Application of self-organizing maps in conformational analysis of lipids.

The characteristics of lipid assemblies are important for the functions of biological membranes. This has led to an increasing utilization of molecular dynamics simulations for the elucidation of the structural features of biomembranes. We have applied the self-organizing map (SOM) to the analysis of the complex conformational data from a 1-ns molecular dynamics simulation of PLPC phospholipids in a membrane assembly. Mapping of 1.44 million molecular conformations to a two-dimensional array of neurons revealed, without human intervention, the main conformational features in hours. Both the whole molecule and the characteristics of the unsaturated fatty acid chains were analyzed. All major structural features were easily distinguished, such as the orientational variability of the headgroup, the mainly trans state dihedral angles of the sn-1 chain, and both straight and bent conformations of the unsaturated sn-2 chain. Furthermore, presentation of the trajectory of an individual lipid molecule on the map provides information on conformational dynamics. The present results suggest that the SOM method provides a powerful tool for routinely gaining rapid insight to the main molecular conformations as well as to the conformational dynamics of any simulated molecular assembly without the requirement of a priori knowledge.     

Stability of a protein tethered to a surface

Surface-tethered proteins are increasingly being used in a variety of experimental situations, and they are the basis for many new technologies. Nevertheless, a thorough understanding of how a surface can impact the native state stability of an attached protein is lacking. In this work, the authors use molecular dynamics simulations of a model beta-barrel protein to investigate how surface tethering influences native state stability. They find that stability, as measured by the folding temperature Tf, can be either increased, decreased, or remain unchanged as a result of tethering. Observed shifts are highly dependent on the location of residue used as the tether point, and stability is influenced by a number of factors, both energetic and entropic. These factors include native state vibrations, loss of bulk unfolded conformations, changes to the unfolded state ensemble, and the emergence of an entropic term not present for the bulk protein. They discuss each of these contributions in detail and comment on their relative importance and connection to experiment.     

Clustering Approach for Multidisciplinary Optimum Design of Cross‐Linked Polymer

This paper proposes a new and systematic approach for optimum design of thermosetting resin systems based on molecular‐dynamics simulations. Specifically, the results of simulations for chemical reaction (cross‐linking) and mechanical properties of epoxy resin are clustered with a self‐organizing map (SOM) that enables to comprehensibly visualize the characteristics of complex structured polymers. Moreover, the scatter‐plot matrix (SPM) is introduced to analyze the specific data. Thus, SOM is used to find common features in a molecular structure, and SPM helps to clarify molecular‐scale mechanism in the clusterization. Through the analysis, the authors find that base resins with multireactive functional groups contribute to superior mechanical properties, and these properties stem from the hydrogen‐bond network distributed throughout the system. The approach, which is thought to be one of chemical informatics, has broad ranges of applications that are not limited to epoxy resin but can be applied to any kind of thermosetting resins.

     

Reactive Bond-Order Simulations Using Both Spatial and Temporal Approaches to Parallelism

We describe two different approaches to exploiting parallel computing architecture that have been used successfully for reactive molecular simulation using bond-order potentials. These potentials are based on the Tersoff bond-order formalism, and allow accurate treatement of covalent bonding reactions in the framework of a classical potential. They include both Brenner's reactive empirical bond order (REBO) potential and our adaptive intermolecular version of this potential (AIREBO). Traditional spatial and atom-based parallel decompositioon techniques have been employed in the RMD-CE program developed for parallel molecular dynamics simulations with a variety of reactive potentials. Key features of this implementation, including the object-oriented approach and novel algorithms for the integrator and neighbor lists, are discussed. The resulting code provides efficient scaling down to system sizes of 400 atoms per processor, and has been applied successfully to systems of as many as half a million atoms. For smaller systems, the parallel replica dynamics algorithm has been successfully applied to take advantage of parallelism in the time domain for rare-event systems. This approach takes advantage of the independence of different parts of a dynamics trajectory, and provides excellent parallel efficiencies for systems as small as tens of atoms, where other parallel simulation techniques are not applicable. This technique has been used to model the pyrolysis of hexadecane on the microsecond timescale, at more realistic temperatures than are achievable with other simulation methods.     

Computational protocols for prediction of solute NMR relative chemical shifts. a case study of L-tryptophan in aqueous solution

In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L-tryptophan in aqueous solution, namely a molecular dynamics simulation and a molecular mechanics conformational search with subsequent geometry re-optimization of the stable conformers using a quantum mechanically based method. These spanning protocols represent standard ways of obtaining a set of conformations on which NMR calculations may be performed. The results stemming from the solute-solvent configurations extracted from the MD simulation at 300 K are found to be inferior to the results stemming from the conformations extracted from the MM conformational search in terms of replicating an experimental reference as well as in achieving the correct sequence of the NMR relative chemical shifts of L-tryptophan in aqueous solution. We find this to be due to missing conformations visited during the molecular dynamics run as well as inaccuracies in geometrical parameters generated from the classical molecular dynamics simulations.     

Undergraduate Projects in the Application of Artificial Intelligence to Chemistry. II Self-Organizing Maps

It is often necessary in science to identify samples that have features in common. For example, one might wish to find those NMR spectra in a large database that have similar patterns of resonances or identify samples amongst a large number of specimens of river water that analysis shows have similar biochemical oxygen demand, heavy metals concentration, organochlorine content, and so on.The determination of relationships among samples is a task to which Artificial Intelligence is increasingly being applied. In this paper, we investigate the Self-Organizing Map (SOM), whose role is to perform just this kind of task; in other words, to cluster data samples so as to reveal the relationships that exist among them. The self-organizing map is a method, which, unusually, combines a mathematical foundation with an intuitive interpretation.We will describe how a simple SOM operates, what kinds of data may be analyzed using one, and how a computer program to run a SOM can be written by anyone-whether student or teacher-with modest programming skills. Portions of sample source code are included in this paper, and program listings for the examples that are discussed are available in the supporting materials. The supporting files can also be used to see the maps in operation.     

Open science grid study of the coupling between conformation and water content in the interior of a protein

Computational grids are a promising resource for modeling complex biochemical processes such as protein folding, penetration of gases or water into proteins, or protein structural rearrangements coupled to ligand binding. We have enabled the molecular dynamics program CHARMM to run on the Open Science Grid. The implementation is general, flexible, easily modifiable for use with other molecular dynamics programs and other grids and automated in terms of job submission, monitoring, and resubmission. The usefulness of grid computing was demonstrated through the study of hydration of the Glu-66 side chain in the interior of protein staphylococcal nuclease. Multiple simulations started with and without two internal water molecules shown crystallographically to be associated with the side chain of Glu-66 yielded two distinct populations of rotameric states of Glu-66 that differed by as much as 20%. This illustrates how internal water molecules can bias protein conformations. Furthermore, there appeared to be a temporal correlation between dehydration of the side chain and conformational transitions of Glu-66. This example demonstrated how difficult it is to get convergence even in the relatively simple case of a side chain oscillating between two conformations. With grid computing, we also benchmarked the self-guided Langevin dynamics method against the Langevin dynamics method traditionally used for temperature control in molecular dynamics simulations and showed that the two methods yield comparable results.     

A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations

We study how the results of molecular dynamics (MD) simulations are affected by various choices during the setup, e.g., the starting velocities, the solvation, the location of protons, the conformation of His, Asn, and Gln residues, the protonation and titration of His residues, and the treatment of alternative conformations. We estimate the binding affinity of ligands to four proteins calculated with the MM/GBSA method (molecular mechanics combined with a generalized Born and surface area solvation energy). For avidin and T4 lysozyme, all variations gave similar results within 2 kJ/mol. For factor Xa, differences in the solvation or in the selection of alternative conformations gave results that are significantly different from those of the other approaches by 4-6 kJ/mol, whereas for galectin-3, changes in the conformations, rotations, and protonation gave results that differed by 10 kJ/mol, but only if residues close to the binding site were modified. This shows that the results of MM/GBSA calculations are reasonably reproducible even if the MD simulations are set up with different software. Moreover, we show that the sampling of phase space can be enhanced by solvating the systems with different equilibrated water boxes, in addition to the common use of different starting velocities. If different conformations are available in the crystal structure, they should also be employed to enhance the sampling. Protonation, ionization, and conformations of Asn, Gln, and His may also be used to enhance sampling, but great effort should be spent to obtain as reliable predictions as possible close to the active site.     

Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamics

We have applied molecular dynamics to investigate the structural properties and activity of recently synthesized amphiphilic polymethacrylate derivatives, designed to mimic the antimicrobial activity of natural peptides. The composition, molecular weight, and hydrophobicity (ratio of hydrophobic and cationic units) of these short copolymers can be modulated to achieve structural diversity, which is crucial in controlling the antimicrobial activity. We have carried out all-atom molecular dynamics to systematically investigate the conformations adopted by these copolymers in water and at the water-lipid interface as a function of sequence and the chemical nature of the monomers. For two sequences, we observe partial insertion into the bilayer. Formation of strong interactions between the lipid headgroups and the amine groups of the polymers assists in the initial association with the lipids. However, the primary driving force for the observed partial insertion appears to be the hydrophobic effect. Our results indicate sensitive dependence of the overall shape on the sequence, suggesting that experimentally observed changes in activity can be correlated with particular sequences, providing an avenue for rational design.     

Correlation between molecular conformation, packing, and dynamics in oligofluorenes: a theoretical/experimental study

Fluorene-based systems have shown great potential as components in organic electronics and optoelectronics (organic photovoltaics, OPVs, organic light emitting diodes, OLEDs, and organic transistors, OTFTs). These systems have drawn attention primarily because they exhibit strong blue emission associated with relatively good thermal stability. It is well-known that the electronic properties of polymers are directly related to the molecular conformations and chain packing of polymers. Here, we used three oligofluorenes (trimer, pentamer, and heptamer) as model systems to theoretically investigate the conformational properties of fluorene molecules, starting with the identification of preferred conformations. The hybrid exchange-correlation functional, OPBE, and ZINDO/S-CI showed that each oligomer exhibits a tendency to adopt a specific chain arrangement, which could be distinguished by comparing their UV/vis electronic absorption and (13)C NMR spectra. This feature was used to identify the preferred conformation of the oligomer chains in chloroform-cast films by comparing experimental and theoretical UV/vis and (13)C NMR spectra. Moreover, the oligomer chain packing and dynamics in the films were studied by DSC and several solid-state NMR techniques, which indicated that the phase behavior of the films may be influenced by the tendency that each oligomeric chain has to adopt a given conformation.     

Exploring the similarities between potential smoothing and simulated annealing

Simulated annealing and potential function smoothing are two widely used approaches for global energy optimization of molecular systems. Potential smoothing as implemented in the diffusion equation method has been applied to study partitioning of the potential energy surface (PES) for N‐Acetyl‐Ala‐Ala‐N‐Methylamide (CDAP) and the clustering of conformations on deformed surfaces. A deformable version of the united‐atom OPLS force field is described, and used to locate all local minima and conformational transition states on the CDAP surface. It is shown that the smoothing process clusters conformations in a manner consistent with the inherent structure of the undeformed PES. Smoothing deforms the original surface in three ways: structural shifting of individual minima, merging of adjacent minima, and energy crossings between unrelated minima. A master equation approach and explicit molecular dynamics trajectories are used to uncover similar features in the equilibrium probability distribution of CDAP minima as a function of temperature. Qualitative and quantitative correlations between the simulated annealing and potential smoothing approaches to enhanced conformational sampling are established. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 531–552, 2000     

Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins

The transferability of molecular mechanics parameters derived for small model systems to larger biopolymers such as proteins can be difficult to assess. Even for small peptides, molecular dynamics simulations are typically too short to sample structures significantly different than initial conformations, making comparison to experimental data questionable. We employed a PC cluster to generate large numbers of native and non-native conformations for peptides with experimentally measured structural data, one predominantly helical and the other forming a beta-hairpin. These atomic-detail sets do not suffer from slow convergence, and can be used to rapidly evaluate important force field properties. In this case a suspected bias toward alpha-helical conformations in the ff94 and ff99 force fields distributed with the AMBER package was verified. The sets provide critical feedback not only on force field transferability, but may also predict modifications for improvement. Such predictions were used to modify the ff99 parameter set, and the resulting force field was used to test stability and folding of model peptides. Structural behavior during molecular dynamics with the modified force field is found to be very similar to expectations, suggesting that these basis sets of conformations may themselves have significant transferability among force fields. We continue to improve and expand this data set and plan to make it publicly accessible. The calculations involved in this process are trivially parallel and can be performed using inexpensive personal computers with commodity components.     

Spin-labeled alkylphospholipids in a dipalmitoylphosphatidylcholine bilayer: molecular dynamics simulations

Molecular dynamics simulation has been performed to investigate the structural properties of perifosine and its synthetic spin-labeled alkylphospholipid analogues. The conformations adopted by these compounds in water and in a dipalmitoylphosphatidylcholine bilayer as a function of the presence and position of the N-oxyl-4',4'-dimethyloxazolidine ring (doxyl group) have been investigated by all-atom molecular dynamics. No predominant conformation was observed in water, but the molecules adopt specific orientations and conformations in the lipid bilayer. As is expected, alkyl chains tend to insert into the hydrophobic core, while charged groups stay at the lipid-water interface. A doxyl group in the middle of the alkyl chain moves up to the interface region, thus preventing adoption of the extended conformation. Compounds with a doxyl group close to the polar head group adopt conformations similar to that of unlabeled perifosine within the first nanoseconds of simulation. When the doxyl group is at the end of alkyl chain, the spin-labeled molecule needs more time to reach equilibrium. These results indicate a considerable effect of the doxyl position within the alkyl chain on its localization in the lipid bilayer and can be extended further to other similar spin probes used in the electron paramagnetic resonance spectroscopy of biological membranes.     

A fast and efficient method to generate biologically relevant conformations

Summary Mutual binding between a ligand of low molecular weight and its macromolecular receptor demands structural complementarity of both species at the recognition site. To predict binding properties of new molecules before synthesis, information about possible conformations of drug molecules at the active site is required, especially if the 3D structure of the receptor is not known. The statistical analysis of small-molecule crystal data allows one to elucidate conformational preferences of molecular fragments and accordingly to compile libraries of putative ligand conformations. A comparison of geometries adopted by corresponding fragments in ligands bound to proteins shows similar distributions in conformation space. We have developed an automatic procedure that generates different conformers of a given ligand. The entire molecule is decomposed into its individual ring and open-chain torsional fragments, each used in a variety of favorable conformations. The latter ones are produced according to the library information about conformational preferences. During this building process, an extensive energy ranking is applied. Conformers ranked as energetically favorable are subjected to an optimization in torsion angle space. During minimization, unfavorable van der Waals interactions are removed while keeping the open-chain torsion angles as close as possible to the experimentally most frequently observed values. In order to assess how well the generated conformers map conformation space, a comparison with experimental data has been performed. This comparison gives some confidence in the efficiency and completeness of this approach. For some ligands that had been structurally characterized by protein crystallography, the program was used to generate sets of some 10 to 100 conformers. Among these, geometries are found that fall convincingly close to the conformations actually adopted by these ligands at the binding site.     

Protein structure predictions by parallel simulated annealing molecular dynamics using genetic crossover

We propose a conformational search method to find a global minimum energy structure for protein systems. The simulated annealing is a powerful method for local conformational search. On the other hand, the genetic crossover can search the global conformational space. Our method incorporates these attractive features of the simulated annealing and genetic crossover. In the previous works, we have been using the Monte Carlo algorithm for simulated annealing. In the present work, we use the molecular dynamics algorithm instead. To examine the effectiveness of our method, we compared our results with those of the normal simulated annealing molecular dynamics simulations by using an α-helical miniprotein. We used genetic two-point crossover here. The conformations, which have lower energy than those obtained from the conventional simulated annealing, were obtained.     

Computational insights into octyl-D-xyloside isomers towards understanding the liquid crystalline structure: physico-chemical features

We applied density functional theory to study octyl-D-xyloside isomers in order to explain the features responsible for the liquid crystal mesophases. Compared to a glucoside, the xylose headgroup has a proton instead of the hydroxymethyl group on C5. Thus, a xyloside has a reduced headgroup volume that renders it less hydrophilic. Our results have shown that the xylose headgroup may adopt stable pyranose and furanose conformations, which may lead to different effective headgroup hydrophilicities. These features are probably responsible for forming two non-equivalent inverse micelles, which are self-assembled into a cubic discontinuous phase with a space group of Fd3m commonly found for xylosides. While different factors are responsible for controlling the relative stability of each isomer, the role of intramolecular hydrogen bonding was highlighted for the investigated single molecule. The polarisable continuum model was used to take into account the solvent effect in order to understand the molecular behaviour in very polar systems. Results from calculations carried out in gas phase were used for comparative purposes. The molecular electrostatic potential calculations for these xylolipids demonstrate sugar amphoterism, which is implicated in the heterogeneity nature of lipid self-assembly.     

Modeling of the triglyceride-rich core in lipoprotein particles

Triglycerides are a major component of many important biological entities such as lipoproteins and lipid droplets. This work focuses on two common triglycerides, tripalmitin and triolein, which have been simulated through atomistic molecular dynamics at temperatures of 310 and 350 K for 300-700 ns. In these systems, both structural and dynamical properties have been characterized, paying particular attention to understanding the packing of triglyceride molecules and their molecular conformations. Additionally, we study the liquid-to-crystalline phase transition of tripalmitin through a temperature quench from the high-temperature isotropic liquid phase to 310 K, corresponding to a polymorphic, crystalline-like phase. The transition is characterized in detail through density, average molecular shape, and, in particular, the relevant order parameter describing the transition.