Parameter optimization for the Gaussian model of protein folding

Computational models of protein folding and ligand docking are large and complex. Few systematic methods have yet been developed to optimize the parameters in such models. We describe here an iterative parameter optimization strategy that is based on minimizing a structural error measure by descent in parameter space. At the start, we know the ‘correct’ native structure that we want the model to produce, and an initial set of parameters representing the relative strengths of interactions between the amino acids. The parameters are changed systematically until the model native structure converges as closely as possible to the correct native structure. As a test, we apply this parameter optimization method to the recently developed Gaussian model of protein folding: each amino acid is represented as a bead and all bonds, covalent and noncovalent, are represented by Hooke's law springs. We show that even though the Gaussian model has continuous degrees of freedom, parameters can be chosen to cause its ground state to be identical to that of Go-type lattice models, for which the global ground states are known. Parameters for a more realistic protein model can also be obtained to produce structures close to the real native structures in the protein database.     

Immobilization of a cyclodextrin glucanotransferase (CGTase) onto polyethylene film with a carboxylic acid group and production of cyclodextrins from corn starch using CGTase‐immobilized PE film

Carboxylic acid groups were introduced onto polyethylene (PE) film by radiation‐induced graft copolymerization. Subsequently, the clodextrin glucanotransferase (CGTase) was immobilized on the PE film with a carboxylic acid group. The activity of the immobilized CGTase on PE film was in the range of 0.40–1.04 U/cm² per min. The production of cyclodextrins (CDs) from corn starch was examined using the CGTase‐immobilized PE film. The production ratios of CDs using CGTase‐immobilized PE film was in the following order: α–CD > β–CD > γ–CD. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 85: 2451–2457, 2002     

Synthesis of syndiotacticity‐rich high molecular weight poly(vinyl alcohol) by suspension polymerization of vinyl pivalate and saponification

Vinyl pivalate (VPi) was suspension‐polymerized to synthesize high molecular weight (HMW) poly(vinyl pivalate) (PVPi) with a high conversion above 95% for a precursor of syndiotacticity‐rich HMW poly(vinyl alcohol) (PVA). Also, the effects of the polymerization conditions on the conversion, molecular weight, and degree of branching (DB) of PVPi and PVA prepared by the saponification of PVPi were investigated. Bulk polymerization was slightly superior to suspension polymerization in increasing the molecular weight of PVA. On the other hand, the latter was absolutely superior to the former in increasing the conversion of the polymer, indicating that the suspension polymerization rate of VPi was faster than that of the bulk one. These effects could be explained by a kinetic order of a 2,2′‐azobis(2,4‐dimethylvaleronitrile) concentration calculated by the initial rate method. Suspension polymerization of VPi at 55°C by controlling various polymerization factors proved to be successful in preparing PVA of HMW [number‐average degree of polymerization (P_n): 8200–10,500], high syndiotactic diad content (58%), and very high yield (ultimate conversion of VPi into PVPi: 94–98%). In the case of the bulk polymerization of VPi at the same conditions, the maximum P_n and conversion of 10,700–11,800 and 32–43% were obtained, respectively. The DB was lower and the P_n was higher with PVA prepared from PVPi polymerized at lower initiator concentrations. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 88: 832–839, 2003     

Measurement and numerical simulation of three‐dimensional fiber orientation states in injection‐molded short‐fiber‐reinforced plastics

To determine three‐dimensional fiber orientation states in injection‐molded short‐fiber composites, a confocal laser scanning microscope (CLSM) is used. Since the CLSM optically sections the specimen, more than two images of the cross sections on and below the surface of the composite can be obtained. Three‐dimensional fiber orientation states can be determined by using geometric parameters of fiber images obtained from two parallel cross sections. For experiments, carbon‐fiber‐reinforced polystyrene is examined by the CLSM and geometric parameters of fibers on each cross‐sectional plane are measured by an image analysis. In order to describe fiber orientation states compactly, orientation tensors are determined at different positions of the prepared specimen. Three‐dimensional orientation states are obtained without any difficulty by determining the out‐of‐plane angles utilizing fiber images on two parallel planes acquired by the CLSM. Orientation states are different at different positions and show the shell–core structure along the thickness of the specimen. Fiber orientation tensors are predicted by a numerical analysis and the numerically predicted orientation states show good agreement with measured ones. However, some differences are found at the end of cavity. They may result from the fountain flow effects, which are not considered in the numerical analysis. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 88: 500–509, 2003     

Preparation of water‐soluble syndiotacticity‐rich high molecular weight poly(vinyl alcohol) microfibrillar fibers using copolymerization of vinyl pivalate and vinyl acetate and saponification

Water‐soluble high molecular weight (HMW) syndiotactic poly(vinyl alcohol) (s‐PVA) microfibrillar fibers were prepared by the saponification with various conditions such as amount of alkali solution, saponification temperature, and saponification concentration from copoly(vinyl pivalate (VPi)/vinyl acetate (VAc)) copolymerized using various VPi/VAc feed ratios. To produce s‐PVA microbrillar fibers having various water‐soluble temperatures for many industrial applications, the intrinsic viscosities, syndiotactic diad (S‐diad) contents, and degrees of saponification (DS)s of PVAs were finely controlled to 1.2–3.6 dL/g, 56.3–58.3%, and 91.4–98.3%, respectively. Through a series of experiments, it was found that the amount of alkali may alter the structure of the saponified polymers, primarily the DS, and the structural variation changes viscosity. That is, intrinsic viscosity was sharply decreased as the amount of alkali solution was increased. DS was increased with an increase in the amount of alkali solution. S‐diad content was increased with an increase in the VPi content. HMW s‐PVA microfibrillar fibers having S‐diad content of 56.3–58.3% prepared by the saponification of copoly(VPi/VAc) were completely soluble in water at 100°C. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 88: 1482–1487, 2003     

Poly(cytidylic acid) and poly(adenylic acid) analogues: synthesis and catalytic activity for hydrolysis of dinucleotides and nucleic acids

Poly(cytidylic acid) and poly(adenylic acid) analogues, resembling closely the structures of the natural polymers, were synthesized by the alternating cyclocopolymerization of a nucleoside derivative and acrylic anhydride, and subsequent hydrolysis. The polymers catalyzed the cleavage of dinuleotides and nucleic acids (DNA and RNA). Poly(cytidylic acid) and poly(adenylic acid) analogues accelerated the hydrolysis of GpG and TpT, respectively, faster than other dinucleotides due to the base pairing.     

Optical and surface properties of whey protein isolate coatings on plastic films as influenced by substrate,protein concentration,and plasticizer type

Composite film structures of common plastic polymers including polypropylene (PP) or poly(vinyl chloride) (PVC) with whey protein isolate (WPI) coatings may be obtained by a casting method. Optical and surface properties of the resulting WPI‐coated plastic films, as affected by protein concentration and plasticizer type, were investigated to examine the biopolymer coating effects on surface modification with polymeric substrates of opposite polarity. The measured properties involved specular gloss, color, contact angle, and critical surface energy. Regardless of the substrates, WPI‐coated films possessed excellent gloss and no color, as well as good adhesion between the coating and the substrate when an appropriate plasticizer was added to the coating formulations. The protein concentration did not significantly affect gloss of WPI‐coated plastic films. Among five plasticizers applied, sucrose conferred the most highly reflective and homogeneous surfaces to the coated films. The WPI coatings were very transparent and the coated films with various protein concentrations and plasticizers showed no noticeable changes in color. Experimental results suggest that WPI coatings formulated with a proper plasticizer can improve the visual characteristics of the polymeric substrate and enhance water wettability of the coated plastic films. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 92: 335–343, 2004     

Effect of blending polyethersulfone on the cure kinetics and physical properties of dicyanate resin

The curing behavior and thermomechanical properties of dicyanate/polyethersulfone (PES) blends were investigated. Differential scanning calorimetry (DSC) was used to study the curing behavior of the dicyanate/PES blends. A second‐order autocatalytic reaction mechanism was used to describe the cure kinetics of the blends. The reaction kinetic parameters were determined by fitting DSC conversion data to the kinetic equation. The main glass‐transition temperatures of the blends decreased with increasing PES content. Two glass‐transition temperatures indicating phase‐separated morphology of the blends were observed. The thermal decomposition behavior of the blends was measured using thermogravimetric analysis. Mechanical and electrical properties of the blends were investigated. © 2001 John Wiley & Sons, Inc. J Appl Polym Sci 82: 1952–1962, 2001     

Effect of zone drawing on the structure and properties of melt‐spun poly(trimethylene terephthalate) fiber

Melt‐spun poly(trimethylene terephthalate) (PTT) fibers were zone‐drawn and the structures and properties of the fibers were investigated in consideration of the spinning and zone‐drawing conditions. The draw ratio increased up to 4 with increasing drawing temperature to 180°C, at a maximum drawing stress of 220 MPa. Higher take‐up velocity gave lower drawability of the fiber. The PTT fiber taken up at 4000 rpm was hardly drawn, in spite of using maximum drawing stress, because a high degree of orientation had been achieved in the spinning procedure. However, an additional enhancement of birefringence was observed, indicating a further orientation of PTT molecules by zone drawing. The exotherm peak at 60°C disappeared and was shifted to a lower temperature with an increase in the take‐up velocity, which means that the orientation and crystallinity of the fiber increased. The d‐spacing of (002) plane increased with increasing take‐up velocity and draw ratio, whereas those of (010) and (001) planes decreased. In all cases, the crystal size increased with take‐up velocity and draw ratio. The cold‐drawn PTT fiber revealed a kink band structure, which disappeared as the drawing temperature was raised. The physical properties of zone‐drawn PTT fibers were improved as the draw ratio and take‐up velocity increased. © 2001 John Wiley & Sons, Inc. J Appl Polym Sci 81: 3471–3480, 2001