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Molecular dynamics simulation starting from a lamellar crystal model of a single polyethylene chain is performed to investigate the lamellar reorganization during heating at the molecular level. It is shown that three stages are involved in the process of the reorganization: at temperatures 300 K500 K the lamella starts to melt and becomes a random coil in the end. Particularly, the thickening process is investigated in our simulations. It is found that the lamellar thickening occurs in discrete steps and is driven mainly by the van der Waal attraction between the chain segments. There are two mechanisms for the lamellar thickening. At lower temperature the thickening occurs by the sliding diffusion of adjacent chain segments, while at higher temperature the recrystallization after the partial melting of thinner stems leads to the thickening. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The Pi-class GST enzyme (GSTP1) has been extensively studied because of its potential role in disease research. However, a detailed understanding of human GSTP1*D requires an accurate structure, which has not been determined yet. We constructed a high-quality model structure of human GSTP1*D by molecular dynamics simulations and revealed the interactions between the proteins and five inhibitors including chlorambucil, ethacrynic acid, EA-glutathione conjugation and CBL-glutathione conjugation to explore the structure–function relationship. We identified several critical residues, including Phe8, Arg13, Val35, Ile104, Tyr108 and Val113. Our results revealed the specific selectivity of Phe8 and Tyr108 to the substrate. And we provied a new explanation for how does Ile104 influence the substrate binding and a hypothesis about the indirect interaction between Val113 and Tyr108. These results may illustrate the alteration of enzymatic activity in the variants of GSTP1. In addition, the influence of glutathione conjugate on ligands was observed. This work will be a good starting point for further determination of the biological role and structure-based inhibitor design of human Pi-class GST. [ABSTRACT FROM AUTHOR]

Cytochrome P450 (CYP) 7B1 is a steroid cytochrome P450 7α-hydroxylase that has been linked directly with bile salt synthesis and hereditary spastic paraplegia type 5 (SPG5). The enzyme provides the primary metabolic route for neurosteroids dehydroepiandrosterone (DHEA), cholesterol derivatives 25-hydroxycholesterol (25-HOChol), and other steroids such as 5α-androstane-3β,17β-diol (anediol), and 5α-androstene-3β,17β-diol (enediol). A series of investigations including homology modeling, molecular dynamics (MD), and automatic docking, combined with the results of previous experimental site-directed mutagenesis studies and access channels analysis, have identified the structural features relevant to the substrate selectivity of CYP7B1. The results clearly identify the dominant access channels and critical residues responsible for ligand binding. Both binding free energy analysis and total interaction energy analysis are consistent with the experimental conclusion that 25-HOChol is the best substrate. According to 20 ns MD simulations, the Phe cluster residues that lie above the active site, particularly Phe489, are proposed to merge the active site with the adjacent channel to the surface and accommodate substrate binding in a reasonable orientation. The investigation of CYP7B1-substrate binding modes provides detailed insights into the poorly understood structural features of human CYP7B1 at the atomic level, and will be valuable information for drug development and protein engineering. [ABSTRACT FROM AUTHOR]

We apply the multibody dissipative particle dynamics method to exhibit evaporation- and surface-induced morphology of diblock copolymer thin films. We find that when the interactions between A components and B components of the diblock copolymer are symmetric, it is easy to obtain a lamellar morphology perpendicular to the surface. On the contrary, if the interactions between A-blocks and B-blocks are asymmetric, it is easy to obtain a lamellar morphology parallel to the surface. Spherical morphology and disorder morphology are formed when the solvent vapour and surface effect are considered. The order parameter and the film thickness are calculated during the phase-separation process for characterising the film properties. The attractive solvent vapour increases the film thickness and impacts the film morphology of the interface. The attractive surface decreases the film thickness and impacts the film morphology near the surface. Our results are partially helpful for the control of film morphology and film thickness in such kind of materials. [ABSTRACT FROM PUBLISHER]

The extracellular signal-regulated protein kinase 2 (ERK2) is a pivotal member involving in Ras/Raf/MEK/ERK signal transduction pathway, acting as a central point where multiple signaling pathways coalesce to drive transcription. The pyrazolylpyrrole compounds as ATP competitive inhibitors of ERK2 can bind target with a special binding mode and have higher inhibitory potency than other ERK2-inhibitors. We investigated the interaction mode of ERK2-inhibitor using molecular dynamics simulation. The molecular mechanics Poisson–Boltzmann surface area approach is used to calculate the binding free energy of ERK2 with pyrazolylpyrrole inhibitors to analyze the factors of improving the affinity. The results indicated that the electrostatic interactions play the most important role in keeping the stabilization of ERK2-inhibitor. The structural analyses showed that the protein motions can be controlled by changing the structures of inhibitors; furthermore, the full use of available space in the binding site by improving the flexibilities of inhibitors and introducing hydrophobic groups can increase the inhibitory effect. [ABSTRACT FROM AUTHOR]

Human slingshot phosphatase 2 (SSH2) is one of the dual specificity protein tyrosine phosphatases, which can activate cofilin substrate by binding its phosphorylation state. Because the interaction model of SSH2 and phospho-cofilin (P-cofilin) was unknown, we obtained the complex through macromolecular docking method. The molecular dynamics studies were used to investigate the complex dynamics in an aqueous solution. To understand the binding specificity, the free energy was calculated with the molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) approach and the interaction mode in active site was analyzed. The results indicated that the interaction of the P-loop of SSH2 with phosphoserine of human P-cofilin was stabilized by molecular mechanics energy and nonpolar solvation energy components, while polar solvation energy and the entropic contributions were unfavorable for the combination of the two proteins. In addition, the electrostatic contributions were negative for the formation of the complex on the whole, but seen from the active local, the Coulomb interaction between the phosphoserine and the P-loop residues could play an important role in determining substrate specificity. [ABSTRACT FROM AUTHOR]

The heme activate protein (HAP) is a model system for understanding protein–DNA interactions and allosteric mechanisms in gene regulation. Despite the wealth of biochemical data provided by extensive mutations of HAP, the specific recognition mechanism of the target DNA by HAP has remained elusive. This paper gives the results of a study using molecular dynamics simulations performed for a single DNA fragment (USACYC7) and three protein–DNACYC7 complex crystal structures: the HAP-wt and two HAP mutants — HAP-PC7: S63G; HAP-18: S63R. Comparative molecular dynamics simulations reveal that the distributions of protein–DNA interactions recognizing the key base steps (CGC) are consistent with their transcriptional activities. Relative to the similar conformations of three bound DNA, the different flexibilities in involving DNA recognition regions: N-term Arm and Zn2Cys6 Binuclear Cluster in three HAPs may result in a variety of protein–DNA recognitions. Despite different intensities of motions, the essential dynamics (ED) analysis shows that the internal motions of three protein–DNA complexes are similar: three proteins all slide along DNA to find their target sites. Thus, under this condition, during the recognition process, the flexibility of the DNA recognizing regions (N-term Arm and Zn2Cys6 Binuclear Cluster regions) plays a crucial role in determining the abilities of protein's recognizing DNA: the higher is its flexibility, the faster it slides along the DNA to find the targeted DNA. [ABSTRACT FROM AUTHOR]

With homology-modeling techniques, molecular mechanics and molecular dynamics methods, a 3D structure model of the human inosine triphosphatase (ITPase; EC 3.6.1.19) is created and refined. This model is further assessed by Profile-3D and ProStat, which confirm that the refined model is reliable. With this model, a flexible docking study is performed, and the results indicate that Arg178, Lys19 and Glu44 are three important determinant residues in substrate binding because they have prominent interaction energies with ITP and form strong hydrogen bonds with ITP. In addition, we further find that the P32T substitution alters the α-helices of ITPase but the β-sheets are almost not changed, and the mutation induces the interaction energy between ITPase and ITP to increase, which are consistent with the conclusion predicted by Sumi et al.8 The results from the mutagenesis imply that Pro32 is vital for the catalytic activity. [ABSTRACT FROM AUTHOR]

By means of the Homology modeling and the known structure of cyannogenic β-glycosidase from white clover (1CBG, EC 3.2.1.21), we construct a 3D model of the β-primeverosidase (EC 3.2.1.149) and search for the binding site of substrate. The 3D model is then refined by using molecular mechanics (optimization and molecular dynamics) simulation. Finally, the refined model is further assessed by Profile-3D and PROCHECK, and the results showed that the final model is reliable. Furthermore, the docking of the substrates into the active site of the protein indicates that β-primeverosidase is able to hydrolyze β-primeverosides, but not act on 2-phenylethyl β-D-glucopyranoside. These results suggest that β-primeverosidase shows broad substrate specificity with respect to the disaccharide glycon moiety (subsite -2). This is consistent with the experimental observation. Thr271 and Thr415 play important roles in subsite -2 of β-primeverosidase. Our results may be helpful for further experimental investigations. [ABSTRACT FROM AUTHOR]

By means of molecular dynamics simulation, the crystallization process of the copolymer (ethylene-co-propene) with different branch distributions is studied at the molecular level. It is shown that subglobules formed at the branch sites along the copolymer chains and subsequently coalesced into a single globule and then developed to a lamellar structure in the end. This process can be considered as crystal nucleation and growth at the early stage of the copolymer crystallization. In the nucleation the branch acts as a nucleating seed and in the crystal growth the branch is rejected from the crystal region as a defect. The driving force for the relaxation process is the attractive van der Waals interaction between the chain segments. Furthermore, it is found that the branch distribution is an important factor in determining the crystallinity of the copolymer, when the comonomer composition and the molecular weight of the copolymers are fixed, as a blocky type of copolymer will show nearly unhampered crystallization and a true random copolymer will show a hindered one. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Abstract: Ethylene-responsive element (ERE) binding factors is responsible for a consensus nucleotide sequence AGCCGCC (GCC-box) binding in many important process of plant growing through gene regulation and mediating signal transduction pathways in response to environmental stress. The GCC-box binding domain (GBD) as a novel fold for DNA recognition has been analyzed by means of molecular dynamics. The simulations show that the complex of GBD–DNA trajectories show similar fluctuations in the atomic positions as uncomplexed, particularly at three β strands involving DNA binding. The calculations of entropy also affirm that GBD flexibility is basically similar for two ligation states. Further, the two complexation states present similar patterns of concerted motions, indicating that the bound DNA cannot alter GBD flexibility. It is inferred that the flexibility of GBD molecule is independent of its ligation state. So in the protein–DNA recognition, the GBD cannot be easily induced while DNA shows better flexibility. Comparison between simulations of unligated GBD and the complexed GBD (in isolation or DNA-bound) reveals intrinsic flexibilities in some certain parts of the molecule play a key role in DNA recognition. In addition, MD simulation identifies that water molecule may mediate interaction between GBD and DNA. [Copyright &y& Elsevier]

Abstract: Molecular dynamics (MD) simulations were performed for investigating the role of Gln50 in the engrailed homeodomain–DNA recognition. Employing the crystal structure of free engrailed homeodomain and homeodomain–DNA complex as a starting structure, we carried out MD simulations of: (i) the complex between engrailed homeodomain and a 20 base-pair DNA containing TAATTA core sequence; (ii) the free engrailed homeodomain. The simulations show that homeodomain flexibility does not depend on its ligation state. The engrailed homeodomain shows similar flexibility, and the recognition helix-3 shows very similar characteristic of high rigidity and limited conformational space in two complexation states. At the same time, DNA structure has also no obvious conformational fluctuations. These results preclude the possibility of the side chain of Gln50 forming direct hydrogen bonds to the core DNA bases. MD simulations confirm a few well-conserved sites for water-mediated hydrogen bonds from protein to DNA are occupied by water molecules, and Gln50 interacts with corresponding core DNA bases through water-mediated hydrogen bonds. So Gln50 plays a relatively modest role in determining the affinity and specificity of the engrailed homeodomain. In addition, the electrostatic interaction between homeodomain and phosphate backbone of the DNA is a main factor for N- and C-terminal arm becoming ordered upon DNA binding. [Copyright &y& Elsevier]

Abstract: Pyrimidine nucleoside phosphorylase (PYNP) catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway. We have built a model of a closed active conformation of the three-dimensional structure of PYNP from Bacillus subtilis. Using docking, molecular dynamics, and hybrid quantum-mechanical/molecular-mechanical methods to study the reaction mechanics between PYNP and a substrate, we identified the role of each residue in the active site during the entire catalytic process. The results indicate that the function of His82, Arg169, and Lys188 is to stabilize the uridine in a high-energy conformation by means of electrostatic interactions and that these residues are involved in catalysis. In addition, the function of Asp162 is likely to activate Lys188 for phosphorolytic catalysis through polarization effects. [Copyright &y& Elsevier]

The novel C3-like ADP-ribosyltransferase is produced by a Staphylococcus aureus strain that especially ADP-ribosylates RhoE/Rnd3 subtype proteins, and its three-dimensional (3D) structure has not known. In order to understand the catalytic mechanism, the 3D structure of the protein is built by using homology modeling based on the known crystal structure of exoenzyme C3 from Clostridium botulinum (1G24). Then the model structure is further refined by energy minimization and molecular dynamics methods. The putative nicotinamide adenine dinucleotide (NAD+)-binding pocket of exoenzyme C3Stau is determined by Binding-Site Search module. The NAD+–enzyme complex is developed by molecular dynamics simulation and the key residues involved in the combination of enzyme binding to the ligand–NAD+ are determined, which is helpful to guide the experimental realization and the new mutant designs as well. Our results indicated that the key binding-site residues of Arg48, Glu180, Ser138, Asn134, Arg85, and Gln179 play an important role in the catalysis of exoenzyme C3Stau, which is in consistent with experimental observation. [Copyright &y& Elsevier]

Cren7, a novel chromatin protein highly conserved amongcrenarchaea,plays an important role in genome packaging and gene regulation. However,the detail dynamical structural characteristic of the Cren7–DNAcomplex and the detail study of the DNA in the complex have not beendone. Focused on two specific Cren7–DNA complexes (PDB codes 3LWHand 3LWI), we applied moleculardynamics (MD) simulations at four different temperatures (300, 350,400, and 450 K) and the molecular mechanics Poisson–Boltzmannsurface area (MM-PBSA) free energy calculation at 300 and 350 K toexamine the role of Cren7 protein in enhancing the stability of DNAduplexes via protein–DNA interactions, and to study the structuraltransition in DNA. The simulation results indicate that Cren7 stabilizesDNA duplex in a certain temperature range in the binary complex comparedwith the unbound DNA molecules. At the same time, DNA molecules werefound to undergo B-like to A-like form transitions with increasedtemperature. The results of statistical analyses of the H-bond andhydrophobic contacts show that some residues have significant influenceon the structure of DNA molecules. Our work can give important informationto understand the interactions of proteins with nucleic acids andother ligands. [ABSTRACT FROM AUTHOR]

Abstract: The reaction of C2 (A3Πu) with C2H6 has been investigated at the BMC–CCSD//BB1K/6-311+G(2d,2p) level. The classical barrier height for H-abstraction reaction is calculated to be 3.32kcal/mol and the electron transfer behavior is also analyzed in detail. The rate constants are calculated by TST, CVT, and CVT/SCT over a wide temperature range 50–3000K. The results indicate: (1) variational effect is small and nonclassical reflection effect is important to the H abstraction in high temperature region; and (2) variational effect is negligible and tunneling effect cooperating with the nonclassical reflection effect makes the rate constant temperature independence in low-temperature range. The CVT/SCT rate constants are in excellent agreement with experimental values. [Copyright &y& Elsevier]

Abstract: The enediyne ring chromophore with strong DNA cleavage activity of neocarzinostatin is labile and therefore stabilization by forming the complex (carrying protein+chromophore: holo-NCS). Holo-NCS has gained much attention in clinical use as well as for drug delivery systems, but the chromophore-releasing mechanism to trigger binding to the target DNA with high affinity and producing DNA damage remain unclear. Three possible pathways were initially determined by conventional MD, essential dynamics and essential dynamics sampling. One of the paths runs along the naphthoate moiety; another runs along the amino sugar moiety; the third along the enediyne ring. Further, calculated forces and time by FPMD (force-probe molecular dynamics) suggest that the opening of the naphthoate moiety is most favorable pathway and Leu45, Phe76 and Phe78 all are key residues for chromophore release. In addition, conformational analyses indicate that the chromophore release is only local motions for the protein. [Copyright &y& Elsevier]

Abstract: Full atomic molecular dynamics simulations of three kinds of n-heptane layers on the graphite (001) surface have been performed to investigate their melting process. The melting process and the molecule conformation transition during the process are described at the molecular level. The melting mechanism is suggested by analyzing the conformation transitions during the melting process, which is divided into three stages, i.e. the decrease, the fluctuation and the disappearance of the orientation order. The bond-orientation order parameter along the x-direction, the dihedral distribution and the height distribution of the carbonic atom in the n-heptane layers show different behaviors with increasing temperature. Furthermore, the roles of dihedral and van der Waals energy in the melting process are discussed. [Copyright &y& Elsevier]

Abstract: Jasmonic acid (JA) is a plant volatile that acts as an important cellular regulator mediating diverse developmental processes and defense responses. Not only the attacked plant but also neighboring plants are affected, becoming more attractive to herbivore predators and less susceptible to invaders. The three-dimensional (3D) model of methyl jasmonate esterase (MJE), which is only responsible for methyl jasmonate (MeJA)-cleaving activity, is constructed based on the crystal structure of salicylic acid-binding protein 2 (SABP2, PDB code 1XKL) by using InsightII/Homology module, and further refined using unrestrained dynamics simulations. With the aid of understanding the molecular interactions between the natural substrate: MeJA and MJE, a 3D model of the complex MeJA–MJE is developed by molecular docking program, and the result may be helpful to explain the experimental realization and the new mutant designs as well. The results indicate that the general 3D organization of MJE is a typical α/β hydrolase superfamily and comprises a central, parallel or mixes β sheet surrounded by α helices. The catalytic residues always constitute a highly conserved triad: Ser83, Asp211, His240, which is consistent with experimental observation. In addition, the key binding-site residues of Thr107 and Leu214 play an important role in the catalysis of MJE. One important finding is that the identification of the key binding site residues of Ser83, which plays an important role in the catalysis of MJE and this is in consistent with experimental observation. The inhibitor phenylmethanesulfonyl fluoride is docked to MJE. Our results also show that His240 and His82 are important in inhibition and it may be helpful for the future inhibitor study. [Copyright &y& Elsevier]

Abstract: By means of the molecular dynamics simulation method, the miscibility of poly(3-hydroxybutyrate)/polyethylene (PHB/PE) blend has been investigated. Two glass transition temperatures of the PHB/PE are found by scrutinizing its volume–temperature curve, and this result is qualitatively in agreement with the experimental results. To further analyze the miscibility of poly(3-hydroxybutyrate)-based blends, the Flory–Huggins parameters of PHB/PE, poly(3-hydroxybutyrate)/poly(ethylene oxide) (PHB/PEO), poly(ethylene oxide)/polyethylene (PEO/PE) have been calculated via a Monte Carlo scheme, and the morphology of the PHB/PEO and the PHB/PE blend has been simulated using dissipative particle dynamics method. The time evolution of dividing interface for PHB/PEO/PE blend shows a dynamic phase separation process. All these results indicate that PHB and PEO tend to mix together, whereas PE aggregates to form PE-rich domains in the PHB/PE and PHB/PEO/PE blends. [Copyright &y& Elsevier]

Abstract: With homology modeling techniques, molecular mechanics, and molecular dynamics methods, a 3D structure model of Ndx1 is created and refined. This model is further assessed by Profile-3D and ProStat, which confirm that the refined model is reliable. With this model, a flexible docking study is performed and the result indicates that Glu46, Arg88, and Glu90 are three important determinant residues in binding, as they have strong hydrogen bonding interactions and electrostatic interactions with Ap6A. In addition, we further find that three residues, Ser38, Leu39 and Glu46, coordinate enzyme-bound Mg2+ ions in complex N–A. The Glu46 is consistent with the experimental results by Iwai et al., and the other four residues mentioned above may also play vital roles in catalysis of Ndx1. [Copyright &y& Elsevier]

Abstract: In order to understand the mechanisms of ligand binding and the interaction between the ligand and the cyclin-dependent kinase 10 (CDK10), a three-dimensional (3D) model of the CDK10 is generated based on the crystal structure of the cyclin-dependent kinase 2 (CDK2) (PDB code 1AQ1) by using InsightII/Homology module. With the aid of the molecular mechanics and molecular dynamics methods, the last refined model is obtained and is further assessed by Profile-3D and ProStat, which show that the refined model is reliable. With this model, a flexible docking study is performed and the results indicate that the Lys39 and Asp94 form hydrogen bonds and have strong nonbonding interaction with adenosine 5′-triphosphate (ATP). From the docking studies, we also suggest that the Leu141, Tyr21, and Val24 in CDK10 are three important determinant residues in binding as they have strong nonbonding interaction with ATP. The hydrogen bonding interactions also play an important role for the stability of the complex. Our results may be helpful for further experimental investigations. [Copyright &y& Elsevier]

Abstract: The three-dimensional (3D) model of the 3-hydroxykynurenine transaminase (3-HKT) is constructed based on the crystal structure of the alanine-glyoxylate aminotransferase (EC 2.6.1.44, PDB code 1VJO) by using InsightII/Homology module. With the aid of the molecular mechanics and molecular dynamics methods, the last refined model is obtained and further assessed by Profile-3D and ProStat, which confirm that the refined model is reliable. With this model, a flexible docking study is performed and the result indicates that Trp104 and Gln204 are important residues as they have strong hydrogen bonding interactions with 3-HK respectively and they will act as a vital role in catalysis of 3-HKT. The Trp104 is in good agreement with the experimental result by Li et al. From the docking studies, we also suggest that the residues of Lys205 and Pro211 in 3-HKT are two important determinant residues in binding as they have strong van der Waals contacts with the 3-HK. Our results may be helpful for further experimental investigations. [Copyright &y& Elsevier]

Abstract: GPX is a mammalian antioxidant selenoenzyme which protects biomembranes and other cellular components from oxidative damage by catalyzing the reduction of a variety of hydroperoxides (ROOH), using Glutathione (GSH) as the reducing substrate. The single-chain Fv fragment of the monoclonal antibody 2F3 (scFv2F3) can be converted into the selenium-containing Se-scFv2F3 by chemical modification of the serine. The new selenium-containing catalytic antibody Se-scFv2F3 acts as a glutathione peroxidase (GPX) mimic with high catalytic efficiency. In order to investigate which residue of scFv2F3 is converted into selenocysteine and to describe the proper reaction site of GSH to Se-scFv2F3, a three-dimensional structure of scFv2F3 is built by means of homology modeling. The 3D model is assessed by molecular dynamics (MD) simulation to determine its stability and by comparison with those of known protein structures. After the serine in the scFv2F3 is modified to selenocysteine, a catalytic antibody (abzyme) is obtained. From geometrical considerations, the solvent-accessible surface of the protein is examined. The computer-aided docking and energy minimization (EM) calculations of the abzyme–GSH complex are then carried out to explore the possible active site of the glutathione peroxidase mimic Se-scFv2F3. The structural information from the theoretically modeled complex can help us to further understand the catalytic mechanism of GPX. [Copyright &y& Elsevier]

Abstract: Molecular dynamics (MD) simulations of several polyethylene copolymer chains containing 1,2-, 1,3- or 1,4-disubstituted cyclopentane or hexamethylene structures in the main chain (with 500 CH2) are performed to investigate the influence of cyclic units on the crystallization properties of polyethylene (PE). From the isothermal relaxation process it is found that they generally collapse to a globule via a local collapse process. The copolymer chains containing 1,2-disubstituted cycloparaffin structures form more kinks and take shorter time to totally collapse into a single globule than the others. Moreover, from the morphology of the crystal structures after annealing it is found that the copolymer chains containing 1,2-disubstituted cycloparaffin structures can yield more ordered structures with cyclic units rejected to the fold surface. For the copolymer chains containing 1,3- or 1,4-disubstituted cycloparaffin, the lamellar structures are not perfect and some cyclic units are always incorporated in the crystalline phase. [Copyright &y& Elsevier]

Abstract: By means of the molecular dynamics (MD) simulation, the crystallization mechanism of 22,8-polyurethane which contains hydrogen-bond units is investigated and the results show that the crystallization process at a fixed temperature can be characterized by three stages: (1) The extended chain collapses to a globular random coil; (2) The random coil reorganizes into an ordered lamellar structure; (3) Accompanied with the segments clustering due to the hydrogen-bond formation, the lamellar develops with local defects. Two kinds of hydrogen-bond, which are formed between NH group and CN–H⋯Oetween NH group and urethane alkoxy oxygen (N–H⋯O), respectively, are found to play an important role in the crystallization process of 22,8-polyurethane. Furthermore, the effect of temperature on the crystallization is also studied by selecting three temperatures 200, 300 and 400K. The lower the crystal temperature is, the slower the crystallization rate is and the stronger the hydrogen-bonding interactions are presented. This is in harmony with the experimental results. [Copyright &y& Elsevier]

Although the GSK3/SHAGGY-like kinase is a highly conserved serine/threonine kinase implicated in many signaling pathways in eukaryotes, the lack of knowledge of its three-dimensional (3D) structure has hindered efforts to understand the binding specificities of substrate and catalytic mechanism. To understand the structure–activity relationships, the protein 3D structure was built by using homology modeling based on the known X-ray diffraction structure of Glycogen synthase kinase-3β (Gsk3β) and the model structure was further refined using unrestrained molecular dynamics simulations. The research indicates that the general 3D organization of the GSK3/SHAGGY-like kinase is a typical kinase family and comprises an N-terminal domain of β-sheet and a larger C-terminal domain mainly constituted by α-helix. In order to understand the molecular interactions between the natural substrate-ATP and GSK3/SHAGGY-like kinase, a 3D model of the complex ATP–GSK3/SHAGGY-like kinase is developed by molecular docking program, which is helpful to guide the experimental realization and the new mutant designs as well. One important finding is that the identification of the key binding-site residue of Lys69 which plays an important role in the catalysis of GSK3/SHAGGY-like kinase and this is in consistent with experimental observation. [Copyright &y& Elsevier]

By means of full atomistic molecular dynamics simulation, the solubility parameters for pure poly(3-hydroxybutyrate) and poly(ethylene oxide) are calculated and the results are in agreement with the literature values. Furthermore, in order to reveal the blend property, the volume–temperature curve of the PHB/PEO blend system (1:2 blends in terms of repeated units) is simulated by employing the united atom approximation to obtain the glass transition temperature. From the volume–temperature curve, the glass transition temperature is about 258 K, which is compared well with the experimental results. It should be pointed out that the two simulated solubility parameters are similar and there is only one glass transition of the blend system, these indicate that the studied blend system is miscible. [Copyright &y& Elsevier]

Three models (star-shaped, H-shaped, and comb-shaped polyethylenes) are used to study the crystallization behavior of low-density polyethylene at the molecular level by means of molecular dynamics simulation. It is shown that, for the three types of polyethylene corresponding to the models, the neighboring sequences of trans bonds firstly aggregate together to form local ordered domains, and then they coalesce to a lamellar structure. In the process, the branching sites are rejected to the fold surface gradually. The driving force for the relaxation process is the attractive van der Waals interaction between the chain segments. Furthermore, it is found that the number of the branch sites and the length of the branch play an important role in determining the formation of the lamellar structure. The longer the length of the branch and the fewer the number of the branch sites, the more perfect lamellar structure can be formed. [ABSTRACT FROM AUTHOR]