How alkali metal ion binding alters the conformation preferences of gramicidin A: a molecular dynamics and ion mobility study

Here, we present a systematic study combing electrospray ionization-ion mobility experiments and an enhanced sampling molecular dynamics, specifically integrated tempering sampling molecular dynamics simulations (ITS-MDS), to explore the conformations of alkali metal ion (Na, K, and Cs) adducts of gramicidin A (GA) in vacuo. Folding simulation is performed to obtain inherent conformational preferences of neutral GA to provide insights about how the binding of metal ions influences the intrinsic conformations of GA. The comparison between conformations of neutral GA and alkali metal ion adducts reveals a high degree of structural similarity, especially between neutral GA and [GA + Na](+); however, the structural similarities decrease as ionic radius of the metal increases. Collision cross section (CCS) profiles for [GA + Na](+) and [GA + Cs](+) ions obtained from by ITS-MDS compare favorably with the experimental CCS, but there are significant differences from CCS profiles for [GA + K](+) ions. Such discrepancies between the calculated and measured CCS profiles for [GA + K](+) are discussed in terms of limitations in the simulation force field as well as possible size-dependent coordination of the [GA + K](+) ion complex.     

Aqua ions-graphene interfacial and confinement behavior: insights from isobaric-isothermal molecular dynamics

We carry out a systematic microstructural characterization of the solid-fluid interface (SFI) of water and simple metal chloride aqueous solutions in contact with a free-standing plate or with two such plates separated by an interplate distance 0 ≤ h (?) ≤ 30 at ambient conditions via isothermal-isobaric molecular dynamics. With this characterization, we target the interrogation of the system in search for answers to fundamental questions regarding the structure of the "external" and "internal" (confined) SFIs, the effect of the differential hydration behavior among species, and its link to species expulsion from confinement. For water at ambient conditions, we found that the structure of the "external" SFIs is independent of the interplate distance h in the range 0 ≤ h (?) ≤ 30, that is, the absence of wall-mediated correlation effects between "external" and "internal" SFIs, and that for h < 9 ? the slit-pores dewet. Moreover, we observed a selective expulsion of ions caused by the differential hydration between the anion and the cations with a consequent charging of the slit-pore. All these observations were interpreted in terms of the axial profiles for precisely defined order parameters, including tetrahedral configuration, hydrogen bonding, and species coordination numbers.     

Sizing large proteins and protein complexes by electrospray ionization mass spectrometry and ion mobility

Mass spectrometry (MS) and ion mobility with electrospray ionization (ESI) have the capability to measure and detect large noncovalent protein-ligand and protein-protein complexes. Using an ion mobility method of gas-phase electrophoretic mobility molecular analysis (GEMMA), protein particles representing a range of sizes can be separated by their electrophoretic mobility in air. Highly charged particles produced from a protein complex solution using electrospray can be manipulated to produce singly charged ions, which can be separated and quantified by their electrophoretic mobility. Results from ESI-GEMMA analysis from our laboratory and others were compared with other experimental and theoretically determined parameters, such as molecular mass and cryoelectron microscopy and X-ray crystal structure dimensions. There is a strong correlation between the electrophoretic mobility diameter determined from GEMMA analysis and the molecular mass for protein complexes up to 12 MDa, including the 93 kDa enolase dimer, the 480 kDa ferritin 24-mer complex, the 4.6 MDa cowpea chlorotic mottle virus (CCMV), and the 9 MDa MVP-vault assembly. ESI-GEMMA is used to differentiate a number of similarly sized vault complexes that are composed of different N-terminal protein tags on the MVP subunit. The average effective density of the proteins and protein complexes studied was 0.6 g/cm(3). Moreover, there is evidence that proteins and protein complexes collapse or become more compact in the gas phase in the absence of water.     

Collision-induced dissociation of the phenylsilane molecular ion

The high-energy collision-induced dissociation of the phenylsilane molecular ion generated by electron ionization has been investigated using tandem mass spectrometry (MS/MS). It was observed that the dissociation of the molecular ion (M(+*)) occurs mainly via [M-H](+), [M-2H](+*), and [M-3H](+), followed by two consecutive losses of C(2)H(2). The structures of the precursors for the [M-CH(3)](+), [M-SiH](+), and [M-SiH(2)](+*) ions are proposed. The data suggest that the molecular ion undergoes rearrangements to several isomers prior to dissociation, including the ion containing a five-membered carbon ring. Reaction mechanisms are proposed for the dissociations via the isomeric molecular ions.     

Reaction mechanism of soluble epoxide hydrolase: insights from molecular dynamics simulations

Molecular dynamics simulations have been performed to gain insights into the catalytic mechanism of the hydrolysis of epoxides to vicinal diols by soluble epoxide hydrolase (sEH). The binding of a substrate, 1S,2S-trans-methylstyrene oxide, was studied in two conformations in the active site of the enzyme. It was found that only one is likely to be found in the active enzyme. In the preferred conformation the phenyl group of the substrate is pi-sandwiched between two aromatic residues, Tyr381 and His523, whereas the other conformation is pi-stacked with only one aromatic residue, Trp334. Two simulations were carried out to 1 ns for each conformation to evaluate the protonation state of active site residue His523. It was found that a protonated histidine is essential for keeping the active site from being disrupted. Long time scale, 4 ns, molecular dynamics simulation was done for the structure with the most likely combination of binding conformation and protonation state of His523. Near Attack Conformers (NACs) are present 5.3% of the time and nucleophilic attack on either epoxide carbon atom, approximately 75% on C(1) and approximately 25% on C(2), is found. A maximum of one hydrogen bond between the epoxide oxygen and either of the active site tyrosines, Tyr465 and Tyr381, is present, in agreement with experimental mutagenesis results that reveal a slight loss in activity if one tyrosine is mutated and essential loss of all activity upon double mutation of the two tyrosines in question. It was found that a hydrogen bond from Tyr465 to the substrate oxygen is essential for controlling the regioselectivity of the reaction. Furthermore, a relationship between the presence of this hydrogen bond and the separation of reactants was found. Two groups of amino acid segments were identified each as moving collectively. Furthermore, an overall anti-correlation was found between the movements of these two individually collectively moving groups, made up by parts of the cap-region, including the two tyrosines, and the site of the catalytic triad, respectively. This overall anti-correlated collective domain motion is, perhaps, involved in the conversion of E.NAC to E.TS.     

Unimolecular dissociation of aniline molecular ion: A theoretical study

The potential energy surface (PES) for dissociation of aniline ion was determined using density functional theory molecular orbital calculations at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31G(d) level. On the basis of the PES obtained, kinetic analysis was performed by Rice–Ramsperger–Kassel–Marcus (RRKM) calculations. The RRKM dissociation rate constants agreed well with previous experimental data. The most favorable channel was formation of the cyclopentadiene ion by loss of HNC, occurring through consecutive ring opening and re-closure to a five-membered ring. Loss of H could compete with the HNC loss at high energy, which occurred by direct cleavage of an N–H bond or through ring expansion.     

Nanoparticle dispersion and aggregation in polymer nanocomposites: insights from molecular dynamics simulation

It is a great challenge to fully understand the microscopic dispersion and aggregation of nanoparticles (NPs) in polymer nanocomposites (PNCs) through experimental techniques. Here, coarse-grained molecular dynamics is adopted to study the dispersion and aggregation mechanisms of spherical NPs in polymer melts. By tuning the polymer-filler interaction in a wide range at both low and high filler loadings, we qualitatively sketch the phase behavior of the PNCs and structural spatial organization of the fillers mediated by the polymers, which emphasize that a homogeneous filler dispersion exists just at the intermediate interfacial interaction, in contrast with traditional viewpoints. The conclusion is in good agreement with the theoretically predicted results from Schweizer et al. Besides, to mimick the experimental coarsening process of NPs in polymer matrixes (ACS Nano 2008, 2, 1305), by grafting polymer chains on the filler surface, we obtain a good filler dispersion with a large interparticle distance. Considering the PNC system without the presence of chemical bonding between the NPs and the grafted polymer chains, the resulting good dispersion state is further used to investigate the effects of the temperature, polymer-filler interaction, and filler size on the filler aggregation process. It is found that the coarsening or aggregation process of the NPs is sensitive to the temperature, and the aggregation extent reaches the minimum in the case of moderate polymer-filler interaction, because in this case a good dispersion is obtained. That is to say, once the filler achieves a good dispersion in a polymer matrix, the properties of the PNCs will be improved significantly, because the coarsening process of the NPs will be delayed and the aging of the PNCs will be slowed.     

Metastable dissociation dynamics of molecular cluster ions

Metastable uni-cluster dissociation for several hydrogen-bonded and van der Waals cluster ions are observed via resonance-enhanced two-photon ionization reflectron time-of-flight (TOF) mass spectrometry. All of the cluster ions studied show evaporation of a single molecule from the respective parent cluster ions as dominant metastable decay processes. Furthermore, the averaged metastable evaporation rate constants (k _evap) of these cluster ions in a fixed time domain of 0.2–50 µs are obtained by analyzing the relative intensity of metastable ion peaks due to evaporation in the acceleration and the field-free drift regions of the TOF mass spectrometer. An intensity anomaly in some of the observed metastable ion peaks, indicative of magic number stability of the cluster ion, is also presented.     

Enzymatic GTP hydrolysis: insights from an ab initio molecular dynamics study

Ab initio methods were used to shed light on fundamental aspects of the enzymatic mechanism of guanosine triphosphate hydrolysis in the Cdc42/Cdc42GAP complex. The calculations focused on the nucleophilic addition of the catalytic water molecule to the gamma-phosphate phosphorus atom. A large model system was required to correctly reproduce the electrostatic properties on the active site. The model turned out to reproduce most of the electrostatic field of the biological complex at the reactants. Our calculations established the H-bond pattern of the catalytic water (WAT), which turned out to interact with Q61 and T35, in the most stable conformation. This ruled out the possibility that the catalytic water transferred its proton directly to the gamma-phosphate. Furthermore, the calculations suggested that the electronic structure of WAT was very different from that in the bulk. Finally, this study showed that during the reaction, WAT transferred a proton to Gln61, consistent with the available X-ray data on a transition-state analogue/enzyme complex(19) and with the decrease of activity in the Q61E mutant.     

Probing the neutral graphene-ionic liquid interface: insights from molecular dynamics simulations

We study basic mechanisms of the interfacial layer formation at the neutral graphite monolayer (graphene)-ionic liquid (1,3-dimethylimidazolium chloride, [dmim][Cl]) interface by fully atomistic molecular dynamics simulations. We probe the interface area by a spherical probe varying the charge (-1e, 0, +1e) as well as the size of the probe (diameter 0.50 nm and 0.38 nm). The molecular modelling results suggest that: there is a significant enrichment of ionic liquid cations at the surface. This cationic layer attracts Cl(-) anions that leads to the formation of several distinct ionic liquid layers at the surface. There is strong asymmetry in cationic/anionic probe interactions with the graphene wall due to the preferential adsorption of the ionic liquid cations at the graphene surface. The high density of ionic liquid cations at the interface adds an additional high energy barrier for the cationic probe to come to the wall compared to the anionic probe. Qualitatively the results from probes with diameter 0.50 nm and 0.38 nm are similar although the smaller probe can approach closer to the wall. We discuss the simulation results in light of available experimental data on the interfacial structure in ionic liquids.     

Force-induced insulin dimer dissociation: a molecular dynamics study

Understanding the forces and dynamics of insulin dissociation is critical for devising formulations for the treatment of insulin-dependent diabetes. In earlier work, we applied AFM-based force spectroscopy to covalently tethered and oriented insulin monomers to assess the effect of molecular orientation on insulin-insulin binding forces. We report here on steered molecular dynamics simulations of the insulin dissociation force spectroscopy experiment. Consistent with our experiments, our simulation results suggest that insulin dimer dissociation occurs near the limit of extensibility of the B-chain. We have also found that the forced dissociation of the insulin dimer is a rate-dependent process, involving significant conformational changes to the monomer(s). The insulin dimer dissociation pathway also depends on the relative strength of the inter-monomer interactions across the antiparallel beta-sheet interface and the intra-monomer interactions of residues A1 and A30 with the insulin B-chain. Our simulation results strongly support the design of bioactive insulin analogues that involves altering hydrogen bonding and hydrophobic interactions across the beta-sheet dimer interface.     

Unfolding the conformational behavior of peptide dendrimers: insights from molecular dynamics simulations

We present here the first comprehensive structural characterization of peptide dendrimers using molecular simulation methods. Multiple long molecular dynamics simulations are used to extensively sample the conformational preferences of five third-generation peptide dendrimers, including some known to bind aquacobalamine. We start by analyzing the compactness of the conformations thus sampled using their radius of gyration profiles. A more detailed analysis is then performed using dissimilarity measures, principal coordinate analysis, and free energy landscapes, with the aim of identifying groups of similar conformations. The results point to a high conformational flexibility of these molecules, with no clear "folded state", although two markedly distinct behaviors were found: one of the dendrimers displayed mostly compact conformations clustered into distinct basins (rough landscape), while the remaining dendrimers displayed mainly noncompact conformations with no significant clustering (downhill landscape). This study brings new insight into the conformational behavior of peptide dendrimers and may provide better routes for their functional design. In particular, we propose a yet unsynthesized peptide dendrimer that might exhibit enhanced ability to coordinate aquocobalamin.     

Rotamer decomposition and protein dynamics: Efficiently analyzing dihedral populations from molecular dynamics

Molecular mechanics methods have matured into powerful methods to understand the dynamics and flexibility of macromolecules and especially proteins. As multinanosecond to microsecond length molecular dynamics (MD) simulations become commonplace, advanced analysis tools are required to generate scientifically useful information from large amounts of data. Some of the key degrees of freedom to understand protein flexibility and dynamics are the amino acid residue side chain dihedral angles. In this work, we present an easily automated way to summarize and understand the relevant dihedral populations. A tremendous reduction in complexity is achieved by describing dihedral timeseries in terms of histograms decomposed into Gaussians. Using the familiar and widely studied protein lysozyme, it is demonstrated that our approach captures essential properties of protein structure and dynamics. A simple classification scheme is proposed that indicates the rotational state population for each dihedral angle of interest and allows a decision if a given side chain or peptide backbone fragment remains rigid during the course of an MD simulation, adopts a converged distribution between conformational substates or has not reached convergence yet. © 2012 Wiley Periodicals, Inc.     

How natural materials remove heavy metals from water: mechanistic insights from molecular dynamics simulations

Water pollution by heavy metals is of increasing concern due to its devastating effects on the environment and on human health. For the removal of heavy metals from water sources, natural materials, such as spent-coffee-grains or orange/banana/chestnut peels, appear to offer a potential cheap alternative to more sophisticated and costly technologies currently in use. However, in order to employ them effectively, it is necessary to gain a deeper understanding – at the molecular level – of the heavy metals-bioorganic-water system and exploit the power of computer simulations. As a step in this direction, we investigate via atomistic simulations the capture of lead ions from water by hemicellulose – the latter being representative of the polysaccharides that are common components of vegetables and fruit peels − as well as the reverse process. A series of independent molecular dynamics simulations, both classical and ab initio, reveals a coherent scenario which is consistent with what one would expect of an efficient capture, i.e. that it be fast and irreversible: (i) binding of the metal ions via adsorption is found to happen spontaneously on both carboxylate and hydroxide functional groups; (ii) in contrast, metal ion desorption, leading to solvation in water, involves sizable free-energy barriers.

We investigate via atomistic simulations the capture of lead ions from water by hemicellulose – as representative of the polysaccharides that are common components of vegetables and fruit peels – and the reverse process.     

基于毛细管电泳和离子迁移率经验公式测定洛伐他汀的绝对淌度和解离常数

作为一种可以预防动脉粥样硬化和冠心病的潜在药物洛伐他汀,其绝对淌度m₀和解离常数pK_a值的测定有助于其性质与应用的研究。在前期相关研究基础上,该文提出了一种基于毛细管区带电泳(CZE)和离子淌度经验公式测定洛伐他汀m₀和pK_a的新方法。首先,根据经验公式由实际淌度(m_act)、有效淌度(m_eff)和m₀之间的关系推导出m₀的计算公式。对于一元酸HA,根据之前m₀的计算公式,以氢离子的浓度为自变量,m_eff的倒数为因变量可得到一条直线。根据这条直线的斜率计算得到pK_a。为了验证该方法的可行性和可靠性,应用该方法测定了巴比妥酸、苯甲酸、苄胺、苯酚、间甲酚等有机酸碱的m₀和pK_a值。同时,对于pH值低于6的缓冲体系,采用反向毛细管电泳技术,测定其pK_a,并将测得的实验结果与理论参考值进行对比,发现两者具有较高的一致性,m₀的标准偏差小于6.0%, pK_a的标准偏差小于6.2%,且由线性回归方程的相关系数(R)可以看出测定pK_a时的线性回归直线拟合度较好,说明该文建立的新方法具有较高的可靠性。最后基于这种CZE与经验公式结合的新方法,采用二甲基亚砜(DMSO)作为电渗流标记物测定了洛伐他汀的m₀和pK_a,得到的值分别为-1.70×10^-8 m²/(V·s)和9.00。该方法适用于酸性和碱性分析物m₀和pK_a等理化参数的测定,在药物分析尤其是新药理化特性研究中具有重要意义。     

Reduced-diabatic vibrational close coupled treatment of molecular dissociation dynamics

A close coupled treatment in a vibrational adiabatic representation is applied to the study of molecular photodissociation dynamics. The procedure which is developed here involves three steps: transformation from a diabatic to an adiabatic basis set, truncation of the adiabatic basis set, back transformation to a reduced–diabatic basis set. In the two model cases which are studied, dissociation spectra show complicated peaks and dips, patterns interpreted in terms of shape and Feshbach resonances associated to vibrational predissociation with a relatively high potential barrier in the excited state. An important reduction in the number of channels required for a given final accuracy can be reached by using the reduced–diabatic basis set instead of the usual diabatic one. This is very promising for studying energy partitioning in molecular systems with several internal degrees of freedom taking part in the dynamics.     

Mechanism of glucose oxidation by quinoprotein soluble glucose dehydrogenase: insights from molecular dynamics studies

We have generated 3 ns molecular dynamic (MD) simulations, in aqueous solution, of the bacterial soluble glucose dehydrogenase enzyme.PQQ.glucose complex and intermediates formed in PQQ reduction. In the MD structure of enzyme.PQQ.glucose complex the imidazole of His144 is hydrogen bonded to the hydroxyl hydrogen of H[bond]OC1(H) of glucose. The tightly hydrogen-bonded triad Asp163-His144-glucose (2.70 and 2.91 A) is involved in proton abstraction from glucose concerted with the hydride transfer from the C1[bond]H of glucose to the >C5[double bond]O quinone carbon of PQQ. The reaction is assisted by Arg228 hydrogen bonding to the carbonyl oxygen of >C5[double bond]O. The rearrangement of [bond](H)C5(O-)[bond]C4([double bond]O)[bond] of II to [bond]C5(OH)[double bond]C4(OH)[bond] of PQQH(2) hydroquinone is assisted by general acid protonatation of the >C4[double bond]O oxygen by protonated His144 and hydrogen bonds of Arg228 to the oxyanion O5. The continuous hydrogen bonding of the amide side chain of Asn229 to >C4[double bond]O4 oxygen and that of the O5 oxygen of the cofactor to Wat89 is observed throughout the entire reaction.     

Threshold dissociation and molecular modeling of transition metal complexes of flavonoids

The relative threshold dissociation energies of a series of flavonoid/transition metal/auxiliary ligand complexes of the type [MII (flavonoid - H) auxiliary ligand]+ formed by electrospray ionization (ESI) were measured by energy-variable collisionally activated dissociation (CAD) in a quadrupole ion trap (QIT). For each of the isomeric flavonoid diglycoside pairs, the rutinoside (with a 1-6 inter-saccharide linkage) requires a greater CAD energy and thus has a higher dissociation threshold than its neohesperidoside (with a 1-2 inter-saccharide linkage) isomer. Likewise, the threshold energies of complexes containing flavones are higher than those containing flavanones. The monoglycoside isomers also have characteristic threshold energies. The flavonoids that are glycosylated at the 3-O- position tend to have lower threshold energies than those glycosylated at the 7-O- or 4'-O- position, and those that are C- bonded have lower threshold energies than the O- bonded isomers. The structural features that substantially influence the threshold energies include the aglycon type (flavanone versus flavone), the type of disaccharide (rutinose versus neohesperidose), and the linkage type (O- bonded versus C- bonded). Various computational means were applied to probe the structures and conformations of the complexes and to rationalize the differences in threshold energies of isomeric flavonoids. The most favorable coordination geometry of the complexes has a plane-angle of about 62 degrees , which means that the deprotonated flavonoid and 2,2'-bipyridine within a complex do not reside on the same plane. Stable conformations of five cobalt complexes and five deprotonated flavonoids were identified. The conformations were combined with the point charges and helium accessible surface areas to explain qualitatively the differences in threshold energies for isomeric flavonoids.     

In silico model for P-glycoprotein substrate prediction: insights from molecular dynamics and in vitro studies

P-glycoprotein (P-gp) is a plasma membrane efflux transporter belonging to ATP-binding cassette superfamily, responsible for multidrug resistance in tumor cells. Over-expression of P-gp in cancer cells limits the efficacy of many anticancer drugs. A clear understanding of P-gp substrate binding will be advantageous in early drug discovery process. However, substrate poly-specificity of P-gp is a limiting factor in rational drug design. In this investigation, we report a dynamic trans-membrane model of P-gp that accurately identified the substrate binding residues of known anticancer agents. The study included homology modeling of human P-gp based on the crystal structure of C. elegans P-gp, molecular docking, molecular dynamics analyses and binding free energy calculations. The model was further utilized to speculate substrate propensity of in-house anticancer compounds. The model demonstrated promising results with one anticancer compound (NSC745689). As per our observations, the molecule could be a potential lead for anticancer agents devoid of P-gp mediated multiple drug resistance. The in silico results were further validated experimentally using Caco-2 cell lines studies, where NSC745689 exhibited poor permeability (P _app 1.03 ± 0.16 × 10^?6 cm/s) and low efflux ratio of 0.26.