• BMB Reports
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• v.37 no.3
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• pp.304-313
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• 2004

Three-dimensional (3D) models for the 65-kDa activated Cry4A and Cry4B $\delta$-endotoxins from Bacillus thuringiensis subsp. israelensis that are specifically toxic to mosquito-larvae were constructed by homology modeling, based on atomic coordinates of the Cry1Aa and Cry3Aa crystal structures. They were structurally similar to the known structures, both derived 3D models displayed a three-domain organization: the N-terminal domain (I) is a seven-helix bundle, while the middle and C-terminal domains are primarily comprise of anti-parallel $\beta$-sheets. Circular dichroism spectroscopy confirmed the secondary structural contents of the two homology-based Cry4 structures. A structural analysis of both Cry4 models revealed the following: (a) Residues Arg-235 and Arg-203 are located in the interhelical 5/6 loop within the domain I of Cry4A and Cry4B, respectively. Both are solvent exposed. This suggests that they are susceptible to tryptic cleavage. (b) The unique disulphide bond, together with a proline-rich region within the long loop connecting ${\alpha}4$ and ${\alpha}5$ of Cry4A, were identified. This implies their functional significance for membrane insertion. (c) Significant structural differences between both models were found within domain II that may reflect their different activity spectra. Structural insights from this molecular modeling study would therefore increase our understanding of the mechanic aspects of these two closely related mosquito-larvicidal proteins.

• 한국생물공학회:학술대회논문집
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• 2003.10a
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• pp.476-476
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• 2003

• Applied Biological Chemistry
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• v.41 no.8
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• pp.568-571
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• 1998

The conformations of human insulin precursors, proinsulin and preproinsulin, are described in terms of molecular dynamics simulations. Despite the presence of the C-peptide and/or the signal peptide, molecular dynamics calculations utilizing the hydration shell model over a period of 500 ps indicate that the native conformations of the A and B chains are well conserved in both cases. These results further support the NMR spectroscopy results that the C-peptide is relatively disordered and does not influence the overall conformation of the native structure. The robustness of the native structure as demonstrated by experiment and simulation will permit future protein engineering applications, whereby the expression or purification yields can be improved upon sequence modification of the C-peptide and/or the signal peptide.

• Journal of the Semiconductor & Display Technology
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• v.10 no.3
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• pp.49-52
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• 2011

This paper shows the results of classical molecular dynamics modeling for the interaction between spherical nano abrasive and substrate in chemical mechanical polishing processes. Atomistic modeling was achieved from 3-dimensional molecular dynamics simulations using the Morse potential functions for chemical mechanical polishing. The abrasive dynamics was modeled by three cases, such as slipping, rolling, and rotating. Simulation results showed that the different dynamics of the abrasive results the different features of surfaces. The simulation concerning polishing pad, abrasive particles and the substrate has same results.

• Bulletin of the Korean Chemical Society
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• v.18 no.4
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• pp.415-424
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• 1997

Conformational flexibilities of the GlcNAc(β1,3)Gal(β)OMe are investigated through NMR spectroscopy and molecular modeling. Adiabatic energy map generated with a dielectric constant of 50 contains three local minima. All of the molecular dynamics simulations on three local minimum energy structures show fluctuations between two low energy structures, N2 at φ=80° and ψ=60° and N3 at φ=60° and ψ=-40°. We have presented adequate evidences to state that GlcNAc(β1,3)Gal(β)OMe exists in two conformationally discrete forms. Two state model of N2 and N3 conformers with a population ratio of 40:60 is used to calculate the effective cross relaxation rate and reproduces the experimental NOEs very well. Molecular dynamics simulation in conjunction with two state model proves successfully the dynamic equilibrium existed in GlcNAc(β1,3)Gal(β)OMe and can be considered as a powerful method to analyze the motional properties in the structure of carbohydrate. This observation also cautions against the indiscriminate use of a rigid model to analyze NMR data.

• Journal of the Korean Society of Combustion
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• v.2 no.1
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• pp.39-51
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• 1997

A review of probability density function(PDF) methodology and direct numerical simulation for the purpose of modeling turbulent combustion are presented in this study where particular attention is focused on the modeling problem of turbulent molecular mixing term appearing in PDF transport equation. Existing mixing models results were compared to those evaluated by direct numerical simulation in a turbulent premixed medium with finite rate chemistry in which the initial scalar field is composed of pockets of partially burnt gases to simulate autoignition. Two traditional mixing models, the least mean square estimations(LMSE) and Curl#s model are examined to see their prediction capability as well as their modeling approach. Test calculations report that the stochastically based Curl#s approach, though qualitatively demonstrates some unphysical behaviors, predicts scalar evolutions which are found to be in good agreement with statistical data of direct numerical simulation.

• Transactions of Materials Processing
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• v.21 no.6
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• pp.366-371
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• 2012

Atomistic simulations have become useful tools for exploring new insights in materials science, but the length and time scale that can be handled with atomistic simulations are seriously limiting their practical applications. In order to make meaningful quantitative predictions, atomistic simulations are necessarily combined with higher-scale modeling. The present research is thus concerned with the development of a multi-scale model and its application to the prediction of the mechanical properties of body-centered cubic(BCC) iron with an emphasis on the coupling of atomistic molecular dynamics with meso-scale discrete dislocation dynamics modeling. In order to achieve predictive multi-scale simulations, it is necessary to properly incorporate atomistic details into the meso-scale approach. This challenge is handled with the proposed hierarchical information passing strategy from atomistic to meso-scale by obtaining material properties and dislocation mobility. Finally, this fundamental and physics-based meso-scale approach is employed for quantitative predictions of the mechanical response of single crystal iron.

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.16 no.12S
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• pp.1157-1164
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• 2003

This paper shows the results of atomistic modeling for the interaction between spherical nano abrasive and substrate in chemical mechanical polishing processes. Atomistic modeling was achieved from 2-dimensional molecular dynamics simulations using the Lennard-Jones 12-6 potentials. The abrasive dynamics was modeled by three cases, such as slipping, rolling, and rotating. Simulation results showed that the different dynamics of the abrasive results the different features of surfaces. This model can be extended to investigate the 3-dimensional chemical mechanical polishing processes.

• Proceedings of the Korean Biophysical Society Conference
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• 1998.06a
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• pp.21-21
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• 1998

Since the repair efficiency of non-Watson-Crick base pairs in DNA is affected by the mismatched base-pairs and their neighbor sequences, the structural studies are necessary for the elucidation of the repair efficiency. NMR and molecular modeling studies on the DNA duplexes including AA mismatches were performed.(omitted)

• BMB Reports
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• v.41 no.6
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• pp.444-447
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• 2008

Trypanothione reductase is an important target enzyme for structure-based drug design against Leishmania. We used homology modeling to construct a three-dimensional structure of the trypanothione reductase (TR) of Leishmania infantum. The structure shows acceptable Ramachandran statistics and a remarkably different active site from glutathione reductase(GR). Thus, a specific inhibitor against TR can be designed without interfering with host (human) GR activity.