Dokyun Na

Dokyun Na
Chung-Ang University · School of Integrative Engineering

Ph.D

About

68
Publications
18,771
Reads
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2,236
Citations
Additional affiliations
September 2013 - present
Chung-Ang University
Position
  • Assistnat Professor
January 2012 - August 2013
University of British Columbia - Vancouver
Position
  • Research Associate
September 2008 - January 2012
Korea Advanced Institute of Science and Technology
Position
  • PostDoc Position
Education
September 2002 - February 2008
September 2000 - August 2002
Korea University
Field of study
  • Biochemistry
March 1996 - February 2000
Korea University
Field of study
  • Life science

Publications

Publications (68)
Article
Full-text available
Background G-protein coupled receptors (GPCRs) sense and transmit extracellular signals into the intracellular machinery by regulating G proteins. GPCR malfunctions are associated with a variety of signaling-related diseases, including cancer and diabetes; at least a third of the marketed drugs target GPCRs. Thus, characterization of their signalin...
Article
Full-text available
In protein biotechnology, large soluble fusion partners are widely utilized for increased yield and solubility of recombinant proteins. However, the production of additional large fusion partners poses an additional burden to the host, leading to a decreased protein yield. In this study, we identified two highly disordered short peptides that were...
Article
Full-text available
Porphyromonas gingivalis is a Gram-negative pathogenic bacterium associated with chronic periodontitis. The development of a chimeric peptide-based vaccine targeting this pathogen could be highly beneficial in preventing oral bone loss as well as other severe gum diseases. We applied a computational framework to design a multi-epitope-based vaccine...
Article
Full-text available
Since prokaryotic restriction-modification (RM) systems protect the host by cleaving foreign DNA by restriction endonucleases, it is difficult to introduce engineered plasmid DNAs into newly isolated microorganisms whose RM system is not discovered. The prokaryotes also possess methyltransferases to protect their own DNA from the endonucleases. As...
Article
Background Drug-induced liver injury (DILI) is a leading cause of drug failure, accounting for nearly 20% of drug withdrawal. Thus, there has been a great demand for in silico DILI prediction models for successful drug discovery. To date, various models have been developed for DILI prediction; however, building an accurate model for practical use i...
Article
Full-text available
Background As methane is 84 times more potent than carbon dioxide in exacerbating the greenhouse effect, there is an increasing interest in the utilization of methanotrophic bacteria that can convert harmful methane into various value-added compounds. A recently isolated methanotroph, Methylomonas sp. DH-1, is a promising biofactory platform becaus...
Article
Full-text available
Differentiation of oligodendrocytes (ODs) presents a challenge in regenerative medicine due to their role in various neurological diseases associated with dysmyelination and demyelination. Here, we designed a peptide derived from vitronectin (VN) using in silico docking simulation and examined its use as a synthetic substrate to support the differe...
Article
Full-text available
Parkinson’s disease (PD) is a movement disorder caused by progressive degeneration of the midbrain dopaminergic (mDA) neurons in the substantia nigra pars compacta (SNc). Despite intense research efforts over the past decades, the etiology of PD remains largely unknown. Here, we discovered the involvement of trophoblast glycoprotein ( Tpbg ) in the...
Article
Full-text available
AU-rich elements in 5’ untranslated region (UTR) are known to increase translation efficiency by recruiting S1 protein that facilitates the assembly of ribosomes. However, AU-rich elements also serve a binding site for Hfq protein, RNase E, etc. To investigate their roles in translation, mRNAs containing either an AU-rich element, originated from s...
Article
In the past, conventional drug discovery strategies have been successfully employed to develop new drugs, but the process from lead identification to clinical trials takes more than 12 years and costs approximately $1.8 billion USD on average. In recent times, in silico approaches have been attracting considerable interest because of their potentia...
Article
Full-text available
Aptamers are artificial nucleic acid ligands that have been employed in various fundamental studies and applications, such as biological analyses, disease diagnostics, targeted therapeutics, and environmental pollutant detection. This review focuses on the recent advances in aptamer discovery strategies that have been used to detect various chemica...
Article
Microbial bioremediation has gained attention as a cheap, efficient, and sustainable technology to manage the increasing environmental pollution. Since microorganisms in nature are not evolved to degrade pollutants, there is an increasing demand for developing safer and more efficient pollutant-scavengers for enhanced bioremediation. In this review...
Article
The ability to generate astrocytes from human pluripotent stem cells (hPSCs) offers a promising cellular model to study the development and physiology of human astrocytes. The extant methods for generating functional astrocytes required long culture periods and there remained much ambiguity on whether such paradigms follow the innate developmental...
Article
Gas therapy appears promising in treating cancer, ischemia-reperfusion injury, heart attack, and acute situations of shock. Gas therapy is also becoming a good choice in preventive medicine against dementia, reducing cancer occurrence, cardiovascular diseases, and delaying aging. On-demand gas release allows precision therapy with few risks of gas...
Article
Full-text available
In bacterial biotechnology, instead of producing functional proteins from plasmids, it is often necessary to deliver functional proteins directly into live cells for genetic manipulation or physiological modification. We constructed a library of cell-penetrating peptides (CPPs) capable of delivering protein cargo into bacteria and developed an effi...
Article
Full-text available
Background Industrial biofuels and other value-added products can be produced from metabolically engineered microorganisms. Methylomonas sp. DH-1 is a candidate platform for bioconversion that uses methane as a carbon source. Although several genetic engineering techniques have been developed to work with Methylomonas sp. DH-1, the genetic manipula...
Article
Fine control of the expression levels of proteins constitutes a major challenge in synthetic biology and metabolic engineering. However, the dependence of translation initiation on the downstream coding sequence (CDS) obscures accurate prediction of the protein expression levels from mRNA sequences. Here, we present a tunable gene-expression system...
Article
Full-text available
Background Abnormal activation of human nuclear hormone receptors disrupts endocrine systems and thereby affects human health. There have been machine learning-based models to predict androgen receptor agonist activity. However, the models were constructed based on limited numerical features such as molecular descriptors and fingerprints. Result I...
Preprint
Full-text available
Background: Industrial biofuels and other value-added products can be produced from metabolically engineered microorganisms. Methylomonas sp. DH-1 is a candidate platform for bioconversion that uses methane as a carbon source. Although several genetic engineering techniques have been developed to work with Methylomonas sp. DH-1, the genetic manipul...
Preprint
Full-text available
Background: Industrial biofuels and other value-added products can be produced from metabolically engineered microorganisms. Methylomonas sp. DH-1 is a candidate platform for bioconversion that uses methane as a carbon source. Although several genetic engineering techniques have been developed to work with Methylomonas sp. DH-1, the genetic manipul...
Article
Full-text available
The uptake of exogenous DNA materials through the cell membrane by bacteria, known as transformation, is essential for the genetic manipulation of bacteria and, thus, plays key roles in biotechnological and biological research. The efficiency of natural transformation is very low; therefore, various artificial transformation methods have been devel...
Article
Multiple etiologies of liver injury are associated with fibrosis in which the key event is the activation of hepatic stellate cells (HSCs). Although microRNAs (miRNAs) are reportedly involved in fibrogenesis, the complete array of miRNA signatures associated with the disease has yet to be elucidated. Here, deep sequencing analysis revealed that com...
Article
Bone defects are common disease requiring thorough treatments since the bone is a complex vascularized tissue that is composed of multiple cell types embedded within an intricate extracellular matrix (ECM). For past decades, tissue engineering using cells, proteins, and scaffolds has been suggested as one of the promising approaches for effective b...
Article
Full-text available
Synthetic small regulatory RNAs (sRNAs) are gene-silencing tools that can be used to tune gene expression in prokaryotes. A recent study by our group proposed rational design principles, introduced a regulatory system that may be used to implement synthetic sRNAs, and showed their utility in metabolic engineering. The regulatory system employed the...
Article
Full-text available
Protein interactions in cis that can activate or autoinhibit protein function play an important role in the fine-tuning of regulatory and signaling processes in the cell, but thus far cis-regulatory elements (CREs) in proteins have not been systematically identified and studied. Here, we introduce a computational tool that identifies intrinsically...
Article
Full-text available
Porcine circovirus type 2 (PCV2) is the primary causative agent of postweaning multisystemic wasting syndrome, which leads to serious economic losses in the pig industry worldwide. While the molecular basis of PCV2 replication and pathogenicity remains elusive, it is increasingly apparent that the microRNA (miRNA) pathway plays a key role in contro...
Article
The removal of humic acid from soil samples is of great importance for the nucleic acid based detection of pathogenic bacteria because it is one of the main enzyme (polymerase) reaction inhibitors. A simple and effective detection tool that detects pathogens in fertilized soil samples was developed here by the combination of sample preparation step...
Article
Full-text available
Communalities between large sets of genes obtained from high-throughput experiments are often identified by searching for enrichments of genes with the same Gene Ontology (GO) annotations. The GO analysis tools used for these enrichment analyses assume that GO terms are independent and the semantic distances between all parent-child terms are ident...
Article
Full-text available
The emergence of co-infections and the evolution of drug-resistant pathogens limit the utility of current therapies against infections, and developing countries in particular are facing a great challenge in combating infectious disease. Moreover, any failure to control the spread of infectious diseases would also represent a threat to developed cou...
Article
Full-text available
Candidiasis is a disease with skin rashes caused by the infectious fungus, Candida albicans, and can be potentially life-threatening, especially in immunodeficient patients. Amphotericin B (AmB) is a potent antifungal agent with a broad spectrum to treat Candidiasis, but its inherent low solubility and limited skin bioavailability have prevented it...
Article
Phenol is an industrially versatile commodity chemical and is currently produced from fossil resources. Phenol's biological production from renewable resources has been limited due to its toxicity to microorganisms. Here, we simultaneously engineered 18 Escherichia coli strains for the production of phenol by employing the strategy of synthetic reg...
Article
Full-text available
Neurodegenerative diseases (NDs) are characterized by the progressive loss of neurons in the human brain. Although the majority of NDs is sporadic, evidence is accumulating that they have a strong genetic component. Therefore, significant efforts have been made in recent years to not only identify disease-causing genes but also genes that modify th...
Article
Gene knockout experiments are often essential in functional genomics and metabolic engineering studies. However, repeated multiple gene knockout experiments are laborious, time consuming and sometimes impossible to perform for those genes that are essential for cell function. Small regulatory RNAs (sRNAs) are short noncoding RNAs in prokaryotes tha...
Data
Box plot of the distribution of the fraction of intrinsic disorder predicted from sequence of the selected protein segments. Shown here are the distribution of the fraction of predicted disorder for the selected ID segments and the selected ID segments extended by 30 amino acids on each side, respectively. The asterisk indicates that the distributi...
Data
Average number of each amino acid per complex partner in the core (a) and rim (b). The red, magenta, and grey columns represent ID segments, ID segment partner, and 3D complex protein interfaces, respectively. (TIF)
Data
The number of residues in the core and rim regions of proteins in our datasets. (TIF)
Data
Natural log of the radius of gyration (Rg) plotted against natural log of protein length (N). 52 ID segments from the literature and 3D complex proteins are represented by red squares and black triangles, respectively. The slopes of the linear fits (red and black lines, respectively) provide the scaling factors ν of 0.5 and 0.35 for ID segments and...
Data
(a) Scatter plots of change in solvent accessible surface area (SASA) against ΔΔGbind. The top, middle and bottom graphs show data points of hydrophobic, charged and salt-bridging residues of the BP in grey, red and blue circles, respectively. (b) and (c) are box plots of ΔΔGbind of hydrophobic and charged interface residues, respectively, normaliz...
Data
Electrostatic components of the binding free energy. (a) Electrostatic contribution to the desolvation free energy of binding. (b) Coulombic interaction energy of binding. (c) Total electrostatic free energy of binding. Electrostatic contributions for 27 ID complexes found in the literature with high-resolution structures are in red and 109 3D comp...
Data
Classifier performance analysis. (a) ROC curve for the Rg/N classifier. The true positive set contains complexes where one interaction partner is experimentally proven to be ID (ID complexes), and the negative set contains complexes of globular proteins from the 3D complex database (3D complexes). (b) ROC curve with disulfide-rich domains and coile...
Data
Performance of classifiers using varying scaling factors ν on the 52 ID complexes (positive set) and the 3D complex dataset (negative set). a Area under ROC curve. b Matthew's correlation coefficient. c False discovery rate. d Sensitivity. (TIF)
Data
Performance of classifiers using varying scaling factors ν on the 52 ID complexes (positive set) and the 3D complex dataset without coiled coils and disulfide-rich domains (negative set). (TIF)
Data
Residue composition of the identified ID segments (red), the 52 ID segments from our literature search that we used to evaluate the classifier (green) as well as 1150 ID protein segments taken from the DisProt database (purple) relative to 3D complex protein. (TIF)
Data
Gene ontology analysis. (a) P values for the enrichment of gene ontology annotations among the proteins harboring the selected ID segments when compared to the annotations of the proteins in the non-redundant PDB dataset. (b) Gene ontology distribution of proteins harboring the selected ID segments. (TIF)
Data
Interface-normalized electrostatic components of the binding free energy. (a) Electrostatic contribution to the desolvation free energy of binding. (b) Coulombic interaction energy of binding. (c) Total electrostatic free energy of binding. Asterisks identify distributions that are significantly different (p values<0.05; Wilcoxon test). (TIF)
Article
Full-text available
There is a growing recognition for the importance of proteins with large intrinsically disordered (ID) segments in cell signaling and regulation. ID segments in these proteins often harbor regions that mediate molecular recognition. Coupled folding and binding of the recognition regions has been proposed to confer high specificity to interactions i...
Article
Small regulatory RNAs (sRNAs) regulate gene expression in bacteria. We designed synthetic sRNAs to identify and modulate the expression of target genes for metabolic engineering in Escherichia coli. Using synthetic sRNAs for the combinatorial knockdown of four candidate genes in 14 different strains, we isolated an engineered E. coli strain (tyrR-...
Article
Full-text available
Since most of the bioavailable drugs are impermeable through the blood-brain barrier (BBB), development of a rapid and reliable permeability assay system has been a challenge in drug discovery targeting central nervous system (CNS). Here, we designed a microfluidic device to monitor the drug permeability into the CNS. Human umbilical vein endotheli...
Chapter
Microorganisms are small but efficient micro-factories for producing bulk and value-added products. Systems biology and synthetic biology advanced during the last decade are enabling us to unravel the underlying complicated intracellular and intercellular mechanisms, to comprehensively understand them as a whole, and to rationally reconstruct metab...
Article
Full-text available
Growing concerns over limited fossil resources and associated environmental problems are motivating the development of sustainable processes for the production of chemicals, fuels and materials from renewable resources. Metabolic engineering is a key enabling technology for transforming microorganisms into efficient cell factories for these compoun...
Article
Cooperative inter-species interaction is another way of evolution in nature. Such cooperation leading to mutual benefits provides a new view on the interaction of biological systems, and engineering such inter-species interaction offers an opportunity for diverse potential applications in biotechnology. Here we show a synthetic system with artifici...
Article
Full-text available
Motivation: RBSDesigner predicts the translation efficiency of existing mRNA sequences and designs synthetic ribosome binding sites (RBSs) for a given coding sequence (CDS) to yield a desired level of protein expression. The program implements the mathematical model for translation initiation described in Na et al. (Mathematical modeling of transla...
Article
Motivation: RBSDesigner predicts the translation efficiency of existing mRNA sequences and designs synthetic ribosome binding sites (RBSs) for a given coding sequence (CDS) to yield a desired level of protein expression. The program implements the mathematical model for translation initiation described in Na et al. (Mathematical modeling of transla...
Article
Hepatocytes have been used for in vitro hepatotoxicity assays because of their ability to sustain intact liver-specific functions. Here, we demonstrate a hepatotoxicity assay system using primary human hepatocytes trapped in microholes of a microfluidic device, providing a microscale in vivo liver-like environment. We performed microfluidic hepatot...
Data
List of the primers used in our experiments. The primers used to construct the expression vectors, as well as the synthetic RDS-containing mRNA sequences, are listed in this file.
Article
Full-text available
Within the emerging field of synthetic biology, engineering paradigms have recently been used to design biological systems with novel functionalities. One of the essential challenges hampering the construction of such systems is the need to precisely optimize protein expression levels for robust operation. However, it is difficult to design mRNA se...
Article
Metabolic engineering has enabled us to develop strains suitable for their use as microbial factories of chemicals and materials from renewable sources. It has recently become more powerful with the advanced in synthetic biology, which is allowing us to create novel and fine-controlled metabolic and regulatory circuits maximizing metabolic fluxes t...
Article
Although passively administered antibodies are known to suppress the humoral immune response, the mechanism is not fully understood. Here, we developed a mathematical model to better understand the suppression phenomena in mice. Using this model, we tested the generally accepted but difficult to prove "epitope masking hypothesis." To simulate the h...
Article
Full-text available
Subcellular localization is one of the key functional characteristics of proteins. An automatic and efficient prediction method for the protein subcellular localization is highly required owing to the need for large-scale genome analysis. From a machine learning point of view, a dataset of protein localization has several characteristics: the datas...
Conference Paper
Helper T(Th) cells regulate immune response by producing various kinds of cytokines in response to antigen stimulation. The regulatory functions of Th cells are promoted by their differentiation into two distinct subsets, Th1 and Th2 cells. Th1 cells are involved in inducing cellular immune response by activating cytotoxic T cells. Th2 cells trigge...
Conference Paper
Administered antibodies can suppress humoral immune response. Though there are two hypotheses explaining the suppression, such as the epitope-masking and Fc-receptor mediated suppression, the epitope-masking hypothesis has garnered more supports. To better understand how the immune suppression works and to gain a quantitative and qualitative insigh...
Conference Paper
The immune system has unique defense mechanisms such as innate, humoral and cellular immunity. These mechanisms are closely related to prevent pathogens from spreading in the host and to clear them effectively. To get a comprehensive understanding of the immune system, it is necessary to integrate the knowledge through modeling. Many immune models...
Conference Paper
Immune system has unique defense mechanisms such as innate, humoral and cellular immunity. These immunities are closely related to prevent pathogens from spreading in host and to clear them effectively. To achieve those mechanisms, particular processes, such as clonal expansion, positive and negative selection, and somatic hypermutation and so on,...
Article
The delta sleep-inducing peptides (DSIP, Trp-Ala-Gly-Gly-Asp-Ala-Ser-Gly-Glu) is an important regulatory hormone, controlling hypothalamus and pituitary functions. In the current study, an expression system was designed for the rapid and economic expression of recombinant DSIP for biophysical studies. Artificially synthesized oligonucleotides encod...