Carbonic anhydrase binding site parameterization in OPLS-AA force field

The parameterization of carbonic anhydrase binding site in OPLS-AA force field was performed using quantum chemistry calculations. Both OH₂ and OH^? forms of the binding site were considered, showing important differences in terms of atomic partial charges. Three different parameterization protocols were used, and the results obtained highlighted the importance of including an extended binding site in the charge calculation. The force field parameters were subsequently validated using standard molecular dynamics simulations. The results presented in this work should greatly facilitate the use of molecular dynamics simulations for studying the carbonic anhydrase, and more generally, the metallo-enzymes.     

Applications of the Cartesian coordinate tensor transfer technique in the simulations of vibrational circular dichroism spectra of oligonucleotides

The application of the Cartesian coordinate tensor transfer (CCT) technique for simulations of the IR absorption and vibrational circular dichroism (VCD) spectra of relatively large nucleic acid fragments is demonstrated on several case studies. The approach is based on direct ab initio calculations of atomic tensors, determining molecular properties, for relatively small fragments, and subsequent transfer of these tensors to the larger systems in Cartesian coordinates. This procedure enables precise computations of vibrational spectra for large biomolecular systems, currently with up to several thousands of atoms. The versatile ability of the CCT methods is emphasized on the examples of VCD and IR absorption spectra calculations for B- and Z-forms of DNA, single-, double-, and triple-stranded RNA helices and DNA structures with different base content and sequences. The development and recent improvements of the methodology are followed, including utilization of the constrained normal mode optimization (NMO) strategy and combined quantum mechanics and molecular dynamics simulations. Advantages, drawbacks, and recommendations for future improvements of the CCT method as applied to nucleic acid spectra calculations are discussed.     

A few low-frequency normal modes predominantly contribute to conformational responses of hen egg white lysozyme in the tetragonal crystal to variations of molecular packing controlled by environmental humidity

The structures of proteins in crystals are fixed by molecular interactions with neighboring molecules, except in non-contacting flexible regions. Thus, it is difficult to imagine what conformational changes occur in solution. However, if molecular interactions can be changed by manipulating molecular packing in crystals, it may be possible to visualize conformational responses of proteins at atomic resolution by diffraction experiments. For this purpose, it is suitable to control the molecular packing in protein crystals by changing the volume of solvent channels through variation of the environmental relative humidity. Here, we studied conformational responses of hen egg white lysozyme (HEWL) in the tetragonal crystal by X-ray diffraction experiments using a humidity-control apparatus, which provided air flow of 20-98%rh at 298 K. First, we monitored the lattice parameters and crystalline order during dehydration and rehydration of HEWL crystal between 61 and 94%rh at 300 K. Then two crystal structures at a resolution of 2.1 ? using diffraction data obtained at 84.2 and 71.9%rh were determined to discuss the conformational responses of HEWL against the external perturbation induced by changes in molecular packing. The structure at 71.9%rh displayed a closure movement that was likely induced by the molecular contacts formed during dehydration and could be approximated by ten low-frequency normal modes for the crystal structure obtained at 84.2%rh. In addition, we observed reorganization of hydration structures at the molecular interfaces between symmetry neighbors. These findings suggest that humidity-controlled X-ray crystallography is an effective tool to investigate the responses of inherent intramolecular motions of proteins to external perturbations.     

Cell size dependence of orientational order of uniaxial liquid crystals in flat slit

In order to investigate the ordered structure of nematic liquid crystal molecules confined in a nanoslit, we carried out a classical molecular dynamics simulation of uniaxial prolate Gay–Berne particles in a flat, structureless slit at several temperatures. When the slit gap is so small that the system is not assumed as the bulk, particles in the slit possess orientationally ordered structures different from ones in the bulk. The weak spacial orientational correlation existed when the temperature corresponded to the isotropic phase in the bulk system. The first order isotropic–nematic phase transition was not clearly observed and the transitional phenomenon of the creation and annihilation of the uniaxial domains were observed. These results revealed that the ordered structure depends on the number of particles, in other words, cell size, and that the system with 100,000 or more particles gives reasonable results of an infinitely wide slit. The number of particles is converted into up to 220 particles of the length of the base.     

Suppressing Energy Loss due to Triplet Exciton Formation in Organic Solar Cells: The Role of Chemical Structures and Molecular Packing

In the most efficient solar cells based on blends of a conjugated polymer (electron donor) and a fullerene derivative (electron acceptor),ultrafast formation of charge‐transfer (CT) electronic states at the donor‐acceptor interfaces and efficient separation of these CT states into free charges, lead to internal quantum efficiencies near 100%. However, there occur substantial energy losses due to the non‐radiative recombinations of the charges, mediated by the loweset‐energy (singlet and triplet) CT states; for example, such recombinations can lead to the formation of triplet excited electronic states on the polymer chains, which do not generate free charges. This issue remains a major factor limiting the power conversion efficiencies (PCE) of these devices. The recombination rates are, however, difficult to quantify experimentally. To shed light on these issues, here, an integrated multi‐scale theoretical approach that combines molecular dynamics simulations with quantum chemistry calculations is employed in order to establish the relationships among chemical structures, molecular packing, and non‐radiative recombination losses mediated by the lowest‐energy charge‐transfer states.     

Protein interactions and dynamics probed by quantum chemistry, computer simulations and neutron experiments

We review some recent experiments and calculations on aspects of the structure and dynamics of proteins and related systems. The use of quantum chemical techniques to determine geometries and energies of supramolecular complexes of biological interest is illustrated, and the concomitant development of empirical energy functions for use in protein simulations outlined. We describe how simulations of crystalline peptides and amino-acids using an empirical force field can be combined with appropriate coherent and incoherent inelastic neutron scattering experiments to elucidate the characteristics of lattice vibrations and diffusive atomic motions in the crystals. The application of molecular dynamics simulations to the interpretation of incoherent neutron scattering experiments on proteins is examined and the resulting ideas on the general characteristics of protein motion discussed in terms of their functional implications.     

Chromophore Structure of Cyanobacterial Phytochrome Cph1 in the Pr State: Reconciling Structural and Spectroscopic Data by QM/MM Calculations

A quantum mechanics (QM)/molecular mechanics (MM) hybrid method was applied to the Pr state of the cyanobacterial phytochrome Cph1 to calculate the Raman spectra of the bound PCB cofactor. Two QM/MM models were derived from the atomic coordinates of the crystal structure. The models differed in the protonation site of His²⁶⁰ in the chromophore-binding pocket such that either the δ-nitrogen (M-HSD) or the ɛ-nitrogen (M-HSE) carried a hydrogen. The optimized structures of the two models display small differences specifically in the orientation of His²⁶⁰ with respect to the PCB cofactor and the hydrogen bond network at the cofactor-binding site. For both models, the calculated Raman spectra of the cofactor reveal a good overall agreement with the experimental resonance Raman (RR) spectra obtained from Cph1 in the crystalline state and in solution, including Cph1 adducts with isotopically labeled PCB. However, a distinctly better reproduction of important details in the experimental spectra is provided by the M-HSD model, which therefore may represent an improved structure of the cofactor site. Thus, QM/MM calculations of chromoproteins may allow for refining crystal structure models in the chromophore-binding pocket guided by the comparison with experimental RR spectra. Analysis of the calculated and experimental spectra also allowed us to identify and assign the modes that sensitively respond to chromophore-protein interactions. The most pronounced effect was noted for the stretching mode of the methine bridge A-B adjacent to the covalent attachment site of PCB. Due a distinct narrowing of the A-B methine bridge bond angle, this mode undergoes a large frequency upshift as compared with the spectrum obtained by QM calculations for the chromophore in vacuo. This protein-induced distortion of the PCB geometry is the main origin of a previous erroneous interpretation of the RR spectra based on QM calculations of the isolated cofactor.Abbreviations: Agp1, phytochrome from Agrobacterium tumefaciens; α-CPC, α-subunit of C-phycocyanin; BV, biliverdin IXα; B3LYP, three-parameter exchange functional according to Becke, Lee, Yang, and Parr; DFT, density functional theory; DrBphP, phytochrome from Deinococcus radiodurans; GAF, domain found in cGMP-specific phosphodiesterases; MM, molecular mechanics; MD, molecular dynamics; N-H ip, N-H in-plane bending; PCB, phycocyanobilin; PED, potential energy distribution; phyA, plant phytochrome; Pr, Pfr, red- and far-red absorbing parent states of phytochrome; PΦB, phytochromobilin; QM, quantum mechanics; RMSD, root mean-square deviation; RR, resonance Raman     

Analysis of excess Gibbs energy of electrolyte solutions: a new model for aqueous solutions

This paper presents an analysis of the excess Gibbs free energy of aqueous electrolytes. The analysis of experimental data leads to the conclusion that the equilibrium state for dilute univalent electrolytes in water involves an intercalation of water and ionic liquid crystal domains. Excess free energy of the solution is determined by the Madelung energy of hydrated ion-pair liquid crystals, and the energy associated with a shift in the structural equilibrium of water. The data that point to such a model include: molecular orbital-molecular dynamics applied to electrolyte water systems; Raman spectra; infrared spectra; magnetic resonance spectra of ions; the apparent density of water; and the excess free energy of electrolytes in aqueous solutions. Molecular orbital-molecular dynamics calculations of relatively large water clusters containing a molecule of sodium iodide show that the solvent separated ion pair exists in a substantial potential well compared to other possible structures. Raman spectra of univalent electrolyte solutions as a function of concentration can be quantitatively modeled using only the spectra of pure water and electrolyte solution at the concentration of the solvent separated ion pair. The other observations are consistent with the structures proposed from the Raman spectral study. The new model provides a satisfactory account of the fact that the excess free energy of dilute (<0.2 mol/l) solutions is generally more negative than anticipated on the basis of Debye-Hückel theory, and that the equilibrium evidence points to the same functional behavior at very low concentrations as is seen at 0.05 mol/l. We present a testable hypothesis that the excess free energy, and other thermodynamic properties of the solutions do not follow the Debye-Hückel limiting law. The tests of this hypothesis must involve only equilibrium measurements at concentrations between 0.05 and 0.0005 mol/l. This hypothesis concerning the structure of aqueous electrolyte solutions is not in conflict in any way with the Debye-Hückel-Onsager theory of electrical conductivity.     

Theoretical studies of the structure and molecular dynamics of a peptide crystal

Energy minimizations and molecular dynamics simulations have been performed on the cyclic peptide cyclo-(Ala-Pro-D-Phe)2 in both the isolated and crystal states. The results of these calculations have been analyzed, both to investigate our ability to reproduce experimental data (structure and vibrational and NMR spectra) and to investigate the effects of environment on the energy, structure, and dynamics of peptides. Comparison of the minimized and time-averaged crystal systems with the experimental peptide structure shows that the calculations have closely reproduced the experimental structure. Molecular dynamics of the isolated molecule has led to a new conformation, which is approximately equal to 8.5 kcal/mol more stable than the conformation that exists in the crystal, the latter conformation being stabilized by intermolecular (packing) forces. This illustrates the considerable effect that environment can have on the conformation of peptides. The crystal environment has also been shown to significantly reduce the dynamic conformational fluctuations seen for the isolated molecule. The behavior of the peptide during the isolated simulation also supports the experimental NMR observation of a symmetric structure that differs from the asymmetric, instantaneous structures which characterize the molecule during the dynamics. Calculations of vibrational frequencies of the peptide in the crystal and isolated states show the expected shifts in bond-stretching frequencies due to intermolecular interactions. Finally, we have calculated NMR coupling constants from the dynamics simulation of the isolated peptide and have compared these with the experimental values. This has led to a possible reinterpretation of the experimental data.     

Resonance Raman spectra of chlorophylls dissolved in liquid crystal matrices. II. Order parameters of chlorophyll a in an MBBA + EBBA liquid crystalline mixture

The molecular ordering of molecules embedded in a uniaxial liquid crystalline system has been considered. In particular, planar Chl a molecules in an MBBA + EBBA mixture have been studied by using polarized resonance Raman spectroscopy. The second- and fourth-rank order parameters and the orientational distribution function of Chl a in the nematic MBBA + EBBA liquid crystalline phase are discussed.     

Promotion of Crystal Phase Transitions by Mass-of-cell Control in Molecular Dynamics Simulations: Phase Transitions in Benzene Crystals

Abstract

The promotion of crystal phase transitions in molecular dynamics (MD) simulations was realized by controlling the momentum of the MD cell. It was implemented by increasing the mass or velocity of the MD cell instantaneously during simulations within the framework of the constant-pressure method by Parrinello and Rahman. This method induced phase transitions in benzene crystals which have not been obtained in conventional MD simulations. This method is useful for the global search of stable (and metastable) crystal structures.     

Investigations of Nematic-Isotropic Transition by Means of Constant Pressure Molecular Dynamics Simulations

Abstract

Constant pressure molecular dynamics simulations, which secure the system to be under hydrostatic pressure, are used to simulate the behavior of liquid crystals consisting of anisotropic molecules with both translational and orientational freedom. In order to investigate to what extent can the properties known to real liquid crystalline phases be explained by the anisotropy of the shape of the molecules alone, the molecular dynamic (MD) simulation uses purely repulsive short-range pair potentials representing soft spherocylinders. A clear change in the microscopic as well as the macroscopic physical properties are observed near the phase transition from nematic liquid crystal to isotropic liquid.     

Calculations on crystal packing of a flexible molecule, Leu-enkephalin

Crystal packing calculations have been carried out on a substantial number of conformations of Leu-enkephalin; namely, those obtained both from crystal structures and from energy minimizations on isolated molecules, and with and without waters of crystallization. The known crystal structures represent the most energetically stable packings found. The conformations of the enkephalin molecules in the crystal are not the most stable for an isolated molecule; i.e. intermolecular interactions force the isolated molecule to change conformation in order to achieve a small packing volume and an optimal packing energy in the crystal. It is found that the packing energy of an enkephalin molecule is a reasonably smooth function of its molecular volume in the unit cell, if structures with intermolecular hydrogen bonding are excluded, and is substantially independent of other details of the molecular conformation or of the crystal packing. Hydrogen bonding provides additional stabilization of the crystal structure, and would likely permit crystallization of the system if it is sufficiently dense. Solvent molecules further stabilize the structure when they can also provide intermolecular hydrogen bonds.     

NMR structural refinement of a tandem G.A mismatched decamer d(CCAAGATTGG)2 via the hybrid matrix procedure

A complete relaxation matrix approach employing a matrix eigenvalue/eigenvector solution to the Bloch equations is used to evaluate the NMR solution structure of a tandemly positioned G.A double mismatch decamer oligodeoxyribonucleotide duplex, d(CCAAGATTGG)2. An iterative refinement method using a hybrid relaxation matrix combined with restrained molecular dynamics calculations is shown to provide structures having good agreement with the experimentally derived structures. Distances incorporated into the MD simulations have been calculated from the relaxation rate matrix evaluated from a hybrid NOESY volume matrix whose elements are obtained from the merging of experimental and calculated NOESY intensities. Starting from both A- and B-DNA and mismatch syn and anti models, it is possible to calculate structures that are in good atomic RMS agreement with each other (less than 1.6 A RMS) but differ from the reported crystal structure (greater than 3.6 A). Importantly, the hybrid matrix derived structures are in excellent agreement with the experimental solution conformation as determined by comparison of the 200-ms simulated and experimental NOESY spectra, while the crystallographic data provide spectra that are grossly different.     

Analysis of zinc-ligand bond lengths in metalloproteins: trends and patterns

Zinc is one of the biologically most abundant and important metal elements, present in a plethora of enzymes from a broad array of species of all phyla. In this study we report a thorough analysis of the geometrical properties of Zinc coordination spheres performed on a dataset of 994 high quality protein crystal structures from the Protein Data Bank, and complemented with Quantum mechanical calculations at the DFT level of theory (B3LYP/SDD) on mononuclear model systems. The results allowed us to draw interesting conclusions on the structural characteristics of Zn centres and to evaluate the importance of such effects as the resolution of X-ray crystallographic structures, the enzyme class in which the Zn centre is included, and the identity of the ligands at the Zn coordination sphere. Altogether, the set of results obtained provides useful data for the enhancement of the atomic models normally applied to the theoretical and computational study of zinc enzymes at the quantum mechanical level (in particular enzymatic mechanisms), and for the development of molecular mechanical parameters for the treatment of zinc coordination spheres with molecular mechanics or molecular dynamics in studies with the full enzyme.     

Conformational study of cyclolinopeptide A. A distance geometry and molecular dynamics approach

The conformation of cyclolinopeptide A, c(Pro-Pro-Phe-Phe-Leu-Ile-Ile-Leu-Val), a naturally occurring peptide with remarkable cytoprotective activity, has been investigated by means of distance geometry calculations and molecular dynamics simulations. The starting points for all the calculations were an X-ray structure and other structures obtained from distance geometry calculations based on NMR data. Restrained and unrestrained molecular dynamics simulations are reported in vacuo and in CCl4. Structural and dynamic properties are investigated and compared with those experimentally determined. The conformation obtained from the MD simulations which best reproduces the NMR parameters is at the same time one of the most stable ones and is also fairly similar to the crystal structure. An explanation for the occurrence of multiple conformations in solution at room temperature is given.     

Characterization of a catalytic ligand bridging metal ions in phosphodiesterases 4 and 5 by molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations

Cyclic nucleotide phosphodiesterases (PDEs) constitute a large superfamily of enzymes regulating concentrations of intracellular second messengers cAMP and cGMP through PDE-catalyzed hydrolysis. Although three-dimensional x-ray crystal structures of PDE4 and PDE5 have been reported, it is uncertain whether a critical, second bridging ligand (BL2) in the active site is H2O or HO- because hydrogen atoms cannot be determined by x-ray diffraction. The identity of BL2 is theoretically determined by performing molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations, for the first time, on the protein structures resolved by x-ray diffraction. The computational results confirm our previous suggestion, which was based on QM calculations on a simplified active site model, that BL2 in PDE4 should be HO-, rather than H2O, serving as the nucleophile to initialize the catalytic hydrolysis of cAMP. The molecular dynamics simulations and QM/MM calculations on PDE5 demonstrate for the first time that the BL2 in PDE5 should also be HO- rather than H2O as proposed in recently published reports on the x-ray crystal structures, which serves as the nucleophile to initialize the PDE5-catalyzed hydrolysis of cGMP. These fundamental structural insights provide a rational basis for future structure-based drug design targeting PDEs.     

Classical molecular dynamics simulation of the photoinduced electron transfer dynamics of plastocyanin.

Classical molecular dynamics simulations are used to investigate the nuclear motions associated with photoinduced electron transfer in plastocyanin. The blue copper protein is modeled using a molecular mechanics potential; potential parameters for the copper-protein interactions are determined using an x-ray crystallographic structure and absorption and resonance Raman spectra. Molecular dynamics simulations yield a variety of information about the ground (oxidized) and optically excited (charge-transfer) states: 1) The probability distribution of the potential difference between the states, which is used to determine the coordinate and energy displacements, places the states well within the Marcus inverted region. 2) The two-time autocorrelation function of the difference potential in the ground state and the average of the difference potential after instantaneous excitation to the excited state are very similar (confirming linear response in this system); their decay indicates that vibrational relaxation occurs in about 1 ps in both states. 3) The spectral densities of various internal coordinates begin to identify the vibrations that affect the optical transition; the spectral density of the difference potential correlation function should also prove useful in quantum simulations of the back electron transfer. 4) Correlation functions of the protein atomic motions with the difference potential show that the nuclear motions are correlated over a distance of more than 20 A, especially along proposed electron transport paths.