Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures

Bacterial chaperonin, GroEL, together with its co-chaperonin, GroES, facilitates the folding of a variety of polypeptides. Experiments suggest that GroEL stimulates protein folding by multiple cycles of binding and release. Misfolded proteins first bind to an exposed hydrophobic surface on GroEL. GroES then encapsulates the substrate and triggers its release into the central cavity of the GroEL/ES complex for folding. In this work, we investigate the possibility to facilitate protein folding in molecular dynamics simulations by mimicking the effects of GroEL/ES namely, repeated binding and release, together with spatial confinement. During the binding stage, the (metastable) partially folded proteins are allowed to attach spontaneously to a hydrophobic surface within the simulation box. This destabilizes the structures, which are then transferred into a spatially confined cavity for folding. The approach has been tested by attempting to refine protein structural models generated using the ROSETTA procedure for ab initio structure prediction. Dramatic improvements in regard to the deviation of protein models from the corresponding experimental structures were observed. The results suggest that the primary effects of the GroEL/ES system can be mimicked in a simple coarse-grained manner and be used to facilitate protein folding in molecular dynamics simulations. Furthermore, the results Sur port the assumption that the spatial confinement in GroEL/ES assists the folding of encapsulated proteins.

The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions

The effect of the box shape on the dynamic behavior of proteins simulated under periodic boundary conditions is evaluated. In particular, the influence of simulation boxes defined by the near-densest lattice packing (NDLP) in conjunction with rotational constraints is compared to that of standard box types without these constraints. Three different proteins of varying size, shape, and secondary structure content were examined in the study. The statistical significance of differences in RMSD, radius of gyration, solvent-accessible surface, number of hydrogen bonds, and secondary structure content between proteins, box types, and the application or not of rotational constraints has been assessed. Furthermore, the differences in the collective modes for each protein between different boxes and the application or not of rotational constraints have been examined. In total 105 simulations were performed, and the results compared using a three-way multivariate analysis of variance (MANOVA) for properties derived from the trajectories and a three-way univariate analysis of variance (ANOVA) for collective modes. It is shown that application of roto-translational constraints does not have a statistically significant effect on the results obtained from the different simulations. However, the choice of simulation box was found to have a small (5-10%), but statistically significant effect on the behavior of two of the three proteins included in the study. (c) 2005 Wiley Periodicals, Inc.

Kinetic energy conserving integrators for Gaussian thermostatted SLLOD

A new integration scheme is developed for nonequilibrium molecular dynamics simulations where the temperature is constrained by a Gaussian thermostat. The utility of the scheme is demonstrated by its application to the SLLOD algorithm which is the standard nonequilibrium molecular dynamics algorithm for studying shear flow. Unlike conventional integrators, the new integrators are constructed using operator-splitting techniques to ensure stability and that little or no drift in the kinetic energy occurs. Moreover, they require minimum computer memory and are straightforward to program. Numerical experiments show that the efficiency and stability of the new integrators compare favorably with conventional integrators such as the Runge-Kutta and Gear predictor-corrector methods. (C) 1999 American Institute of Physics. [S0021-9606(99)50125-6].

Frontiers in Materials Science and Technology

This special issue aims to provide up-to-date knowledge and the latest scientific concepts and technological developments in the processing, characterization, testing, mechanics, modeling and applications of a broad range of advanced materials. The many contributors, from Denmark, Germany, UK, Iran, Saudi Arabia, Malaysia, Japan, the People’s Republic of China, Singapore, Taiwan, USA, New Zealand and Australia, present a wide range of topics including: nanomaterials, thin films and coatings, metals and alloys, composite materials, materials processing and characterization, biomaterials and biomechanics, and computational materials science and simulation. The work will therefore be of great interest to a broad spectrum of researchers and technologists.

Infrared and Raman spectroscopic studies of archaeological materials

The use of vibrational spectroscopic techniques to characterise historical artefacts and art works continues to grow and to provide the archaeologist and art historian with significant information with which to understand the nature and activities of previous peoples and civilizations. In addition, conservators can gain knowledge of the composition of artworks or historical objects and so are better equipped to ensure their preservation. Both infrared and Raman have been widely used. Microspectroscopy is the preferred sampling technique as it requires only a very small sample, which often can be recovered. The use of synchrotron radiation in conjunction with IR microspectroscopy is increasing because of the substantial benefits in terms of improved spatial resolution and signal-to-noise ratio. The key trend for the future is the growth in the use of portable instruments, both IR and Raman, which are becoming important because they allow non-destructive measurements to be made in situ, for example at an archaeological site or at a museum.

Fine tuning of elasticity via crosslinking collagen-based materials to mediate mechanotransduction and stability using corona treatment

The common goal of tissue engineering is to develop substitutes that can closely mimic the structure of extracellular matrix (ECM). However, similarly important is the intensive material properties which have often been overlooked, in particular, for soft tissues that are not to bear load assumingly. The mechanostructural properties determine not only the structural stability of biomaterials but also their physiological functionality by directing cellular activity and regulating cell fate decision. The aim here is to emphasize that cells could sense intensive material properties like elasticity and reside, proliferate, migrate and differentiate accordinglyno matter if the construct is from a natural source like cartilage, skin etc. or of synthetic one. Meanwhile, the very objective of this work is to provide a tunable scheme for manipulating the elasticity of collagen-based constructs to be used to demonstrate how to engineer cell behavior and regulate mechanotransduction. Articular cartilage was chosen as it represents one of the most complex hierarchical arrangements of collagen meshwork in both connective tissues and ECM-like biomaterials. Corona discharge treatment was used to produce constructs with varying density of crosslinked collagen and stiffness accordingly. The results demonstrated that elastic modulus increased up to 33% for samples treated up to one minute as crosslink density was found to increase with exposure time. According to the thermal analysis, longer exposure to corona increased crosslink density as the denaturation enthalpy increased. However the spectroscopy results suggested that despite the stabilization of the collagen structure the integrity of the triple helical structure remained intact. The in vitro superficial culture of heterologous chondrocytes also determined that the corona treatment can modulate migration with increased focal adhesion of cells due to enhanced stiffness, without cytotoxicity effects, and providing the basis for reinforcing three-dimensional collagen-based biomaterials in order to direct cell function and mediate mechanotransduction.

TEM characterization of nanostructure and chemistry of semiconductor quantum structures

The power of advanced transmission electron microscopy in determining the nanostructures and chemistry of nanosized materials on the applications in semiconductor quantum structures was demonstrated.

Hydrothermal Synthesis of Layered Double Hydroxides (LDHs) from Mixed MgO and Al2O3: LDH Formation Mechanism

The formation of MgA1 layered double hydroxide (LDH) from physically mixed MgO and Al2O3 oxides upon hydrothermal treatment has been extensively investigated, and a formation mechanism has been proposed. We observed that the formation of LDH from the oxide mixture occurs upon heating at 110 degreesC. In general, LDH is the major component while the minor phases are mainly determined by the initial pH of the oxide suspension as well as the MgO/Al2O3 ratio. The neutrality in the initial suspension results in a minor Mg(OH)(2) as the impure phase, while the alkalinity in the suspension keeps some MgO unreacted throughout the whole hydrothermal treatment. We suggest that MgO and Al2O3 be hydrated into Mg(OH)(2) and Al(OH)(3), respectively, in the initial stage for all samples. We further Suggest that in the neutral condition Mg(OH)2 be quickly dissociated to Mg2+ and OH- which then deposit on the surface of Al(OH)(3)/Al2O3 to form a M-Al pre-LDH material. Al(OH)(4)(-), ionized from Al(OH)(3) in the basic solution, deposits on the surface of Mg(OH)(2)/MgO to result in a similar MgAl pre-LDH material. Such a pre-LDH material is then well crystallized upon continuous heating via the diffusion of metal ions in the solid lattice. Such a dissociation-deposition-diffusion mechanism via two pathways has been supported by the phase composition, morphological features of crystallites, and [Mg]/[Al] ratios on the crystallite surface. and presumably applied to the general formation of LDHs with various synthetic methods. Such as coprecipitation, homogeneous preparation, and reconstruction.

Characterization of commercial double-walled carbon nanotube material : composition, structure, and heat capacity

A purified commercial double-walled carbon nanotube (DWCNT) sample was investigated by transmission electron microscopy (TEM), thermogravimetry (TG), and Raman spectroscopy. Moreover, the heat capacity of the DWCNT sample was determined by temperature-modulated differential scanning calorimetry in the range of temperature between -50 and 290 °C. The main thermo-oxidation characterized by TG occurred at 474 °C with the loss of 90 wt% of the sample. Thermo-oxidation of the sample was also investigated by high-resolution TG, which indicated that a fraction rich in carbon nanotube represents more than 80 wt% of the material. Other carbonaceous fractions rich in amorphous coating and graphitic particles were identified by the deconvolution procedure applied to the derivative of TG curve. Complementary structural data were provided by TEM and Raman studies. The information obtained allows the optimization of composites based on this nanomaterial with reliable characteristics.

Purity evaluation and influence of carbon nanotube on carbon nanotube/graphite thermal stability

High resolution thermogravimetry has been used to evaluate the carbonaceous content in a commercial sample of single-walled carbon nanotube (SWNT). The content of SWNTs in the sample was found to be at least 77mass% which was supported by images obtained with scanning and transmission electron microscopies (SEM and TEM). Furthermore, the influence of SWNT addition on the thermal stability of graphite in mixtures of SWNT/graphite at different proportions was investigated. The graphite stability decreased with the increased of SWNT content in the overall range of composition. This behavior could be due to the close contact between these carbonaceous species as determined by SEM analysis.