Determination of the aggregation constants of bile salts by capillary electrophoresis

Summary Capillary electrophoresis has been investigated as a novel experimental method for determination of the aggregation constants of surfactants. The tendency of sodium cholate and sodium taurodeoxycholate to associate was studied in phosphate buffers of pH 8.0 and pH 7.0, respectively. Stepwise aggregation equilibria of bile salt monomers has been described in terms of massbalance equations. The Offord equation was used to model the electrophoretic mobility of the bile salt associates, and the experimental mobility values could be fitted to the model. Interestingly, only even-membered aggregates-dimers and tetramers-besides the monomers were proposed from the results of the curve-fitting for both bile salts. The aggregation constants calculated were (in molar units): cholate logK _A2=1.37, logK _A4=4.98 taurodeoxycholate logK _A2=1.68, logK _A4=6.46. From these values, more pronounced aggregation of taurodeoxycholate starting at lower concentrations has been deduced, supporting the back-to-back association model of bile salts.     

Molecular dynamics simulation of the aggregation of colloidal particles

The spontaneous time evolution of systems containing N colloidal particles (N = 12, 24, 100) in a spherical cell of volume V at a constant volume fraction φ=0.1 was studied by a molecular dynamics method in the NVT ensemble. The starting velocities of the particles are allocated according to the Maxwell distribution at T=273 K.

Pairwise interaction of the particles was specified by molecular, electrostatic and elastic forces. The changes in the potential energy of the systems were calculated during the establishment of dynamic equilibrium. Coagulation takes place at sufficiently high values of the Hamaker constant. The value of the coefficient of Brownian diffusion, which is calculated from the half-time of coagulation, is found to be close to the known value for aqueous dispersions. The inclusion of electrostatic forces prevents coagulation.

The results obtained are in agreement with those obtained using theories of aggregate formation. Some structural characteristics of aggregates and stable systems are discussed.     

Spontaneous formation of annular structures observed in molecular dynamics simulations of polyglutamine peptides

Annular structures have been observed experimentally in aggregates of polyglutamine-containing proteins and other proteins associated with diseases of the brain. Here we report the observation of annular structures in molecular-level simulations of large systems of model polyglutamine peptides. A system of 24 polyglutamine chains 16 residues long at a concentration of 5 mM spontaneously formed large beta sheets which curved to form tube-like annular structures that resemble beta barrels. This work was accomplished by extending the PRIME model to polyglutamine. PRIME is an off-lattice, unbiased, intermediate-resolution protein model based on an amino acid representation of between three and seven united atoms depending on the residue being modeled. Our results are interesting not only because of the recent discovery of tubular protofibrils in experiments on aggregation of mutant huntingtin fragments containing expanded polyglutamine tracts but also because Perutz predicted that polyglutamine forms water filled nanotubes.     

Controlling J aggregation in fluorescein by bile salt hydrogels

Aggregation of the well-known xanthene dye, fluorescein has been studied in the restricted environment of a bile salt hydrogel and in the bile salt micelles. It has been observed that the hydrogel can be used to some extent “control” the type of aggregation in fluorescein, since J-aggregate formation is favored at the expense of H-aggregates in the gel. In contrast to the hydrogel, the effect of normal bile salt micelles is less dramatic, i.e., bile salt micelles do not lead to significant change in the type of dye aggregation.     

Molecular dynamics simulations of atomistic hydration structures of poly(vinyl methyl ether)

Molecular dynamics simulations have been performed on the aqueous solutions of poly(vinyl methyl ether) (PVME) at various concentrations. Both radial and spatial distribution functions are used to investigate the detailed hydration structures. The structures of water are found to get increasingly concentrated when polymers are introduced and the water motions are severely hindered by the polymer matrix. At low concentrations, larger populations of tt conformers in meso dyads than those at higher concentrationsare found and this phenomenon is believed to be due to the increasing in bonding of water molecule to two ether oxygens in meso dyad. At higher concentrations, the size and conformations of polymers are quite similar to those in bulk. A transition of hydrogen bond fractions between PVME and water at around the concentration of 0.3 is observed and this value is perfectly in agreement with the results of conformational analysis and Raman spectra. Second neighbor hydrogen bond statistics revealed the domination of complicated hydrogen bond networks at low concentrations, but single hydrogen bonds as well as isolated clusters composed of 2-4 water molecules are usual around each polymer repeat unit.     

Molecular dynamics simulations of oligonucleotides in solution: Visualisation of intrinsic curvature

Summary We have undertaken molecular dynamics simulations on the d(CGCAAAAAAGCG)d(CGCTTTTTTGCG) dodecamer in solution. In this study, we focus on aspects of conformation and dynamics, including the possibility of cross-strand hydrogen bonds. We compare our results with those from crystallography as well as infrared, Raman and NMR spectroscopy and cyclization kinetics. Our method of analysis allows us to visualise the curvature of the helix as a function of time during the simulation. We find that the major distortions of the helix axis path occur at the junctions between the (essentially straight) A-tract and the CG-and GC-tracts, although at one junction this is due to hyperflexibility (i.e., regions of high flexibility with no preferred direction of curvature), while at the other junction a static curvature is found (i.e., a preferred, sustained direction of curvature).     

Molecular dynamics simulations of the isolated domain 1 of annexin I

Annexin molecules consist of a symmetrical arrangement of four domains of identical folds but very different sequences. Nuclear magnetic resonance (NMR) experiments on the isolated domains of annexin I in aqueous solution have indicated that domain 1 retains its native structure whereas domain 2 unfolds. Therefore these two domains constitute interesting models for comparative simulations of structural stability using molecular dynamics. Here we present the preliminary results of molecular dynamics simulations of the isolated domain 1 in explicit water at 300 K, using two different simulation protocols. For the first, domain 1 was embedded in a 46 ? cubic box of water. A group-based non-bonded cut-off of 9 ? with a 5–9 ? non-bonded switching function was used and a 2 fs integration step. Bonds containing hydrogens were constrained with the SHAKE algorithm. These conditions led to unfolding of the domain within 400 ps at 300 K. In the second protocol, the domain was embedded in a 62 ? cubic box of water. An atom-based non-bonded cut-off of 8–12 ? using a force switching function for electrostatics and a shifting function for van der Waals interactions were used with a 1 fs integration step. This second protocol led to a native-like conformation of the domain in accord with the NMR data which was stable over the whole trajectory (∼2 ns). A small, but well-defined relaxation of the structure, from that observed for the same domain in the entire protein, was observed. This structural relaxation is described and methodological aspects are discussed. Received: 10 May 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

Free Energy Change of Micelle Formation for Sodium Dodecyl Sulfate from a Dispersed State in Solution to Complete Micelles along Its Aggregation Pathways Evaluated by Chemical Species Model Combined with Molecular Dynamics Calculations

Surfactant molecules, when dispersed in solution, have been shown to spontaneously form aggregates. Our previous studies on molecular dynamics(MD) calculations have shown that ionic sodium dodecyl sulfate molecules quickly aggregated even when the aggregation number is small. The aggregation rate, however, decreased for larger aggregation numbers. In addition, studies have shown that micelle formation was not completed even after a 100 ns-long MD run(Chem. Phys. Lett. 2016, 646, 36). Herein, we analyze the free energy change of micelle formation based on chemical species model combined with molecular dynamics calculations. First, the free energy landscape of the aggregation, ?G_(i+j)~+, where two aggregates with sizes i and j associate to form the(i + j)-mer, was investigated using the free energy of micelle formation of the i-mer, G_i~+, which was obtained through MD calculations. The calculated ?G_(i+j)~+ was negative for all the aggregations where the sum of DS ions in the two aggregates was 60 or less. From the viewpoint of chemical equilibrium, aggregation to the stable micelle is desired. Further, the free energy profile along possible aggregation pathways was investigated, starting from small aggregates and ending with the complete thermodynamically stable micelles in solution. The free energy profiles, G(l, k), of the aggregates at l-th aggregation path and k-th state were evaluated by the formation free energy ∑_in_i( l,k)G_i~+ and the free energy of mixing ∑_in_i( l,k)k_BTln( n_i( l,k)/n( l,k)), where ni(l, k) is the number of i-mer in the system at the l-th i aggregation path and k-th state, with n(l,k)= ∑_n_i( l,k). All the aggregation pathways were obtained from the initial i state of 12 pentamers to the stable micelle with i = 60. All the calculated G(l, k) values monotonically decreased with increasing k. This indicates that there are no free energy barriers along the pathways. Hence, the slowdown is not due to the thermodynamic stability of the aggregates, but rather the kinetics that inhibit the association of the fragments. The time required for a collision between aggregates, one of the kinetic factors, was evaluated using the fast passage time, t_(FPT). The calculated t_(FPT) was about 20 ns for the aggregates with N = 31. Therefore, if aggregation is a diffusion-controlled process, it should be completed within the 100 ns-simulation. However, aggregation does not occur due to the free energy barrier between the aggregates, that is, the repulsive force acting on them. This may be caused by electrostatic repulsions produced by the overlap of the electric double layers, which are formed by the negative charge of the hydrophilic groups and counter sodium ions on the surface of the aggregates.     

离子液体表面活性剂1-丁基-3-甲基咪唑烷基硫酸酯的合成及其在水溶液中的聚集行为

采用离子交换法,由1-丁基-3甲基咪唑氯盐（C4mimCl）和烷基硫酸钠合成了一系列无卤素的阴离子表面活性离子液体—1-丁基-3-甲基咪唑烷基硫酸酯[C4mim][CnH2n 1SO4](n=8,12,16),利用表面张力仪、稳态荧光光谱等手段考察了表面活性离子液体在水溶液表面及体相中的聚集行为,结果表明,与传统无机反离子相比,有机咪唑阳离子[C4mim] 作为反离子的离子液体型表面活性剂具有较高的表面活性,[C4mim] 产生的氢键引起的抑制分子规则排列的作用小于其促进分子有序排列的疏水作用。长烷基链的阴离子是界面膜及胶束的主要组成成分,阴离子疏水烷基碳链的增长虽然可促进胶束的形成,但却在一定程度上抑制[C4mim] 离子参与界面或胶束的形成;阴离子所带烷基链越长,越不利于阳离子[C4mim]＋参与界面膜或胶束的形成,界面膜或胶束中表面活性剂排布越松散,即界面张力越大,体系中胶束聚集数较小。     

Molecular dynamics simulations of aggregation behavior of sodium dodecyl sulfate on SiO2 and CaCO3 surfaces

Molecular dynamics simulations were carried out to investigate the aggregation behavior of anionic surfactant sodium dodecyl sulfate (SDS) on the surfaces of SiO₂ and CaCO₃. The results indicate that SDS molecules formed a spherical micelle structure near the SiO₂ surface; moreover, there were more head groups near the SiO₂ surface. However, they could form a self‐assemble film on the CaCO₃ surface. The self‐assemble film of SDS on the CaCO₃ surface was more stable than that on the SiO₂ surface. Our simulation results have a certain significance to understand the aggregation behavior of SDS on different surfaces on molecular level.     

Molecular dynamics simulations of self-diffusion coefficient and thermal conductivity of methane at low and moderate densities

This article demonstrates a highly accurate molecular dynamics (MD) simulation of thermal conductivity of methane using an ab initio intermolecular potential. The quantum effects of the vibrational contribution to thermal conductivity are more efficiently accounted for in the present MD model by an analytical correction term as compared to by the Monte Carlo method. The average deviations between the calculated thermal conductivity and the experimental data are 0.92% for dilute methane and 1.29% for methane at moderate densities, as compared to approximately 20% or more in existing MD calculations. The results demonstrate the importance of considering vibrational contribution to the thermal conductivity which is mainly through the self-diffusion process.     

Molecular dynamics simulations of the hexagonal structure of crystals with long methylene sequences

An unconstrained polymethylene crystal, consisting of 9600 CH₂ groups, in which each CH₂ is permitted to carry out stretching, bending, and torsional motion, has been studied at various temperatures using molecular dynamics simulations. Information about the atomistic details of the dynamics and structure of these crystals is presented. A significant disorder exists at tempratures well below the melting point. Close to melting, the disordered crystals have about 2% of gauche bonds that are distributed mainly at positions close to the surface of the crystal. The major disorder consists, however, of a collective twisting of the chains leading to a hexagonal crystal structure. The hexagonal structure of the symmetric motifs is caused by a dynamic multidomain arrangement of the chains. © 1993 John Wiley & Sons, Inc.     

Molecular modeling and dynamics of neuropeptide Y

Summary A combination of molecular modeling and molecular dynamics (MD) is used to determine a theoretical structure for neuropeptide Y (NPY). Starting with the X-ray structure for avian pancreatic polypeptide (APP), the substituted amino acids were mutated, the side chains oriented to local potential energy minima, and the entire structure minimized and subjected to an MD simulation. Comparison of the resulting NPY structure with APP X-ray and MD results showed secondary structural elements to be maintained and RMS fluctuations to be similar, although differences in both were observed. The approach presented offers a means to study the structure-function relationships of NPY and other similar polypeptides when combined with pharmacological measurements.Abbreviations NPY Neuropeptide Y - APP Avian pancreatic polypeptide - ABNR Adopted-basis Newton Raphson - MD Molecular dynamics     

Modeling dimerizations of transmembrane proteins using Brownian dynamics simulations

The dimerizations of membrane proteins, Outer Membrane Phospholipase A (OMPLA) and glycophorin A (GPA), have been simulated by an adapted Brownian Dynamics program. To mimic the membrane protein environment, we introduced a hybrid electrostatic potential map of membrane and water for electrostatic interaction calculations. We added a van der Waals potential term to the force field of the current version of the BD program to simulate the short-range interactions of the two monomers. We reduced the BD sampling space from three dimensions to two dimensions to improve the efficiency of BD simulations for membrane proteins. The OMPLA and GPA dimers predicted by our 2D-BD simulation and structural refinement is in good agreement with the experimental structures. The adapted 2D-BD method could be used for prediction of dimerization of other membrane proteins, such as G protein-coupled receptors, to help better understanding of the structures and functions of membrane proteins.     

Spin and fluorescence label studies on bile salt micelles

The interior structure of micelles formed by bile salts, which differ in the number and location of the hydroxyl groups attached to the steroid nucleus, was studied by the spin label and fluorescence label methods. The results show that the interior structure of micelles formed by bile salts possessing two hydroxyl groups is more rigid than that of micelles formed by trihydroxy bile salts regardless of the terminal hydrophilic group. Even in the case of dihydroxy bile salts possessing two hydroxyl groups in the same location, the interior structures of their micelles are different from each other depending on the orientation of their hydroxyl groups. It is considered that hydroxyl groups as well as the terminal hydrophilic group play an important role in the micellar formation of bile salts.     

Behaviors of sodium glycochenodeoxycholate and sodium glycoursodeoxycholate in binary mixed micelles of bile salt and nonionic surfactant

The behavior of sodium glycochenodeoxycholate (NaGCDC) and sodium glycoursodeoxycholate (NaGUDC) in binary mixed micelles consisting of bile salt and octaoxyethylene glycol mono n-decyl ether (C₁₀E₈) has been studied on the basis of micellar compositions, polarities of the interior of intramicelles, mean aggregation numbers and ¹H NMR measurements. Micellar compositions for both NaGCDC---C₁₀E₈ and NaGUDC---C₁₀E₈ systems showed a tendency to change from C₁₀E₈-rich micelles to bile-salt-rich micelles with an increase on the mole fraction of bile salts from the results of both theoretical calculations using the critical micelle concentration and the micellar polarity. The microenvironment of intramicelles for the NaGCDC---C₁₀E₈ system was found to be more hydrophobic than that for the NaGUDC---C₁₀E₈ system. Mean aggregation numbers of mixed micelles for both systems decreased abruptly with an increase in the mole fraction of bile salts in the range of low mole fraction, but those for NaGCDC were larger than those for NaGUDC. Furthermore, from the results of ¹H NMR measurements, the motions of the methyl group protons in the 18 position of the molecular structure of NaGCDC were slightly restricted with an increase in the mole fraction of NaGCDC. In contrast, the methyl group protons in the 18 and 19 positions of the molecular structure of NaGUDC became freer with an increase in the mole fraction of NaGUDC.     

Molecular dynamics simulation study on the structural stabilities of polyglutamine peptides

It is known that Huntington's disease patients commonly have glutamine (Q) repeat sequences longer than a critical length in the coding area of Huntingtin protein in their genes. As the polyglutamine (polyQ) region becomes longer than the critical length, the disease occurs and Huntingtin protein aggregates, both in vitro and in vivo, as suggested by experimental and clinical data. The determination of polyglutamine structure is thus very important for elucidation of the aggregation and disease mechanisms. Here, we perform molecular dynamics calculations on the stability of the structure based on the β-helix structure suggested by Perutz et al. (2002) [Perutz, M.F., Finch, J.T., Berriman, J., Lesk, A., 2002. Amyloid fibers are water-filled nanotubes. Proc. Natl. Acad. Sci. USA 99, 5591]. We ensure that perfect hydrogen bonds are present between main chains of the β-helix based on the previous studies, and perform simulations of stretches with 20, 25, 30, 37 and 40 glutamine residues (20Q, 25Q, 30Q, 37Q and 40Q) for the Perutz models with 18.5 and 20 residues per turn (one coil). Our results indicate that the structure becomes more stable with the increase of repeated number of Q, and there is a critical Q number of around 30, above which the structure of the Perutz model is kept stable. In contrast to previous studies, we started molecular dynamics simulations from conformations in which the hydrogen bonds are firmly formed between stacked main chains. This has rendered the initial β-helix structures of polyQ much more stable for longer time, as compared to those proposed previously. Model calculations for the initial structures of polyQ dimer and tetramer have also been carried out to study a possible mechanism for aggregation.     

Molecular dynamics simulations on the inhibition of Cyclin-Dependent Kinases 2 and 5 in the presence of activators

Interests in CDK2 and CDK5 have stemmed mainly from their association with cancer and neuronal migration or differentiation related diseases and the need to design selective inhibitors for these kinases. Molecular dynamics (MD) simulations have not only become a viable approach to drug design because of advances in computer technology but are increasingly an integral part of drug discovery processes. It is common in MD simulations of inhibitor/CDK complexes to exclude the activator of the CDKs in the structural models to keep computational time tractable. In this paper, we present simulation results of CDK2 and CDK5 with roscovitine using models with and without their activators (cyclinA and p25). While p25 was found to induce slight changes in CDK5, the calculations support that cyclinA leads to significant conformational changes near the active site of CDK2. This suggests that detailed and structure-based inhibitor design targeted at these CDKs should employ activator-included models of the kinases. Comparisons between P/CDK2/cyclinA/roscovitine and CDK5/p25/roscovitine complexes reveal differences in the conformations of the glutamine around the active sites, which may be exploited to find highly selective inhibitors with respect to CDK2 and CDK5.     

Molecular dynamics simulations of ligand-induced backbone conformational changes in the binding site of the periplasmic lysine-, arginine-, ornithine-binding protein

The periplasmic lysine-, arginine-, ornithine-binding protein (LAOBP) traps its ligands by a large hinge bending movement between two globular domains. The overall geometry of the binding site remains largely unchanged between the open (unliganded) and closed (liganded) forms, with only a small number of residues exhibiting limited movement of their side chains. However, in the case of the ornithine-bound structure, the backbone peptide bond between Asp11 and Thr12 undergoes a large rotation. Molecular dynamics simulations have been used to investigate the origin and mechanism of this backbone movement. Simulations allowing flexibility of a limited region and of the whole binding site, with and without bound ligands, suggest that this conformational change is induced by the binding of ornithine, leading to the stabilisation of an energetically favourable alternative conformation.