Cation radicals of xanthophylls

Carotenes and xanthophylls are well known to act as electron donors in redox processes. This ability is thought to be associated with the inhibition of oxidative reactions in reaction centers and light-harvesting pigment–protein complexes of photosystem II (PSII). In this work, cation radicals of neoxanthin, violaxanthin, lutein, zeaxanthin, β-cryptoxanthin, β-carotene, and lycopene were generated in solution using ferric chloride as an oxidant and then studied by absorption spectroscopy. The investigation provides a view toward understanding the molecular features that determine the spectral properties of cation radicals of carotenoids. The absorption spectral data reveal a shift to longer wavelength with increasing π-chain length. However, zeaxanthin and β-cryptoxanthin exhibit cation radical spectra blue-shifted compared to that of β-carotene, despite all of these molecules having 11 conjugated carbon–carbon double bonds. CIS molecular orbital theory quantum computations interpret this effect as due to the hydroxyl groups in the terminal rings selectively stabilizing the highest occupied molecular orbitals of preferentially populated s-trans-isomers. The data are expected to be useful in the analysis of spectral results from PSII pigment–protein complexes seeking to understand the role of carotene and xanthophyll cation radicals in regulating excited state energy flow, in protecting PSII reaction centers against photoinhibition, and in dissipating excess light energy absorbed by photosynthetic organisms but not used for photosynthesis.     

Binding free energy calculation with QM/MM hybrid methods for Abl-Kinase inhibitor

We report a Quantum mechanics/Molecular Mechanics–Poisson-Boltzmann/ Surface Area (QM/MM-PB/SA) method to calculate the binding free energy of c-Abl human tyrosine kinase by combining the QM and MM principles where the ligand is treated quantum mechanically and the rest of the receptor by classical molecular mechanics. To study the role of entropy and the flexibility of the protein ligand complex in a solvated environment, molecular dynamics calculations are performed using a hybrid QM/MM approach. This work shows that the results of the QM/MM approach are strongly correlated with the binding affinity. The QM/MM interaction energy in our reported study confirms the importance of electronic and polarization contributions, which are often neglected in classical MM-PB/SA calculations. Moreover, a comparison of semi-empirical methods like DFTB-SCC, PM3, MNDO, MNDO-PDDG, and PDDG-PM3 is also performed. The results of the study show that the implementation of a DFTB-SCC semi-empirical Hamiltonian that is derived from DFT gives better results than other methods. We have performed such studies using the AMBER molecular dynamic package for the first time. The calculated binding free energy is also in agreement with the experimentally determined binding affinity for c-Abl tyrosine kinase complex with Imatinib.     

QM/MM investigation of structure and spectroscopic properties of a vanadium-containing peroxidase

We present a comprehensive analysis of the most likely ground state configuration of the resting state of vanadium dependent chloroperoxidase (VCPO) based on quantum mechanics/molecular mechanics (QM/MM) evaluations of ground state properties, UV-vis spectra and NMR chemical shifts. Within the QM/MM framework, density functional theory (DFT) calculations are used to characterize the resting state of VCPO via time-dependent density functional theory (TD-DFT) calculations of electronic excitation energies and NMR chemical shifts. Comparison with available experimental data allows us to determine the most likely protonation state of VCPO, a state which results in a doubly protonated axial oxygen, a site largely stabilized by hydrogen bonds. We found that the bulk of the protein that is beyond the immediate layer surrounding the cofactor, has an important electrostatic effect on the absorption maximum. Through examination of frontier orbitals, we analyze the nature of two bound water molecules and the extent to which relevant residues in the active site influence the spectroscopy calculations.     

The evolutionary pathway from anoxygenic to oxygenic photosynthesis examined by comparison of the properties of photosystem II and bacterial reaction centers

In photosynthetic organisms, such as purple bacteria, cyanobacteria, and plants, light is captured and converted into energy to create energy-rich compounds. The primary process of energy conversion involves the transfer of electrons from an excited donor molecule to a series of electron acceptors in pigment–protein complexes. Two of these complexes, the bacterial reaction center and photosystem II, are evolutionarily related and structurally similar. However, only photosystem II is capable of performing the unique reaction of water oxidation. An understanding of the evolutionary process that lead to the development of oxygenic photosynthesis can be found by comparison of these two complexes. In this review, we summarize how insight is being gained by examination of the differences in critical functional properties of these complexes and by experimental efforts to alter pigment–protein interactions of the bacterial reaction center in order to enable it to perform reactions, such as amino acid and metal oxidation, observable in photosystem II.     

Interactions of cholesterol with lipid bilayers: the preferred configuration and fluctuations.

The free energy difference associated with the transfer of a single cholesterol molecule from the aqueous phase into a lipid bilayer depends on its final location, namely on its insertion depth and orientation within the bilayer. We calculated desolvation and lipid bilayer perturbation contributions to the water-to-membrane transfer free energy, thus allowing us to determine the most favorable location of cholesterol in the membrane and the extent of fluctuations around it. The electrostatic and nonpolar contributions to the solvation free energy were calculated using continuum solvent models. Lipid layer perturbations, resulting from both conformational restrictions of the lipid chains in the vicinity of the (rigid) cholesterol backbone and from cholesterol-induced elastic deformations, were calculated using a simple director model and elasticity theory, respectively. As expected from the amphipathic nature of cholesterol and in agreement with the available experimental data, our results show that at the energetically favorable state, cholesterol's hydrophobic core is buried within the hydrocarbon region of the bilayer. At this state, cholesterol spans approximately one leaflet of the membrane, with its OH group protruding into the polar (headgroup) region of the bilayer, thus avoiding an electrostatic desolvation penalty. We found that the transfer of cholesterol into a membrane is mainly driven by the favorable nonpolar contributions to the solvation free energy, whereas only a small opposing contribution is caused by conformational restrictions of the lipid chains. Our calculations also predict a strong tendency of the lipid layer to elastically respond to (thermally excited) vertical fluctuations of cholesterol so as to fully match the hydrophobic height of the solute. However, orientational fluctuations of cholesterol were found to be accompanied by both an elastic adjustment of the surrounding lipids and by a partial exposure of the hydrophobic cholesterol backbone to the polar (headgroup) environment. Our calculations of the molecular order parameter, which reflects the extent of orientational fluctuations of cholesterol in the membrane, are in good agreement with available experimental data.     

Theoretical study of the excited states of the photosynthetic reaction center in photosystem II: electronic structure, interactions, and their origin

The excited states of the chlorophyll 6-mer in the photosystem II (PSII) reaction center (RC) were investigated theoretically using ab initio quantum chemical calculations, and the results are compared with those of the bacterial reaction center (bRC). A significant difference in the peak at the lowest energy in the absorption spectra arises from the structural asymmetry of the special pair (SP). The origin can be traced back to the structural difference in the CD helix. The low-lying excited states are characterized as a linear combination of the excited states of the chlorophyll monomers, which verifies the applicability of exciton theory. Analysis of the molecular interactions clearly explains the cause of the constructive/destructive interferences in the state transition moment. The protein electrostatic potential (ESP) decreases the energy of the charge-transfer (Chl(D1)→Pheo(D1)) state. The ESP also localizes the HOMO distribution to the P(D1) moiety and increases the ionization potential.     

How does the protein environment optimize the thermodynamics of thiol sulfenylation? Insights from model systems to QM/MM calculations on human 2-Cys peroxiredoxin

Protein thiol/sulfenic acid oxidation potentials provide a tool to select specific oxidation agents, but are experimentally difficult to obtain. Here, insights into the thiol sulfenylation thermodynamics are obtained from model calculations on small systems and from a quantum mechanics/molecular mechanics (QM/MM) analysis on human 2-Cys peroxiredoxin thioredoxin peroxidase B (Tpx-B). To study thiol sulfenylation in Tpx-B, our recently developed computational method to determine reduction potentials relatively compared to a reference system and based on reaction energies reduction potential from electronic energies is updated. Tpx-B forms a sulfenic acid (R-SO^?) on one of its active site cysteines during reactive oxygen scavenging. The observed effect of the conserved active site residues is consistent with the observed hydrogen bond interactions in the QM/MM optimized Tpx-B structures and with free energy calculations on small model systems. The ligand effect could be linked to the complexation energies of ligand L with CH₃S^? and CH₃SO^?. Compared to QM only calculations on Tpx-B’s active site, the QM/MM calculations give an improved understanding of sulfenylation thermodynamics by showing that other residues from the protein environment other than the active site residues can play an important role.     

Investigation of the acylation mechanism of class C beta-lactamase: pKa calculation, molecular dynamics simulation and quantum mechanical calculation

β-Lactamases are bacterial enzymes that act as a bacterial defense system against β-lactam antibiotics. β-Lactamase cleaves the β-lactam ring of the antibiotic by a two step mechanism involving acylation and deacylation steps. Although class C β-lactamases have been investigated extensively, the details of their mechanism of action are not well understood at the molecular level. In this study, we investigated the mechanism of the acylation step of class C β-lactamase using pKa calculations, molecular dynamics (MD) simulations and quantum mechanical (QM) calculations. Serine64 (Ser64) is an active site residue that attacks the β-lactam ring. In this study, we considered three possible scenarios for activation of the nucleophile Ser64, where the activation base is (1) Tyrosine150 (Tyr150), (2) Lysine67 (Lys67), or (3) substrate. From the pKa calculation, we found that Tyr150 and Lys67 are likely to remain in their protonated states in the pre-covalent complex between the enzyme and substrate, although their role as activator would require them to be in the deprotonated state. It was found that the carboxylate group of the substrate remained close to Ser64 for most of the simulation. The energy barrier for hydrogen abstraction from Ser64 by the substrate was calculated quantum mechanically using a large truncated model of the enzyme active site and found to be close to the experimental energy barrier, which suggests that the substrate can initiate the acylation mechanism in class C β-lactamase.     

Photophysical properties of Prochlorococcus marinus SS120 divinyl chlorophylls and phycoerythrin in vitro and in vivo

Prochlorococcus marinus SS120 is an ecologically important and biochemically intriguing marine cyanobacterium. In addition to divinyl chlorophylls (DV-Chls) a and b it possesses a particular form of phycoerythrin (PE), but no other phycobilins and therefore no complete phycobilisomes. Here, a spectroscopic characterisation of these DV-Chls and PE is provided. Comparison of fluorescence quantum yields, excited state lifetimes and absorption characteristics indicate similar light-harvesting properties of the DV-Chls as their monovinyl counterparts. PE, which is present only in tiny amounts, was purified and considerably enriched. A phycourobilin to phycoerythrobilin ratio of 3:1 chromophores per (alphabeta) PE monomer is suggested. The in vitro fluorescence lifetime of PE is 1.74 ns. In vivo time-resolved fluorescence measurements with synchrotron radiation were used to investigate the possible role of PE in light-harvesting. The fluorescence decay time for PE is about 550 ps, indicating an unusually slow excitation energy transfer. The decay time slowed to 1 ns after addition of glycerol to cell cultures. The contribution of PE to total light-harvesting capacity was estimated to be about one (alphabeta) PE monomer per 330 DV-Chl b molecules. Thus, the capacity of PE to function primarily as a photosynthetic light-harvesting pigment in P. marinus SS120 is low.     

Catalytic mechanism and energy barriers for butyrylcholinesterase-catalyzed hydrolysis of cocaine

The geometries of the transition states, intermediates, and prereactive enzyme-substrate complex and the corresponding energy barriers have been determined by performing hybrid quantum mechanical/molecular mechanical (QM/MM) calculations on butyrylcholinesterase (BChE)-catalyzed hydrolysis of (-)- and (+)-cocaine. The energy barriers were evaluated by performing QM/MM calculations with the QM method at the MP2/6-31+G* level and the MM method using the AMBER force field. These calculations allow us to account for the protein environmental effects on the transition states and energy barriers of these enzymatic reactions, showing remarkable effects of the protein environment on intermolecular hydrogen bonding (with an oxyanion hole), which is crucial for the transition state stabilization and, therefore, on the energy barriers. The calculated energy barriers are consistent with available experimental kinetic data. The highest barrier calculated for BChE-catalyzed hydrolysis of (-)- and (+)-cocaine is associated with the third reaction step, but the energy barrier calculated for the first step is close to the highest and is so sensitive to the protein environment that the first reaction step can be rate determining for (-)-cocaine hydrolysis catalyzed by a BChE mutant. The computational results provide valuable insights into future design of BChE mutants with a higher catalytic activity for (-)-cocaine.     

<Emphasis Type="Italic">Cis</Emphasis>–<Emphasis Type="Italic">trans</Emphasis> photoisomerization properties of GFP chromophore analogs

The photoswitching behaviour of the green fluorescent protein (GFP) chromophore and its analogs opens up exciting horizons for the engineering and development of molecular devices for high sensitivity in vivo studies. In this work we present the synthesis and photophysical study of four GFP chromophore analogs belonging to butenolide and pyrrolinone classes. These chromophores possess an intriguing photoinduced cis–trans isomerization mechanism. Stereochemical structural assignment was unambiguously performed by 1D Nuclear Overhauser Effect NMR measurements. The spectroscopic properties of both cis and trans isomers were studied, and photoconversion quantum yield for cis–trans isomerization was assessed to be in the 0.1–0.4 range. Finally, the ³J_C,H coupling constant in the ¹³C–C=C–H motif was in excellent agreement with theoretical DFT calculations, thus providing a further confirmation of cis–trans photoisomerization of the structurally analog GFP chromophore.     

A computational study of the deacylation mechanism of human butyrylcholinesterase

To investigate the mechanism of the deacylation reaction in the active site of human butyrylcholinesterase (BuChE), we carried out quantum mechanical (QM) calculations on cluster models of the active site built from a crystallographic structure. The models consisted of the substrate butyrate moiety, the catalytic triad of residues (Ser198, Glu325, and His438), the "oxy-anion hole" (Gly116, Gly117, and Ala199), the side chain of Glu197, four water molecules, the side chain of Ser225, and the peptide linkage between Val321 and Asn322. Analyses of the equilibrium geometries, electronic properties, and energies of the QM models gave insights into the catalytic mechanism. In addition, the QM calculations provided the data required to build a molecular mechanics representation of the reactive BuChE region that was employed in molecular dynamics simulations followed by molecular-mechanics-Poisson-Boltzmann (MM-PB) calculations. Subsequently, we combined the QM energies with average MM-PB energies to estimate the free energy of the reactive structures in the enzyme. The rate-determining step corresponds to the formation of a tetrahedral intermediate with a free-energy barrier of approximately 14.0 kcal/mol. The modulation of the BuChE activity, exerted by either neutral molecules (glycerol, GOL) or a second butyrylcholine (CHO) molecule bound to the cation-pi site, does not involve any significant allosteric effect. Interestingly, the presence of GOL or CHO stabilizes a product complex formed between a butyric acid molecule and BuChE. These results are in consonance with the crystallographic structure of BuChE, in which the catalytic Ser198 interacts with a butyric fragment, while the cation-pi site is occupied by one GOL molecule.     

How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: a theoretical study

Phosphorylation mediates the function of many proteins and enzymes. In the catalytic subunit of cAMP-dependent protein kinase, phosphorylation of Thr 197 in the activation loop strongly influences its catalytic activity. In order to provide theoretical understanding about this important regulatory process, classical molecular dynamics simulations and ab initio QM/MM calculations have been carried out on the wild-type PKA-Mg(2) ATP-substrate complex and its dephosphorylated mutant, T197A. It was found that pThr 197 not only facilitates the phosphoryl transfer reaction by stabilizing the transition state through electrostatic interactions but also strongly affects its essential protein dynamics as well as the active site conformation.     

Disentangling the low-energy states of the major light-harvesting complex of plants and their role in photoprotection

The ability to dissipate large fractions of their absorbed light energy as heat is a vital photoprotective function of the peripheral light-harvesting pigment–protein complexes in photosystem II of plants. The major component of this process, known as qE, is characterised by the appearance of low-energy (red-shifted) absorption and fluorescence bands. Although the appearance of these red states has been established, the molecular mechanism, their site and particularly their involvement in qE are strongly debated. Here, room-temperature single-molecule fluorescence spectroscopy was used to study the red emission states of the major plant light-harvesting complex (LHCII) in different environments, in particular conditions mimicking qE. It was found that most states correspond to peak emission at around 700 nm and are unrelated to energy dissipative states, though their frequency of occurrence increased under conditions that mimicked qE. Longer-wavelength emission appeared to be directly related to energy dissipative states, in particular emission beyond 770 nm. The ensemble average of the red emission bands shares many properties with those obtained from previous bulk in vitro and in vivo studies. We propose the existence of at least three excitation energy dissipating mechanisms in LHCII, each of which is associated with a different spectral signature and whose contribution to qE is determined by environmental control of protein conformational disorder. Emission at 700 nm is attributed to a conformational change in the Lut 2 domain, which is facilitated by the conformational change associated with the primary quenching mechanism involving Lut 1.     

Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods

The [NiFe] hydrogenases catalyse the reversible conversion of H₂ to protons and electrons. The active site consists of a Fe ion with one carbon monoxide, two cyanide, and two cysteine (Cys) ligands. The latter two bridge to a Ni ion, which has two additional terminal Cys ligands. It has been suggested that one of the Cys residues is protonated during the reaction mechanism. We have used combined quantum mechanical and molecular mechanics (QM/MM) geometry optimisations, large QM calculations with 817 atoms, and QM/MM free energy simulations, using the TPSS and B3LYP methods with basis sets extrapolated to the quadruple zeta level to determine which of the four Cys residues is more favourable to protonate for four putative states in the reaction mechanism, Ni-SI_a, Ni-R, Ni-C, and Ni-L. The calculations show that for all states, the terminal Cys-546 residue is most easily protonated by 14–51 kJ/mol, owing to a more favourable hydrogen-bond pattern around this residue in the protein.     

Combined quantum and molecular mechanics calculations on metalloproteins

The combination of quantum mechanics and molecular mechanics (QM/MM) methods is one of the most promising approaches to study the structure, function and properties of proteins. The number of QM/MM applications on metalloproteins is steadily increasing, especially studies with density functional methods on redox-active metal centres. Recent developments include new parameterised methods to treat covalent bonds between the quantum and classical systems, methods to obtain free energy from QM/MM results, and the combination of quantum chemistry and protein crystallography.     

The energy transfer model of nonphotochemical quenching: Lessons from the minor CP29 antenna complex of plants

Antenna complexes in photosystems of plants and green algae are able to switch between a light-harvesting unquenched conformation and a quenched conformation so to avoid photodamage. When the switch is activated, nonphotochemical quenching (NPQ) mechanisms take place for an efficient deactivation of excess excitation energy. The molecular details of these mechanisms have not been fully clarified but different hypotheses have been proposed. Among them, a popular one involves excitation energy transfer (EET) from the singlet excited Chls to the lowest singlet state (S₁) of carotenoids. In this work, we combine such model with μs-long molecular dynamics simulations of the CP29 minor antenna complex to investigate how conformational fluctuations affect the electronic couplings and the final EET quenching. The computational framework is applied to both CP29 embedding violaxanthin and zeaxantin in its L2 site. Our results demonstrate that the EET model is rather insensitive to physically reasonable variations in single chlorophyll-carotenoid couplings, and that very large conformational changes would be needed to see the large variation of the complex lifetime expected in the switch from light-harvesting to quenched state. We show, however, that a major role in regulating the EET quenching is played by the S₁ energy of the carotenoid, in line with very recent spectroscopy experiments.     

Molecular mechanism for the initial process of visual excitation. IV. Energy surfaces of visual pigments and photoisomerization mechanism

Using the twisted conformations of the chromophores for visual pigments and intermediates which were theoretically determined in the previous paper, energy surfaces of the pigment at −190‡ C were obtained as functions of the torsional anglesθ _9–10 andθ _11–12 or of the torsional anglesθ _9–10 andθ _13–14. In these calculations, the existence of specific reaction paths between rhodopsin (R) and bathorhodopsin (B), between isorhodopsin I (I) and bathorhodopsin, and between isorhodopsin II (I′) and bathorhodopsin were assumed. It was shown that the total energy surfaces of the excited states had minimaC ₁ atθ _9–10 ∼ −10‡ andθ _11–12 ∼ −80‡,C ₂ atθ _9–10 ∼ −85‡ andθ _11–12 ∼ −5‡, andC ₃ atθ _9–10 ∼ 0‡ andθ _13–14 ∼ −90‡. These minima are considered to correspond to the thermally barrierless common states as denoted by Rosenfeld et al. Using the total energy surfaces in the ground and excited states, the molecular mechanism of the photoisomerization reaction was suggested. Quantum yields for the photoconversions among R, I, I′ and B were related to the rates of vibrational relaxations, radiationless transitions and thermal excitations. Some discussion was made of the temperature effect on the quantum yield. Similar calculations of the energy surfaces were also made at other temperatures where lumirhodopsin or metarhodopsin I is stable. Relative energy levels of the pigments and the intermediates were discussed.