An efficient molecular docking using conformational space annealing

Lee, Kyoungrim,Czaplewski, Cezary,Kim, Seung-Yeon,Lee, Jooyoung John Wiley Sons, Inc. 2005 Journal of computational chemistry Vol.26 No.1

<P>Molecular docking falls into the general category of global optimization problems because its main purpose is to find the most stable complex consisting of a receptor and its ligand. Conformational space annealing (CSA), a powerful global optimization method, is incorporated with the Tinker molecular modeling package to perform molecular docking simulations of six receptor–ligand complexes (3PTB, 1ULB, 2CPP, 1STP, 3CPA, and 1PPH) from the Protein Data Bank. In parallel, Monte Carlo with the minimization (MCM) method is also incorporated into the Tinker package for comparison. The energy function, consisting of electrostatic interactions, van der Waals interactions, and torsional energy terms, is calculated using the AMBER94 all-atom empirical force field. Rigid docking simulations for all six complexes and flexible docking simulations for three complexes (1STP, 3CPA, and 1PPH) are carried out using the CSA and the MCM methods. The simulation results show that the docking procedures using the CSA method generally find the most stable complexes as well as the native-like complexes more efficiently and accurately than those using the MCM, demonstrating that CSA is a promising search method for molecular docking problems. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 78–87, 2005</P> <B>Graphic Abstract</B> <img src='wiley_img/01928651-2005-26-1-JCC20147-gra001.gif' alt='wiley_img/01928651-2005-26-1-JCC20147-gra001'>

Using quaternions to calculate RMSD

Coutsias, Evangelos A.,Seok, Chaok,Dill, Ken A. John Wiley Sons, Inc. 2004 Journal of computational chemistry Vol.25 No.15

<P>A widely used way to compare the structures of biomolecules or solid bodies is to translate and rotate one structure with respect to the other to minimize the root-mean-square deviation (RMSD). We present a simple derivation, based on quaternions, for the optimal solid body transformation (rotation-translation) that minimizes the RMSD between two sets of vectors. We prove that the quaternion method is equivalent to the well-known formula due to Kabsch. We analyze the various cases that may arise, and give a complete enumeration of the special cases in terms of the arrangement of the eigenvalues of a traceless, 4 × 4 symmetric matrix. A key result here is an expression for the gradient of the RMSD as a function of model parameters. This can be useful, for example, in finding the minimum energy path of a reaction using the elastic band methods or in optimizing model parameters to best fit a target structure. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1849–1857, 2004</P> <B>Graphic Abstract</B> <img src='wiley_img/01928651-2004-25-15-JCC20110-gra001.gif' alt='wiley_img/01928651-2004-25-15-JCC20110-gra001'>

Electrically conductive polystyrene nanocomposites incorporated with aspect ratio‐controlled silver nanowires

Kim, Jung Mock,Jang, Keon‐,Soo,Lee, Seong Jae John Wiley Sons, Inc. 2019 Journal of applied polymer science Vol.136 No.36

<P><B>ABSTRACT</B></P><P>Polymer nanocomposites consisting of electrically conductive nanofillers with high aspect ratios are widely utilized for high‐performance applications such as sensors and electronics. Silver nanowires (AgNWs) synthesized through polyol reduction have been reported to show excellent electrical conductivity, hydrophilicity, and high aspect ratios. In this study, the influence of the aspect ratios of the AgNWs on the rheological and electrical properties of the fabricated polystyrene (PS)/AgNW nanocomposites was chiefly investigated. The nanocomposites were made by combining a dispersion of AgNWs with a suspension of PS particles, followed by freeze‐drying the PS/AgNW mixture harnessing the latex technology. Scanning electron microscopy, UV–Vis spectroscopy, and thermogravimetric analysis were performed on the nanocomposites to investigate the morphological, optical, and thermal properties, respectively; in addition, X‐ray photoelectron spectroscopy was performed to examine the hydrophilic polymer poly(vinylpyrrolidone)‐capped AgNW surfaces. The rheological behavior of the nanocomposites changed from liquid‐like to solid‐like after the addition of AgNWs with high aspect ratios. The electrical percolation threshold of the AgNWs in the nanocomposites was determined by the aspect ratio of the nanofiller rather than by its length. Thus, the various properties of the PS/AgNW nanocomposites could be tuned by tailoring the aspect ratios of the AgNWs. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. <B>2019</B>, <I>136</I>, 47927.</P>

Ideal scaffold design for total ear reconstruction using a three‐dimensional printing technique

Jung, Bok Ki,Kim, Jae Yoon,Kim, Young Seok,Roh, Tai Suk,Seo, Anna,Park, Keun‐,Ho,Shim, Jin‐,Hyung,Yun, In Sik John Wiley Sons, Inc. 2019 JOURNAL OF BIOMEDICAL MATERIALS RESEARCH PART B Vol.107 No.4

<P><B>Abstract</B></P><P>Ear reconstruction using three‐dimensional (3D) printing technique has been considered as a good substitute for conventional surgery, because it can provide custom‐made 3D framework. However, there are difficulties with its application in clinical use. Researchers have reported 3D scaffolds for ear cartilage regeneration, but the designs of the 3D scaffolds were not appropriate to be used in surgery. Hence, we propose the design of an ideal 3D ear scaffold for use in ear reconstruction surgery. Facial computed tomography (CT) images of the unaffected ear were extracted using a “segmentation” procedure. The selected data were converted to a 3D model and mirrored to create a model of the affected side. The design of 3D model was modified to apply to Nagata's two‐stage surgery. Based on the 3D reconstructed model, a 3D scaffold was 3D printed using polycaprolactone. The 3D scaffold closely resembled the real cartilage framework used in current operations in terms of ear anatomy. To account for skin thickness, the 3D scaffold was made 4 mm smaller than the real ear. Furthermore, 2 mm pores were included to allow the implantation of diced cartilage to promote regeneration of the cartilage. 3D printing technology can overcome the limitations of previous auricular reconstruction methods. Further studies are required to achieve a functional and stable substitute for auricular cartilage and to extend the clinical use of the 3D‐printed construct. Additionally, the ethical and legal issues regarding the transplantation of 3D‐printed constructs and cell culture technologies using human stem cells remain to be solved. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 107B: 1295–1303, 2019.</P>

Downregulation of GFAP, TSP-1, and p53 in human glioblastoma cell line, U373MG, by IE1 protein from human cytomegalovirus

Lee, Karim,Jeon, Kipyoung,Kim, Jong-Mook,Kim, Vic Narry,Choi, Dong Hee,Kim, Seung U.,Kim, Sunyoung John Wiley & Sons, Inc. 2005 Glia Vol.51 No.1

<P>Human cytomegalovirus (HCMV) is a member of the β-herpesvirus family, which has tropism for glial cells. It was recently reported that HCMV might play important roles in the pathogenesis of malignant glioma. In this study, we investigated the effects of the HCMV IE1 protein on the gene expression profile in the human glioblastoma cell line, U373MG by employing cDNA microarray technology. Using DNA chips containing approximately 1,000 human cDNAs, RNA samples from U373MG cells stably expressing IE1 were compared with those from the control cells lacking IE1 cDNA. Fluorescence intensities of 13 genes were significantly decreased in IE1-expressing cells, while one gene was found to be upregulated. Among these 14 genes, we chose to work further on glial fibrillary acidic protein (GFAP), thrombospondin-1 (TSP-1), and p53, because of their previously known involvement in tumorigenesis. The mRNA levels of all these genes were found to be decreased in IE1-expressing glioblastoma cells by real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR) as well as Northern blot analysis. The decreased expression of these genes was also observed at protein levels as measured by immunocytochemistry or fluorescence-activated cell sorting (FACS) analysis. Our data strongly suggested that HCMV IE1 could modulate the expression of cellular genes that might play important roles in the pathogenesis of glial tumors. © 2005 Wiley-Liss, Inc.</P>

Resident microglia die and infiltrated neutrophils and monocytes become major inflammatory cells in lipopolysaccharide-injected brain

Ji, Kyung-Ae,Yang, Myung-Soon,Jeong, Hey-Kyeong,Min, Kyoung-Jin,Kang, Seung-Hee,Jou, Ilo,Joe, Eun-Hye John Wiley & Sons, Inc. 2007 Glia Vol.55 No.15

<P>Generally, it has been accepted that microglia play important roles in brain inflammation. However, recently several studies suggested possible infiltration of blood neutrophils and monocytes into the brain. To understand contribution of microglia and blood inflammatory cells to brain inflammation, the behavior of microglia, neutrophils, and monocytes was investigated in LPS (lipopolysaccharide)-injected substantia nigra pars compacta, cortex, and hippocampus of normal and/or leukopenic rats using specific markers of neutrophils (myeloperoxidase, MPO), and microglia and monocytes (ionized calcium binding adaptor molecule-1, Iba-1), as well as a general marker for these inflammatory cells (CD11b). CD11b-immunopositive (CD11b<SUP>+</SUP>) cells and Iba-1<SUP>+</SUP> cells displayed similar behavior in intact and LPS-injected brain at 6 h after the injection. Interestingly, however, CD11b<SUP>+</SUP> cells and Iba-1<SUP>+</SUP> cells displayed significantly different behavior at 12 h: Iba-1<SUP>+</SUP> cells disappeared while CD11b<SUP>+</SUP> cells became round in shape. We found that CD11b/Iba-1-double positive (CD11b<SUP>+</SUP>/Iba-1<SUP>+</SUP>) ramified microglia died within 6 h after LPS injection. The round CD11b<SUP>+</SUP> cells detected at 12 h were MPO<SUP>+</SUP>. These CD11b<SUP>+</SUP>/MPO<SUP>+</SUP> cells were not found in leukopenic rats, suggestive of neutrophil infiltration. MPO<SUP>+</SUP> neutrophils expressed inducible nitric oxide synthase, interleukin-1β, cyclooxygenase-2, and monocyte chemoattractant protein-1, but died within 18 h. CD11b<SUP>+</SUP> cells detected at 24 h appeared to be infiltrated monocytes, since these cells were once labeled with Iba-1 and were not found in leukopenic rats. Furthermore, transplanted monocytes were detectable in LPS-injected brain. These results suggest that at least a part of neutrophils and monocytes could have been misinterpreted as activated microglia in inflamed brain. © 2007 Wiley-Liss, Inc.</P>

Accelerated long‐range corrected exchange functional using a two‐gaussian operator combined with one‐parameter progressive correlation functional [LC‐BOP(2Gau)]

Song, Jong‐,Won,Hirao, Kimihiko John Wiley Sons, Inc. 2019 Journal of computational chemistry Vol.40 No.1

<P>Recently, we proposed a simple yet efficient method for the computation of a long‐range corrected (LC) hybrid scheme [LC‐DFT(2Gau)], which uses a modified two‐Gaussian attenuating operator instead of the error function for the long‐range HF exchange integral. This method dramatically reduced the computational time while maintaining the improved features of the LC density functional theory (DFT). Here, we combined an LC hybrid scheme using a two‐Gaussian attenuating operator with one‐parameter progressive correlation functional and Becke88 exchange functional with varying range‐separation parameter values [LC‐BOP(2Gau) with various <I>μ</I> values of 0.16, 0.2, 0.25, 0.3, 0.35, 0.4, and 0.42] and demonstrated that LC‐BOP(2Gau) reproduces well the thermochemical and frontier orbital energies of LC‐BOP. Additionally, we revised the scaling factors of the Gaussian multipole screening scheme for LC‐DFT(2Gau) to correspond to the angular momentum of orbitals, which decreased the energy deviations from the energy with the no‐screening scheme. © 2018 Wiley Periodicals, Inc.</P>

Fabrication and electrochemical characterization of polyimide‐derived carbon nanofibers for self‐standing supercapacitor electrode materials

Han, Nam Koo,Ryu, Ji Hyung,Park, Do Un,Choi, Jae Hak,Jeong, Young Gyu John Wiley Sons, Inc. 2019 Journal of applied polymer science Vol.136 No.32

<P><B>ABSTRACT</B></P><P>We report the electrochemical performance of aromatic polyimide (PI)‐based carbon nanofibers (CNFs), which were fabricated by electrospinning, imidization, and carbonization process of poly(amic acid) (PAA) as an aromatic PI precursor. For the purpose, PAA solution was electrospun into nanofibers, which were then converted into CNFs via one‐step (PAA‐CNFs) or two‐step heat treatment (PI‐CNFs) of imidization and carbonization. The FTIR and Raman spectra demonstrated a successful structural evolution from PAA nanofibers to PI nanofibers to CNFs at the molecular level. The SEM images revealed that the average diameter of the nanofibers decreased noticeably via imidization and carbonization, while it decreased slightly with increasing the carbonization temperature from 800 °C to 1000 °C. In case of PI‐CNF carbonized at 1000 °C, a porous structure was developed on the surface of nanofibers. The electrical conductivity of PI‐CNFs, which was even higher than that of PAA‐CNFs, increased significantly from 0.41 to 2.50 S/cm with increasing the carbonization temperature. From cyclic voltammetry and galvanostatic charge/discharge tests, PI‐CNF carbonized at 1000 °C was evaluated to have a maximum electrochemical performance of specific capacitance of ~126.3 F/g, energy density of ~12.2 Wh/kg, and power density of ~160 W/kg, in addition to an excellent operational stability. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. <B>2019</B>, <I>136</I>, 47846.</P>

Novel green composites from styrene butadiene rubber and palm oil derivatives for high performance tires

Lee, Chung Kyeong,Seo, Jin Gwan,Kim, Hyun Jun,Song, Sung Ho John Wiley Sons, Inc. 2019 Journal of applied polymer science Vol.136 No.25

<P><B>ABSTRACT</B></P><P>In rubber compounding, renewable, nontoxic, and degradable palm oil is used as a safe alternative softener or stabilizer process oil. In the tire industry, with the development of environment‐friendly “green tires,” silica has been used as a reinforcing filler for tread compounds. To make the hydrophilic silica compatible with the hydrophobic rubber matrix, the addition of amphiphilic oil is required. We, for the first time, prepared an amphiphilic palm oil derivative (PO) with hydrophobic and hydrophilic functional groups in bulk. Rubber composites prepared with the PO exhibited remarkable improvements in mechanical properties, including tensile strength, elongation, and fatigue. These improvements are attributed to the enhanced dispersion of the fillers in the rubber matrix due to the PO. Also, the mixing of PO in the rubber matrix resulted in outstanding abrasion, rebound resilience, and heat buildup properties at low loadings. We then prepared pneumatic tires with a tread composite using PO, and conducted virtual tests using a vehicle‐mounted pneumatic tire. The pneumatic tire exhibited enhanced high speed durability, dry and wet braking. The strong interfacial interactions between the silica and the rubber matrix due to the PO resulted in improved viscoelastic properties. These results show that PO is a renewable potential replacement for conventional aromatic oils in tire engineering applications. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. <B>2019</B>, <I>136</I>, 47672.</P>

Increasing the tissue thickness at implant sites using guided bone regeneration and an additional collagen matrix: Histologic observations in beagle dogs

Seo, Gi‐,Young,Thoma, Daniel Stefan,Jung, Ui‐,Won,Lee, Jung‐,Seok John Wiley Sons, Inc. 2019 JOURNAL OF BIOMEDICAL MATERIALS RESEARCH PART B Vol.107 No.3

<P><B>ABSTRACT</B></P><P><B>Objectives</B></P><P>To histologically determine the alteration in horizontal mucosal thickness at sites that received guided bone regeneration (GBR) with additional use of collagen matrix and to assess whether bone formation is affected by adding collagen matrix at GBR sites at 8 weeks of healing.</P><P><B>Materials and methods</B></P><P>Eight weeks after bilateral extraction of maxillary premolars, standardized defects were created on buccal side of edentulous ridges in four beagle dogs. One side was randomly allocated as control (biphasic calcium phosphate plus collagen membrane; GBR only), while contralateral side was allocated as test (biphasic calcium phosphate plus collagen membrane plus an additional layer of collagen matrix). Histologic observations, histomorphometric and micro‐computed tomography analyses were performed after 8 weeks.</P><P><B>Results</B></P><P>Membrane complex comprising residual collagen membrane and adjacent dense connective tissue was observed at both control and test sites. The thickness in the histologic analysis were 1.69 ± 0.23 mm (control) and 1.76 ± 0.07 mm (test) in histologic analysis and were 2.03 ± 0.26 mm (control) and 2.14 ± 0.24 mm (test) in radiographic analysis. The thickness of the membrane complex in soft‐tissue layer were 723.0 ± 241.6 μm (control) and 984.6 ± 334.4 μm (test). The percentage of new bone formation were 22.30 ± 5.92% (control) and 25.50 ± 8.08% (test). All measured outcome did not show significant differences between control and test groups.</P><P><B>Conclusion</B></P><P>The addition of collagen matrix on top of standard GBR procedure did not increase the soft tissue thickness and dense connective tissue formation at 8 weeks of healing. Bone regeneration was not affected by the addition of collagen matrix. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 107B: 741–749, 2019.</P>