Thermodynamics of peptide insertion and aggregation in a lipid bilayer

A variety of biomolecules mediate physiological processes by inserting and reorganizing in cell membranes, and the thermodynamic forces responsible for their partitioning are of great interest. Recent experiments provided valuable data on the free energy changes associated with the transfer of individual amino acids from water to membrane. However, a complete picture of the pathways and the associated changes in energy of peptide insertion into a membrane remains elusive. To this end, computational techniques supplement the experimental data with atomic-level details and shed light on the energetics of insertion. Here, we employed the technique of umbrella sampling in a total 850 ns of all-atom molecular dynamics simulations to study the free energy profile and the pathway of insertion of a model hexapeptide consisting of a tryptophan and five leucines (WL5). The computed free energy profile of the peptide as it travels from bulk solvent through the membrane core exhibits two minima: a local minimum at the water-membrane interface or the headgroup region and a global minimum at the hydrophobic-hydrophilic interface close to the lipid glycerol region. A rather small barrier of roughly 1 kcal mol (-1) exists at the membrane core, which is explained by the enhanced flexibility of the peptide when deeply inserted. Combining our results with those in the literature, we present a thermodynamic model for peptide insertion and aggregation which involves peptide aggregation upon contact with the membrane at the solvent-lipid headgroup interface.     

Thermodynamics and kinetics of competing aggregation processes in a simple model system

A simple model system has been used to develop thermodynamics and kinetics for bulk and surface aggregation processes capable of competing with each other. The processes are the stepwise aggregation of monomers in a fluid medium and on an impenetrable solid surface bounding the fluid medium, besides the adsorption and desorption of the same species at the solid-fluid interface. Emphasis is on aggregation processes in the high friction limit. The theoretical model is used to compare the kinetics and thermodynamics of the processes and to infer the conditions in which one process dominates another, in the high friction limit, such as in a liquid. The motivation of this study is obtaining insight into competition between aggregation in solution and on an adjoining surface, such as a cell membrane.     

Thermodynamics of peptide dimer formation

The Replica Exchange Statistical Temperature Molecular Dynamics algorithm is used to study the equilibrium properties of a peptide monomer and dimer and the thermodynamics of peptide dimer formation. The simulation data are analyzed by the Statistical Temperature Weighted Histogram Analysis Method. Each 10-residue peptide is represented by a coarse-grained model with hydrophobic side chains and has an α-helix as its minimum energy configuration. It is shown that the configurational behavior of the dimer can be divided into four regions as the temperature increases: two folded peptides; one folded and one unfolded peptide; two unfolded peptides; and two spatially separated peptides. Two important phenomena are discussed: in the dimer, one peptide unfolds at a lower temperature than the isolated monomer and the other peptide unfolds at a higher temperature than the isolated monomer. In addition, in the temperature region where one peptide is folded and the other unfolded, the unfolded peptide adopts an extended structure that minimizes the overall surface area of the aggregate. It is suggested that combination of destabilization due to aggregation and the resulting extended configuration of the destabilized peptide could have implications for nucleating β-sheet structures and the ultimate formation of fibrils.     

Optical trapping for the characterization of amyloid-beta aggregation kinetics

Alzheimer's disease (AD) is marked by the accumulation of neuronal plaques from insoluble amyloid-beta (Aβ) peptides. Growing evidence for the role of Aβ oligomers in neuronal cell cytotoxicity and pathogenesis has prompted the development of novel techniques to better understand the early stages of aggregation. Near infrared (NIR) optical trapping was applied to characterize the early stages of Aβ aggregation in the presence of a β-sheet intercalating dye, Congo Red (CR), as the fluorescent marker. The integration of fluorescence analysis with NIR optical trapping has provided a new outlook into the first two hours of Aβ aggregation.     

Cluster aggregation and fragmentation kinetics model for gelation

Gelation can occur in polymer, hydrogel, and colloid systems that undergo reversible aggregation-fragmentation (crosslinking accompanied by breakage). Gelation, characterized by rapid divergence of weight-average molecular weight and viscosity due to initial network formation, can be reversed if conditions change. In this paper, reversible aggregation and fragmentation in the pre-gelation time period are modeled with distribution kinetics. Moment equations are obtained from the population balance equation, and solved for eight different rate kernels. We identify the cases for which gelation is possible and obtain the critical values for the rate constants that allow gelation. The model provides a good simulation of published experimental data for aggregation and degradation of plasticized wheat gluten during thermo-mechanical treatments. We also evaluate two closure approximations based on Gamma and log-normal distributions, and conclude that log-normal closure predicts all five possible steady states, in agreement with the Vigil-Ziff criterion, and Gamma closure predicts only three. However, Gamma closure approximates the steady state either closely or exactly, whereas log-normal closure only poorly approximates the steady-state distribution.     

Thermodynamics and kinetics of PNA-DNA quadruplex-forming chimeras

PNA-DNA chimeras present the interesting properties of PNA, such as the high binding affinity to complementary single-strand (DNA or RNA), and the resistance to nuclease and protease degradation. At the same time, the limitations of an oligomer containing all PNA residues, such as low water solubility, self-aggregation, and low cellular uptake, are effectively overcome. Further, PNA-DNA chimeras possess interesting biological properties as antisense agents. We have explored the ability of PNA-DNA chimeric strands to assemble in quadruplex structures. The rate constant for association of the quadruplexes and their thermodynamic properties have been determined by CD spectroscopy and differential scanning calorimetry (DSC). Thermal denaturation experiments indicated higher thermal and thermodynamic stabilities for chimeric quadruplexes in comparison with the corresponding unmodified DNA quadruplex. Singular value decomposition analysis (SVD) suggests the presence of kinetically stable intermediate species in the quadruplex formation process. The experimental results have been discussed on the basis of molecular dynamic simulations. The ability of PNA-DNA chimeras to form stable quadruplex structures expands their potential utility as therapeutic agents.     

Thermodynamics and kinetics of NaAlH4 nanocluster decomposition

Reactive nanoparticles are of great interest for applications ranging from catalysis to energy storage. However, efforts to relate cluster size to thermodynamic stability and chemical reactivity are hampered by broad pore size distributions and poorly characterized chemical environments in many microporous templates. Metal hydrides are an important example of this problem. Theoretical calculations suggest that reducing their critical dimension to the nanoscale can in some cases considerably destabilize these materials and there is clear experimental evidence for accelerated kinetics, making hydrogen storage applications more attractive in some cases. However, quantitative measurements establishing the influence of size on thermodynamics are lacking, primarily because carbon aerogels often used as supports provide inadequate control over size and pore chemistry. Here, we employ the nanoporous metal-organic framework (MOF) Cu-BTC (also known as HKUST-1) as a template to synthesize and confine the complex hydride NaAlH(4). The well-defined crystalline structure and monodisperse pore dimensions of this MOF allow detailed, quantitative probing of the thermodynamics and kinetics of H(2) desorption from 1-nm NaAlH(4) clusters (NaAlH(4)@Cu-BTC) without the ambiguity associated with amorphous templates. Hydrogen evolution rates were measured as a function of time and temperature using the Simultaneous Thermogravimetric Modulated Beam Mass Spectrometry method, in which sample mass changes are correlated with a complete analysis of evolved gases. NaAlH(4)@Cu-BTC undergoes a single-step dehydrogenation reaction in which the Na(3)AlH(6) intermediate formed during decomposition of the bulk hydride is not observed. Comparison of the thermodynamically controlled quasi-equilibrium reaction pathways in the bulk and nanoscale materials shows that the nanoclusters are slightly stabilized by confinement, having an H(2) desorption enthalpy that is 7 kJ (mol H(2))(-1) higher than the bulk material. In addition, the activation energy for desorption is only 53 kJ (mol H(2))(-1), more than 60 kJ (mol H(2))(-1) lower than the bulk. When combined with first-principles calculations of cluster thermodynamics, these data suggest that although interactions with the pore walls play a role in stabilizing these particles, size exerts the greater influence on the thermodynamics and reaction rates.     

新型储氢材料及其热力学与动力学问题

氢能作为一种理想的二次能源受到了国内外科研工作者的广泛关注,研制可以在室温和较低压力下方便、安全、高效地储存氢能的材料是氢能发展的瓶颈.到目前为止,固态储氢材料以能量密度高及安全性好等优势被认为极具应用前景,其中以轻质元素构成的氢化物(包括硼氢化物/铝氢化物(可用通式A(MH4)n表示,其中A是碱金属(Li,Na,K)或碱土金属(Be,Mg,Ca);M是硼或铝;n=1～4)、氨基氢化物(如LiNH2等))、氨硼烷(NH3BH3)、金属有机骨架材料(MOFs)是新型储氢材料研究领域的热点,本文将着重就目前这几类储氢材料的研究当中所涉及到的一些热力学及动力学问题进行总结探讨.     

Determination of coagulation coefficients and aggregation kinetics for charged aerosols

A new method has been developed which allows determination of the coagulation coefficient of two oppositely charged particles experimentally. For this purpose, quasi-monodisperse particles of different sizes and morphology were used to study the influence of different parameters on the coagulation coefficient. A good agreement between experimental results and the classic Fuchs' theory was obtained when including a method accounting for particle nonsphericity. In experiments with polydisperse bipolarly charged aerosols, no principal differences to uncharged aerosols were found when a dimensionless representation was used. Changes in particle number concentration and geometric mean diameter can be described by simple empirical expressions.     

Thermodynamics and kinetics of evaporative crystallization of sodium gluconate

Thermodynamic properties of sodium gluconate (SG) aqueous solution have been measured over the 303.15–343.15 K temperature range including solubility, density, and viscosity. For proper crystallization of SG, the kinetics of evaporative crystallization with spontaneous nucleation was subsequently investigated in a semi-batch mode. The crystals present a size-dependent growth rate, and the number particle size distribution (PSD) data were well fitted with the MJ2 model. The effects of supersaturation, suspension density, and agitation intensity were carefully analyzed to contribute to a better understanding for the control of crystal size of SG.     

Thermodynamics and kinetics of immersion of coal by n-alcohols

The heats of immersion of Pocahontas No. 3 coal (325 mesh) have been measured at 36°C for a series of n-alcohols in a Calvet MS 70 microcalorimeter. The 200 mg coal samples were outgassed at ∼ 1 × 10⁻⁵ torr for 1h at room temperature. The evacuated sample bulbs with break-off tips were broken in 5 cm³ of the alcohols after establishment of an initial steady state. The rate at which the steady state was reestablished after immersion of the coal was followed. The heat of immersion decreased non-linearly from 20.2 J/g for methanol to 5.8 J/g for n-dodecanol. The immersion times of coal by methanol and n-dodecanol were 330 and 475 min/g, resp. A maximum in immersion time of 1220 min/g was observed for n-butanol. The results suggest limited penetration of the immersion liquids into the coal structure as the alcohol chain length increases.     

Adsorbate-induced silver nanoparticle aggregation kinetics

Metal sols are often stabilized in solution by the presence of a charged double layer surrounding each colloidal nanoparticle that produces a coulomb barrier to aggregation. The nanoparticles can be induced to aggregate by replacing the charged surface species by uncharged adsorbate. We present a simple analysis that produces an expression for the initial rate constant describing the aggregation process, which is shown to depend nontrivially on the adsorbate concentration. The expression is tested experimentally by following and analyzing the time rate of decrease of the surface plasmon resonance absorption of isolated Ag nanoparticles in aqueous solution. The experimental result accords well with theory, producing a rough estimate of the (adsorbate-concentration dependent) barrier to aggregation that in the absence of added adsorbate is approximately equal to 0.08 eV.     

Thermodynamics and kinetics of protonated merocyanine photoacids in water

Metastable-state photoacids (mPAHs) are chemical species whose photo-activated state is long-lived enough to allow for proton diffusion. Liao''s photoacid (1) represents the archetype of mPAHs, and is being widely used on account of its unique capability to change the acidity of aqueous solutions reversibly. The behavior of 1 in water, however, still remains poorly understood. Herein, we provide in-depth insights on the thermodynamics and kinetics of 1 in water through a series of comparative ¹H NMR and UV-Vis studies and relative modelling. Under dark conditions, we quantified a three-component equilibrium system where the dissociation (K_a) of the open protonated form (MCH) is followed by isomerization (K_c) of the open deprotonated form (MC) to the closed spiropyran form (SP) – i.e., in the absence of light, the ground state acidity can be expressed as K^GS_a = K_a(1 + K_c). On the other hand, under powerful and continuous light irradiation we were able to assess, for the first time experimentally, the dissociation constant (K^MS_a) of the protonated metastable state (cis-MCH). In addition, we found that thermal ring-opening of SP is always rate-determining regardless of pH, whereas hydrolysis is reminiscent of what is found for Schiff bases. The proposed methodology is general, and it was applied to two other compounds bearing a shorter (ethyl, 2) and a longer (butyl, 3) alkyl-1-sulfonate bridge. We found that the pK_a remains constant, whereas both pK_c and pK^MS_a linearly increase with the length of the alkyl bridge. Importantly, all results are consistent with a four-component model cycle, which describes perfectly the full dynamics of proton release/uptake of 1–3 in water. The superior hydrolytic stability and water solubility of compound 3, together with its relatively high pK^GS_a (low K_c), allowed us to achieve fully reversible jumps of 2.5 pH units over 18 consecutive cycles (6 hours).

We rationalize the behaviour of protonated merocyanines in water through cross-validation of ¹H NMR, UV-Vis and pH measurements, and show their capability to act as reversible photoacids along light/dark cycles can be described by a four-state model.     

Thermodynamics and kinetics of bubble nucleation: Simulation methodology

The simulation of homogeneous liquid to vapor nucleation is investigated using three rare-event algorithms, boxed molecular dynamics, hybrid umbrella sampling Monte Carlo, and forward flux sampling. Using novel implementations of these methods for efficient use in the isothermal-isobaric ensemble, the free energy barrier to nucleation and the kinetic rate are obtained for a Lennard-Jones fluid at stretched and at superheated conditions. From the free energy surface mapped as a function of two order parameters, the global density and largest bubble volume, we find that the free energy barrier height is larger when projected over bubble volume. Using a regression analysis of forward flux sampling results, we show that bubble volume is a more ideal reaction coordinate than global density to quantify the progression of the metastable liquid toward the stable vapor phase and the intervening free energy barrier. Contrary to the assumptions of theoretical approaches, we find that the bubble takes on cohesive non-spherical shapes with irregular and (sometimes highly) undulating surfaces. Overall, the resulting free energy barriers and rates agree well between the methods, providing a set of complementary algorithms useful for studies of different types of nucleation events.