Monte Carlo simulation study of melittin: Protein folding and temperature dependence

The tetramerization of melittin, a 26-amino-acid peptide, is considered as a model for protein folding. The Monte Carlo simulation was used to study the folding arrangement of melittin, and the results are compared with the experiment. An acceptance rate of 50% for new configurations is achieved by using ranges of ±0.001 Å for the translations and ±15°C for the rotations. Around 311 K, the folded structure of the protein has the greatest stability; the range from −40 to −80 shows the best ϕ angles for melittin. The final optimized structure of melittin strongly depends on the temperature. The melittin tetramer is found to have a temperature of maximum stability ranging from 35.5 to 43°C.

     

Microphase separation in the melts of diblock copolymers composed of linear and amphiphilic blocks

Computer-aided simulation performed via two independent methods (the Monte Carlo method and method of dissipative particle dynamics) is performed for studying the effect of microphase separation in concentrated solutions of diblock copolymers composed of linear blocks A and amphiphilic blocks A-graft-B. The type of microstructures generated by strong incompatibility between units A and B is shown to be controlled by the ratio of block lengths. For example, in the case of short amphiphilic blocks, elongated micelles with correlated mutual alignment are formed. In the case of longer amphiphilic blocks, lamellar structures are produced; with an increase in the length of this block, these structures are transformed into sequences of lamellas containing parallel layers, lamellas with intersecting layers, and perforated lamellas. When the system contains long amphiphilic blocks, bicontinuous structures arise.     

A new technique for metropolis Monte Carlo simulation to capture aggregate structures of fine particles: Cluster-moving Monte Carlo algorithm

We present a new Monte Carlo simulation procedure which is capable of capturing aggregate structures in a suspension where fine particles are dispersed. The algorithm we call the “cluster-moving” Monte Carlo algorithm involves moving aggregates (clusters) as unitary particles at every certain Monte Carlo step. We discuss here the theoretical background of the cluster-moving Monte Carlo algorithm and the availability of the algorithm for simulations of systems where fine particles aggregate. The results of simulations for two model systems, magnetic fluids and colloidal dispersions, have shown that the new algorithm produces much more rapid convergence than the conventional one for unstable dispersion systems and reproduces physically reasonable aggregate structures of fine particles.     

A comparative study of the simulated-annealing and Monte Carlo-with-minimization approaches to the minimum-energy structures of polypeptides: [Met]-enkephalin

A comparison of two methods for surmounting the multiple-minima problem, Simulated Annealing (SA) and Monte Carlo with Minimization (MCM), is presented with applications to [Met]-enkephalin in the absence and in the presence of water. SA explores a continuous space of internal variables, while MCM explores a discrete space consisting of the local energy minima on that space. Starting from random conformations chosen from the whole conformational space in both cases, it is found that, while SA converges to low-energy structures significantly faster than MCM, the former does not converge to a unique minimum whereas the latter does. Furthermore, the behavior of the RMS deviations with respect to the apparent global minimum (for enkephalin in the absence of water) shows no correlation with the observed overall energy decrease in the case of SA, whereas such a correlation is quite evident with MCM; this implies that, even though the potential energy decreases in the annealing process, the Monte Carlo SA trajectory does not proceed towards the global minimum. Possible reasons for these differences between the two methods are discussed. It is concluded that, while SA presents attractive prospects for possibly improving or refining given structures, it must be considered inferior to MCM, at least in problems where little or no structural information is available for the molecule of interest.     

The Structure of Liquid 4He across the λ-point

Abstract

Reverse Monte Carlo (RMC) modelling has been used to create three dimensional particle configurations of condensed ⁴He that are consistent with diffraction data at ten different temperatures across the superfluid transition. Here it is shown that all observable changes in the data are within the experimental uncertainties, so no conclusions can be drawn concerning possible structural differences between normal fluid and superfluid. The local structure is found to be dominantly icosahedral.     

Density distributions in the water shell of myoglobin

Two different approaches were used to explain the distribution of water coordinates in the crystallographically invisible part of the unit cell. Monte Carlo calculations were done starting from different initial water structures. Extended Monte Carlo calculations using equal initial structures were also used to obtain two further water structures. The differences between the Monte Carlo water structures were used to calculate the mean-square displacements of the water molecules. Monte Carlo calculations starting from different structures lead to a mean-square displacement of 0.58 Ų, whereas extended Monte Carlo moves using the same initial structure only show a mean-square displacement of 0.17 Ų. The mean-square displacement of 0.58 Ų can be used to explain the experimental data. © 1996 John Wiley & Sons, Inc.     

Fluorescence Assay for Membrane Lytic Peptides

Abstract

Lytic peptides such as melittin and mastoparan are usually assayed by measuring the leakage of cell contents; e.g., hemolysis. When such peptides lyse liposomes containing concentration-quenched 6-carboxyfluorescein (6CF), the resulting fluorescence increase is proportional to the amount of lytic peptide added. Using this 6CF-liposome system, one can assay nanogram quantities of melittin. A protocol was developed to survey peptides for lytic activity and at the same time, to test for mast cell degranulating activity. Peptides possessed either, both, or neither of these activities. The dye-liposome system was used to assay HPLC fractions of bee venom. This fluorescence assay for lytic activity is more sensitive and convenient than the hemolysis method, does not require removal of unlysed structures, and does not require animal cells.     

Ordering in Stretched Bernoullian Copolymers

A new approach is suggested to estimate the theoretical maximum capability to order for stretched Bernoullian copolymers AB, provided interchain AB contacts are unfavorable. A simple Monte Carlo procedure simulating the ordering of such copolymers via rotation of ring‐shaped chains reveals the capability to order even for quite long copolymer chains. The analytical probabilistic consideration is elaborated, which enables one to interpret the ordering via rotation in terms of a sliding of periodic Bernoullian chains. Using both the probabilistic analysis and Monte Carlo simulations it is shown that estimations of a capability to order given by the rotation procedure are also good for a sliding of true Bernoullian copolymers. Therefore, the simple Monte Carlo procedure seems suitable for estimating ordering in other classes of copolymers for which an analytical approach is more complicated. Such estimations might be useful for a consideration of various properties of irregular copolymers connected with their tendency to order.

Ordering by rotation of rings. As an example, an ordering for M = 10 000 chains of length N = 20 and composition p = 0.50 (p is the mole fraction of A units) is shown. See text.     

Influence of the Screening Function on Theoretical Calculations of the Structure Factor of Liquid Aluminum

Abstract

The structure factor S(k) of liquid aluminum is calculated using the Metropolis Monte Carlo method. The effective two-body ion-ion interaction used in the calculations are the Shaw optimized model and the local approximation suggested by Harrison calculated using two screening function in each case, the screening function of Vashishta and Singwi and that of Utsumi and Ichimaru. The calculated structure factors from each case are compared with experiment.     

Molecular imprinting of the endogenous neuropeptide Leu5-enkephalin and some derivatives thereof

We have undertaken the molecular imprinting of Leu⁵-enkephalin, and derivatives related to this endogenous neuropeptide, in highly cross-linked methacrylic acid/ethylene dimethacrylate copolymers. The underivatized enkephalin peptide yielded polymers with poor recognition abilities, since the imprinting of this compound had to be performed using dimethyl sulfoxide, which was found to interfere with the imprint inducement, as the solvent of polymerisation. In order to circumvent this problem, the amino- and carboxy-protected derivatives Boc-Leu⁵-enkephalin and Leu⁵-enkephalin anilide, which are soluble in apolar solvents, were investigated as alternative imprint molecules. Both compounds led to polymers which are highly specific for the imprint species. The anilide derivative was shown to be a good substitute for the free peptide since the resultant polymers showed efficient recognition of the parent enkephalin structure.     

Some novel cholesteric liquid crystals

Abstract

We investigate the possibility of inferring the absence of an ordered phase using Monte Carlo simulations. The example we have chosen is that of a one dimensional Lebwohl-Lasher model, where an analytic solution is available. We argue that Monte Carlo can be of help even in this delicate sector notwithstanding the complications created by periodic boundary conditions.     

Generalized boublick equation: an accurate expression for the equation of state of hard fused spheres

Abstract

A simple expression to calculate the shape factor of hard bodies is proposed. Introducing this factor in the Boublik equation of state, very good results are obtained for hard dumbells and more complicated systems of linear homonuclear hard fused spheres. Agreement with available Monte Carlo results are also satisfactory enough for heteronuclear molecules. Furthermore, the new expression is reduced to the classical shape factor for hard convex bodies and provides a common basis to manage to concave and convex hard bodies.     

Monte Carlo determination of the oscillator strength and excited state lifetime for the Li 22S → 22P transition

A recently developed Monte Carlo method is used to compute the 2²S → 2²P transition dipole moment of Li. This approach employs a guided Metropolis random walk with quantum Monte Carlo “side” walks to sample the required probability distributions. The transition dipole moment is employed to obtain the oscillator strength and excited-state lifetime. Our most accurately converged calculations yield an oscillator strength of 0.742(7) and excited-state lifetime of 27.41(35) ns. These results are in excellent agreement with precise experimental measurements of 0.742(1) and 27.29(4) ns, respectively. In addition, single-state expectation values are computed for both states. Monte Carlo parameters, such as the time step size and the convergence time, are varied in order to study their effect on computed results.     

X-ray diffraction study of [M<Superscript>I</Superscript>(NH<Subscript>3</Subscript>)<Subscript>5</Subscript>Cl] [M<Superscript>II</Superscript>Br<Subscript>6</Subscript>] (M<Superscript>I</Superscript> = Rh,Ir; M<Superscript>II</Superscript> = Re,Ir) polycrystals

Based on the X-ray diffraction data for polycrystals, the crystal structures of double complex salts [Rh(NH₃)₅Cl][ReBr₆] and [Ir(NH₃)₅Cl][ReBr₆] are refined. The structure of [Rh(NH₃)₅Cl][IrBr₆] is determined. Initial models are constructed using the Monte Carlo method in the straight space. Further refinement is made by the Rietveld method. It is shown that such an approach is suitable for the refinement of crystal structures composed of isolated rigid polyhedra and can be used to determine the structure of salts without structural analogues     

The nature of base stacking: a Monte Carlo study

To elucidate the physical origin of the preference of nucleic acid bases for stacking over hydrogen bonding in water, Monte Carlo simulations were performed starting from Watson?CCrick structures of the adenine?Cthymine, adenine?Curacil and guanine?Ccytosine base pairs, as well as from the Hoogsteen adenine?Cthymine base pair, in clusters comprising 400 and 800 water molecules. The simulations employed a newly implemented Metropolis Monte Carlo algorithm based on the extended cluster approach. All simulations reached stacked structures, confirming that such structures are preferred over the hydrogen-bonded Watson?CCrick and Hoogsteen base pairs. The Monte Carlo simulations show the complete transition from hydrogen-bonded base pairs to stacked structures in the Monte Carlo framework. Analysis of the average energies shows that the preference of stacked over hydrogen-bonded structures is due to the increased water?Cbase interaction in these structures. This is corroborated by the increased number of water?Cbase hydrogen bonds in the stacked structures.     

Molecular dynamics simulations of hydrophobic and amphiphatic proteins interacting with a lipid bilayer membrane

Molecular dynamics simulations of polypeptides at high dilution near a fully hydrated bilayer membrane have been performed. In contrast to previous theoretical predictions, Monte Carlo simulations and conclusions from experiments a spontaneous insertion of amphiphatic or hydrophobic proteins into a membrane is not observed. Rather it is found that an amphiphatic chain has the tendency to remain in proximity to the membrane surface, whereas the location of a hydrophobic chain is more unbound. This is shown using two proteins, melittin and polyleucine. The conformation of the proteins and their orientation with respect to the membrane surface are discussed.     

The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides

Molecular simulation by using force field parameters has been widely applied in the fields of peptide and protein research for various purposes. We recently proposed a new all‐atom protein force field, called the SAAP force field, which utilizes single amino acid potentials (SAAPs) as the fundamental elements. In this article, whole sets of the SAAP force field parameters in vacuo, in ether, and in water have been developed by ab initio calculation for all 20 proteinogenic amino acids and applied to Monte Carlo molecular simulation for two short peptides. The side‐chain separation approximation method was employed to obtain the SAAP parameters for the amino acids with a long side chain. Monte Carlo simulation for Met‐enkephalin (CHO‐Tyr‐Gly‐Gly‐Phe‐Met‐NH₂) by using the SAAP force field revealed that the conformation in vacuo is mainly controlled by strong electrostatic interactions between the amino acid residues, while the SAAPs and the interamino acid Lennard‐Jones potentials are predominant in water. In ether, the conformation would be determined by the combination of the three components. On the other hand, the SAAP simulation for chignolin (H‐Gly‐Tyr‐Asp‐Pro‐Glu‐Thr‐Gly‐Thr‐Trp‐Gly‐OH) reasonably reproduced a native‐like β‐hairpin structure in water although the C‐terminal and side‐chain conformations were different from the native ones. It was suggested that the SAAP force field is a useful tool for analyzing conformations of polypeptides in terms of intrinsic conformational propensities of the single amino acid units. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Study of caffeine-DNA interaction in aqueous solution by parallel Monte Carlo simulation

Monte Carlo simulation of caffeine aqueous solutions containing a superhelical B-DNA fragment is performed using parallel computing. The binding sites of caffeine molecules with DNA were identified as well as the most probable structures of the resultant complexes. The degrees of caffeine molecule association in aqueous solutions with different concentrations were estimated and the main configuration types of molecular aggregates were revealed.     

Molecular theory of surfactant micelles in aqueous solution

This paper presents an overview of recent theoretical work on the molecular theory of micelle formation. A primary emphasis is given to the role of computer simulation of condensed materials in understanding micelle structure and thermodynamics. Much of the detailed discussion focuses on recent Monte Carlo studies of a simple molecular model of micellar aggregates. For clarity of presentation, a compact, physical organization of micelle thermodynamic equilibrium ratios is advocated. This procedure provides a simple basis for physical reasoning about the molecular roles of attractive and repulsive forces in micellization thermodynamics. The molecularly coarse-grained micellar structural information available from current small angle neutron scattering (SANS) measurements is surveyed. The structural predictions of the reviewed Monte Carlo calculations are shown to be in good qualitative agreement with the SANS data. The Monte Carlo results indicate that micelles should be viewed as fluid aggregates with a low surface free energy relative to water-hydrocarbon interfaces. The computer experimental results suggest that dynamic surface and shape fluctuations should be considered in understanding micelle structure at a molecular level. Several instantaneous structures are graphically displayed to illustrate that these transitory structures could be qualitatively described as “dry” but irregularly shaped. Configurations drawn from Monte Carlo calculations on cylindrical and bilayer structures of infinite extent are used to illustrate the role of surface flexibility in these systems.     

Structure of hydrogenated silicon clusters. Small clusters

The ground state structures of silicon hydride clusters Si_nH_m containing up to 12 silicon atoms are obtained by numerical modeling. The cluster geometry is optimized for a wide set of initial structures using the MINDO/3 approximation for Monte Carlo simulation of interatomic interactions. The energy of the cluster depending on the content of hydrogen is studied, and it is shown that the Si-H and Si-Si bond energies depend little on the cluster size.