分子间相互作用对蛋白质晶体生长的影响

采用原子力显微镜对溶菌酶和刀豆蛋白A的分子间相互作用力的情况进行了研究,并用动态光散射研究了此二种分子间相互作用力有较大差异的蛋白质在晶体生长条件和非生长条件下,溶液中的聚集体的状态(大小和分散度)随浓度和温度的变化情况.实验结果表明,范德华力强的刀豆蛋白A在成核前,溶液中的聚集体不能很快转变为生长基元,导致晶体生长时间长;而范德华力弱的溶菌酶,溶液中的聚集体可以很快转变成生长基元,晶体生长时间也较短.

Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated. We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard-Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.

Instability Analysis Of Torsional Mems/Nems Actuators Under Capillary Force

The static and dynamic instabilities of a torsional MEMS/NEMS actuator caused by capillary effects are studied, respectively. An instability number, eta, is defined, and the critical gap distance, g(cr), between the mainplate and the substrate is derived. According to the values of eta and g, the instability criteria of the actuator are presented. The dimensionless motion equation of the MEMS/NEMS torsional actuator is derived when it makes nonlinear oscillation under capillary force. The qualitative analysis of the nonlinear equation is made, and the phase portraits are presented on the phase plane. In addition, the bifurcation phenomena in the system are also analyzed. (C) 2008 Elsevier Inc. All rights reserved.

Spectroscopic studies of gas-phase molecular clusters

Spectroscopic investigations of hydrogen-bonding and van der Waals' interactions m molecular clusters were studied by the techniques of infrared predissociation and resonance-enhanced multiphoton ionization spectroscopies (REMPI). Ab initio calculations were applied in conjunction for data interpretation.

The infrared predissociation spectroscopy of CN^-•(H_2O)_n (n = 2 - 6) clusters was reported in the region of 2950 - 3850 cm^(-1). The hydrogen bondings for the C-site and N-site binding, and among the water molecules were identified for n = 2 to 4. A spectral transition was observed for n = 5 and 6, implying that the anion was surface-bound onto the water aggregates in larger clusters.

The infrared predissociation spectroscopy of Br^-•(NH_3) and I^-•(NH_3)_n (n =1-3) clusters was reported in the region of 3050-3450 cm^(-1). For the Br^-•(NH_3) complex, a dominating ionic NH stretch appeared at 3175 cm^(-1), and the weaker free NH stretch appeared at 3348 cm^(-1). The observed spectrum was consistent to the structure in which there was one nearly linear hydrogen bond between Br^- and the NH_3 moiety. For the I^- •(NH_3) complex, five distinct IR absorption bands were observed in the spectrum. The spectrum was not consistent with basic frequency patterns of three geometries considered in the ab initio calculations - complex with one, two and three hydrogen bondings between I^- and the NH_3 moiety. Substantial inhomogenous broadening were displayed in the spectra for I^-•(NH_3)_n (n =2-3), suggesting the presence of multiple isomers.

The REMPI spectroscopy of the bound 4p ^2П 1/2 and ^2П 3/2 states, and the dissociative 3d ^2Σ^+ 1/2 state in the Al•Ar complex was reported. The dissociative spectrum at Al^+ channel suggested the coupling of the 4p ^2П 1/2,3/2 states to the repulsive 3d ^2Σ^+ 1/2 state. The spin-electronic coupling was further manifested in the dissociative Al^+ spectrum of the 3d ^2Σ^+ 1/2 state. Using the potential energy curves obtained from ab initio calculations, a bound → continuum Franck-Condon-intensity simulation was performed and compared with the one-photon 3d ^2Σ^+ 1/2 profile. The agreement provided evidence for the petturbation above the Al(3d)Ar dissociation limit, and the repulsive character of the 3d ^2Σ^+ 1/2 state.

Numerical modeling of optical levitation and trapping of the "stuck" particles with a pulsed optical tweezers

We present the theoretical analysis and the numerical modeling of optical levitation and trapping of the stuck particles with a pulsed optical tweezers. In our model, a pulsed laser was used to generate a large gradient force within a short duration that overcame the adhesive interaction between the stuck particles and the surface; and then a low power continuous - wave (cw) laser was used to capture the levitated particle. We describe the gradient force generated by the pulsed optical tweezers and model the binding interaction between the stuck beads and glass surface by the dominative van der Waals force with a randomly distributed binding strength. We numerically calculate the single pulse levitation efficiency for polystyrene beads as the function of the pulse energy, the axial displacement from the surface to the pulsed laser focus and the pulse duration. The result of our numerical modeling is qualitatively consistent with the experimental result. (C) 2005 Optical Society of America.

Electron transfer in chemically and genetically modified myoglobins

The temperature dependences of the reduction potentials (E^o') of wildtype human myoglobin (Mb) and three site-directed mutants have been measured by using thin-layer spectroelectrochemistry. Residue Val68, which is in van der Waals contact with the heme in Mb, has been replaced by Glu, Asp, and Asn. At pH 7.0, reduction of the heme iron (III) in the former two proteins is accompanied by uptake of a proton by the protein. The changes in E^o', and the standard entropy (ΔS^o') and enthalpy (ΔH^o') of reduction in the mutant proteins were determined relative to values for wild-type; the change in E^o' at 25°C was about -200 millivolts for the Glu and Asp mutants, and about -80 millivolts for the Asn mutant. Reduction of Fe(III) to Fe(II) in the Glu and Asp mutants is accompanied by uptake of a proton. These studies demonstrate that Mb can tolerate substitution of a buried hydrophobic group by potentially charged and polar residues, and that such amino acid replacements can lead to substantial changes in the redox thermodynamics of the protein.

Through analysis of the temperature dependence and shapes of NMR dispersion signals, it is determined that a water molecule is bound to the sixth coordination site of the ferric heme in the Val68Asp and in the Val68Asn recombinant proteins while the carboxyl group of the sidechain of Glu68 occupies this position in Val68Glu. The relative rhombic distortions in the ESR spectra of these mutant proteins combined with H₂¹⁷O and spin interconversion experiments performed on them confirm the conclusions of the NMRD study.

The rates of intramolecular electron transfer (ET) of (NH₃)₅Ru-His48 (Val68Asp, His81GIn, Cys110AIa)Mb and (NH₃)₅Ru-His48 (Val68GIu,His81GIn,Cys110Ala)Mb were measured to be .85(3)s^-1 and .30(2)s^-1, respectively. This data supports the hypothesis that entropy of 111 reduction and reorganization energy of ET are inversely related. The rates of forward and reverse ET for (NH₃)₅ Ru-His48 (Val68GIu, His81 GIn, Cys110AIa)ZnMb -7.2(5)•10⁴s^-1and 1.4(2)•10⁵s^-1, respectively- demonstrate that the placement of a highly polar residue nearby does not significantly change the reorganization energy of the photoactive Zn porphyrin.

The distal histidine imidazoles of (NH₃)₄isnRu-His48 SWMb and (NH₃)₅Ru-His48 SWMb were cyanated with BrCN. The intramolecular ET rates of these BrCN-modified Mb derivatives are 5.5(6)s^-1 and 3.2(5)s^-1, respectively. These respective rates are 20 and 10 times faster than those of their noncyanated counterparts after the differences in ET rate from driving force are scaled according to the Marcus equation. This increase in ET rate of the cyanated Mb derivatives is attributed to lower reorganization energy since the cyanated Mb heme is pentacoordinate in both oxidation states; whereas, the native Mb heme loses a water molecule upon reduction so that it changes from six to five coordinate. The reorganization energy from Fe-OH₂ dissociation is estimated to be .2eV. This conclusion is used to reconcile data from previous experiments in our lab. ET in photoactive porphyrin-substituted myoglobins proceed faster than predicted by Marcus Theory when it is assumed that the only difference in ET parameters between photoactive porphyrins and native heme systems is driving force. However, the data can be consistently fit to Marcus Theory if one corrects for the smaller reorganization in the photoactive porphyrin systems since they do not undergo a coordination change upon ET.

Finally, the intramolecular ET rate of (NH₃)₄isnRu-His48 SWMb was measured to be 3.0(4)s^-1. This rate is within experimental error of that for (NH₃)₄pyrRu-His48 SWMb even though the former has 80mV more driving force. One likely possibility for this observation is that the tetraamminepyridineruthenium group undergoes less reorganization upon ET than the tetraammineisonicotinamideruthenium group. Moreover, analysis of the (NH₃)₄isnRu-His48 SWMb experimental system gives a likely explanation of why ET was not observed previously in (NH₃)₄isnRu-Cytochrome C.

Effects of KI encapsulation in single-walled carbon nanotubes by Raman and optical absorption spectroscopy.

The effect of KI encapsulation in narrow (HiPCO) single-walled carbon nanotubes is studied via Raman spectroscopy and optical absorption. The analysis of the data explores the interplay between strain and structural modifications, bond-length changes, charge transfer, and electronic density of states. KI encapsulation appears to be consistent with both charge transfer and strain that shrink both the C-C bonds and the overall nanotube along the axial direction. The charge transfer in larger semiconducting nanotubes is low and comparable with some cases of electrochemical doping, while optical transitions between pairs of singularities of the density of states are quenched for narrow metallic nanotubes. Stronger changes in the density of states occur in some energy ranges and are attributed to polarization van der Waals interactions caused by the ionic encapsulate. Unlike doping with other species, such as atoms and small molecules, encapsulation of inorganic compounds via the molten-phase route provides stable effects due to maximal occupation of the nanotube inner space.

Molecular modeling on human CCR5 receptors and complex with CD4 antigens and HIV-1 envelope glycoprotein gp120

AIM: To investigate the interaction between human CCR5 receptors (CCR5) and HIV-1 envelope glycoprotein gp120 (HIV-1 gp120) and HIV-1 receptor CD4 antigens (CD4). METHODS: The structurally con served regions (SCR) of human CCR5 was built by the SYBYL/Biopolymer module using the corresponding transmembrane (TM) domain of bacteriorhodopsin (bR) as the template. The coordinates for amino-ter minal residue sequence, and carboxyl-terminal residue sequence, extracellular and cytoplasmic loops were generated using LOOP SEARCH algorithm. Subsequently the structural model was merged into the complex with HIV-1 gp120 and CD4. RESULTS: Human CCR5 interacted with both an HIV-1 gp120 and CD4. The N-terminal residues (especially Met1 and Gln4) of human CCR5, contacted with CD4 residues, mainly 7Nith one span (56 - 59) of CD4 in electrostatic interaction and hydrogen-bonds. The binding sites of human CCR5 were buried in a hydrophobic center surrounded by a highly basic periphery. On the other hand, direct interatomic contacts were made between ? CCR5 residues and 6 gp120 amino-acid residues, which included van der Waals contacts, hydrophobic interaction, and hydrogen bonds. CONCLUSION: The interaction model should be helpful for rational design of novel anti-HIV drugs.

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

Dispersion of carbon nanotubes: Mixing, sonication, stabilization, and composite properties

Advances in functionality and reliability of carbon nanotube (CNT) composite materials require careful formulation of processing methods to ultimately realize the desired properties. To date, controlled dispersion of CNTs in a solution or a composite matrix remains a challenge, due to the strong van der Waals binding energies associated with the CNT aggregates. There is also insufficiently defined correlation between the microstructure and the physical properties of the composite. Here, we offer a review of the dispersion processes of pristine (non-covalently functionalized) CNTs in a solvent or a polymer solution. We summarize and adapt relevant theoretical analysis to guide the dispersion design and selection, from the processes of mixing/sonication, to the application of surfactants for stabilization, to the final testing of composite properties. The same approaches are expected to be also applicable to the fabrication of other composite materials involving homogeneously dispersed nanoparticles. © 2012 by the authors; licensee MDPI, Basel, Switzerland.

In situ intercalation dynamics in inorganic-organic layered perovskite thin films.

The properties of layered inorganic semiconductors can be manipulated by the insertion of foreign molecular species via a process known as intercalation. In the present study, we investigate the phenomenon of organic moiety (R-NH3I) intercalation in layered metal-halide (PbI2)-based inorganic semiconductors, leading to the formation of inorganic-organic (IO) perovskites [(R-NH3)2PbI4]. During this intercalation strong resonant exciton optical transitions are created, enabling study of the dynamics of this process. Simultaneous in situ photoluminescence (PL) and transmission measurements are used to track the structural and exciton evolution. On the basis of the experimental observations, a model is proposed which explains the process of IO perovskite formation during intercalation of the organic moiety through the inorganic semiconductor layers. The interplay between precursor film thickness and organic solution concentration/solvent highlights the role of van der Waals interactions between the layers, as well as the need for maintaining stoichiometry during intercalation. Nucleation and growth occurring during intercalation matches a Johnson-Mehl-Avrami-Kolmogorov model, with results fitting both ideal and nonideal cases.

Effect of microwave on formation/decomposition of natural gas hydrate

Natural gas hydrate (NGH) reservoirs have been considered as a substantial future clean energy resource and how to recover gas from these reservoirs feasibly and economically is very important. Microwave heating will be taken as a promising method for gas production from gas hydrates for its advantages of fast heat transfer and flexible application. In this work, we investigate the formation/decomposition behavior of natural gas hydrate with different power of microwave (2450MHZ), preliminarily analyze the impact of microwave on phase equilibrium of gas hydrate,and make calculation based on van der Waals-Platteeuw model. It is found that microwave of a certain amount of power can reduce the induction time and sub-cooling degree of NGH formation, e.g., 20W microwave power can lead to a decrease of about 3A degrees C in sub-cooling degree and the shortening of induction time from 4.5 hours to 1.3 hours. Microwave can make rapid NGH decomposition, and water from NGH decomposition accelerates the decomposition of NGH with the decomposition of NGH. Under the same pressure, microwave can increase NGH phase equilibrium temperature. Different dielectric properties of each composition of NGH may cause a distinct difference in temperature in the process of NGH decomposition. Therefore, NGH decomposition by microwave can be affected by many factors.

Hydrate dissociation conditions for gas mixtures containing carbon dioxide, hydrogen, hydrogen sulfide, nitrogen, and hydrocarbons using SAFT

A new method, a molecular thermodynamic model based on statistical mechanics, is employed to predict the hydrate dissociation conditions for binary gas mixtures with carbon dioxide, hydrogen, hydrogen sulfide, nitrogen, and hydrocarbons in the presence of aqueous solutions. The statistical associating fluid theory (SAFT) equation of state is employed to characterize the vapor and liquid phases and the statistical model of van der Waals and Platteeuw for the hydrate phase. The predictions of the proposed model were found to be in satisfactory to excellent agreement with the experimental data.

Theoretical foundation of Zisman's empirical equation for wetting of liquids on solid surfaces

Theories of wetting of liquids on solid surfaces under the condition that van der Waals force is dominant are briefly reviewed. We show theoretically that Zisman's empirical equation for wetting of liquids on solid surfaces is a linear approximation of the Young-van der Waals equation in the wetting region, and we express the two parameters in Zisman's empirical equation in terms of the dielectric polarizabilities of the solid and liquids. The materials contained in this paper are suitable for physics teaching of wetting phenomena for undergraduate, graduate, general physicist, etc.

Effects of pH on the Interactions and Conformation of Bovine Serum Albumin: Comparison between Chemical Force Microscopy and Small-Angle Neutron Scattering

The conformation of bovine serum albumin (BSA), as well as its interactions with negatively charged mica surfaces in saline solutions of different pH values, have been studied by small-angle neutron scattering (SANS) and chemical force microscopy (CFM), respectively. A new approach to extract the contribution of elementary interactions from the statistically averaged force-extension curves through self-consistent fitting was proposed and used to understand the effects of pH on the interactions and conformation of BSA in saline solutions. When pH increases, the SANS results reveal that the sizes of BSA molecules increase slightly, while the statistical analysis of the CFM results shows that the averaged pull-off force for the elongation monotonously decreases. The decrease of pull-off force with the increase of pH results from the decrease in the strength of hydrogen bonding and the number of interaction pairs, as well as the slight increase of the strength of van der Waals interaction. When pH approaches the isoelectric point (pI) of BSA, results from both SANS and CFM suggest a loss of long-range interactions in BSA molecules. Our results also suggest that the force-extension curve is mainly contributed by the van der Waals interaction. The combination of SANS and CFM provides new insight to understand the interactions and conformation of BSA molecules