Use Of Molecular Dynamics Research Articles

Fluorescence-quenched solid phase combinatorial libraries in the characterization of cysteine protease substrate specificity.

To map the substrate specificity of cysteine proteases, two combinatorial peptide libraries were synthesized and screened using the archetypal protease, papain. The use of PEGA resin as the solid support for library synthesis facilitated the application of an on-resin fluorescence-quenched assay. Results from the screening of library 2 indicated a preference for Pro or Val in the S3 subsite and hydrophobic residues in S2; the most prevalent residue not being Phe but Val. The S1 subsite exhibited a dual specificity for both small, nonpolar residues, Ala or Gly, as well as larger, Gln, and charged residues, Arg. Small residues predominated in the S1'-S4' subsites. Active peptides from the libraries and variations thereof were resynthesized and their kinetics of hydrolysis by papain assessed in solution phase assays. Generally, there was a good correlation between the extent of substrate cleavage on solid phase and the kcat/KM's obtained in solution phase assays. Several good substrates for papain were obtained, the best substrates being Y(NO2)PMPPLCTSMK(Abz) (kcat/KM = 2109 (mM s)-1), Y(NO2)PYAVQSPQK(Abz) (kcat/KM = 1524 (mM s)-1), and Y(NO2)PVLRQQRSK(Abz) (kcat/KM = 1450 (mM s)-1). These results were interpreted in structural terms by the use of molecular dynamics (MD). These MD calculations indicated two different modes for the binding of substrates in the narrow enzyme cleft.

Stability and Activity of Mesophilic Subtilisin E and Its Thermophilic Homolog: Insights from Molecular Dynamics Simulations

Herein we examine the origin of the high-temperature (350 K) behavior of a thermophilic mutant enzyme (labeled as 5-3H5; see Zhao and Arnold Prot. Eng. 1999, 12, 47−53) derived from subtilisin E by eight amino acid substitutions. Through the use of molecular dynamics (MD) simulations, we have provided molecular-level insights into how point mutations can affect protein structure and dynamics. From our simulations we observed a reduced rmsd in several key regions, an increased overall flexibility, an increase in the number of hydrogen bonds, and an increase in the number of stabilizing interactions in the thermophilic system. We also show that it is not a necessary requirement that thermophilic enzymes be less flexible than their mesophilic counterparts at low temperatures. However, thermophilic enzymes must retain their three-dimensional structures and flexibility at high temperatures in order to retain activity. Furthermore, we have been able to point out the effects of some of the single substitutions. Even if it is not possible yet to give general rules for rational protein design, we are able to make some predictions on how a protein should be stabilized in order to be thermophilic. In particular, we suggest that a promising strategy toward speeding up the design of thermally stable proteins would be to identify fluxional regions within a protein through the use of MD simulations (or suitable experiments). Presumably these regions allow for autocatalytic reactions to occur and are also involved in allowing water to gain access to the interior of the protein and initiate protein unfolding. These fluxional regions could also adversely affect the positioning of the catalytic machinery, thereby decreasing catalytic efficiency. Thus, once these locations have been identified, “focused” directed evolution studies could be designed that stabilize these “fluxional” regions.

The Use of Molecular Dynamics to Simulate the Temperature Dependence of the Calculated Absorption Spectrum for Nd<sup>3+</sup>:YAG

The use of molecular dynamics (MD) and the inclusion of configuration interaction (CI) effects have been shown to be important in the simulation of polarized absorption spectra for rare-earth doped compounds. This work, focuses on how well the MD approach can account for the temperature dependence of the calculated absorption spectrum for Nd3+:YAG, using the standard MD pair-potential of the Born-Mayer-Huggins form. All simulated spectra are compared to the corresponding experimental spectra. The results indicate that the simple pair-potential must be replaced by a many-body potential to describe the motion of the ions with sufficient accuracy. They also suggest that an “effective temperature” (T') should be used in the MD simulation of the form T'=aT+b

Rationalization of the Enantioselectivity of Subtilisin in DMF

Herein we examine the origin of enantioselectivity in the serine protease subtilisin in DMF through the use of molecular dynamics (MD) and free energy perturbation (FEP) simulations. In particular, we are interested in the resolution of a racemic mixture of sec-phenethyl alcohol by a transesterification reaction with the acylating agent vinyl acetate, catalyzed by subtilisin in anhydrous dimethylformamide (DMF). To study the enantioselectivity in this case, we examined the tetrahedral intermediate as a model of the enzyme transition state (as has been done in the past). A critical aspect of this study was the determination of the charge distribution of the two (R and S) tetrahedral intermediates through the use of a combined quantum mechanical/molecular mechanical electrostatic potential fitting methodology. In designing the active site charge model, we found that the R and S tetrahedral intermediates have significantly different charge distributions due to the presence of the stereodifferentiating enviro...

Diffusion of a Mixture of Methane and Xenon in Silicalite: A Molecular Dynamics Study and Pulsed Field Gradient Nuclear Magnetic Resonance Experiments

The diffusion of a mixture of methane and xenon in the zeolite silicalite is studied by use of molecular dynamics (MD) simulations and pulsed field gradient (PFG) nuclear magnetic resonance (NMR). For a fixed total number of guest molecules, the ratio of xenon to methane is varied in order to examine the special properties of diffusion in a mixture. High xenon concentrations were found to slow the methane diffusivity in the mixture, while the diffusion of xenon is nearly unaffected by high methane concentrations. The reason for the dominance of xenon is the larger local heat of adsorption of xenon and the larger mass of xenon compared to methane in combination with channel size and topology in silicalite. Simulated and experimental data are in very good agreement with each other. Diffusion anisotropy as resulting from the MD simulations is discussed in terms of the correlation rule for diffusion in the interconnected pore system of ZSM-5 (Karger, J. J. Phys. Chem. 1991, 98, 5558).

Macro- and microscopic simulation of materio-thermo-mechanical fields

Two kinds of computer simulation are made for some engineering processes incorporating phase transformation. One is the macroscopic or continuum mechanics approach based on the theory of metallo-thermo-mechanics developed byt eh authors, and the other is the microscopic, or atomic ledvei simulation by use of molecular dynamics. In each case, emphasis is focussed on the effect of coupling among material structures, temperature and stress/strain during in-solid or liquid-solid phase transformations. Some illustrative examples are presented.

Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations

Specific amino acid binding by aminoacyl-tRNA synthetases is necessary for correct translation of the genetic code. To obtain insight into the origin of the specificity, the binding to aspartyl-tRNA synthetase (AspRS) of the negatively charged substrate aspartic acid and the neutral analogue asparagine are compared by use of molecular dynamics and free energy simulations. Simulations of the Asn - AspRS complex show that although Asn cannot bind in the same position as Asp, several possible positions exist 1.5 to 2 Å away from the Asp site. The binding free energy of Asn in three of these positions was compared to that of Asp through alchemical free energy simulations, in which Asp is gradually mutated ito Asn in the complex with the enzyme. To correctly account for the electrostatic interactions in the system (including bulk solvent), a recently developed hybrid approach was used, in which the region of the mutation site is treated microscopically, whereas distant protein and solvent are treated by continuum electrostatics. Seven free energy simulations were performed in the protein and two in solution. The various Asn positions and orientations sampled at the Asn endpoints of the protein simulations yielded very similar free energy differences. The calculated Asp → Asn free energy change is 79.8(±1.5) kcal/mol in solution and 95.1(±2.8) kcal/mol in the complex with the protein. Thus, the substrate Asp is predicted to bind much more strongly than Asn, with a binding free energy difference of 15.3 kcal/mol. This implies that erroneous binding of Asn by AspRS is highly improbable, and cannot account for any errors in the translation of the genetic code. Almost all of the protein contributions to the Asp versus Asn binding free energy difference arise from an arginine and a lysine residue that hydrogen bond to the substrate carboxylate group and an Asp and a Glu that hydrogen bond to these; all four amino acid residues are completely conserved in AspRSs. The protein effectively “solvates” the Asp side-chain more strongly than water does. The simulations are analyzed to determine the interactions that Asn is able to make in the binding pocket, and which sequence differences between AspRS and the highly homologous AsnRS are important for modifying the amino acid specificity. A double or triple mutation of AspRS that could make it specific for Asn is proposed, and supported by preliminary simulations of a mutant complex.

Analysis of Serial and Parallel Algorithms for Use in Molecular Dynamics.

This work analyzes the stability and accuracy of multistep methods, either for serial or parallel calculations, applied to molecular dynamics simulations. Numerical testing is made by evaluating the equilibrium configurations of mono-elemental crystalline lattices of metallic and semiconducting type (Ag and Si, respectively) and of a cubic CuY compound.

Molecular dynamics simulations to investigate wafer bonded interfaces

The physical processes of wafer bonding and the resulting structure of interfaces are studied by the combined use of molecular dynamics (MD) structure modelling and high resolution electron microscopy (HREM) structure imaging.

Using Molecular Dynamics to Predict Factors Affecting Binding Strength and Magnetic Relaxivity of MRI Contrast Agents

We demonstrate the use of molecular dynamics and molecular mechanics methods to calculate properties and behavior of metal-chelate complexes that can be used as MRI contrast agents. Static and dynamic properties of several known agents were calculated and compared with experiment. We calculated the static properties such as the q-values (number of inner shell waters) and binding distances of chelate atoms to the metal ion for a set of chelates with known X-ray structure. The dynamic flexibility of the chelate arms was also calculated. These computations were extended to a series of exploratory chelate structures in order to estimate their potential as MRI contrast agents. We have also calculated for the first time the NMR relaxivity of an MRI contrast agent using a long (5 nsec) molecular dynamics simulation. Our predictions are promising enough that the method should prove useful for evaluating novel candidate compounds before they are synthesized. One novel static property, the projected area of chelate atoms onto a virtual surface centered on the metal ion (gnomonic projection), was found to give an effective measure of how well the chelate atoms use the free space around the metal ion.

Structural Basis for Calcium Binding by Uteroglobins

Uteroglobins, i.e. proteins with similar three-dimensional structure and ligand binding specificity to uteroglobin from rabbit uterus, have been found in rat, mouse and human lung. We have recently demonstrated the binding of calcium by human uteroglobin, and we have therefore tried to find potential binding sites for metals in the three-dimensional structure of uteroglobin by the use of two different computational procedures. A putative binding site for calcium in uteroglobin was identified by means of a hydrophobic contrast function. The spatial disposition of atoms that could ligand calcium in the putative calcium-binding site appears similar to that of the primary calcium-binding site of secretory phospholipase A 2enzymes, consisting of the carboxyl group of an aspartic acid residue and a loop providing three backbone carbonyl oxygens. From inspection of their primary sequences and three-dimensional structures, it became clear that this putative calcium-binding motif is conserved among uteroglobins from different species. The potential significance of the predicted site was investigated by site-directed point mutagenesis of human uteroglobin in which Asp46 was replaced by Asn or Lys. In both mutants, the ruthenium red and 45Ca 2+binding was significantly reduced. Sodium dodecyl sulphate/polyacrylamide gel electrophoresis under non-reducing conditions indi cated that the mutant proteins had the expected molecular masses and that their ability to dimerize was not disturbed by these mutations. Valence calculations also identified the putative calcium-binding site, but only after optimization of its conformation by the use of molecular dynamics with a restrained calcium ion. Our results support the notion that Asp46 of uteroglobins acts as a "cap" residue in a calcium-binding site structurally similar to the primary calcium binding sites of phospholipases A 2.

Some Recent Developments in Computational Chemistry

Abstract Some recent developments in the use of computational methods to predict the properties of condensed phases are discussed; the use of Gibbs ensemble Monte Carlo to predict the phase equilibria of bulk phases, the use of molecular dynamics to elucidate Atomic Force Microscopy experiments on organic films, and the use of combined Monte Carlo/molecular dynamics techniques to enable the direct prediction of particle fluxes along pressure gradients in model microporous materials.

Molecular Dynamics Studies of Initiation in Energetic Materials

In this paper an overview of Molecular Dynamics simulations of chemically reacting systems is described. In particular, molecular dynamics simulations of shock initiation in a model energetic material are reported. The use of Molecular Dynamics to model thermal initiation and determine reactions rates in energetic materials is also discussed. Finally, the future potential of MD techniques for energetic materials applications is considered.

Transmission of low-energy oxygen ions through ultrathin rare-gas films: Molecular-dynamics simulation.

By use of molecular dynamics we simulate a recent experiment by Sack et al. in which oxygen ions are desorbed by electron impact from a ${\mathrm{WO}}_{\mathit{x}}$ surface, and their transmission through rare-gas films of a few monolayer thickness has been measured. When using only elastic scattering cross sections between ${\mathrm{O}}^{+}$ and rare-gas atoms in the simulation, we find fair quantitative agreement with the measured transmission yield, and energy, and angular distributions, for Xe and Kr films. The large number of transmitted oxygen ions can be traced back to the small ${\mathrm{O}}^{+}$ radius. The discrepancy between measured and simulated transmission behavior through Ar films is attributed to either electronically inelastic losses or structural effects in these films. The im pact of this work on the depth of origin of sputtered particles is discussed.

Conformational properties of the Arg-Leu-Gly tripeptide--DMSO--water clusters with the combined use of molecular dynamics and energy minimization studies.

The Arg-Leu-Gly tripeptide is the repeating fragment of sequential arginine-rich polypeptides capable of interacting with DNA. The conformational influence of solvent molecules (DMSO/H2O) were investigated with the combined use of molecular dynamics and energy minimization. It was found that water molecules greatly contribute to the peptide structure by solvating all its hydrophylic sites even in the presence of DMSO excess, whereas one water molecule links the ammonium and carboxylic ends of the Arg-Leu-Gly. The persistence of residual water, which was confirmed by varying the computer simulation parameters, indicates that pretreatment of peptide segments in aqueous solutions should greatly affect their conformational properties in organic media. A satisfactory agreement between experimental data (1H-NMR and IR spectroscopy) and the presented computational study deserves also to be noted.

Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2.

Temperature-induced unfolding of chymotrypsin inhibitor 2 in water was investigated by molecular dynamics simulations. The major transition state of unfolding was identified on the basis of structural and conformational changes in the protein during the unfolding reaction. The native tertiary contacts in the hydrophobic core were considerably disrupted in the transition state, whereas the secondary structure was partially intact. The extent of structural change of the protein around a particular residue was represented quantitatively by the ratio of the number of contacts the residue makes in the transition state relative to the native state, phi MD, which allows quantitative comparison with the experimentally determined phi F values. For the region of the unfolding trajectory that is identified as the transition state, the phi MD and phi F values are in good agreement, suggesting that the transition state identified in the unfolding simulation corresponds to that probed with protein engineering methods. Although speculative, the transition state identified in the simulation is consistent with available experimental data and provides an in-depth view of what the transition state of unfolding may look like.

A molecular dynamics study on the collisional and cooling phases of cascade damage

Abstract Presented at the IEA Workshop on the Use of Molecular Dynamics in Modelling Radiation Effects and Other Non-equilibrium Phenomena, May 6–8, 1991 at La Jolla, USA Molecular dynamics calculations were performed to study the cascade damage evolution initiated from a primary knock-on atom of 250 eV. The thermodynamic characterization of the cascade was investigated by the Morse potential and it is found that during the cooling phase of the cascade local equilibrium was realized. Cascade evolution by the simple embedded atom method (EAM) potential was also calculated and the effects of initial target temperatures on the cascade processes were discussed.

Vibrational densities of states from molecular-dynamics calculations.

A method for calculating the vibrational densities of states of crystalline materials by use of molecular dynamics (MD) is presented. It consists mainly of starting the calculation with all atoms at rest in their equilibrium positions, except one which is given an initial velocity; the time evolution of this velocity is Fourier transformed to give the local vibrational density of states, and the procedure repeated for nonequivalent atoms in the lattice. It is shown with examples that the vibrational densities of states are unbiased and show very low noise and that calculations with this method require much fewer MD steps than those performed using standard random initializations.

Conformational sampling and ensemble generation by molecular dynamics simulations: 18‐Crown‐6 as a test case

AbstractUsing the crown ether 18‐crown‐6 as a test system, molecular dynamics has been evaluated as a technique for conformational searching and thermodynamic ensemble generation. By running a series of 200 ps and 2 ns simulations, an “optimum” temperature range for conformational searching, i.e., the temperature at which one finds the largest number of low energy structures, was demonstrated to be dependent on the time interval at which one examines the structure. By considering conformational degeneracy and entropy with the rigid rotor harmonic oscillator approximation we have been able to demonstrate that the ensemble generated approaches thermodynamic equilibrium in about 6 ns of simulation. To our knowledge this is the first time this has been demonstrated for a complex organic molecule and it highlights the power and usefulness of molecular dynamics as a method for thermodynamic ensemble generation and conformational searching.

Intermolecular Potential Variation due to Intramolecular Rotation in Molecules

Abstract The changes in charge and polarization densities of ethane, methanol and formamide upon internal rotation is studied using SCF-HF calculations. For formamide the charge density changes with dihedral angle are seen in the rapidly varying molecular dipole moment, whereas these changes are only moderate in the methanol molecule. In ethane the quadrupole moment variation is about 15%. The barriers to rotation are found to be 3.47 kcal/mole for ethane, 0.84 kcal/mole for methanol and 14.94 kcal/mol for formamide. The total molecular polarizability, which is estimated using perturbation theory, is varying slowly with rotation angle, but the individual atomic components change rapidly for all three molecules investigated. The calculations indicate that solvent effects upon intramolecular configuration are reflected in variations of intermolecular interactions. These implications are discussed in connection with modelling internally flexible molecules for use in molecular dynamics and Monte Carlo simulations. Similarly, water-water interactions are affected by small vibrations which alter the equilibrium charge density and polarizability of the individual molecule.