Comparative Molecular Dynamics Study Research Articles

Comparative molecular field analysis and molecular dynamics studies of α/β hydrolase domain containing 6 (ABHD6) inhibitors.

The endocannabinoid system remains an attractive molecular target for pharmacological intervention due to its roles in the central nervous system in learning, thinking, emotional function, regulation of food intake or pain sensation, as well as in the peripheral nervous system, where it modulates the action of cardiovascular, immune, metabolic or reproductive function. α/β hydrolase domain containing 6 (ABHD6)—an enzyme forming part of the endocannabinoid system—is a newly discovered post-genomic protein acting as a 2-AG (2-arachidonoylglycerol) serine hydrolase. We have recently reported a series of 1,2,5-thiadiazole carbamates as potent and selective ABHD6 inhibitors. Here, we present comparative molecular field analysis (CoMFA) and molecular dynamics studies of these compounds. First, we performed a homology modeling study of ABHD6 based on the assumption that the catalytic triad of ABHD6 comprises Ser148–His306–Asp 278 and the oxyanion hole is formed by Met149 and Phe80. A total of 42 compounds was docked to the homology model using the Glide module from the Schrödinger suite of software and the selected docking poses were used for CoMFA alignment. A model with the following statistics was obtained: R2 = 0.98, Q2 = 0.55. In order to study the molecular interactions of the inhibitors with ABHD6 in detail, molecular dynamics was performed with the Desmond program. It was found that, during the simulations, the hydrogen bond between the inhibitor carbonyl group and the main chain of Phe80 is weakened, whereas a new hydrogen bond with the side chain of Ser148 is formed, facilitating the possible formation of a covalent bond.Graphical Left–right: Docking pose of 1 in the binding pocket of α/β hydrolase domain containing 6 (ABHD6) selected for molecular alignment; CoMFA steric and electrostatic contour fields; changes in potential energy of the complex during simulations for the complex of 6 and ABHD6Electronic supplementary materialThe online version of this article (doi:10.1007/s00894-015-2789-8) contains supplementary material, which is available to authorized users.

Comparative molecular dynamics studies of Si, GaN and SiC thermal conductivity

Comparative molecular dynamics studies of Si, GaN and SiC thermal conductivity

Allosterism in human complement component 5a (hC5a): a damper of C5a receptor (C5aR) signaling

The phenomena of allosterism continues to advance the field of drug discovery, by illuminating gainful insights for many key processes, related to the structure–function relationships in proteins and enzymes, including the transmembrane G-protein coupled receptors (GPCRs), both in normal as well as in the disease states. However, allosterism is completely unexplored in the native protein ligands, especially when a small covalent change significantly modulates the pharmacology of the protein ligands toward the signaling axes of the GPCRs. One such example is the human C5a (hC5a), the potent cationic anaphylatoxin that engages C5aR and C5L2 to elicit numerous immunological and non-immunological responses in humans. From the recently available structure–function data, it is clear that unlike the mouse C5a (mC5a), the hC5a displays conformational heterogeneity. However, the molecular basis of such conformational heterogeneity, otherwise allosterism in hC5a and its precise contribution toward the overall C5aR signaling is not known. This study attempts to decipher the functional role of allosterism in hC5a, by exploring the inherent conformational dynamics in mC5a, hC5a and in its point mutants, including the proteolytic mutant des-Arg74-hC5a. Prima facie, the comparative molecular dynamics study, over total 500 ns, identifies Arg74-Tyr23 and Arg37-Phe51 “cation-π” pairs as the molecular “allosteric switches” on hC5a that potentially functions as a damper of C5aR signaling.

Study of Two Xanthene Dyes Using Spectrally Resolved Three-Pulse Photon Echo Spectroscopy

Comparative study of the molecular dynamics of two xanthene dye derivatives (Rhodamine-6G and Fluorescein-548) is reported using spectrally resolved three-pulse photon echo spectroscopy. An appreciable change in the coherence and population dynamics was observed between the two xanthene derivatives due to the presence of different functional groups. Solution of Rhodamine-6G in methanol behaves in a more coherent fashion compared to that of Fluorescein-548 dye.

Binding of the Antagonist Caffeine to the Human Adenosine Receptor hA2AR in Nearly Physiological Conditions.

Lipid composition may significantly affect membrane proteins function, yet its impact on the protein structural determinants is not well understood. Here we present a comparative molecular dynamics (MD) study of the human adenosine receptor type 2A (hA2AR) in complex with caffeine—a system of high neuro-pharmacological relevance—within different membrane types. These are POPC, mixed POPC/POPE and cholesterol-rich membranes. 0.8-μs MD simulations unambiguously show that the helical folding of the amphipathic helix 8 depends on membrane contents. Most importantly, the distinct cholesterol binding into the cleft between helix 1 and 2 stabilizes a specific caffeine-binding pose against others visited during the simulation. Hence, cholesterol presence (~33%-50% in synaptic membrane in central nervous system), often neglected in X-ray determination of membrane proteins, affects the population of the ligand binding poses. We conclude that including a correct description of neuronal membranes may be very important for computer-aided design of ligands targeting hA2AR and possibly other GPCRs.

Differential Interactions of Cytochrome P450 3A5 and 3A4 with Chemotherapeutic Agent-Vincristine: A Comparative Molecular Dynamics Study

The chemotherapeutic agent vincristine, used for treatment of acute lymphoblastic leukemia is metabolized preferentially by polymorphic cytochrome P450 3A5 (CYP3A5) with higher clearance rate than cytochrome P450 3A4 (CYP3A4). As a result, CYP3A5 expressers have a reduced amount of vincristine-induced peripheral neuropathy than non-expressers. We modeled the structure of CYP3A5 and its interaction with vincristine, compared with CYP3A4-vincristine complex using molecular docking and simulation studies. This relative study helped us to understand the molecular mechanisms behind the interaction at the atomic level through interaction energy, binding free energy, hydrogen bond and solvent accessible surface area analysis - giving an insight into the binding mode and the main residues involved in this particular interaction. Our results show that the interacting groups get closer in CYP3A5-vincristine complex due to different orientation of vincristine. This leads to higher binding affinity of vincristine towards CYP3A5 compared to CYP3A4 and explains the preferential metabolism of vincristine by CYP3A5. We believe that, the results of the current study will be helpful for future studies on structure-based drug design in this area.

Comparative molecular dynamics study of fcc-Ni nanoplate stress corrosion in water

Abstract Reactive molecular dynamics studies of stress corrosion properties of Ni metal nanoplate structures in pressurized water at different temperatures, chemical environments and mechanical boundary conditions have been performed. The results indicate reduction of dislocation nucleation barriers due to the water reactions on material surfaces, simulated loading rate and elevated temperature, resulting in reduction of material strength and ductility. It is also found that pre-oxidized surfaces yield increased initial dislocation nucleation barriers. Likewise, significant effects of stress triaxiality on strength, ductility and surface reactivity are also observed by comparison of boundary conditions. Size dependent structure failure modes and distributions of stress and strain have been explored. A possible Ni dissolution mechanism is identified and validated using DFT calculations and metadynamics simulations.

Comparative molecular dynamics study of melting and crystallization of Ni and Au nanoclusters

The melting and crystallization hysteresis for nanoclusters of two transition metals (nickel and gold) have been comparatively studied using the molecular dynamics method and the tight-binding potential. It is established that the onset and end temperatures of the corresponding first kind of phase transition (i.e., melting and crystallization temperatures) should be considered for Ni nanoclusters, whereas Au nanoclusters are melted and crystallized at certain temperatures. The size dependence of the melting temperature of Au nanoclusters determined using the computation results is compared with the molecular dynamics data from other researchers and the results of two independent laboratory experiments. It is shown that our molecular dynamics results are in much better agreement with the experimental data than those obtained by other researchers.

A comparative molecular dynamics study of crystalline, paracrystalline and amorphous states of cellulose

The quintessential form of cellulose in wood consists of microfibrils that have high aspect ratio crystalline domains embedded within an amorphous cellulose domain. In this study, we apply united-atom molecular dynamics simulations to quantify changes in different morphologies of cellulose. We compare the structure of crystalline cellulose with paracrystalline and amorphous phases that are both obtained by high temperature equilibration followed by quenching at room temperature. Our study reveals that the paracrystalline phase may be an intermediate, kinetically arrested phase formed upon amorphisation of crystalline cellulose. The quenched structures yield isotropic amorphous polymer domains consistent with experimental results, thereby validating a new computational protocol for achieving amorphous cellulose structure. The non-crystalline cellulose compared to crystalline structure is characterized by a dramatic decrease in elastic modulus, thermal expansion coefficient, bond energies, and number of hydrogen bonds. Analysis of the lattice parameters shows that Iβ cellulose undergoes a phase transition into high-temperature phase in the range of 450–550 K. The mechanisms of the phase transition elucidated here present an atomistic view of the temperature dependent dynamic structure and mechanical properties of cellulose. The paracrystalline state of cellulose exhibits intermediate mechanical properties, between crystalline and amorphous phases, that can be assigned to the physical properties of the interphase regions between crystalline and amorphous cellulose in wood microfibrils. Our results suggest an atomistic structural view of amorphous cellulose which is consistent with experimental data available up to date and provide a basis for future multi-scale models for wood microfibrils and all-cellulose nanocomposites.

Mechanisms of Trf1/Trf2 Binding Properties and DNA Sequence Recognition as Studied by Molecular Dynamics

Telomeres are complex nucleoprotein structures, formed at the ends of linear chromosomes as means of termini protection and stabilization. They were developped in response to the so-called termini replication problem, which caused steady shortening of Eukaryota chromosomes over the course of cell divisions. In numerous species, including humans, telomeric DNA consists of tandem 5'-TTAGGG-3' repeats of various length (ca. 10 kbp in case of human chromosomes); this portion of non-coding DNA can be lost during proliferation with no loss in genetic information. Constitutively proliferating cells, however, need to produce telomerase -- a ribonucleoprotein which is able to elongate the termini by use of its own RNA template. Telomere-deficient chromosomes might undergo ligation by cellular mechanisms of DNA repair and, further, trigger apoptosis; at the same time, telomere shortening is considered to be a cellular marker of aging. These two reasons make telomeres subject to particular attention in fields of drug design and senescence research.The telomere structure is stabilized by a number of distinct proteins, building up the shelterin complex. Two of these are responsible for specifically recruiting the complex to the telomeric sequence: Telomere repeat-binding factors 1 and 2 (TRF1 and TRF2). Here we present a detailed comparative Molecular Dynamics study of their mechanism of binding and sequence recognition. A decomposed free energy profile is used to quantify the key determinants of binding. We reproduce the experimental affinity data on the fully atomic scale, and propose a novel mechanism of sequence specificity. Moreover, we have computed a 2D PMF profile that enables us to draw conclusions about the association-dissociaton dynamics.

Non-planar grain boundary structures in fcc metals and their role in nano-scale deformation mechanisms

This work presents the results of a comparative molecular dynamics study showing that relaxed random grain boundary structures can be significantly non-planar at the nano-scale in fcc metals characterized by low stacking fault values. We studied the relaxed structures of random [1 1 0] tilt boundaries in a polycrystal using interatomic potentials describing Cu and Pd. Grain boundaries presenting non-planar features were observed predominantly for the Cu potential but not for the Pd potential, and we relate these differences to the stacking fault values. We also show that these non-planar structures can have a strong influence on dislocation emission from the grain boundaries as well as on grain boundary strain accommodation processes, such as grain boundary sliding. We studied the loading response in polycrystals of 40 nm grain size to a level of 9% strain and found that the non-planar grain boundaries favour dislocation emission as a deformation mechanism and hinder grain boundary sliding. This has strong implications for the mechanical behaviour of nano-crystalline materials, which is determined by the competition between dislocation activity and grain boundary accommodation of the strain. Thus, the two interatomic potentials for Cu and Pd considered in this work resulted in the same overall stress–strain curve, but significantly different fractions of the strain accommodated by the intergranular versus intragranular deformation mechanisms. Strain localization patterns are also influenced by the non-planarity of the grain boundary structures.

Comparative Molecular Dynamics Study of Human Islet Amyloid Polypeptide (IAPP) and Rat IAPP Oligomers

Human islet amyloid polypeptide (hIAPP or amylin) is a causative agent in pancreatic amyloid deposits found in patients with type 2 diabetes. The aggregation of full-length hIAPP(1-37) into small oligomeric species is increasingly believed to be responsible for cell dysfunction and death. However, rat IAPP (rIAPP(1-37)), which differs from hIAPP in only six of 37 residues, loses its aggregation ability to form toxic amyloid species. Atomic details of the effect of sequence on the structure and toxicity between the amyloidogenic, toxic hIAPP peptide and the nonamyloidogenic, nontoxic rIAPP peptide remain unclear. Here, we probe sequence-induced differences in structural stability, conformational dynamics, and driving forces between different hIAPP and rIAPP polymorphic forms from monomer to pentamer using molecular dynamics simulations. Simulations show that hIAPP forms from trimer to pentamer exhibit high structural stability with well-preserved in-register parallel β-sheet and the U-bend conformation. The hIAPP trimer appears to be a smallest minimal seed in solution. The stabilities of parallel hIAPP oligomers increase with the number of peptides. Conversely, replacement of hIAPP sequence by rIAPP sequence causes a significant loss of favorable interpeptide interactions in all rIAPP oligomers, destabilizing the C-terminal β-sheet, turn conformation, and overall stability. A less β-sheet-rich structure and a disturbed U-shaped topology exert a large energy penalty on the self-assemble of the rIAPP peptides into highly ordered, in-register β-sheet-rich protofibrils and fibrils, which explains the nonamyloidogenic activity of rIAPP. Moreover, the absence of interior water within the U-turn region in the well-packed higher-order hIAPP oligomers, not in the poorly packed rIAPP oligomers, also stabilizes peptide association. This work provides atomic details of the sequence-structure relationship between the amyloidogenic hIAPP and its analogues such as the nonamyloidogenic rIAPP and some mutants, which could help in the development of novel therapeutic agents to block the formation of toxic hIAPP oligomeric species for type 2 diabetes.

A Comparative Study of Mechanical Stability of Circular Permutants during Co-Translocational Unfolding of Proteins through Mitochondrial Pore

Mitochondrial import machinery catalyses unfolding of the native precursor proteins by trapping some faster local unfolding fluctuations due to specific secondary structural element adjacent to the targeting sequence. On the rupture of the first resistant structure, the rest of the protein unfolds rapidly by cooperative unfolding during import into the mitochondrial matrix. The process of circular permutation on the protein chain can give important information about the connectivity, structure and folding or unfolding kinetics which guides its translocation and subsequent function in the cell. To study the process of co-translocational unfolding and its dependence on the secondary structure at the N-terminus of the protein imported, we conduct a comparative molecular dynamics study of circular permutants of Dihydrofolate reductase(DHFR) using atomistic model in CHARMM. Six Circular Permutants - CP25, CP38, CP78, CP97, CP108, CP133 - are generated such that the new N-terminus leads either to an alpha helix or a beta-strand. using Steered Molecular Dynamics we compute the work distributions for the forced unfolding of each of the CP's and native DHFR using two processes - unfolding through the geometrical constriction of the model pore as in mitochondrial translocation and mechanical unfolding with the C-terminus fixed. In both cases the unfolding force is applied at the N-terminus. A comparison of the free energy profile along the reaction coordinate for each circular permutant can lead to identification of different unfolding pathways and hence import efficiency based on first resistant structure adjacent to the targeting sequence.

From protein denaturant to protectant: Comparative molecular dynamics study of alcohol/protein interactions

It is well known that alcohols can have strong effects on protein structures. For example, monohydric methanol and ethanol normally denature, whereas polyhydric glycol and glycerol protect, protein structures. In a recent combined theoretical and NMR experimental study, we showed that molecular dynamics simulations can be effectively used to understand the molecular mechanism of methanol denaturing protein. In this study, we used molecular dynamics simulations to investigate how alcohols with varied hydrophobicity and different numbers of hydrophilic groups (hydroxyl groups) exert effects on the structure of the model polypeptide, BBA5. First, we showed that methanol and trifluoroethanol (TFE) but not glycol or glycerol disrupt hydrophobic interactions. The latter two alcohols instead protect the assembly of the α- and β-domains of the polypeptide. Second, all four alcohols were shown to generally increase the stability of secondary structures, as revealed by the increased number of backbone hydrogen bonds formed in alcohol/water solutions compared to that in pure water, although individual hydrogen bonds can be weakened by certain alcohols, such as TFE. The two monohydric alcohols, methanol and TFE, display apparently different sequence-dependence in affecting the backbone hydrogen bond stability: methanol tends to enhance the stability of backbone hydrogen bonds of which the carbonyl groups are from polar residues, whereas TFE tends to stabilize those involving non-polar residues. These results demonstrated that subtle differences in the solution environment could have distinct consequences on protein structures.

Structural Effects of L16Q, S20G, and L16Q‐S20G Mutations on hIAPP: A Comparative Molecular Dynamics Study

AbstractThe conformation change picture of human islet amyloid polypeptide (hIAPP) is outlined using molecular dynamics simulation, and the structural influences of L16Q, S20G, and L16Q‐S20G mutations on the conformation of hIAPP are analyzed. Particularly, the conformational changes of the amyloidogenic‐related regions of residues 15–17 and 20–29 are emphasized. Our studies find that, for WT hIAPP, residues 15–17 always maintain a stable α‐helix structure, residues 20–25 structurally fluctuate between turn and 5‐helix, and residues 26–29 mainly adopt coil and bend structures. The hydrogen bonds between the polar groups of hIAPP, long‐rang van der Waals forces between the residues, and hydrophobic interactions between the residues of hIAPP are important driving forces to maintain the secondary structure of hIAPP. The replacement of leucine16 by glutamine stabilizes the helix structure of residues 15–17 and 20–23 of hIAPP monomer, and the structure of residues 24–29 fluctuates between helix and turn. The relatively stable helix structures of residues 15–17 and 20–29 are supposed to be beneficial for L16Q hIAPP to resist the aggregation as observed in the experiment. The substitution of serine20 by glycine drives residues 15–17 and 20–29 of hIAPP to transform from helix structure to β‐strands or coil structures with higher extension and flexibility, which may promote the aggregation of hIAPP as the experiments reported. These results are significant to understand the aggregation mechanism of hIAPP monomer into the dimer, trimer, oligomers and fibrils associated with the type 2 diabetes at the atomic level.

A Comparative Molecular Dynamics Study of Methylation State Specificity of JMJD2A

Histone modifications have great importance in epigenetic regulation. JMJD2A is a histone demethylase which is selective for di- and trimethyl forms of residues Lys9 and Lys36 of Histone 3 tail (H3K9 and H3K36). We present a molecular dynamics simulations of mono-, di- and trimethylated histone tails in complex with JMJD2A catalytic domain to gain insight into how JMJD2A discriminates between the methylation states of H3K9. The methyl groups are located at specific distances and orientations with respect to Fe(II) in methylammonium binding pocket. For the trimethyllysine the mechanism which provides the effectual orientation of methyl groups is the symmetry, whereas for the dimethyllysine case the determining factors are the interactions between methyllysine head and its environment and subsequently the restriction on angular motion. The occurrence frequency of methyl groups in a certain proximity of Fe(II) comes out as the explanation of the enzyme activity difference on di- and tri-methylated peptides. Energy analysis suggests that recognition is mostly driven by van der Waals and followed by Coulombic interactions in the enzyme-substrate interface. The number (mono, di or tri) and orientations of methyl groups and water molecules significantly affect the extent of van der Waals interaction strengths. Hydrogen bonding analysis suggests that the interaction between JMJD2A and its substrates mainly comes from main chain-side chain interactions. Binding free energy analysis points out Arg8 as an important residue forming an intra-substrate hydrogen bond with tri and dimethylated Lys9 of the H3 chain. Our study provides new insights into how JMJD2A discriminates between its substrates from both a structural and dynamical point of view.

Structural Role of Compensatory Amino Acid Replacements in the α-Synuclein Protein

A subset of familial Parkinson's disease (PD) cases is associated with the presence of disease-causing point mutations in human α-synuclein [huAS(wt)], including A53T. Surprisingly, the human neurotoxic amino acid 53T is present in non-primate, wild-type sequences of α-synucleins, including that expressed by mice [mAS(wt)]. Because huAS(A53T) causes neurodegeneration when expressed in rodents, the amino acid changes between the wild-type human protein [huAS(wt)] and mAS(wt) might act as intramolecular suppressors of A53T toxicity in the mouse protein, restoring its physiological structure and function. The lack of structural information for mAS(wt) in aqueous solution has prompted us to conduct a comparative molecular dynamics study of huAS(wt), huAS(A53T), and mAS(wt) in water at 300 K. The calculations are based on an ensemble of nuclear magnetic resonance-derived huAS(wt) structures. huAS(A53T) turns out to be more flexible and less compact than huAS(wt). Its central (NAC) region, involved in fibril formation by the protein, is more solvent-exposed than that of the wild-type protein, in agreement with nuclear magnetic resonance data. The compactness of mAS(wt) is similar to that of the human protein. In addition, its NAC region is less solvent-exposed and more rigid than that of huAS(A53T). All of these features may be caused by an increase in the level of intramolecular interactions on passing from huAS(A53T) to mAS(wt). We conclude that the presence of "compensatory replacements" in the mouse protein causes a significant change in the protein relative to huAS(A53T), restoring features not too dissimilar to those of the human protein.

Characterizing the Dynamics and Ligand-Specific Interactions in the Human Leukocyte Elastase through Molecular Dynamics Simulations

The human leukocyte elastase (HLE), a neutrophil serine protease of the chymotrypsin superfamily, is a major therapeutic target for a number of inflammatory diseases, such as chronic obstructive pulmonary disease (COPD). In this work, we present a comparative explicit water molecular dynamics (MD) study on the free and inhibitor-bound HLE. Knowledge of the flexibility and conformational changes induced by this irreversible inhibitor, whether in a prebound stage or covalently bound at the enzyme binding site, encases fundamental biological interest and is particularly relevant to ongoing structure-based drug design studies. Our results suggest that HLE operates by an induced-fit mechanism with direct intervention of a surface loop which is open toward the solvent in the free enzyme and closed while in the presence of the ligand. MM-PBSA free energy calculations furthermore elucidate the energetic contributions to the distinct conformations adopted by this loop. Additionally, a survey of the major contributions to the inhibitor binding free energies was attained. Our findings enforce the need to account for HLE flexibility, whether through the use of MD-generated ensembles of HLE conformations as targets for molecular docking or via sophisticated flexible-docking algorithms. We anticipate that inclusion of the observed HLE dynamic behavior into future drug design methodologies will have a relevant impact in the development of novel, more efficient, inhibitors.

Comparative Molecular Dynamics Study of Vapor-Exposed Basal, Prismatic, and Pyramidal Surfaces of Ice

We present the results of molecular dynamics simulations in which ice I(h) slabs with free basal, prismatic, 28° pyramidal, and 14° pyramidal facets are exposed to vapor. All simulations were carried out at 250 K using a six-site intermolecular potential. Characteristics common to all facets include spontaneous development of a quasi-liquid layer (QLL) within ∼10 ns and QLL stratification into outer (ε(1)) and inner (ε(2)) sublayers having on average two and three hydrogen bonds, respectively. Vapor pressure, based on the rate of escape of molecules from the QLL to the vapor phase, is found to be greatest for the 14° pyramidal and basal facets (∼230 Pa), while significantly lower values are obtained for the prismatic and 28° pyramidal facets (∼200 Pa). The geometric thickness of the QLL also varies between facets, with the 14° pyramidal having the greatest thickness. The free prismatic and pyramidal facets exhibit significant anisotropic diffusivity, in-plane motion being faster in the trans-prismatic direction than in the basal-to-basal direction. The in-plane diffusion length is greatest for the 28° pyramidal facet and smallest for the prismatic facet. This diversity of facet-specific properties provides a rich set of possibilities for mechanisms of ice crystal growth and ablation.

A Comparative Molecular Dynamics Study of the Effect of Alpha-Tocopherol and Cholesterol on Phospholipid Bilayers having Different Levels of Acyl Chain Unsaturation

Cholesterol and alpha-tocopherol (vitamin E) are important constituents of cell membranes having similar molecular shapes and sizes. These two molecules, however, exhibit very different properties in membranes and are thought to play different roles in the biology of the cell. Cholesterol is found in high concentrations in membranes, especially those composed of saturated phospholipids such as 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), while recent experiments suggest that alpha-tocopherol, which is typically found in much smaller concentrations, preferentially accumulates in membranes containing highly polyunsaturated lipids such as 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (SDPC). Here we examine the structural and dynamic properties of alpha-tocopherol and cholesterol and their effects on phospholipid bilayers using molecular dynamics (MD) computer simulation methods. Six long simulations (hundreds of nanosecond each) have been carried out, one for each neat lipid (DPPC and SDPC), and one for each solute in each lipid. The dramatically different effect on membrane properties that is observed in the simulation is explained in terms of unique solute-lipid interactions arising from polyunsaturation of the lipid acyl chains.