Characterization of a complete cycle of acetylcholinesterase catalysis by <Emphasis Type="Italic">ab initio</Emphasis> QM/MM modeling

The reaction mechanism of acetylcholine hydrolysis by acetylcholinesterase, including both acylation and deacylation stages from the enzyme-substrate (ES) to the enzyme-product (EP) molecular complexes, is examined by using an ab initio type quantum mechanical – molecular mechanical (QM/MM) approach. The density functional theory PBE0/aug-6–31+G* method for a fairly large quantum part trapped inside the native protein environment, and the AMBER force field parameters in the molecular mechanical part are employed in computations. All reaction steps, including the formation of the first tetrahedral intermediate (TI1), the acylenzyme (EA) complex, the second tetrahedral intermediate (TI2), and the EP complex, are modeled at the same theoretical level. In agreement with the experimental rate constants, the estimated activation energy barrier of the deacylation stage is slightly higher than that for the acylation phase. The critical role of the non-triad Glu202 amino acid residue in orienting lytic water molecule and in stabilizing the second tetrahedral intermediate at the deacylation stage of the enzymatic process is demonstrated. Figure The computed energy diagram for the reaction path from the enzyme – substrate complex (ES) to the enzyme-product complex (EP).     

Interactions in pseudorotoxanes based on crown ether-secondary ammonium motifs. A theoretical study

A theoretical analysis of the nature of the interactions in dibenzo[24]crown-8 (DB24C8)-n-dibutylammonium (DBM)—pseudorotaxane complex at the MP2 and DFT levels shows that the main contribution to the binding energy is the electrostatic interaction with moderate (20–25%) correlation stabilization. The total binding energy in the DB24C8-DBM complex represents a sum of the binding energies of two NH–O and one CH–O hydrogen bonds and the latter constitutes about 25% of the total interaction energy, giving the total binding energy of −41.2 kcal mol⁻¹ at the BHandHLYP/6-311++G** level. Deprotonation of the DB24C8-DBM complex reduces the binding energy by some 50 kcal mol⁻¹, giving metastable complexes DB24C8-DBA-1 or DB24C8-DBA-2, which will dissociate to give free crown ether and n-dibutylamine because of the strong exchange repulsion that prevails in neutral complexes. Figure Formation of DB24C8-DBM pseudorotoxane complex     

Calculation of chromophore excited state energy shifts in response to molecular dynamics of pigment-protein complexes

The absorption and energy transfer properties of photosynthetic pigments are strongly influenced by their local environment or “site.” Local electrostatic fields vary in time with protein and chromophore molecular movement and thus transiently influence the excited state transition properties of individual chromophores. Site-specific information is experimentally inaccessible in many light-harvesting pigment–proteins due to multiple chromophores with overlapping spectra. Full quantum mechanical calculations of each chromophores excited state properties are too computationally demanding to efficiently calculate the changing excitation energies along a molecular dynamics trajectory in a pigment–protein complex. A simplified calculation of electrostatic interactions with each chromophores ground to excited state transition, the so-called charge density coupling (CDC) for site energy, CDC, has previously been developed to address this problem. We compared CDC to more rigorous quantum chemical calculations to determine its accuracy in computing excited state energy shifts and their fluctuations within a molecular dynamics simulation of the bacteriochlorophyll containing light-harvesting Fenna–Mathews–Olson (FMO) protein. In most cases CDC calculations differed from quantum mechanical (QM) calculations in predicting both excited state energy and its fluctuations. The discrepancies arose from the inability of CDC to account for the differing effects of charge on ground and excited state electron orbitals. Results of our study show that QM calculations are indispensible for site energy computations and the quantification of contributions from different parts of the system to the overall site energy shift. We suggest an extension of QM/MM methodology of site energy shift calculations capable of accounting for long-range electrostatic potential contributions from the whole system, including solvent and ions.     

Synthesis and luminescence properties of novel 8‐hydroxyquinoline derivatives and their Eu(III) complexes

Six novel 8‐hydroxyquinoline derivatives were synthesized using 2‐methyl‐8‐hydroxyquinoline and para‐substituted phenol as the main starting materials, and were characterized by ¹H nuclear magnetic resonance (NMR), mass spectrometry (MS), ultraviolet (UV) light analysis and infra‐red (IR) light analysis. Their complexes with Eu(III) were also prepared and characterized by elemental analysis, molar conductivity, UV light analysis, IR light analysis, and thermogravimetric–differential thermal analysis (TG–DTA). The results showed that the ligand coordinated well with Eu(III) ions and had excellent thermal stability. The structure of the target complex was EuY^1–6(NO₃)₃.2H₂O. The luminescence properties of the target complexes were investigated, the results indicated that all target complexes had favorable luminescence properties and that the introduction of an electron‐donating group could enhance the luminescence intensity of the corresponding complexes, but the addition of an electron‐withdrawing group had the opposite effect. Among all the target complexes, the methoxy‐substituted complex (–OCH₃) had the highest fluorescence intensity and the nitro‐substituted complex (–NO₂) had the weakest fluorescence intensity. The results showed that 8‐hydroxyquinoline derivatives had good energy transfer efficiency for the Eu(III) ion. All the target complexes had a relatively high fluorescence quantum yield. The fluorescence quantum yield of the complex EuY³(NO₃)₃.2H₂O was highest among all target complexes and was up to 0.628. Because of excellent luminescence properties and thermal stabilities of the Eu(III) complexes, they could be used as promising candidate luminescent materials.     

Dynamics of electron transfer from high-potential cytochrome <Emphasis Type="Italic">c</Emphasis> to bacteriochlorophyll dimer in photosynthetic reaction centers as probed using laser-induced temperature jump

Laser-induced temperature jump experiments were used for testing the rates of thermoinduced conformational transitions of reaction center (RC) complexes in chromatophores of Chromatium minutissimum. The thermoinduced transition of the macromolecular RC complex to a state providing effective electron transport from the multiheme cytochrome c to the photoactive bacteriochlorophyll dimer within the temperature range 220–280 K accounts for tens of seconds with activation energy 0.166 eV/molecule. The rate of the thermoinduced transition in the cytochrome–RC complex was found to be three orders of magnitude slower than the rate of similar thermoinduced transition of the electron transfer reaction from the primary to secondary quinone acceptors studied in the preceding work (Chamorovsky et al. in Eur Biophys J 32:537–543, 2003). Parameters of thermoinduced activation of the electron transfer from the multiheme cytochrome c to the photoactive bacteriochlorophyll dimer are discussed in terms of cytochrome c docking onto the RC.     

A computational approach to studying monomer selectivity towards the template in an imprinted polymer

A computational approach was proposed to study monomer–template interactions in a molecularly imprinted polymer (MIP) in order to gain insight at the molecular level into imprinting polymer selectivity, regarding complex formation between template and monomer at the pre-polymerisation step. This is the most important step in MIP preparation. In the present work, chlorphenamine (CPA), diphenhydramine (DHA) and methacrylic acid (MAA), were chosen as the template, non-template, and monomer, respectively. The attained complexes were optimised, and changes in the interaction energies, atomic charges, IR spectroscopy results, dipole moment, and polarisability were studied. The effects of solvent on template–monomer interactions were also investigated. According to a survey of the literature, this is the first work in which dipole moment and polarisability were used to predict the types of interactions existing in pre-polymerisation complexes. In addition, the density functional tight-binding (DFTB) method, an approximate version of the density functional theory (DFT) method that was extended to cover the London dispersion energy, was used to calculate the interaction energy.     

Carbostyril derivatives as antenna molecules for luminescent lanthanide chelates

Luminescent lanthanide complexes consisting of a lanthanide-binding chelate and organic-based antenna molecule have unusual emission properties, including millisecond excited state lifetimes and sharply spiked spectra, compared to standard organic fluorophores. We have previously used carbostyril (cs124, 7-amino-4-methyl-2(1H)-quinolinone) as an antenna molecule (Li and Selvin, J. Am. Chem. Soc., 1995) attached to a polyaminocarboxylate chelate such as DTPA. Here, we report the chelate syntheses of DTPA conjugated with cs124 derivatives substituted on the 1-, 3-, 4-, 5-, 6-, and 8-position. Among them, the DTPA chelate of cs124-6-SO(3)H has similar lifetime and brightness for both Tb(3+) and Eu(3+) compared to the corresponding DTPA-cs124 complexes, yet it is significantly more soluble in water. The Tb(3+) complex of DTPA-cs124-8-CH(3) has significantly longer lifetime compared to DTPA-cs124 (1.74 vs 1.5 ms), indicating higher lanthanide quantum yield resulting from the elimination of back emission energy transfer from Tb(3+) to the antenna molecule. Thiol-reactive forms of chelates were made for coupling to proteins. These lanthanide complexes are anticipated to be useful in a variety of fluorescence-based bioassays.     

Intermolecular interactions between gold clusters and selected amino acids cysteine and glycine: a DFT study

The intermolecular interactions between Au_n (n = 3–4) clusters and selected amino acids cysteine and glycine have been investigated by means of density functional theory (DFT). Present calculations show that the complexes possessing Au-NH₂ anchoring bond are found to be energetically favored. The results of NBO and frontier molecular orbitals analysis indicate that for the complex with anchoring bonds, lone pair electrons of sulfur, oxygen, and nitrogen atoms are transferred to the antibonding orbitals of gold, while for the complex with the nonconventional hydrogen bonds (Au···H–O), the lone pair electrons of gold are transferred to the antibonding orbitals of O-H bonds during the interaction. Furthermore, the interaction energy calculations show that the complexes with Au-NH₂ anchoring bond have relatively high intermolecular interaction energy, which is consistent with previous computational studies.     

A novel one-step strategy for the preparation of HLA/HBc<Subscript>18–27</Subscript> and HLA/CEA<Subscript>694–702</Subscript> complexes with ion exchange chromatography

The heavy chain protein of HLA-peptide complexes (HLA/HBc_18–27 and HLA/CEA_694–702) immobilized onto an ion exchange chromatography column and then the dilution-refolded HBc_18–27-fused or CEA_694–702-fused β2m protein was able to pass through the column. Using this method, HLA/peptide complexes were prepared within 30 h with a refolding yield of at least 20% (w/w) and purity of over 80% (w/w). This strategy refolds, concentrates, and purifies HLA/peptide complexes in a single integrated step and offers a potential tool to refold multiple-subunit proteins other than the major histocompatibility complex (MHC)/peptide complexes.     

Density functional theory study of model complexes for the revised nitrate reductase active site in Desulfovibrio desulfuricans NapA

[Mo(SSCH₃)(S₂C₂(CH₃)₂)₂] ^x complexes with charges x between −3 and +3 were investigated by density functional theory computations as minimal nitrate reductase active-site models. The strongly reduced species (x = −2, −3) exist preferentially as pentacoordinate sulfo complexes separated from a thiolate anion. The oxidized extremes (x > 0) clearly prefer hexacoordinate complexes with an η²-MeSS ligand. Among the neutral and especially for the singly negatively charged species structures with η²-MeSS and η¹-MeSS ligands are energetically close to the sulfo methyl sulfide complex without SS bonding. For x = −1 the three isomers lie in a 1.5 kcal mol⁻¹ energy range. Putative mechanistic pathways for nitrate reduction from the literature were investigated computationally: (1) reduction at a pentacoordinate sulfo complex, (2) reduction at the ligand, and (3) reduction at the molybdenum center with an R–S–S ligand. All three pathways could be traced at least for some overall charges but no definite conclusion can be drawn about the mechanism. Complexes with larger dithiolato ligands were also computed in order to model the tricyclic metallopterin framework more accurately: the first heterocyclus (5,6-dihydro-2H-pyran) stabilizes the nitrate complex and the molybdenum oxo product complex by approximately 10 kcal mol⁻¹ and also reduces the activation barrier (by approximately 5 kcal mol⁻¹). The effect of the second (1,2,3,4-tetrahydropyrazin) and third heterocyclus (2-amino-3H-pyrimidin-4-one) on the relative energies is relatively small. For bigger models derived from an experimental protein structure, nitrate reduction at a persulfo molybdenum(IV) complex fragment (mechanism 3) is clearly favored over the oxidation of a molybdenum-bound sulfur atom (mechanism 2). Mechanism 1 could not be investigated for the big models but seems the least favorable on the basis of the results from smaller models.     

Recognizing protein–protein interfaces with empirical potentials and reduced amino acid alphabets

Background  

In structural genomics, an important goal is the detection and classification of protein–protein interactions, given the structures of the interacting partners. We have developed empirical energy functions to identify native structures of protein–protein complexes among sets of decoy structures. To understand the role of amino acid diversity, we parameterized a series of functions, using a hierarchy of amino acid alphabets of increasing complexity, with 2, 3, 4, 6, and 20 amino acid groups. Compared to previous work, we used the simplest possible functional form, with residue–residue interactions and a stepwise distance-dependence. We used increased computational ressources, however, constructing 290,000 decoys for 219 protein–protein complexes, with a realistic docking protocol where the protein partners are flexible and interact through a molecular mechanics energy function. The energy parameters were optimized to correctly assign as many native complexes as possible. To resolve the multiple minimum problem in parameter space, over 64000 starting parameter guesses were tried for each energy function. The optimized functions were tested by cross validation on subsets of our native and decoy structures, by blind tests on series of native and decoy structures available on the Web, and on models for 13 complexes submitted to the CAPRI structure prediction experiment.     

Modeling Lanthanide Complexes: Towards the Theoretical Design of Light Conversion Molecular Devices

Theoretical techniques have been developed and/or improved to predict the molecular structure of lanthanide complexes which were used to calculate their electronic properties, in particular, their electronic spectra and energy levels necessary to calculate the rates of energy transfer from the ligands to the metal ion. The molecular structure has been obtained by the SMLC/AM1 (Sparkle Model for the Calculation of Lanthanide Complexes – Austin Model 1) model where the lanthanide ion is simulated by a sparkle implemented into the AM1 Hamiltonian used to perform a HF-SCF (Hartree-Fock Self-Consistent Field) calculation. The previous implementation of the SMLC/AM1 model (sparkle/1) involving only two parameters has been generalized to be consistent with the AM1 Hamiltonian and the new model (sparkle/2) significantly improved the prediction of molecular structures of Eu(III) complexes. For the electronic spectra and energy level calculations of the lanthanide complexes the model replaces the metal ion by a point charge with the ligands held in their positions as determined by the SMLC/AM1 model, and uses a INDO/S-CI (intermediate neglect of differential overlap/spectroscopic-configuration interaction) model. A preliminary study of the solvent effects on the absorption spectra of the free ligand is also presented. For the ligand-lanthanide ion energy transfer Fermi's golden rule is used with the multipolar and exchange mechanisms being implemented and tested for several complexes. These theoretical techniques have been applied to several complexes yielding very good results when compared to experimental data as well as predictions for the molecular and electronic structures and the relative contributions of the mechanisms for the energy transfer rates. This revised version was published online in June 2006 with corrections to the Cover Date.     

Possible dynamic anchor points in a benzoxazinone derivative–human oxytocin receptor system — a molecular docking and dynamics calculation

In this study, we performed a molecular docking and dynamics simulation for a benzoxazinone–human oxytocin receptor system to determine the possible hydrophobic and electrostatic interaction points in the dynamic complex. After the homology modeling, the ligand was docked into the putative active using AutoDock 3.05. After the application of energetic and structural filters, the complexes obtained were further refined with a simulated annealing protocol (AMBER8) to remove steric clashes. Three complexes were selected for subjection to the molecular dynamics simulation (5 ns), and the results on the occurrence of average anchor points showed a stable complex between the benzoxazinone derivative and the receptor. The complex could be used as a good starting point for further analysis with site-directed mutagenesis, or further computational research. Figure The location of the ligands (complex B – blue; complex E – red; and complex F – green) in the transmembrane regions (TM1 – red; TM2 – blue; TM3 – yellow; TM4 – purple; TM5 – orange; TM6 – cyan; TM7 – pink) of the hOTR. For clarity, the EC and IC loops are not shown Electronic Supplementary Material Supplementary material is available at     

Hybrid system based on quantum dots and photosystem 2 core complex

We show that semiconductor nanocrystals (quantum dots, QD) can be used to increase the absorption capacity of pigment-protein complexes. In a mixture of photosystem 2 core complex (PS2) and QD, the fluorescence of the latter decreases several-fold due to the transfer of the absorbed energy to the PS2 core complex. We discuss Forster’s inductive-resonance mechanism as a possible way of energy transfer in donor-acceptor pairs QD-PS2 core complex. Calculations based on the experimental data show that the enhancement of PS2 fluorescence and the rate of Q_A reduction increase up to 60% due to efficient energy migration from QD to PS2.     

Characteristics and nature of the intermolecular interactions in boron-bonded complexes with carbene as electron donor: an <Emphasis Type="Italic">ab initio</Emphasis>, SAPT and QTAIM study

We report geometries, stabilization energies, symmetry adapted perturbation theory (SAPT) and quantum theory of atoms in molecules (QTAIM) analyses of a series of carbene–BX₃ complexes, where X = H, OH, NH₂, CH₃, CN, NC, F, Cl, and Br. The stabilization energies were calculated at HF, B3LYP, MP2, MP4 and CCSD(T)/aug-cc-pVDZ levels of theory using optimized geometries of all the complexes obtained from B3LYP/aug-cc-pVTZ. Quantitatively, all the complexes indicate the presence of B–C_carbene interaction due to the short B–C_carbene distances. Inspection of stabilization energies reveals that the interaction energies increase in the order NH₂ > OH > CH₃ > F > H > Cl > Br > NC > CN, which is the opposite trend shown in the binding distances. Considering the SAPT results, it is found that electrostatic effects account for about 50% of the overall attraction of the studied complexes. By comparison, the induction components of these interactions represent about 40% of the total attractive forces. Despite falling in a region of charge depletion with ∇² ρ _BCP >0, the B–C_carbene bond critical points (BCPs) are characterized by a reasonably large value of the electron density (ρ _BCP) and H_BCP <0, indicating that the potential energy overcomes the kinetic energy density at BCP and the B–C_carbene bond is a polar covalent bond.     

Degradation of 2-chlorobenzoic and 2,5-dichlorobenzoic acids in pure culture byPseudomonas stutzeri

A strain ofPseudomonas stutzeri KS25 utilizing 2-chlorobenzoic and 2,5-dichlorobenzoic acids as the sole carbon and energy source was isolated from polychlorophenol-contaminated soil and sewage, using the method of enrichment cultures. This strain was also able to grow on 2-fluoro-, 2-iodo-, 2-bromo- and 2,5-dihydroxybenzoate, but did not utilize 3-, 4-chloro-, 2,4- and 2,6-dichlorobenzoates as the sole carbon and energy source, however, it cometabolized 3-chloro-, 2,4-and 2,6-dichlorobenzoates, but not 4-chlorobenzoate. The yield of released chlorine during utilization of 2-chloro- and 2,5-dichlorobenzoates amounted to 100 % of the theoretical. The concentration of 2-chloro- and 2,5-dichlorobenzoates, not substantially inhibiting the isolated microorganism, was within the range 0.25–0.5 and 2.5–3.0 g/L, respectively.     

The Equilibrium of Phosphatidylcholine–Amino Acid System in Monolayer at the Air/water Interface

Monolayers of phosphatidylcholine, tyrosine, and phenylalanine and binary mixtures phosphatidylcholine–tyrosine or phosphatidylcholine–phenylalanine were investigated at the air/water interface. Phosphatidylcholine (lecithin, PC), tyrosine (Tyr), and phenylalanine (Phe) were used in the experiment. The surface tension values of pure and mixed monolayers were used to calculate π–A isotherms. The surface tension measurements were carried out at 22°C using an improved Teflon trough and a Nima 9000 tensiometer. The Teflon trough was filled with a subphase of triple-distilled water. Known amounts of lipid dissolved in 1-chloropropane were placed at the surface using a syringe. The interactions between lecithin and amino acid result in significant deviations from the additivity rule. An equilibrium theory to describe the behavior of monolayer components at the air/water interface was developed in order to obtain the stability constants of PC–Tyr as well as PC–Phe complexes. We considered the equilibrium between the individual components and the complex and established that lecithin and amino acid formed highly stable 1:1 complex.     

Conformational stabilities, infrared, and vibrational dichroism spectroscopy studies of tris(ethylenediamine) zinc(II) chloride

The conformational stabilities of the transition metal complex of Zn (en)₃Cl₂ were studied using density functional theory (DFT). Deformational potential energy profiles (PEPs), and pathways between the different isomeric conformational energies were calculated using DFT/B3LYP/6–31G. The relative conformational energies of Δ(λλλ), Δ(λλδ), Δ(λδδ) and Δ(δδδ) are 10.48, 7.08, 3.56, and 0.0 kcal/mol, respectively, which are small compared to the barrier heights for reversible phase transitions (49.56, 49.55, 49.52 kcal/mol, respectively). Frequency assignment was carried out by decomposing Fourier transform infrared (FTIR) spectra using Gaussian and Gaussview. The theoretical IR and vibrational dichroism spectroscopy (VCD) absorption spectra are presented for all conformations within the range of 400–3,500 cm^-1.     

Study on the fluorescent enhancement effect in terbium-gadolinium-protein-sodium dodecyl benzene sulfonate system and its application on sensitive detection of protein at nanogram level

The co-luminescence effect in a terbium-gadolinium-protein-sodium dodecyl benzene sulfonate (SDBS) system is reported here. Based on it, the sensitive quantitative analysis of protein at nanogram levels is established. The co-luminescence mechanism is studied using fluorescence, resonance light scattering (RLS), absorption spectroscopy and NMR measurement. It is considered that protein could be unfolded by SDBS, then a efficacious intramolecular fluorescent energy transfer occurs from unfolded protein to rare earth ions through SDBS acting as a "transfer bridge" to enhance the emission fluorescence of Tb3+ in this ternary complex of Tb-SDBS-BSA, where energy transfer from protein to SDBS by aromatic ring stacking is the most important step. Cooperating with the intramolecular energy transfer above is the intermolecular energy transfer between the simultaneous existing complexes of both Tb3+ and Gd3+. The fluorescence quantum yield is increased by an energy-insulating sheath, which is considered to be another reason for the resulting enhancement of the fluorescence. F?rster theory is used to calculate the distribution of enhancing factors and has led to a greater understanding of the mechanisms of energy transfer.     

DFT and MP2 investigations of <Emphasis Type="SmallCaps">L</Emphasis>-proline and its hydrated complexes

A theoretical study of L-proline-nH₂O (n = 1–3) has been performed using the hybrid DFT-B3LYP and MP2 methods together with the 6-311++G(d,p) basis set. The results show that the P2 conformer is energetically favorable when forming a hydrated structure, and the hydration of the carboxyl group leads to the greatest stability. For hydrated complexes, the adiabatic and vertical singlet–triplet excitation energies tend to decrease with the addition of water molecules. The hydration energy indicates that in the hydrated complexes the order of stability is: binding site 2 > binding site 1 > binding site 3, and binding site 12 > binding site 23 > binding site 13. As water molecules are added, the stabilities of these hydrated structures gradually increase. In addition, an infrared frequency analysis indicated that there are some differences in the low-frequency range, which are mainly dominated by the O–H stretching or bending vibrations of different water molecules. All of these results should aid our understanding of molecular behavior and provide reference data for further studies of biological systems.