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PubMed2006

Probing the importance of hydrogen bonds in the active site of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation.

Hydrogen bonds occurring in the catalytic triad (Asp32, His64 and Ser221) and the oxyanion hole (Asn155) are very important to the catalysis of peptide bond hydrolysis by serine proteases. For the subtilisin NK (nattokinase), a bacterial serine protease, construction and analysis of a three-dimensional structural model suggested that several hydrogen bonds formed by four residues function to stabilize the transition state of the hydrolysis reaction. These four residues are Ser33, Asp60, Ser62 and Thr220. In order to remove the effect of these hydrogen bonds, four mutants (Ser33-->Ala33, Asp60-->Ala60, Ser62-->Ala62, and Thr220-->Ala220) were constructed by site-directed mutagenesis. The results of enzyme kinetics indicated that removal of these hydrogen bonds increases the free-energy of the transition state (DeltaDeltaG(T)). We concluded that these hydrogen bonds are more important for catalysis than for binding the substrate, because removal of these bonds mainly affects the kcat but not the K(m) values. A substrate, SUB1 (succinyl-Ala-Ala-Pro-Phe-p-nitroanilide), was used during enzyme kinetics experiments. In the present study we have also shown the results of FEP (free-energy perturbation) calculations with regard to the binding and catalysis reactions for these mutant subtilisins. The calculated difference in FEP also suggested that these four residues are more important for catalysis than binding of the substrate, and the simulated values compared well with the experimental values from enzyme kinetics. The results of MD (molecular dynamics) simulations further demonstrated that removal of these hydrogen bonds partially releases Asp32, His64 and Asn155 so that the stability of the transition state decreases. Another substrate, SUB2 (H-D-Val-Leu-Lys-p-nitroanilide), was used for FEP calculations and MD simulations.

Bacillus subtilis↗

PubMed2001

Multimodal inclusion complexes between barbiturates and 2-hydroxypropyl-beta-cyclodextrin in aqueous solution: isothermal titration microcalorimetry, (13)C NMR spectrometry, and molecular dynamics simulation.

Multiple types (structures) of inclusion complexes between barbiturates and 2-hydroxypropyl-beta-cyclodextrin (HPCD) were evaluated by isothermal titration microcalorimetry and (13)C NMR spectroscopy. The geometries of the inclusion complexes were suggested by molecular dynamics simulation. Barbituric acid (BA), barbital (B), amobarbital (AB), pentobarbital (PB), secobarbital (SB), cyclobarbital (CB), and phenobarbital (PHB) were used as barbiturates with different substituents on the barbituric acid ring and compared for inclusion types in aqueous solution. The association constants (K), stoichiometries, and thermodynamic parameters change in free energy (DeltaG) change in enthalpy (DeltaH), and change in entropy [DeltaS] for each type of complex were determined from the calorimetric data. The inclusion complexation was largely entropy driven because of hydrophobic interactions. The values of K increased in the order BA<B<AB<PB<SB<CB<PHB. Barbiturates, except B and BA, form two types of inclusion complex with a 1:1 stoichiometry in the un-ionized forms. The first type of inclusion complex with high affinity (K(1)) was characterized by small negative values of DeltaH(1) and large positive DeltaS(1), where the substituent R2 of the barbiturate was initially inserted into the cavity of HPCD through hydrophobic interactions. There was a good relationship between DeltaG(1) obtained from the calorimetric data for the first type of inclusion complex and DeltaG(R2) calculated from the changes in (13)C Nuclear Magnetic Resonance (NMR) chemical shifts for the substituent R2 of barbiturates. These types were very stable in aqueous solution at various pHs. The second type of complex, with low affinity (K(2)), was characterized by large negative values of DeltaH(2) and small positive DeltaS(2), reflecting van der Waals' interactions in the un-ionized forms of barbiturates at pH values less than pK(a). The values of K(2) were markedly decreased to <10(3) M(-1) as the barbiturates were ionized over pH 8. Thus, in the second type, the barbituric acid ring contributed to forming the complexes. The geometries were stabilized by hydrogen bond formation between the hetero atoms in the barbituric acid ring and the secondary hydroxyl groups on the rim of the cyclodextrin. The (13)C NMR chemical shifts of C4 and C6 carbons in the barbituric acid ring were moved upfield significantly by the inclusion complexation. On the other hand, B and BA could form only one type of complex, the lid-type supramolecular complex with small association constants.

2-Hydroxypropyl-beta-cyclodextrin↗

PubMed2003

Molecular dynamics simulation reveals a surface salt bridge forming a kinetic trap in unfolding of truncated Staphylococcal nuclease.

Surface salt bridges are ubiquitous in globular proteins. Their contribution to protein stability has been extensively debated in the past decade. Here, molecular dynamics simulations are performed starting from a non-equilibrium state of Staphylococcal nuclease (SNase) with C-terminal truncation (SNaseDelta). The results indicate a key role in the unfolding of the surface salt bridge between arginine 105 and glutamate 135. Experimentally, SNaseDelta is known to be partially unfolded. However, in simulations over 1 ns at 300 K and over 500 ps at 400 K, SNaseDelta remains stable in the native-like folded conformation, the salt bridge hindering unfolding. When the potential function is altered so as to selectively weaken the salt bridge, which then breaks rapidly at 430 K, the protein starts to unfold. The results suggest that breaking of this salt bridge presents a significant barrier to the unfolding transition of SNaseDelta from a native-like state to the unfolded state. Potential of mean force calculations indicate that the barrier height for this transition is approximately 7 kcal/mol.

Arginine↗

PubMed2005

A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides.

Recently, the importance of proline ring pucker conformations in collagen has been suggested in the context of hydroxylation of prolines. The previous molecular mechanics parameters for hydroxyproline, however, do not reproduce the correct pucker preference. We have developed a new set of parameters that reproduces the correct pucker preference. Our molecular dynamics simulations of proline and hydroxyproline monomers as well as collagen-like peptides, using the new parameters, support the theory that the role of hydroxylation in collagen is to stabilize the triple helix by adjusting to the right pucker conformation (and thus the right phi angle) in the Y position.

Collagen↗

PubMed2005

Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations.

We use an integrated computational approach to reconstruct accurately the transition state ensemble (TSE) for folding of the src-SH3 protein domain. We first identify putative TSE conformations from free energy surfaces generated by importance sampling molecular dynamics for a fully atomic, solvated model of the src-SH3 protein domain. These putative TSE conformations are then subjected to a folding analysis using a coarse-grained representation of the protein and rapid discrete molecular dynamics simulations. Those conformations that fold to the native conformation with a probability (P(fold)) of approximately 0.5, constitute the true transition state. Approximately 20% of the putative TSE structures were found to have a P(fold) near 0.5, indicating that, although correct TSE conformations are populated at the free energy barrier, there is a critical need to refine this ensemble. Our simulations indicate that the true TSE conformations are compact, with a well-defined central beta sheet, in good agreement with previous experimental and theoretical studies. A structured central beta sheet was found to be present in a number of pre-TSE conformations, however, indicating that this element, although required in the transition state, does not define it uniquely. An additional tight cluster of contacts between highly conserved residues belonging to the diverging turn and second beta-sheet of the protein emerged as being critical elements of the folding nucleus. A number of commonly used order parameters to identify the transition state for folding were investigated, with the number of native Cbeta contacts displaying the most satisfactory correlation with P(fold) values.

Models, Molecular↗

PubMed2004

Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations.

The experimentally well-established folding mechanism of the src-SH3 domain, and in particular the phi-value analysis of its transition state, represents a sort of testing table for computational investigations of protein folding. Here, parallel molecular dynamics simulations of the src-SH3 domain have been performed starting from denatured conformations. By rescuing and restarting only trajectories approaching the folding transition state, an ensemble of conformations was obtained with a completely structured central beta-sheet and a native-like packing of residues Ile-110, Ala-121, and Ile-132. An analysis of the trajectories shows that there are several pathways leading to the formation of the central beta-sheet whereas its two hairpins form in a different but consistent way.

Computer Simulation↗

PubMed1999

Molecular dynamics simulations of human alpha-lactalbumin: changes to the structural and dynamical properties of the protein at low pH.

Two 700-ps molecular dynamics simulations of human alpha-lactalbumin have been compared. Both were initiated from an X-ray structure determined at pH 6.5. One simulation was designed to represent native conditions and the other the protein in solution at pH 2.0 without a bound calcium ion. The low pH conditions were modelled by protonating the aspartate, glutamate, and histidine side chains and the protein C-terminus. Significant changes were observed for the C-terminal region of the sequence in the simulation at low pH. Most notably an alpha-helix, helix D, and the C-terminal 3(10) helix were substantially disrupted relative to the simulation at high pH. These perturbations to the native fold are similar to those observed in an X-ray structure of alpha-lactalbumin at pH 4.2. In addition, larger fluctuations about side chain torsion angles were observed in the low pH simulation than in that corresponding to the higher pH. These structural and dynamical changes might be representative of the early stages of the transition to the molten-globule state of the protein known to be formed under low pH conditions in solution.

Humans↗

PubMed2000

Molecular-dynamics simulation of the beta domain of metallothionein with a semi-empirical treatment of the metal core.

The three-metal-containing beta domain of rat liver metallothionein-2 in aqueous solution was simulated with different metal contents. The Cd(3), the CdZn(2), and the Zn(3) variant were investigated using a conventional molecular dynamics simulation, as well as a simulation with a semi-empirical quantum-chemical description (MNDO and MNDO/d) of the metal core embedded in a classical environment. For the purely classical simulations, the standard GROMOS96 force-field parameters were used, and parameters were estimated for cadmium. The results of both kinds of simulations were compared to each other and to the corresponding experimental X-ray crystallographic and NMR solution data. The purely classical simulations were found to produce a too compact metal cluster with partially incorrect geometries, which affected the enfolding protein backbone structure. The inclusion of MNDO/d for the treatment of the metal cluster improved the results to give correct cluster geometries and an overall protein structure in agreement with the experiment. The metal cluster and the cysteine residues bound to it are structurally stable, while the irregular polypeptide backbone loops between the cysteines exhibit a considerable flexibility. MNDO without extension to d orbitals failed to maintain the structure of the metal core.

Animals↗

PubMed2005

Molecular dynamics simulation of discontinuous volume phase transitions in highly-charged crosslinked polyelectrolyte networks with explicit counterions in good solvent.

The volumetric properties of highly-charged defect-free polyelectrolyte networks with tetrafunctional crosslinks are studied through molecular dynamics simulations in the canonical ensemble. The network backbone monomers, which are monovalent, and the counterions, which are mono-, di-, or trivalent, are modeled explicitly in the simulations, but the solvent is treated implicitly as a dielectric medium of good solvation quality. The osmotic pressure of the network-solvent system is found to depend greatly on the strength of electrostatic interactions. Discontinuous volume phase transitions are observed when the electrostatic interactions are strong, and the onset of these transitions shifts to higher solvent dielectricity as the counterion valency increases. The roles of the various virial contributions to the osmotic pressure are examined. The network elasticity entropy is found to behave nearly classically. As the network contracts and collapses with increasing strength of electrostatic interactions, the loss of counterion entropy leads to increased counterion osmotic pressure contributions via two mechanisms. The reduction in available configurational space increases the counterion translational entropy contribution to the ideal part of the osmotic pressure, and the greater number of counterion-monomer contacts formed due to counterion condensation and confinement increases the counterion excluded-volume entropy contribution to the excess part of the osmotic pressure. These observations contrast the decrease in the single ideal-gas-like counterion translational entropy contribution to the osmotic pressure predicted by the counterion condensation-charge renormalization theory. An accompanying decrease in the total electrostatic energy balances the loss of counterion excluded-volume entropy as the polyelectrolyte networks collapse in low-dielectric solvents. This interplay between the electrostatic energy and the counterion excluded-volume entropy appears to be responsible for the discontinuous volume phase transitions that are observed in polyelectrolyte networks. The structure of the polyelectrolyte network is also found to be affine in the swollen state, with constituent chains nearly fully extended, and nonaffine in the collapsed state, with the chains adopting a Gaussian conformation.

Journal Article↗

PubMed2000

Clumps of randomly charged polymers: molecular dynamics simulation of condensation, crystallization, and swelling

The behavior of randomly charged polyampholytes against a wide range of the Coulomb coupling parameter Gamma (the ratio of the Coulomb energy to thermal energy) is studied with the use of molecular dynamics simulations. Neutral polyampholyte collapses for Gamma>1, where large volume changes are due to multichain effects. Charged chains reptate significantly in a globule. Polyampholyte with widely extensible bonds condenses to a cubic crystal for Gamma>>1, while that with finitely extensible bonds remains in an imperfectly ordered glass structure. Non-neutral polyampholyte whose charge offset exceeds 1 / 2N(1/2) behaves as polyelectrolyte: it consists of nonoverlapped chains for Gamma>1, and shrinks to the noncharged polymer regime for Gamma<1 (N is the number of charged monomers). Condensed counterions on polyampholyte screen the electric field, making non-neutral polyampholyte close to the neutral one. Added salt of comparable charge density as that of the polyampholyte further compactifies it. However, the addition of more salt results in the weakening of the polyampholyte nature and reentrant swelling of non-neutral polyampholyte.

Journal Article↗

PubMed2006

Mechanism of beta-purothionin antimicrobial peptide inhibition by metal ions: molecular dynamics simulation study.

Wheat beta-purothionin is a highly potent antimicrobial peptide which, however, is inactivated by metal ions. The key structural properties and mechanisms of inhibition of beta-purothionin were investigated for the first time using unconstrained molecular dynamics simulations in explicit water. A series of simulations were performed to determine effects of temperature and the metal ions. Analyses of the unconstrained simulations allowed the experimentally unavailable structural and dynamic details to be unambiguously examined. The global fold and the alpha1 helix of beta-purothionin are thermally stable and not affected by metal ions. In contrast, the alpha2 helix unfolds with shift of temperature from 300 K and in the presence of metal ions. The network of conserved residues including Arg30 and Lys5 is sensitive to environmental changes and triggers unfolding. Loop regions display high flexibility and elevated dynamics, but are affected by metal ions. Our study provides insights into the mechanism of metal ion-based inhibition.

Anti-Infective Agents↗

PubMed2006

Molecular dynamics simulations of melting of perfect crystalline hexahydro-1,3,5-trinitro-1,3,5-s-triazine.

The melting mechanism of superheated perfect crystalline hexahydro-1,3,5-trinitro-1,3,5-s-triazine (alpha-RDX) has been investigated using molecular dynamics simulations with the fully flexible force field developed by Smith and Bharadwaj [J. Phys. Chem. B 103, 3570 (1999)]. Sequential 50 ps equilibration simulations of the constant stress-constant temperature ensemble were performed at 10 K intervals over the range of 300-650 K, corresponding to a heating rate of 2.0 x 10(11) Ks. A solid-solid phase transition is observed between 480 and 490 K, followed by melting, which occurs between 500 and 510 K. The solid-solid phase transition, both displacive and rotational, is characterized by an abrupt decrease in the lengths of the unit cell edges a and b and an increase of the length of edge c. The molecular conformation in the new phase is AAE, although the axial nitro groups have different changes: one shift is more axial and the other is more equatorial. Phases other than alpha-RDX have been observed experimentally, however, there are insufficient data for comparisons to ascertain that the new phase observed here corresponds to a real phase. At the high heating rate (2.0 x 10(11) Ks) used in the simulations, the melted RDX reaches full orientational disorder at about 540 K and translational freedom at around 580 K. If the simulation at the melting temperature (510 K) is run sufficiently long complete rotational freedom is achieved in a few hundreds of picoseconds, while complete translational freedom requires much longer. These results show that given a sufficiently high heating rate, the system can exist for significant periods of time in a near-liquid state in which the molecules are not as free to rotate and diffuse as in the true liquid state. The bond lengths and bond angles undergo little change upon melting, while there are significant changes in the dihedral angles. The molecular conformation of RDX changes from AAE to EEE upon melting. The ramification of this for formulating force fields that accurately describe melting is that it is important that the torsional motions are accurately described.

Journal Article↗

PubMed1995

Molecular dynamics simulation of cytochrome b5: implications for protein-protein recognition.

Cytochrome b5 participates in electron-transfer reactions with a variety of different proteins. To explore how this protein might discern between structurally varied proteins, we have performed a molecular dynamics simulation focusing on its structural stability and dynamic behavior in solution. The protein was simulated in water at 298 K and pH 6.9 for 2.5 ns. The protein deviated significantly from the crystal structure midway through the simulation, but ultimately the crystalline conformation was regained. The simulation was at all times well behaved as judged by comparison to structural NMR data obtained in solution. One region of the protein backbone that deviated from the crystal conformation contains acidic residues implicated in electrostatic-based protein-protein recognition. The mobility in this region caused the protein to display different patterns of residues at the surface with time, as well as the formation of a large cleft partially exposing the hydrophobic core lining the heme pocket. Furthermore, the position and cyclical formation of this cleft suggest that hydrophobic interactions may be important in protein-protein recognition events and possibly even electron transfer, as the cleft allows for easy access to the heme group. These results indicate that thermal motion could provide a low-energy mechanism for controlling recognition events. Thus, the dynamical behavior observed through the varying solution conformations sampled may be important in influencing the diverse range of protein-protein interactions in which cytochrome b5 participates.

Computer Simulation↗

PubMed2005

The role of Phe in the formation of well-ordered oligomers of amyloidogenic hexapeptide (NFGAIL) observed in molecular dynamics simulations with explicit solvent.

We observed fast aggregation of partially ordered oligomers in an earlier simulation study of an amyloidogenic hexapeptide NFGAIL. In this work, the nucleation of highly ordered oligomers was further investigated by a combined total of 960 ns molecular dynamics simulations with explicit solvent on NFGAIL and its nonamyloidogenic mutant NAGAIL. In these simulations, four dimer subunits that each was constrained by harmonic forces as a two-strand beta-sheet were used to enhance the rate of formation. It was found that a critical role played by the aromatic residue Phe was to direct the stacking of beta-sheets to form ordered multilayer aggregates. We also found that many molecular arrangements of the peptide satisfied the "cross-beta-structure", a hallmark of amyloid fibrils. The tendency for the peptide to form either parallel or antiparallel beta-sheet was comparable, as was the tendency for the beta-sheets to stack either in parallel or antiparallel orientation. Overall, approximately 85% of the native hexapeptide formed octamers. The fact that only 8% of the octamers were well-ordered species suggests that the dissociation of the disordered oligomers be the rate-limiting step in the formation of highly ordered oligomers. Among the well-ordered subunit pairs, about half was formed by the beta-sheet extension along the main-chain hydrogen-bond direction, whereas the other half was formed by the beta-sheet stacking. Hence, a delicate balance between intersheet and intrasheet interactions appeared to be crucial in the formation of a highly ordered nucleus of amyloid fibrils. The disordered oligomers were mainly stabilized by nonspecific hydrophobic interactions, whereas the well-ordered oligomers were further stabilized by cross-strand hydrogen bonds and favorable side-chain stacking.

Amyloid↗

PubMed2006

Molecular dynamics simulations applied to electric field induced second harmonic generation in dipolar chromophore solutions.

Electric field induced second harmonic generation (EFISH) is an important experimental technique in extracting the first hyperpolarizability of an organic chromophore molecule. Such experiments are carried out in solutions with chromophore molecules dissolved in some common solvents. A known fact is that the first hyperpolarizabilities extracted from EFISH experiments are subject to the use of local field factors. In this work, we apply simulations to study the EFISH properties of chromophore solutions. By combining quantum chemistry calculations with the results derived from molecular dynamics simulations, we show how macroscopic EFISH properties can be modeled, using 4-(dimethylamino)-4'-nitroazobenzene dissolved in chloroform as a demonstration case. The focus of the study is on deriving accurate local field factors. We find that the local field approach applies very well to dipolar solutions, such as the one studied here, but that the local field factors derived are much smaller than the commonly used Onsager or Lorentz local field factors. Our study indicates that many of the reported first hyperpolarizabilities for dipolar molecules from EFISH experiments are most probably underestimated because the Onsager/Lorentz approach, commonly used in extracting the molecular first hyperpolarizability, neglects the effects of the shapes of dipolar chromophore molecules on the local field factors.

Journal Article↗

PubMed2007

Structural and dynamic properties of concentrated alkali halide solutions: a molecular dynamics simulation study.

The physicochemical properties of alkali halide solutions have long been attributed to the collective interactions between ions and water molecules in the solution, yet the structure of water in these systems and its effect on the equilibrium and dynamic properties of these systems are not clearly understood. Here, we present a systematic view of water structure in concentrated alkali halide solutions using molecular dynamics simulations. The results of the simulations show that the size of univalent ions in the solution has a significant effect on the dynamics of ions and other transport properties such as the viscosity that are correlated with the structural properties of water in aqueous ionic solution. Small cations (e.g., Li+) form electrostatically stabilized hydrophilic hydration shells that are different from the hydration shells of large ions (e.g., Cs+) which behave more like neutral hydrophobic particles, encapsulated by hydrogen-bonded hydration cages. The properties of solutions with different types of ion solvation change in different ways as the ion concentration increases. Examples of this are the diffusion coefficients of the ions and the viscosities of solutions. In this paper we use molecular dynamics (MD) simulations to study the changes in the equilibrium and transport properties of LiCl, RbCl, and CsI solutions at concentrations from 0.22 to 3.97 M.

Journal Article↗

PubMed1994

Open "back door" in a molecular dynamics simulation of acetylcholinesterase.

The enzyme acetylcholinesterase generates a strong electrostatic field that can attract the cationic substrate acetylcholine to the active site. However, the long and narrow active site gorge seems inconsistent with the enzyme's high catalytic rate. A molecular dynamics simulation of acetylcholinesterase in water reveals the transient opening of a short channel, large enough to pass a water molecule, through a thin wall of the active site near tryptophan-84. This simulation suggests that substrate, products, or solvent could move through this "back door," in addition to the entrance revealed by the crystallographic structure. Electrostatic calculations show a strong field at the back door, oriented to attract the substrate and the reaction product choline and to repel the other reaction product, acetate. Analysis of the open back door conformation suggests a mutation that could seal the back door and thus test the hypothesis that thermal motion of this enzyme may open multiple routes of access to its active site.

Acetylcholine↗

PubMed2005

A statistical approach to the interpretation of molecular dynamics simulations of calmodulin equilibrium dynamics.

A sample of 35 independent molecular dynamics (MD) simulations of calmodulin (CaM) equilibrium dynamics was prepared from different but equally plausible initial conditions (20 simulations of the wild-type protein and 15 simulations of the D129N mutant). CaM's radius of gyration and backbone mean-square fluctuations were analyzed for the effect of the D129N mutation, and simulations were compared with experiments. Statistical tests were employed for quantitative comparisons at the desired error level. The computational model predicted statistically significant compaction of CaM relative to the crystal structure, consistent with the results of small-angle X-ray scattering (SAXS) experiments. This effect was not observed in several previously reported studies of (Ca2+)(4)-CaM, which relied on a single MD run. In contrast to radius of gyration, backbone mean-square fluctuations showed a distinctly non-normal and positively skewed distribution for nearly all residues. Furthermore, the D129N mutation affected the backbone dynamics in a complex manner and reduced the mobility of Glu123, Met124, Ile125, Arg126, and Glu127 located in the adjacent alpha-helix G. The implications of these observations for the comparisons of MD simulations with experiments are discussed. The proposed approach may be useful in studies of protein equilibrium dynamics where MD simulations fall short of properly sampling the conformational space, and when the comparison with experiments is affected by the reproducibility of the computational model.

Calmodulin↗