Molecular dynamics simulations of helix-forming, amine-functionalized m-poly(phenyleneethynylene)s

We present here the results of all-atom and united-atom molecular dynamics (MD) simulations that were used to examine the folding behavior of an amine-functionalized m-poly(phenyleneethynylene) (m-PPE) oligomer in aqueous environment. The parallelized GROMACS MD simulation code and OPLS force field were used for multiple MD simulations of m-PPE oligomers containing 24 phenyl rings in extended, coiled and helix conformations separately in water to determine the minimum energy conformation of the oligomer in aqueous solvent and what interactions are most important in determining this structure. Simulation results showed that the helix is the preferred minimum energy conformation of a single oligomer in water and that Lennard-Jones interactions are the dominant forces for the stabilization of the helix. In addition, these solvophobic interactions are strong enough to maintain the helix conformation at temperatures up to 523 K.     

Convergence of replica exchange molecular dynamics

Replica exchange molecular dynamics (REMD) method is one of the generalized-ensemble algorithms which performs random walk in energy space and helps a system to escape from local energy traps. In this work, we studied the accuracy and efficiency of REMD by examining its ability to reproduce the results of multiple extended conventional molecular dynamics (MD) simulations and to enhance conformational sampling. Two sets of REMD simulations with different initial configurations, one from the fully extended and the other from fully helical conformations, were conducted on a fast-folding 21-amino-acid peptide with a continuum solvent model. Remarkably, the two REMD simulation sets started to converge even within 1.0 ns, despite their dramatically different starting conformations. In contrast, the conventional MD within the same time and with identical starting conformations did not show obvious signs of convergence. Excellent convergence between the REMD sets for T>300 K was observed after 14.0 ns REMD simulations as measured by the average helicity and free-energy profiles. We also conducted a set of 45 MD simulations at nine different temperatures with each trajectory simulated to 100.0 and 200.0 ns. An excellent agreement between the REMD and the extended MD simulation results was observed for T>300 K, showing that REMD can accurately reproduce long-time MD results with high efficiency. The autocorrelation times of the calculated helicity demonstrate that REMD can significantly enhance the sampling efficiency by 14.3+/-6.4, 35.1+/-0.2, and 71.5+/-20.4 times at, respectively, approximately 360, approximately 300, and approximately 275 K in comparison to the regular MD. Convergence was less satisfactory at low temperatures (T<300 K) and a slow oscillatory behavior suggests that longer simulation time was needed to reach equilibrium. Other technical issues, including choice of exchange frequency, were also examined.     

An improved replica-exchange sampling method: temperature intervals with global energy reassignment

In a molecular dynamics (MD) simulation, representative sampling over the entire phase space is desired to obtain an accurate canonical distribution at a given temperature. For large molecules, such as proteins, this is problematic because systems tend to become trapped in local energy minima. The extensively used replica-exchange molecular dynamics (REMD) simulation technique overcomes this kinetic-trapping problem by allowing Boltzmann-weighted configuration exchange processes to occur between numerous thermally adjacent and compositionally identical simulations that are thermostated at sequentially higher temperatures. While the REMD method provides much better sampling than conventional MD, there are two substantial difficulties that are inherent in its application: (1) the large number of replicas that must be used to span a designated temperature range and (2) the subsequent long time required for configurations sampled at high temperatures to exchange down for potential inclusion within the low-temperature ensemble of interest. In this work, a new method based on temperature intervals with global energy reassignment (TIGER) is presented that overcomes both of these problems. A TIGER simulation is conducted as a series of short heating-sampling-quenching cycles. At the end of each cycle, the potential energies of all replicas are simultaneously compared at the same temperature using a Metropolis sampling method and then globally reassigned to the designated temperature levels. TIGER is compared with regular MD and REMD methods for the alanine dipeptide in water. The results indicate that TIGER increases sampling efficiency while substantially reducing the number of central processing units required for a comparable conventional REMD simulation.     

On the modeling of aggregates of an optically active regioregular polythiophene

The conformational properties of the optically active regioregular poly[(R)-3-(4-(4-ethyl-2-oxazolin-2-yl) phenyl) thiophene] (PEOPT) were explored by molecular dynamics on a single chain using several solvents of increasing polarity. Furthermore, their aggregate formation was studied over a wide range of temperatures using a replica exchange molecular dynamics simulation providing simulation data representative of the equilibrium behaviour of their aggregates. Results show a clear tendency of PEOPT to keep a syn-gauche conformation between continuous backbone thiophene rings favouring a bent chain structure in solvent. After studying their aggregation behaviour in acetonitrile, a strong tendency to pack stabilizing structures that reinforce the chirality of the polymer, in concordance with experimental data, was found. Two different aggregated structures were observed depending on oligomer length, a self-assembled helical aggregate based on stacked octamers and a bent double helix aggregate in large oligomers.     

On achieving experimental accuracy from molecular dynamics simulations of flexible molecules: aqueous glycerol

The rotational isomeric states (RIS) of glycerol at infinite dilution have been characterized in the aqueous phase via a 1 micros conventional molecular dynamics (MD) simulation, a 40 ns enhanced sampling replica exchange molecular dynamics (REMD) simulation, and a reevaluation of the experimental NMR data. The MD and REMD simulations employed the GLYCAM06/AMBER force field with explicit treatment of solvation. The shorter time scale of the REMD sampling method gave rise to RIS and theoretical scalar 3J(HH) coupling constants that were comparable to those from the much longer traditional MD simulation. The 3J(HH) coupling constants computed from the MD methods were in excellent agreement with those observed experimentally. Despite the agreement between the computed and the experimental J-values, there were variations between the rotamer populations computed directly from the MD data and those derived from the experimental NMR data. The experimentally derived populations were determined utilizing limiting J-values from an analysis of NMR data from substituted ethane molecules and may not be completely appropriate for application in more complex molecules, such as glycerol. Here, new limiting J-values have been derived via a combined MD and quantum mechanical approach and were used to decompose the experimental 3J(HH) coupling constants into population distributions for the glycerol RIS.     

Experimental resolution of early steps in protein folding: testing molecular dynamics simulations

Time-resolved Tyr fluorescence spectroscopy coupled with a laser-induced temperature-jump (T-jump) was employed to follow the folding relaxation dynamics of the B-domain of Staphylococcal protein A. The single Tyr is located in helix 1 (H1) and is a sensitive probe of the structure of this helix and the overall helical bundle structure. The results from this study were compared to those from a complementary infrared T-jump study on this protein [Vu, D. M.; Myers, J. K.; Oas, T. G.; Dyer, R. B. Biochemistry 2004, 43, 3582]. Both methods detect a microsecond process that follows the cooperative relaxation of the helical bundle core. However, a fast process (10-7 s) that follows the relaxation of the individual helices was observed only with the infrared probe. Thus, fast formation of H1 is not observed, but rather H1 forms in the microsecond phase, concomitantly with the docking to (and stabilization by) the other two helices to form the helical bundle structure. This observation validates the results of several previous molecular dynamics simulations that predict H1 formation only in the final assembly of the helix bundle.     

MD simulations of homomorphous PNA, DNA, and RNA single strands: characterization and comparison of conformations and dynamics

MD simulations of homomorphous single-stranded PNA, DNA, and RNA with the same base sequence have been performed in aqueous solvent. For each strand two separate simulations were performed starting from a (i) helical conformation and (ii) random coiled state. Comparisons of the simulations with the single-stranded helices (case i) show that the differences in the covalent nature of the backbones cause significant differences in the structural and dynamical properties of the strands. It is found that the PNA strand maintains its nice base-stacked initial helical structure throughout the 1.5-ns MD simulation at 300 K, while DNA/RNA show relatively larger fluctuations in the structures with a few local unstacking events during -ns MD simulation each. It seems that the weak physical coupling between the bases and the backbone in PNA causes a loss of correlation between the dynamics of the bases and the backbone compared to the DNA/RNA and helps maintain the base-stacked helical conformation. The global flexibility of a single-stranded PNA helix was also found to be lowest, while RNA appears to be the most flexible single-stranded helix. The sugar pucker of several nucleotides in single-stranded DNA and RNA was found to adopt both C2'-endo and C3'-endo conformations for significant times. This effect is more pronounced for single strands in completely coiled states. The simulations with single-stranded coils as the initial structure also indicate that a PNA can adopt a more compact globular structure, while DNA/RNA of the same size adopts a more extended coil structure. This allows even a short PNA in the coiled state to form a significantly stable nonsequentially base-stacked globular structure in solution. Due to the hydrophobic nature of the PNA backbone, it interacts with surrounding water rather weakly compared to DNA/RNA.     

Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent

Replica exchange methods (REMs) are increasingly used to improve sampling in molecular dynamics (MD) simulations of biomolecular systems. However, despite having been shown to be very effective on model systems, the application of REM in complex systems such as for the simulation of protein and peptide folding in explicit solvent has not been objectively tested in detail. Here we present a comparison of conventional MD and temperature replica exchange MD (T-REMD) simulations of a beta-heptapeptide in explicit solvent. This system has previously been shown to undergo reversible folding on the time scales accessible to MD simulation and thus allows a direct one-to-one comparison of efficiency. The primary properties compared are the free energy of folding and the relative populations of different conformers as a function of temperature. It is found that to achieve a similar degree of precision T-REMD simulations starting from a random set of initial configurations were approximately an order of magnitude more computationally efficient than a single 800 ns conventional MD simulation for this system at the lowest temperature investigated (275 K). However, whereas it was found that T-REMD simulations are more than four times more efficient than multiple independent MD simulations at one temperature (300 K) the actual increase in conformation sampling was only twofold. The overall gain in efficiency using REMD resulted primarily from the ordering of different conformational states over temperature, as opposed to a large increase of conformational sampling. It is also shown that in this system exchanges are accepted primarily based on (random) fluctuations within the solvent and are not strongly correlated with the instantaneous peptide conformation raising questions in regard to the efficiency of T-REMD in larger systems.     

Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study

Molecular dynamics (MD) simulation is the standard computational technique used to obtain information on the time evolution of the conformations of proteins and many other molecular systems. However, for most biological systems of interest, the time scale for slow conformational transitions is still inaccessible to standard MD simulations. Several sampling methods have been proposed to address this issue, including the accelerated molecular dynamics method. In this work, we study the extent of sampling of the phi/psi space of alanine dipeptide in explicit water using accelerated molecular dynamics and present a framework to recover the correct kinetic rate constant for the helix to beta-strand transition. We show that the accelerated MD can drastically enhance the sampling of the phi/psi conformational phase space when compared to normal MD. In addition, the free energy density plots of the phi/psi space show that all minima regions are accurately sampled and the canonical distribution is recovered. Moreover, the kinetic rate constant for the helix to beta-strand transition is accurately estimated from these simulations by relating the diffusion coefficient to the local energetic roughness of the energy landscape. Surprisingly, even for such a low barrier transition, it is difficult to obtain enough transitions to accurately estimate the rate constant when one uses normal MD.     

Comparison of Ethene Diffusion Characteristics in H[Al]ZSM‐5 at 300 K and 400 K by Molecular Dynamics

The ethene diffusion characteristics in the framework of H[Al]ZSM‐5 at 300 K and 400 K have been studied by molecular dynamics (MD) simulation. The data have been obtained for the molecular kinetic, potential and total energies, mean square displacement and self‐diffusion coefficient, interaction and beat of adsorption. The dependence of molecular diffusion on temperature has been explored.     

Optical absorption of methoxy and carboethoxy derivatives of 1,3-diphenyl-1H-pyrazolo[3,4-b]quinoline

Paper deals with experimental investigations and quantum chemical calculations of the optical absorption spectra of methoxy and carboethoxy 1,3-diphenyl derivatives of the pyrazoloquinoline ([PQ]): 6-methoxy-1,3-dyphenil-[PQ], 6-methoxy-1,3-(p-methoxyphenyl)-[PQ], 6-methoxy-1-(p-methoxyphenyl)-[PQ] and 6-carboethoxy-1,3-diphenyl-[PQ]. The quantum chemical calculations are performed by means of the semiempirical quantum chemical methods (AM1 or PM3) applied to: (a) the equilibrium molecular conformation in vacuo (T=0 K); (b) the molecular dynamic (MD) trajectory (T=300 K) which includes the dynamics of a certain molecular fragment (moiety) only (fragmental MD simulations); or (c) the MD trajectory obtained for most general case within the total MD simulations at T=300 K. The results of these calculations are compared with the measured spectra of the optical absorption. The quantum chemical simulations show that the dynamics of the methoxy or carboethoxy groups practically does not influence the absorption spectrum whereas the strongest its modification (300相似文献   

Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles

The authors propose explicit symplectic integrators of molecular dynamics (MD) algorithms for rigid-body molecules in the canonical and isobaric-isothermal ensembles. They also present a symplectic algorithm in the constant normal pressure and lateral surface area ensemble and that combined with the Parrinello-Rahman algorithm. Employing the symplectic integrators for MD algorithms, there is a conserved quantity which is close to Hamiltonian. Therefore, they can perform a MD simulation more stably than by conventional nonsymplectic algorithms. They applied this algorithm to a TIP3P pure water system at 300 K and compared the time evolution of the Hamiltonian with those by the nonsymplectic algorithms. They found that the Hamiltonian was conserved well by the symplectic algorithm even for a time step of 4 fs. This time step is longer than typical values of 0.5-2 fs which are used by the conventional nonsymplectic algorithms.     

Ab initio molecular dynamics studies of ionic dissolution and precipitation of sodium chloride and silver chloride in water clusters, NaCl(H2O)n and AgCl(H2O)n, n = 6, 10, and 14

An ab initio molecular dynamics method was used to compare the ionic dissolution of soluble sodium chloride (NaCl) in water clusters with the highly insoluble silver chloride (AgCl). The investigations focused on the solvation structures, dynamics, and energetics of the contact ion pair (CIP) and of the solvent-separated ion pair (SSIP) in NaCl(H(2)O)(n) and AgCl(H(2)O)(n) with cluster sizes of n = 6, 10 and 14. We found that the minimum cluster size required to stabilize the SSIP configuration in NaCl(H(2)O)(n) is temperature-dependent. For n = 6, both configurations are present as two distinct local minima on the free-energy profile at 100 K, whereas SSIP is unstable at 300 K. Both configurations, separated by a low barrier (<10 kJ mol(-1)), are identifiable on the free energy profiles of NaCl(H(2)O)(n) for n = 10 and 14 at 300 K, with the Na(+)/Cl(-) pairs being internally solvated in the water cluster and the SSIP configuration being slightly higher in energy (<5 kJ mol(-1)). In agreement with the low bulk solubility of AgCl, no SSIP minimum is observed on the free-energy profiles of finite AgCl(H(2)O)(n) clusters. The AgCl interaction is more covalent in nature, and is less affected by the water solvent. Unlike NaCl, AgCl is mainly solvated on the surface in finite water clusters, and ionic dissolution requires a significant reorganization of the solvent structure.     

Molecular dynamics study of tryptophylglycine: a dipeptide nanotube with confined water

To investigate the mechanism of structural changes of a peptide nanotube and water confined inside the channel, the helical peptide tryptophylglycine monohydrate (WG.H2O) was studied by molecular dynamics (MD) simulations using the three-dimension parallel MD program ddgmq (software package) and a consistent force field. Simulations were performed on both the water-containing system and a model system without water molecules. The details of the structural behavior with temperature are investigated for the entire simulated temperature range. Phase transitions were obtained at 115, 245, 270, 310, and 385 K, due to the contributions of both the peptide and the confined water subsystems. The crystalline, amorphous, liquidlike, liquid, and superheated phases of water were observed in the temperature ranges 40-115, 115-245, 245-310, 310-385, and >385 K, respectively. At 300 K, the diffusion constant of the confined water is 0.46 x 10-5 cm2 s-1, a value comparable to that of other peptide nanotubes. The empty peptide system melts at 440 K. Mechanisms of the negative thermal expansion (NTE) along the tube axis were investigated for different temperature ranges. The contraction of the crystalline water (or amorphous water) draws also the tube walls in and leads to NTE below 245 K. The other NTEs appear to be connected to the collapse of the ice network or the solid peptide network between 245 K and room temperature or from 310 to 440 K, respectively.     

Activation mechanism of the human histamine H4 receptor--an explicit membrane molecular dynamics simulation study

Molecular dynamics (MD) simulations in a membrane-embedded environment were carried out on the homology model of the human histamine H4 receptor (hH4R) alone and in complex with its endogenous activator histamine and with the first reported selective hH4R antagonist JNJ7777120. During the simulation of the histamine-hH4R complex, considerable changes occurred in the hH4R structure as well as in the interaction pattern of histamine at the binding site. These changes are in agreement with experimental data published on GPCR activation. In particular, the intracellular side of TM helix VI moved significantly away from TM helices III and VII. Moreover, histamine formed an interaction with Asn147 (4.57) that was previously proved to be important in hH4R activation. Results of the MD simulations of the native hH4R and the JNJ7777120-hH4R complex suggest that these models represent an inactive conformation of hH4R. MD simulation in the presence of JNJ7777120 resulted in the movement of the intracellular side of TM helix VI in the direction of TM helix III. Snapshots of the simulations may serve as functionally relevant models in the development of novel hH4R ligands in the future.     

应用ABEEMσπ／MM模型探讨小α-螺旋在显性水中折叠／展开的可逆过程

应用ABEEMσπ／MM模型进行分子动力学模拟,研究了显性水溶液中小α-螺旋（短肽Ala5）折叠／展开的可逆过程．动力学分析显示,300K下α-螺旋可以保存2ns的时间,该结果支持Margulis等人的结论．每个结构与α-螺旋结构骨架重原子的均方根偏差的时间轨迹指出,“300K下螺旋成核现象在0．1ns内快速发生”的结论是不恰当的．通过对300、400和500K温度下的研究,首次定量地给出各温度下螺旋保存的时间分别为2ns、1～1．5ns和0．8ns,并且增加温度并不改变折叠／展开的方式,只是改变折叠／展开的速率．本文对“转化态集合”结构的分析表明,从螺旋到卷曲的转换,主要通过螺旋端的氢键断裂发生（92％）、尤其是C端的氢键断裂发生（50％）．氢键的破坏和形成在0．1ns的时间内完成．     

Computational study of ketosteroid isomerase: insights from molecular dynamics simulation of enzyme bound substrate and intermediate

Delta(5)-3-Ketosteroid Isomerase (KSI) catalyzes the isomerization of 5,6-unsaturated ketosteroids to their 4,5-unsaturated isomers at a rate approaching the diffusion limit. The isomerization reaction follows a two-step general acid-base mechanism starting with Asp38-CO(2)(-) mediated proton abstraction from a sp(3)-hybridized carbon atom, alpha to carbonyl group, providing a dienolate intermediate. In the second step, Asp38-CO(2)H protonates the C6 of the intermediate providing a 4,5-unsaturated ketosteroid. The details of the mechanism have been highly controversial despite several experimental and computational studies of this enzyme. The general acid-base catalysis has been proposed to involve either a catalytic diad or a cooperative hydrogen bond mechanism. In this paper, we report our results from the 1.5 nanosecond molecular dynamics (MD) simulation of enzyme bound natural substrate (E.S) and enzyme bound intermediate (E.In) solvated in a TIP3P water box. The final coordinates from our MD simulation strongly support the cooperative hydrogen bond mechanism. The MD simulation of E.S and E.In shows that both Tyr14 and Asp99 are hydrogen bonded to the O3 of the substrate or intermediate. The average hydrogen bonding distance between Tyr14-OH and O3 becomes shorter and exhibits less fluctuation on E.S --> E.In. We also observe dynamic motions of water moving in and out of the active site in the E.S structures. This free movement of water disappears in the E.In structures. The active site is shielded by hydrophobic residues, which come together and squeeze out the waters from the active site in the E.In complex.     

Adsorption of collagen onto single walled carbon nanotubes: a molecular dynamics investigation

Classical molecular dynamics (MD) simulation has been carried out to understand the adsorption of collagen like peptides onto single walled carbon nanotubes (CNT) in an aqueous environment. It is observed that the triple helical structure of all the model collagen like peptides (CPs) has been unaltered upon adsorption onto CNT. The model CPs do not wrap around the CNT, however, the axis of the triple helix subtends a cross angle with respect to the axis of the CNT. The interaction between the CPs and CNT as well as that between the CPs and water molecules was observed by MD simulation snapshots. The inherent nature of the interaction of CPs with CNT facilitates the penetration of CPs into the water/CNT interface. During this process, water molecules trapped between the CPs and CNT are appreciably displaced. Although, hydrophobic-hydrophobic interaction is crucial for the interaction, the role of πR (R = OH and NH(2)) interactions are also observed from the geometrical parameters. The sequence specific interaction of CPs with CNT is evident from the results. It is found that the length of the CNT, curvature of the CNT and length of the CPs do not significantly influence interaction between the two systems. Overall the findings provide important information for the development of nanocomposite materials from collagen and CNT.     

多巴胺第三受体蛋白三维结构及其活性位点氨基酸残基

基于牛视紫红质模板蛋白,同源模建多巴胺第三受体（D₃R）蛋白三维结构,在1-棕榈酰-2-油酰-卵磷脂（POPC）膜-水模型环境,开展300 ns分子动力学模拟提炼优化其结构,取得稳定的D₃R蛋白三维结构（2B08-D₃R）.在该蛋白基础上,采用MP2/6-31G（d,p）方法,计算多巴胺（Dop）与氨基酸残基相互作用的结合能,确定五个残基（Asp117、Ser208、His272、Phe269和Thr276）为活性位点.五个活性位点残基分别位于D₃R蛋白跨膜螺旋区TM3、TM5和TM6,组成活性空腔结构.多巴胺分子以其苯基平面与TM2-TM7包围的圆柱体空腔平行和非共价键结合方式保留在D₃R蛋白中,与D₃R蛋白结合能E_b为-97.8 kJ·mol^-1基于3PBL D₃R突变体晶体结构,构建了另外一个含有多巴胺分子的D₃R蛋白结构（Dop-3PBL-D₃R）,确定在该蛋白结构中,多巴胺的活性位点氨基酸是Asp83、His272、Phe269、Phe268和Trp265.在该蛋白结构中,多巴胺分子同样以其苯基平面与TM2-TM7包围的圆柱体空腔平行和非共价键方式结合,与该蛋白相互作用的结合能是-80.5 kJ·mol^-1.     

Multidimensional umbrella sampling and replica‐exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers

Structural information of a transmembrane (TM) helix dimer is useful in understanding molecular mechanisms of important biological phenomena such as signal transduction across the cell membrane. Here, we describe an umbrella sampling (US) scheme for predicting the structure of a TM helix dimer in implicit membrane using the interhelical crossing angle and the TM–TM relative rotation angles as the reaction coordinates. This scheme conducts an efficient conformational search on TM–TM contact interfaces, and its robustness is tested by predicting the structures of glycophorin A (GpA) and receptor tyrosine kinase EphA1 (EphA1) TM dimers. The nuclear magnetic resonance (NMR) structures of both proteins correspond to the global free‐energy minimum states in their free‐energy landscapes. In addition, using the landscape of GpA as a reference, we also examine the protocols of temperature replica‐exchange molecular dynamics (REMD) simulations for structure prediction of TM helix dimers in implicit membrane. A wide temperature range in REMD simulations, for example, 250–1000 K, is required to efficiently obtain a free‐energy landscape consistent with the US simulations. The interhelical crossing angle and the TM–TM relative rotation angles can be used as reaction coordinates in multidimensional US and be good measures for conformational sampling of REMD simulations. © 2013 Wiley Periodicals, Inc.