• Macromolecular Research
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• 제8권5호
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• pp.224-230
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• 2000

Molecular mechanics technique has been used for finding energy-minimized conformation to understand the mechanism of yielding of glassy polymers in atomistic level. As a model polymer, amor- phous isotactic polypropylene (iPP) was generated by molecular mechanics and molecular dynamics methods. The stress-strain cone was successfully obtained by using molecular mechanics technique. The torsional angle distribution showed no significant change during extension, although the torsional angles of certain bonds in polymer backbone changed more largely than other bonds. No significant change in the van der Waals interaction is observed at yielding point, whereas the torsional angle energy starts to decrease at yield strain.

• 한국기계가공학회지
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• 제8권1호
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• pp.43-47
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• 2009

Recently, an approach for nano-scale material deformation has been developed that couples the atomistic and continuum approaches using Finite Element Method (FEM) and Molecular Dynamics (MD). However, this approach still has problems to connect two approaches because of the difference of basic assumptions, continuum and atomistic modeling. To solve this problem, an alternative way is developed that connects the QuasiMolecular Dynamics (QMD) and molecular dynamics. In this paper, we suggest the way to make and validate the MD-QMD coupled model.

• Nuclear Medicine and Molecular Imaging
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• 제42권2호
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• pp.145-152
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• 2008

Nuclear medicine imaging has an unique advantage of absolute quantitation of radioactivity concentration in body. Tracer kinetic analysis has been known as an useful investigation methods in quantitative study of in-vivo physiological function. The use of nuclear medicine imaging and kinetic analysis together can provide more useful and powerful intuition in understanding biochemical and molecular phenomena in body. There have been many development and improvement in kinetic analysis methodologies, but the conventional basic concept of kinetic analysis is still essential and required for further advanced study using new radiopharmaceuticals and hybrid molecular imaging techniques. In this paper, the basic theory of kinetic analysis and imaging techniques for suppressing noise were summarized.

• 통합자연과학논문집
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• 제9권3호
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• pp.161-165
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• 2016

The p21-activated kinase-1 (PAK1) has emerged as a potential target for anticancer therapy. It is overexpressed in ovarian, breast and bladder cancers. This suggests that PAK1 may contribute to tumorigenesis. 4-azaindole derivatives are reported as potent PAK1 inhibitors. The present work deals with the molecular docking studies of 4-azaindoles with PAK1. Probable binding mode of these inhibitors has been identified by molecular modeling. Docking results indicated that hydrogen bonding interactions with Glu345 and Leu347 are responsible for governing inhibitor potency of the compounds. Additionally, Val284, Val328, Met344 and Leu396 were found to be accountable for hydrophobic interactions inside the active site of PAK1.

• Macromolecular Research
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• 제8권2호
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• pp.59-65
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• 2000

We simulated the conformational changes of polymethacrylates which have side chains with different lengths (methyl and butyl) by molecular dynamics simulation technique. Bulk states of atactic amorphous polymers relaxed at a higher temperature were generated. The chain behaviors of polymethacrylates were investigated upon varying temperatures. Molecular structural information was then obtained by characterizing radial distribution function(RDF), mean square displacement, self diffusion constant, and Connolly surfaces, among others. The estimated self diffusion constants and RDF values of PMMA and PBMA were found to be in good agreement with our expectation in view of the chain flexibility.

• BMB Reports
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• 제56권1호
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• pp.32-42
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• 2023

Heart disease is one of the major life-threatening diseases with high mortality and incidence worldwide. Several model systems, such as primary cells and animals, have been used to understand heart diseases and establish appropriate treatments. However, they have limitations in accuracy and reproducibility in recapitulating disease pathophysiology and evaluating drug responses. In recent years, three-dimensional (3D) cardiac tissue models produced using tissue engineering technology and human cells have outperformed conventional models. In particular, the integration of cell reprogramming techniques with bioengineering platforms (e.g., microfluidics, scaffolds, bioprinting, and biophysical stimuli) has facilitated the development of heart-on-a-chip, cardiac spheroid/organoid, and engineered heart tissue (EHT) to recapitulate the structural and functional features of the native human heart. These cardiac models have improved heart disease modeling and toxicological evaluation. In this review, we summarize the cell types for the fabrication of cardiac tissue models, introduce diverse 3D human cardiac tissue models, and discuss the strategies to enhance their complexity and maturity. Finally, recent studies in the modeling of various heart diseases are reviewed.

• Computers and Concrete
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• 제33권3호
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• pp.325-340
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• 2024

The growing demands for sustainable and high-performance construction materials necessitate a deep understanding of their physicochemical properties by that of these heterogeneities. This paper presents a comprehensive review of the state-of-the-art hierarchical multiscale modeling approach aimed at predicting the intricate physicochemical characteristics of construction materials. Emphasizing the heterogeneity inherent in these materials, the review briefly introduces single-scale analyses, including the ab initio method, molecular dynamics, and micromechanics, through a scale-bridging technique. Herein, the limitations of these models are also overviewed by that of effectively scale-bridging methods of length or time scales. The hierarchical multiscale model demonstrates these physicochemical properties considering chemical reactions, material defects from nano to macro scale, microscopic properties, and their influence on macroscopic events. Thereby, hierarchical multiscale modeling can facilitate the efficient design and development of next-generation construction.

• Journal of Microbiology and Biotechnology
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• 제14권4호
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• pp.881-884
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• 2004

Apoptosis inducers for cancer therapy have been studied. Among hundreds of inducers, peptide anticancer drugs have many advantages such as being not harmful to humans, high selectivity, and dependence on their structures. Naltriben (NTB) is an octapeptide consisting of DPhe-Cys-Tyr-DTrp-Orn-Thr-Pen-Thr-$NH_2$. Several NTB analogues are known. In this experiment, apoptotic activities of NTB analogues with 8 amino acids were tested using flow cytometry. The conformational study of NTB was carried out using NMR spectroscopy and molecular modeling. Here, the relationships between conformations of NTB analogues and their apoptotic effects are reported.

• BMB Reports
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• 제50권5호
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• pp.269-274
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• 2017

The biological activities of macrophage migration inhibitory factor (MIF) might be mediated through a classical receptor-mediated or non-classical endocytic pathway. JAB1 (C-Jun activation domain-binding protein-1) promotes the degradation of the tumor suppressor, p53, and the cyclin-dependent kinase inhibitor, p27. When MIF and JAB1 are bound to each other in various intracellular sites, MIF inhibits the positive regulatory effects of JAB1 on the activity of AP-1. The intestinal parasite, Anisakis simplex, has an immunomodulatory effect. The molecular mechanism of action of As-MIF and human JAB1 are poorly understood. In this study, As-MIF and hJAB1 were expressed and purified with high solubility. The structure of As-MIF and hJAB1 interaction was modeled by homology modeling based on the structure of Ace-MIF. This study provides evidence indicating that the MIF domain of As-MIF interacts directly with the MPN domain of hJAB1, and four structure-based mutants of As-MIF and hJAB1 disrupt the As-MIF-hJAB1 interaction.

• Bulletin of the Korean Chemical Society
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• 제33권8호
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• pp.2508-2512
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• 2012

Cold shock proteins (CSPs) are a family of proteins induced at low temperatures. CSPs bind to single-stranded nucleic acids through the ribonucleoprotein 1 and 2 (RNP 1 and 2) binding motifs. CSPs play an essential role in cold adaptation by regulating transcription and translation via molecular chaperones. The solution nuclear magnetic resonance (NMR) or X-ray crystal structures of several CSPs from various microorganisms have been determined, but structural characteristics of psychrophilic CSPs have not been studied. Therefore, we optimized the purification process to obtain highly pure Lm-Csp and determined the three-dimensional structure model of Lm-Csp by comparative homology modeling using MODELLER on the basis of the solution NMR structure of Bs-CspB. Lm-Csp consists of a ${\beta}$-barrel structure, which includes antiparallel ${\beta}$ strands (G4-N10, F15-I18, V26-H29, A46-D50, and P58-Q64). The template protein, Bs-CspB, shares a similar ${\beta}$ sheet structure and an identical chain fold to Lm-Csp. However, the sheets in Lm-Csp were much shorter than those of Bs-CspB. The Lm-Csp side chains, E2 and R20 form a salt bridge, thus, stabilizing the Lm-Csp structure. To evaluate the contribution of this ionic interaction as well as that of the hydrophobic patch on protein stability, we investigated the secondary structures of wild type and mutant protein (W8, F15, and R20) of Lm-Csp using circular dichroism (CD) spectroscopy. The results showed that solvent-exposed aromatic side chains as well as residues participating in ionic interactions are very important for structural stability. Further studies on the three-dimensional structure and dynamics of Lm-Csp using NMR spectroscopy are required.