Femtosecond laser-induced cleaving of protein crystal in water solution

For precise X-ray diffraction (XRD) measurement giving the three-dimensional structure of proteins, it is important to prepare high-quality single crystals with suitable shape. As a new processing technique to obtain such protein crystals, we employed femtosecond laser-induced cleaving of protein crystal in a growth vessel containing water solution. An intact protein crystal was precisely processed without mechanical contact in its sealed growth vessel by focusing femtosecond laser pulses. We confirmed that three-dimensional processing of the crystal in its supersaturated solution was realized using multiphoton absorption and that the processing was efficiently enhanced by the cleaving behavior attributed to a photomechanical mechanism of the femtosecond laser ablation.     

Thin layers of bovine serum albumin by matrix assisted pulsed laser evaporation

Thin films of bovine serum albumin were prepared by cryogenic matrix assisted pulsed laser evaporation technique under various deposition conditions. Energy density of laser beam changed in the range 0.1-0.5 J cm⁻². Films were deposited in vacuum or in nitrogen ambient. Targets were prepared from bovine serum albumin solution in phosphate buffered physiological saline and with an addition of UV absorbers as dimethylsulphoxide, phthalic acid, or adenine. Polyethylene and silicon (1 1 1) were used as substrates. Film properties were studied with atomic force microscopy and Fourier transform infrared spectroscopy attenuated total reflection. The deposition changed native conformation of albumin, resulting in the formation of water-insoluble aggregates. Addition of laser light absorbers in target solutions did not prevent the damage of albumin structure.     

Structural class tendency of polypeptide: A new conception in predicting protein structural class

Prediction of protein domain structural classes is an important topic in protein science. In this paper, we proposed a new conception: structural class tendency of polypeptides (SCTP), which is based on the fact that a given amino acid fragment tends to be presented in certain type of proteins. The SCTP is obtained from an available training data set PDB40-B. When using the SCTP to predict protein structural classes by Intimate Sorting predictive method, we got the predictive accuracy (jackknife test) with 93.7%, 96.5%, and 78.6% for the testing data set PDB40-j, Chou&Maggiora and CHOU. These results indicate that the SCTP approach is quite encouraging and promising. This new conception provides an effective tool to extract valuable information from protein sequences.     

Excimer laser-induced crystallization of CdSe thin films

We have investigated ArF (λ=193 nm) excimer laser-induced crystallization of amorphous CdSe semiconductor thin films. The crystallization has been monitored by a related photoluminescence emission in the free-exciton and defect-band transition regions. For different irradiation conditions, we have observed formation of nanorods, up to 2 μm long, as well as the formation of arrays of CdSe nanobeads with a narrow size distribution and characteristic dimensions corresponding to λ/2 and λ/8. The successful crystallization has also been confirmed by confocal Raman spectroscopy.     

Bubble creation and collapse during excimer laser ablation of weak absorbing polymers

We present evidence suggesting that XeCl laser ablation of a weakly absorbing poly-methyl-methacrylate (PMMA) polymer, done by chemical, thermal bond breaking of the polymer chain or optical breakdown of the material, which involves plasma generation, creates a cloud of small asymmetric near the surface bubbles, which subsequently expand and aggregate during the same laser pulse duration or in subsequent pulses depending on the laser pulse energy. When a critical volume is reached each bubble collapses in a high pressure and temperature central point and rebounds ejecting a hot jet of material on the non-irradiated area of the polymer and creating craters on the surface. A characteristic bipolar pressure wave corresponding to the bubble collapse, explosion and rebound is observed. The number density of the craters on the surface is a function of the laser pulse sequence number and the laser pulse energy density.     

Derivation of extremely slow dynamics of protein motion based on entropy invariance

It is a mysterious fact that protein systems often show an extremely slow dynamics of their molecular motions with time scales much longer than nanosecond order, although their characteristic frequencies obtained by the normal mode analysis fall in much shorter temporal regions. This Letter provides a heuristic account for why and how such extremely slow modes of protein motions naturally emerge from fast molecular modes on the basis of an idea of entropy invariance in the principal component analysis.     

Distinct conformational properties determined by implicit and explicit representation of protein-solvent interactions. An analytical and computer simulation study

In the protein folding problem, solvent-mediated forces are commonly represented by intra-chain pairwise contact energy. Although this approximation has proven to be useful in several circumstances, it is limited in some other aspects of the problem. Here we show that it is possible to achieve two models to represent the chain-solvent system, one of them with implicit and other with explicit solvent, such that both reproduce the same thermodynamic results. Firstly, lattice models treated by analytical methods, were used to show that the implicit and explicitly representation of solvent effects can be energetically equivalent only if local solvent properties are time and spatially invariant. Following, applying the same reasoning used for the lattice models, two inter-consistent Monte Carlo off-lattice models for implicit and explicit solvent are constructed, being that now in the latter the solvent properties are allowed to fluctuate. Then, it is shown that the chain configurational evolution as well as the globule equilibrium conformation are significantly distinct for implicit and explicit solvent systems. Actually, strongly contrasting with the implicit solvent version, the explicit solvent model predicts: (i) a malleable globule, in agreement with the estimated large protein-volume fluctuations; (ii) thermal conformational stability, resembling the conformational heat resistance of globular proteins, in which radii of gyration are practically insensitive to thermal effects over a relatively wide range of temperatures; and (iii) smaller radii of gyration at higher temperatures, indicating that the chain conformational entropy in the unfolded state is significantly smaller than that estimated from random coil configurations. Finally, we comment on the meaning of these results with respect to the understanding of the folding process.     

Femtosecond laser ablation of aluminium

We investigate femtosecond laser ablation of aluminium using a hybrid simulation scheme. Two equations are solved simultaneously: one for the electronic system, which accounts for laser energy absorption and heat conduction, the other for the dynamics of the lattice where the ablation process takes place. For the electron-temperature a generalized heat-conduction equation is solved by applying a finite difference scheme. For the lattice properties, e.g. pressure, density or temperature, we use common molecular dynamics. Energy transfer between the subsystems is allowed by introducing an electron-phonon coupling term. This combined treatment of the electronic and atomic systems is an extension of the well known two-temperature model [Anisimov, Kapeliovich, Perel’man, Electron emission from metal surfaces exposed to ultra short laser pulses, JETP Lett. 39 (2)].     

A study of Barstar folding events using boundary value simulations

From extensive biophysical studies of protein folding, two competing mechanisms emerged: hydrophobic collapse and the framework model. Our protein of choice is Barstar—a barnase inhibitor. The approximation algorithm we used to study Barstar folding trajectories is called SDEL—stochastic difference equation in length. Using the native structure as the final boundary value and a collection of unfolded structures as the varying initial boundary value, SDEL calculates an ensemble of least action pathways between these boundaries. The results are atomically detailed folding pathways, with as many intermediate structures as you request in the input. We generated 12 pathways, starting from a structurally wide selection of unfolded conformations. Using the protein's radius of gyration as our primary reaction coordinate, we tracked H-bonds, dihedral angles, native and non-native contacts, and energy along the folding pathways. This paper will follow our findings, with special emphasis on pinpointing hydrophobic collapse as a more appropriate mechanism for Barstar. Comparison with pathway predictions for Barstar using experimental techniques will also be discussed.     

Effect of ionization on laser-induced plume self-similar expansion

The dynamics of a laser ablation plume during the first stage of its expansion, just after the termination of the laser pulse is modelled. The one-dimensional expansion of the evaporated material, considered as an ideal fluid, is governed by one-fluid Euler equations. For high energetic ions, the charge separation can be neglected and the hydrodynamics equations solved using self-similar formulation. Numerical solution is obtained, first when the laser fluence range is low enough to deal with a neutral vapor, and in a second stage, when ionization effects on the expansion are taken into account, for different material targets. As a main result, we found that the presence of ions in the evaporated gas enhances the self-similar expansion.     

Minireview: The compact phase in polymers and proteins

Proteins are linear molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed characteristics of protein structures. Here we review some recent works tackling this problem. In particular, we will show that there is a growing evidence suggesting that the compact structures of folded proteins are selected in their gross topological features based on geometry and symmetry rather than on sequence consideration. They are poised at the edge of compaction, thus accounting for their flexibility. Different aspects of protein behavior can be rationalized by studying how the energy landscape of a single chain in the marginally compact phase can be modified.     

Effect of Pulse Width and Fluence of Femtosecond Laser on Electron--Phonon Relaxation Time

The electron phonon relaxation time as functions of pulse width and fluence of femtosecond laser is studied based on the two-temperature model. The two-temperature model is solved using a finite difference method for copper target. The temperature distribution of the electron and the lattice along with space and time for a certain laser fluence is presented. The time-dependence of lattice and electron temperature of the surface for different pulse width and different laser fluence are also performed, respectively. Moreover, the variation of heat-affected zone per pulse with laser Auence is obtained. The satisfactory agreement between our numerical results and experimental data indicates that the electron-phonon relaxation time is reasonably accurate with the influences of pulse width and Auence of femtosecond laser.     

Nd:YAG Laser-aided ceramic brackets debonding: Effects on shear bond strength and enamel surface

In order to evaluate the efficiency of Nd:YAG laser-aided ceramic brackets debonding technique, both ceramic brackets and metallic brackets were bonded with orthodontic adhesive to 30 freshly extracted premolars. The specimens were divided into three groups, 10 in each, according to the brackets employed and the debonding techniques used: (1) metallic brackets with shear debonding force, (2) ceramic brackets with shear debonding force, and (3) ceramic brackets with Nd:YAG laser irradiation. The result showed that laser irradiation could diminish shear bond strength (SBS) significantly and produce the most desired ARI scores. Moreover, scanning electron microscopy investigation displayed that laser-aided technique induced little enamel scratch or loss. It was concluded that Nd:YAG laser could facilitate the debonding of ceramic brackets and diminish the amount of remnant adhesive without damaging enamel structure.     

Simplified models for vibrational energy transfer in proteins

We consider the transfer of vibrational energy in proteins and derive a simplified model for the resonant energy exchange between different vibrational modes. We use the parameters of an earlier study [K. Moritsugu, et al., Phys. Rev. Lett. 85 (2000) 3970 ] to compare our predictions with the results of the molecular dynamics simulations, and reveal an excellent agreement.     

Investigation of Chlorophyll Protein 43 and 47 Denaturation by Terahertz Time-Domain Spectroscopy

We demonstrate the applications of terahertz time-domain spectroscopy to distinguish conformation changes of the chlorophyll proteins CP43 and CP47 induced by the treatment of guanidine hydrochloride, light irradiation and heating. It is indicated that THz transmission spectroscopy can be used for monitoring protein denaturation and associated conformation change processes in a feasible and effective way.     

Metal and polymer melt jet formation by the high-power laser ablation

The laser-induced metal and polymer melt jets are studied experimentally. Two classes of physical phenomena of interest are: first, the process of explosive phase change of laser induced surface ablation and second, the hydrodynamic jetting of liquid melts ejected from a beamed spot. We focus on the dynamic link between these two distinct physical phenomena in a framework of forming and patterning of metallic and polymer jets using a high-power Nd:YAG laser. The microexplosion of ablative spot on a target first forms a pocket of hot liquid melt and then it is followed by a sudden volume change of gas-liquid mixture leading to a pressure-induced spray jet ejection into surrounding medium.     

Compositional analysis of ferroelectric films coated with carbon layer using laser-induced plasmas spectroscopy

An experimental investigation of the effect of different thickness of carbon layer coated on ferroelectric films on the atomic emission intensity using laser-induced plasmas spectroscopy technique with charge-coupled device (CCD) experimental system has been conducted. The experimental results show that the intensity of the spectra emitted with the carbon layer thickness of 15 μm is much higher than that of pure ferroelectric films. By using this best experimental condition, the atomic concentration ratios of ferroelectric films are evaluated by rationing the integrated intensities of selected spectral emission lines of the plasma produced from the films. And the experimental results show that N_La/N_Co and N_Sr/N_Co atomic concentration ratios are almost in agreement with the corresponding values obtained by traditional compositional analysis techniques of inductively coupled plasma (ICP).     

Co-ion dependence of DNA nuclease activity suggests hydrophobic cavitation as a potential source of activation energy

The source of the activation energy that allows cutting of DNA by restriction enzymes is unclear. A systematic study of the cutting efficiency of the type-II restriction endonuclease EcoRI, with varying background electrolyte ion pair and buffer reported here, shows only a modest dependence of efficiency on cation type. Surprisingly, efficiency does depend strongly on the presumed indifferent anion of the background salt. What emerges is that competition between the background salt anion and the buffer anion for the enzyme and DNA surfaces is crucial. The results are unexpected and counterintuitive from the point of view of conventional electrolyte theory. However, taken together with recent developments in surface chemistry, the results do fall into place and could also suggest a novel mechanism for enzyme activity as an alternative to metal-activated hydrolysis: microscopic cavitation in a hydrophobic pocket might be the source of activation energy. Received 19 June 2000 and Received in final form 17 October 2000     

Measurement of Binding Force between Microtubule-Associated Protein and Microtubule

Microtubule-associated proteins （MAPs） are important proteins in cells. They can regulate the organization, dynamics and function of microtubules. We measure the binding force between microtubule and a new plant MAP, i.e. AtMAP65-1, by dual-optical tweezers. The force is obtained to be 14.6 ± 3.5 pN from the data statistics and analysis. This force measurement is helpful to understand the function and mechanism of MAPs from the mechanical point of view and lays the groundwork for future measurements of the mechanical properties of other biological macro-molecules.