http://chineseinput.net/에서 pinyin(병음)방식으로 중국어를 변환할 수 있습니다.
변환된 중국어를 복사하여 사용하시면 됩니다.
Application of the multiensemble sampling to the equilibrium folding of proteins
Son, Hyeon S.,Kim, Seung-Yeon,Lee, Jooyoung,Han, Kyu-Kwang Oxford University Press 2006 Bioinformatics Vol.22 No.15
<P><B>Motivation:</B> Conventional Monte Carlo and molecular dynamics simulations of proteins in the canonical ensemble are of little use, because they tend to get trapped in states of energy local minima at low temperatures. One way to surmount this difficulty is to use a non-Boltzmann sampling method in which conformations are sampled upon a general weighting function instead of the conventional Boltzmann weighting function. The multiensemble sampling (MES) method is a non-Boltzmann sampling method that was originally developed to estimate free energy differences between systems with different potential energies and/or at different thermodynamic states. The method has not yet been applied to studies of complex molecular systems such as proteins.</P><P><B>Results:</B> MES Monte Carlo simulations of small proteins have been carried out using a united-residue force field. The proteins at several temperatures from the unfolded to the folded states were simulated in a single MC run at a time and their equilibrium thermodynamic properties were calculated correctly. The distributions of sampled conformations clearly indicate that, when going through states of energy local minima, the MES simulation did not get trapped in them but escaped from them so quickly that all the relevant parts of conformation space could be sampled properly. A two-step folding process consisting of a collapse transition followed by a folding transition is observed. This study demonstrates that the use of MES alleviates the multiple-minima problem greatly.</P><P><B>Availability:</B> Available on request from the authors</P><P><B>Contact:</B> khan@pcu.ac.kr</P><P><B>Supplementary information:</B> A FORTRAN90 code of MES algorithm for MC simulation and its sample input have been deposited as Supplementary data available at <I>Bioinformatics</I> online.</P>
Cancer-selective Mechanisms of Oncolytic Viruses
Myeongji Cho,Hyeon S. Son 서울대학교 보건환경연구소 2015 보건학논집 Vol.52 No.1
Viruses that can be used for the treatment of cancer are referred to as oncolytic viruses. These viruses selectively infect cancer cells and induce cell death through a process of viral replication, proliferation, and budding. Diverse oncolytic viruses exist, and the genetic mechanisms of their cancer-selective killing strategies vary with the genetic diversity of each virus. Therefore, accurate information on viral genes and an understanding of cancer-selective killing mechanisms are required to study the treatment of cancer using oncolytic viruses. These require the storage and utilization of large amounts of data related to oncolytic viruses and cancer and studies based on enormous data sets using computer-based bioinformatics approaches. Such resources will aid in the development of novel cancer therapeutics using oncolytic viruses by providing the scientific basis for problem solving and decision making. In this study, we discuss the anti-cancer mechanisms of oncolytic viruses, classify them into four categories, and investigate the anti-cancer activities of different viruses. In addition, we evaluate the need for interdisciplinary research on oncolytic viruses by considering future research and therapy directions based on our understanding of molecular mechanisms, genetic mechanisms, and research achievements.
Ahn, Insung,Son, Hyeon S. National Research Council 2007 Canadian journal of microbiology Vol.53 No.7
<P>To investigate the genomic patterns of influenza A virus subtypes, such as H3N2, H9N2, and H5N1, we collected 1842 sequences of the hemagglutinin and neuraminidase genes from the NCBI database and parsed them into 7 categories: accession number, host species, sampling year, country, subtype, gene name, and sequence. The sequences that were isolated from the human, avian, and swine populations were extracted and stored in a MySQL<SUP>®</SUP>database for intensive analysis. The GC content and relative synonymous codon usage (RSCU) values were calculated using JAVA codes. As a result, correspondence analysis of the RSCU values yielded the unique codon usage pattern (CUP) of each subtype and revealed no extreme differences among the human, avian, and swine isolates. H5N1 subtype viruses exhibited little variation in CUPs compared with other subtypes, suggesting that the H5N1 CUP has not yet undergone significant changes within each host species. Moreover, some observations may be relevant to CUP variation that has occurred over time among the H3N2 subtype viruses isolated from humans. All the sequences were divided into 3 groups over time, and each group seemed to have preferred synonymous codon patterns for each amino acid, especially for arginine, glycine, leucine, and valine. The bioinformatics technique we introduce in this study may be useful in predicting the evolutionary patterns of pandemic viruses.</P>
Colloidal synthesis and thermoelectric properties of La-doped SrTiO3 nanoparticles
Park, K.,Son, J.,Woo, S.,Shin, K.,Oh, M. W.,Park, S. D.,Hyeon, T. Royal Society of Chemistry 2014 Journal of Materials Chemistry A Vol.2 No.12
We describe n-type nanostructured bulk thermoelectric La-doped SrTiO3 materials produced by spark plasma sintering of chemically synthesized colloidal nanocrystals. The La doping levels could be readily controlled from 3 to 9.0 at% by varying the experimental conditions. We found that nanoscale interfaces were preserved even after the sintering process, and the thermoelectric properties of the nanostructured bulk La-doped SrTiO3 were characterized. An enhanced thermoelectric efficiency was observed and attributed to the large decrease in thermal conductivity obtained with no significant change in the Seebeck coefficient or electrical conductivity. The nanostructured bulk of the La-doped SrTiO3 exhibited a maximum ZT of similar to 0.37 at 973 K at 9.0 at% La doping, which is one of the highest values reported for doped SrTiO3. Furthermore, the materials showed high thermal stability, which is important for practical high-temperature thermoelectric applications. This report demonstrates the high potential for low-cost thermoelectric energy production using highly stable and inexpensive oxide materials.
Screen printed carbon nanotube field emitter array for lighting source application
Park, Jae-Hong,Son, Gil-Hwan,Moon, Jin-San,Han, Jae-Hee,Berdinsky, Alexander S.,Kuvshinov, D. G.,Yoo, Ji-Beom,Park, Chong-Yun,Nam, Joong-Woo,Park, Jonghwan,Lee, Chun Gyoo,Choe, Deok Hyeon American Vacuum Society 2005 JOURNAL OF VACUUM SCIENCE & TECHNOLOGY B - Vol.23 No.2
Park, J.,Kang, E.,Son, S. U.,Park, H. M.,Lee, M. K.,Kim, J.,Kim, K. W.,Noh, H.-J.,Park, J.-H.,Bae, C. J.,Park, J.-G.,Hyeon, T. WILEY-VCH Verlag 2005 Advanced Materials Vol.17 No.4
<B>Graphic Abstract</B> <P>Monodisperse spherical Ni nanoparticles with diameters of 2 nm, 5 nm, and 7 nm were synthesized from the thermal decomposition of a Ni–oleylamine complex. Ni nanocrystal superlattices were generated via the controlled evaporation of solvent (see Figure). The nanoparticles were successfully used as catalysts for the Suzuki coupling reaction, and were readily oxidized to produce NiO nanoparticles. <img src='wiley_img/09359648-2005-17-4-ADMA200400611-content.gif' alt='wiley_img/09359648-2005-17-4-ADMA200400611-content'> </P>
Analysis of evolutionary and genetic patterns in structural genes of primate lentiviruses
Cho Myeongji,Min Xianglan,Son Hyeon S. 한국유전학회 2022 Genes & Genomics Vol.44 No.7
Background: Primate lentiviruses (HIV1, HIV2, and Simian immunodeficiency virus [SIV]) cause immune deficiency, encephalitis, and infectious anemia in mammals such as cattle, cat, goat, sheep, horse, and puma. Objective: This study was designed and conducted with the main purpose of confirming the overall codon usage pattern of primate lentiviruses and exploring the evolutionary and genetic characteristics commonly or specifically expressed in HIV1, HIV2, and SIV. Methods: The gag, pol, and env gene sequences of HIV1, HIV2, and SIV were analyzed to determine their evolutionary relationships, nucleotide compositions, codon usage patterns, neutrality, selection pressure (influence of mutational pressure and natural selection), and viral adaptation to human codon usage. Results: A strong 'A' bias was confirmed in all three structural genes, consistent with previous findings regarding HIV. Notably, the ENC-GC3s plot and neutral evolution analysis showed that all primate lentiviruses were more affected by selection pressure than by mutation caused by the GC composition of the gene, consistent with prior reports regarding HIV1. The overall codon usage bias of pol was highest among the structural genes, while the codon usage bias of env was lowest. The virus groups showing high codon bias in all three genes were HIV1 and SIVcolobus. The codon adaptation index (CAI) and similarity D(A, B) values indicated that although there was a high degree of similarity to human codon usage in all three structural genes of HIV, this similarity was not caused by translation pressure. In addition, compared with HIV1, the codon usage of HIV2 is more similar to the human codon usage, but the overall codon usage bias is lower. Conclusion: The origin viruses of HIV (SIVcpz_gor and SIVsmm) exhibit greater similarity to human codon usage in the gag gene, confirming their robust adaptability to human codon usage. Therefore, HIV1 and HIV2 may have evolved to avoid human codon usage by selection pressure in the gag gene after interspecies transmission from SIV hosts to humans. By overcoming safety and stability issues, information from codon usage analysis will be useful for attenuated HIV1 vaccine development. A recoded HIV1 variant can be used as a vaccine vector or in immunotherapy to induce specific innate immune responses. Further research regarding HIV1 dinucleotide usage and codon pair usage will facilitate new approaches to the treatment of AIDS.