Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding

We show that diffusion can play an important role in protein-folding kinetics. We explicitly calculate the diffusion coefficient of protein folding in a lattice model. We found that diffusion typically is configuration- or reaction coordinate-dependent. The diffusion coefficient is found to be decreasing with respect to the progression of folding toward the native state, which is caused by the collapse to a compact state constraining the configurational space for exploration. The configuration- or position-dependent diffusion coefficient has a significant contribution to the kinetics in addition to the thermodynamic free-energy barrier. It effectively changes (increases in this case) the kinetic barrier height as well as the position of the corresponding transition state and therefore modifies the folding kinetic rates as well as the kinetic routes. The resulting folding time, by considering both kinetic diffusion and the thermodynamic folding free-energy profile, thus is slower than the estimation from the thermodynamic free-energy barrier with constant diffusion but is consistent with the results from kinetic simulations. The configuration- or coordinate-dependent diffusion is especially important with respect to fast folding, when there is a small or no free-energy barrier and kinetics is controlled by diffusion.Including the configurational dependence will challenge the transition state theory of protein folding.

Study of controllable aggregation morphology of ABA amphiphilic triblock copolymer in dilute solution by changing the solvent property

We have studied, both experimentally and theoretically, the aggregation morphology of the ABA amphiphilic triblock copolymer in dilute solution by changing the solvent property. Experimental results showed that the micellar morphology changed from spheres to rods and then to vesicles by changing the common solvent from N-N-dimethylformamide (DMF) to dioxane and then to tetrahydrofuran (THF). These controllable aggregates were also obtained by Monte Carlo simulation. The simulative results showed that the solvent property is a key factor that determines the copolymer aggregation morphology. The morphology changed from spheres to rods and then to vesicles by increasing the solvent solubility, corresponding to the change of stretched of the copolymer chains in the micellar cores. This result is in good agreement with the experimental one. Moreover, the simulative results revealed that the end-to-end distant of the ABA triblock copolymer in the vesicle was larger than that in the spheres and rods, indicating that the copolymer chains were more stretched in vesicles than in the spheres and rods. Furthermore, we gave the distribution of the fraction of the chain number with the end-to-end distance. The results indicated that the amount of folded chains is almost the same as that of stretched chains in the vesicle. Although most chains were folded, stretched chains could be found in the rod and sphere micelles.

How does solvent molecular size affect the microscopic structure in polymer solutions?

Monte Carlo simulation has been used to investigate the effects of linear solvent molecular size on polymer chain conformation in solutions. Increasing the solvent molecular size leads to shrinkage of the polymer chains and increase of the critical overlap concentrations. The root-mean-square radius of gyration of polymer chains (R-g) is less sensitive to the variation of polymer concentration in solutions of larger solvent molecules. In addition, the dependency of R-g on polymer concentration under normal solvent conditions and solvent molecular size is in good agreement with scaling laws. When the solvent molecular size approaches the ideal end-to-end distance of the polymer chain, an extra aggregation of polymer chains occurs, and the solvent becomes the so-called medium-sized solvent. When the size of solvent molecules is smaller than the medium size, the polymer chains are swollen or partially swollen. However, when the size of solvent molecules is larger than the medium size, the polymer coils shrink and segregate, enwrapped by the large solvent molecules.

Diffusion and single molecule dynamics on biomolecular interface binding energy landscape

We propose a new approach to study the diffusion dynamics on biomolecular interface binding energy landscape. The resulting mean first passage time (MFPT) has 'U'curve dependence on the temperature. It is shown that the large specificity ratio of gap to roughness of the underlying binding energy landscape not only guarantees the thermodynamic stability and the specificity [P.A. Rejto, G.M. Verkhivker, in: Proc. Natl. Acad. Sci. 93 (1996) 8945; C.J. Tsai, S. Kumar, B. Ma, R. Nussinov, Protein Sci. 8 (1999) 1181; G.A. Papoian, P.G. Wolynes, Biopolymers 68 (2003) 333; J. Wang, G.M. Verkhivker, Phys. Rev. Lett. 90 (2003) 198101] but also the kinetic accessibility. The complex kinetics and the associated fluctuations reflecting the structures of the binding energy landscape emerge upon temperature changes. The theory suggests a way of connecting the models/simulations with single molecule experiments by analysing the kinetic trajectories.

Monte Carlo simulation of the aggregation of rod-flexible triblock copolymers in a thin film

The aggregation of rod-flexible ABA and BAB triblock (A was rod block and repulsive with block B) copolymers in a thin film was studied as a function of varying the rigidity (eta) and the length of the rod block by Monte Carlo simulation. The rigidity of block A was defined as eta = R-c/R-max in this study. R-c, was the end-to-end distance below which the conformation of the block was not allowed, whereas R-max, was the longest end-to-end distance that the block could be. If eta = 0 the block was flexible, whereas if eta = 1 the block was a straight rod. The simulation results showed that the ABA triblock copolymer film were likely to form lamella structure with increasing the rigidity (eta) of block A. The lamellas were parallel each other and perpendicular to the film surface. However, the aggregation of BAB triblock copolymers tended to change from lamella to cylinder structure with increasing the rigidity (eta) of block A. Typical lamella and cylinder co-exist structure was obtained at eta = 0.504 for the BAB copolymer film. On the other hand, the simulation results indicated that the film changed from disorder to order, then to disorder structure with increasing the relative length of B block for both ABA and BAB copolymer films.

First-passage time distribution and non-Markovian diffusion dynamics of protein folding

We study the kinetics of protein folding via statistical energy landscape theory. We concentrate on the local-connectivity case, where the configurational changes can only occur among neighboring states, with the folding progress described in terms of an order parameter given by the fraction of native conformations. The non-Markovian diffusion dynamics is analyzed in detail and an expression for the mean first-passage time (MFPT) from non-native unfolded states to native folded state is obtained. It was found that the MFPT has a V-shaped dependence on the temperature. We also find that the MFPT is shortened as one increases the gap between the energy of the native and average non-native folded states relative to the fluctuations of the energy landscape. The second- and higher-order moments are studied to infer the first-passage time distribution. At high temperature, the distribution becomes close to a Poisson distribution, while at low temperatures the distribution becomes a Levy-type distribution with power-law tails, indicating a nonself-averaging intermittent behavior of folding dynamics. We note the likely relevance of this result to single-molecule dynamics experiments, where a power law (Levy) distribution of the relaxation time of the underlined protein energy landscape is observed.

Diffusion dynamics, moments, and distribution of first-passage time on the protein-folding energy landscape, with applications to single molecules

We study the dynamics of protein folding via statistical energy-landscape theory. In particular, we concentrate on the local-connectivity case with the folding progress described by the fraction of native conformations. We found that the first passage-time (FPT) distribution undergoes a dynamic transition at a temperature below which the FPT distribution develops a power-law tail, a signature of the intermittent nonexponential kinetic phenomena for the folding dynamics. Possible applications to single-molecule dynamics experiments are discussed.

Nanometer scale mechanical study on well defined nanostructured chain aggregation of polyethylene

Two kinds of polyethylene chain aggregation with chain axis perpendicular and parallel to the supported substrate were designed and successfully obtained from melt under an electric field and by melt-drawn method

Branched crystal morphology of linear polyethylene crystallized in a two-dimensional diffusion-controlled growth field

The branched crystal morphology of linear polyethylene formed at various temperatures from thin films has been studied by atomic-force microscopy (AFM), transmission electron microscopy (TEM), electron diffraction (ED) pattern and polymer decoration technique. Two types of branched patterns, i.e. dendrite and seaweed patterns, have been visualized. The fractal dimension d(f) = 1.65 of both dendrite and some of seaweed patterns was obtained by using the box-counting method, although most of the seaweed patterns are compact. Selected-area ED patterns indicate that the fold stems tilt about 34.5degrees around the b-axis and polymer decoration patterns show that the chain folding direction and regularity in two (200). regions are quite different from each other. Because of chain tilting, branched crystals show three striking features: 1) the lamella-like branches show two (200) regions with different thickness; 2) the crystals usually bend towards the thin region; 3) the thick region grows faster by developing branches, thus branches usually occur outside the thick region. The branched patterns show a characteristic width w, which gives a linear relationship with the crystallization temperature on a semilogarithmic plot.

Sol-gel derived carbon ceramic electrode containing methylene blue-intercalted alpha-zirconium phosphate micro particles

Methylene blue-intercalated a-zirconium phosphate (MBZrP) micro particles in deionized water were deposited onto the surface of graphite powder to prepare graphite powder-supported MBZrP, which was subsequently dispersed into methyltrimethoxysilane-derived gels to yield a conductive composite. The composite was used as electrode material to fabricate a surface-renewable, rigid, leak-free carbon ceramic composite electrode, bulk-modified with methylene blue (MB). In the configuration, alpha-zirconium phosphate was employed as a solid host for MB, which acted as a catalyst. Graphite powder ensured conductivity by percolation, the silicate provided a rigid porous backbone and the methyl groups endowed hydrophobicity and thus limited the wetting section of the modified electrode. Peak currents of the MBZrP-modified electrode were surface-confined at low scan rates but diffusion-controlled at high scan rates. Square-wave voltammetric study revealed that MBZrP immobilized in carbon ceramic matrix presented a two-electron, three-proton redox process in acidic aqueous solution with pH ranged from 0.44 to 2.94. In addition, the chemically modified electrode showed an electrocatalytic activity toward nitrite reduction at +0.15 V (vs. Ag/AgCl) in acidic aqueous solution (pH=0.44). The linear range and detection limit are 1 x 10(-6)-4 x 10(-3) mol L-1 and 1.5 x 10(-7) mol L-1, respectively.

Aggregation behavior of amphiphilic D-pi-A molecules bearing recognition group

Aggregation behavior of two amphiphilic D-pi -A molecules bearing barbituric acid as both recogniton group and electron-drawing substituent, 5-(4-dodecyl oxybenzylidene)-(1H, 3H)-2,4,6-pyrimidine trione (PB12) and 5-(4-N,N-didodecyl aminobenzylidene)-(1H,3H)-2,4,6-pyrimidine trione (AB(12)) was studied by UV-visible, fluorescence, and surface voltaic spectroscopies (SPS). The experimental results indicate that PB12 tends to form J-aggregate and AB(12) tends to form H-aggregate under increasing concentration. An intramolecular twisted charge transfer (TICT) emission around 500 nm is observed when J-aggregate is formed between PB12 molecules, and an excimer emission around 600 nm is observed when H-aggregate is formed between AB(12) molecules.

Tuning the aggregation of polyimide thin films by modification of their molecular interactions

Thin films of an organo-soluble polyimide based on 1,4-(3,4-dicarboxyphenoxy)benzene dianhydride (HQDPA) and 2,2'-dimethyl-4,4'-methylene dianiline (DMMDA) have been studied. A prism coupler was used to measure the refractive indices. The average refractive indices of thin films prepared by annealing at different temperatures and times were chosen to characterize the condensation states of thin films. Thin films annealed at 200 degrees C show irreversible changes in physical properties, eg solubility. FTIR spectroscopy showed that the chain structures of the above thin films remained unchanged. It is proposed that specific molecular interactions induce the irreversible changes revealed by fluorescence spectroscopy. (C) 2000 Society of Chemical Industry.