibrational spectra of an ensemble consisting of the PYP chromophore surrounded by model compounds used as mimics of the important active-site residues. Predictions of vibrational frequencies on an ab initio corrected semiempirical potential energy surface show remarkable agreement with experimental frequencies for all three states, thus shedding light on the potential along the reaction path. For example, calculated frequencies for vibrational modes of the red-shifted intermediate, PYPL, exhibit an overall average error of 0.82% from experiment. Upon analysis of anharmonicity patterns in the PYP modes we observe a decrease in anharmonicity in the C8-C9 stretching mode nu29 (trans-cis isomerization marker mode) with the onset of the cis configuration in PYPL. This can be attributed to the loss of the hydrogen-bonding character of the adjacent C9-O2 to the methylamine (Cys69 backbone). For several of the modes, the anharmonicity is mostly due to mode-mode coupling, while for others it is mostly intrinsic. This study shows the importance of the inclusion of anharmonicity in theoretical spectroscopic calculations, and the sensitivity of experiments to anharmonicity. The characterization of protein active-site residues by small molecular mimics provides an acceptable chemical structural representation for biomolecular spectroscopy calculations.     

分子间相互作用的研究——-价轨道模型势从头算能量分解法

研究分子间相互作用是了解液体,固体性质和结构以及气体性质的关键,也是研究化学和生物化学催化机制及化学反应途径的重要方面.因此,近几年来这个领域的理论和实验研究引起了人们广泛的兴趣并取得了长足的进步.特别值得指出的是Morokuma等提出的基于单行列式从头算的能量分解法,较好地解决了很多体系中分子间相互作用的本质问题,受到了理论化学界的普遍重视.但是这种方法很费计算机时间,对于较大的体系,特别是含有重原子的体系,应用受到了限制.因此简化这种方法,使它能够比较容