Biomedical subjects

Jeong-Sun Kim

Publications and source records attributed to Jeong-Sun Kim.

17 recordsLinked to original sources

PubMed2006

Construction and characterization of a pseudo-immune human antibody library using yeast surface display.

Lymphocytes from eight individuals out of 60 healthy donors, whose plasmas showed relatively higher antibody titer for a target antigen of death receptor 5 (DR5), were selected for the source of antibody genes to construct so called an anti-DR5 pseudo-immune human single-chain fragment variable (scFv) library on the yeast cell surface (approximately 2x10(6) diversity). Compared with a large nonimmune human scFv library (approximately 1x10(9) diversity), the repertoire of the pseudo-immune scFv library was significantly biased toward the target antigen, which facilitated rapid enrichments of the target-specific high affinity scFvs during selections by fluorescence activated cell sortings. Isolated scFvs, HW5 and HW6, from the pseudo-immune library showed much higher specificity and affinity for the targeted antigen than those from the nonimmune library. Our results suggest that a pseudo-immune antibody library is very efficient to isolate target-specific high affinity antibody from a relatively small sized library.

Humans↗

PubMed2006

Heavy and light chain variable single domains of an anti-DNA binding antibody hydrolyze both double- and single-stranded DNAs without sequence specificity.

Anti-DNA antibodies (Abs) are of biomedical interest because they are associated with autoimmune diseases in human and mice. Previously we isolated an anti-DNA monoclonal Ab 3D8 from an autoimmune-prone MRL-lpr/lpr mouse. Here we have characterized DNA binding kinetics and hydrolyzing activities of the recombinant single chain variable fragment (scFv) and the single variable domains of heavy chain (VH) and light chain (VL) using various single-stranded (ss) and double-stranded (ds) DNA substrates. All the Abs bound to both ds- and ssDNAs without significant preferential sequence specificity showing scFv higher affinities (KD = approximately 17-74 nm) than VH (KD = approximately 2.4-8.4 microm) and VL (KD = approximately 3.2-72 microm), and efficiently hydrolyzed both ds- and ssDNAs without sequence specificity in a Mg2+-dependent manner, except for the poor activity of 3D8 scFv for ss-(dT)40. Elucidated crystal structure-based His to Ala mutations on the complementarity determining regions of VH (His-H35 --> Ala) and/or VL (His-L94 --> Ala) of 3D8 scFv significantly inhibited the catalytic activities, indicating that the His residues are involved in the catalytic mechanism of 3D8 scFv. However, the DNA hydrolyzing activities of single domain VH and VL were not affected by the mutations, indicative of their different catalytic mechanisms from that of 3D8 scFv. Our results demonstrate single domain Abs with DNase activities for the first time, which might provide new insights into substrate recognition and catalytic mechanisms of anti-DNA Abs.

Amino Acid Substitution↗

PubMed2006

Crystal structure of the DUF16 domain of MPN010 from Mycoplasma pneumoniae.

We have determined the crystal structure of the DUF16 domain of unknown function encoded by the gene MPN010 of Mycoplasma pneumoniae at 1.8 A resolution. The crystal structure revealed that this domain is composed of two separated homotrimeric coiled-coils. The shorter one consists of 11 highly conserved residues. The sequence comprises noncanonical heptad repeats that induce a right-handed coiled-coil structure. The longer one is composed of approximately nine heptad repeats. In this coiled-coil structure, there are three distinguishable regions that confer unique structural properties compared with other known homotrimeric coiled-coils. The first part, containing one stutter, is an unusual phenylalanine-rich region that is not found in any other coiled-coil structures. The second part is a highly conserved glutamine-rich region, frequently found in other trimeric coiled-coil structures. The last part is composed of prototype heptad repeats. The phylogenetic analysis of the DUF16 family together with a secondary structure prediction shows that the DUF16 family can be classified into five subclasses according to N-terminal sequences. Based on the structural comparison with other coiled-coil structures, a probable molecular function of the DUF16 family is discussed.

Amino Acid Sequence↗

PubMed2006

Crystal structure of ScpB from Chlorobium tepidum, a protein involved in chromosome partitioning.

Structural maintenance of chromosome (SMC) proteins are essential in chromosome condensation and interact with non-SMC proteins in eukaryotes and with segregation and condensation proteins (ScpA and ScpB) in prokaryotes. The highly conserved gene in Chlorobium tepidum gi 21646405 encodes ScpB (ScpB_ChTe). The high resolution crystal structure of ScpB_ChTe shows that the monomeric structure consists of two similarly shaped globular domains composed of three helices sided by beta-strands [a winged helix-turn-helix (HTH)], a motif observed in the C-terminal domain of Scc1, a functionally related eukaryotic ScpA homolog, as well as in many DNA binding proteins.

Amino Acid Sequence↗

PubMed2006

[Experiences of being tied with drugs in the elderly women in community].

PURPOSE: This study was done to understand elderly women within a community who have used lots of drugs. METHOD: Data was collected through in-depth interviews with four elderly women from April 2001 to February 2002. Data was analyzed by Giorgi's phenomenological method(2000). RESULTS: The components in common with drug usage of elderly women were as follows: 'Awareness of the limitation of physical strength and uncertainty of life', 'Dread of a crisis situation occurring', 'Attachment and dependency on drugs', 'Expectation of a comfortable life and death', 'Prevention of family burden', and 'Pursuit of psychological comfort'. The general structure of experiences was as follows: causal factors were 'Awareness of uncertainty and limitation', 'dread of a crisis situation occurring' the results factor was 'Attachment and dependency on drugs' and the facilitating factors were 'Expectation of a comfortable life and death', 'Prevention of family burden', and 'Pursuit of psychological comfort'. The causal relation was cyclic. This structure showed a realistic adaptation pattern. CONCLUSION: This study contributed to provide fundamental data for nursing interventions for health promotion and promoting quality of life in elderly women by increasing understanding of the experiences of drugs use.

Adaptation, Psychological↗

PubMed2006

Development of e-learning multimedia contents for PBL.

The purpose of this study was to develop a PBL package for maternal and newborn care and apply e-learning multimedia contents for PBL. During the first semester of 2005, 64 Nursing students of a college were subjected to the e-learning multimedia contents for PBL. This course was blended so that part of the class sessions were held in a face to face setting and the other classes were held online. Learners' reactions and their instructional performance were measured.E-learning multimedia contents, composed of a learning contents system, PBL systems and an administrator/professor system, were developed. Ratings of their reactions as learners and of instructional performance averaged 3.3 points and 3.9 points (on a scale of 5) respectively. Some benefits of this program as reported by the learners are: the moving pictures similar to clinical situations, distinctive experience, ease of understanding, time saving, repetitive learning, etc. The nursing students reported this program was a positive experience and that it encouraged self-directed learning.

Education, Distance↗

PubMed2005

Crystal structure of a heat-inducible transcriptional repressor HrcA from Thermotoga maritima: structural insight into DNA binding and dimerization.

All cells have a defense mechanism against a sudden heat-shock stress. Commonly, they express a set of proteins that protect cellular proteins from being denatured by heat. Among them, GroE and DnaK chaperones are representative defending systems, and their transcription is regulated by a heat-shock repressor protein HrcA. HrcA repressor controls the transcription of groE and dnaK operons by binding the palindromic CIRCE element, presumably as a dimer, and the activity of HrcA repressor is modulated by GroE chaperones. Here, we report the first crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima at 2.2A resolution. The Tm_HrcA protein crystallizes as a dimer. The monomer is composed of three domains: an N-terminal winged helix-turn-helix domain (WH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. The Tm_HrcA dimer structure is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains. In the overall dimer structure, the two WH domains are exposed, but the conformation of these two domains seems to be incompatible with DNA binding. We suggest that our structure may represent an inactive form of the HrcA repressor. Structural implication on how the inactive form of HrcA may be converted to the active form by GroEL binding to a conserved C-terminal sequence region of HrcA is discussed.

Bacterial Proteins↗

PubMed2005

X-ray snapshots of peptide processing in mutants of tricorn-interacting factor F1 from Thermoplasma acidophilum.

The tricorn-interacting factor F1 of the archaeon Thermoplasma acidophilum cleaves small hydrophobic peptide products of the proteasome and tricorn protease. F1 mutants of the active site residues that are involved in substrate recognition and catalysis displayed distinct activity patterns toward fluorogenic test substrates. Crystal structures of the mutant proteins complexed with peptides Phe-Leu, Pro-Pro, or Pro-Leu-Gly-Gly showed interaction of glutamates 213 and 245 with the N termini of the peptides and defined the S1 and S1' sites and the role of the catalytic residues. Evidence was found for processive peptide cleavage in the N-to-C direction, whereby the P1' product is translocated into the S1 site. A functional interaction of F1 with the tricorn protease was observed with the inactive F1 mutant G37A. Moreover, small angle x-ray scattering measurements for tricorn and inhibited F1 have been interpreted as formation of transient and substrate-induced complexes.

Alanine↗

PubMed2005

Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications.

Type I restriction-modification enzymes are differentiated from type II and type III enzymes by their recognition of two specific dsDNA sequences separated by a given spacer and cleaving DNA randomly away from the recognition sites. They are oligomeric proteins formed by three subunits: a specificity subunit, a methylation subunit, and a restriction subunit. We solved the crystal structure of a specificity subunit from Methanococcus jannaschii at 2.4-A resolution. Two highly conserved regions (CRs) in the middle and at the C terminus form a coiled-coil of long antiparallel alpha-helices. Two target recognition domains form globular structures with almost identical topologies and two separate DNA binding clefts with a modeled DNA helix axis positioned across the CR helices. The structure suggests that the coiled-coil CRs act as a molecular ruler for the separation between two recognized DNA sequences. Furthermore, the relative orientation of the two DNA binding clefts suggests kinking of bound dsDNA and exposing of target adenines from the recognized DNA sequences.

Amino Acid Sequence↗

PubMed2005

Structural genomics of minimal organisms and protein fold space.

The initial aim of the Berkeley Structural Genomics Center is to obtain a near-complete structural complement of two minimal organisms, closely related pathogens Mycoplasma genitalium and M. pneumoniae. The former has fewer than 500 genes and the latter fewer than 700 genes. To achieve this goal, the current protein targets have been selected starting with those predicted to be most tractable and likely to yield new structural and functional information. During the past 3 years, the semi-automated structural genomics pipeline has been set up from cloning, expression, purification, and ultimately to structural determination. The results from the pipeline substantially increased the coverage of the protein fold space of M. pneumoniae and M. genitalium. Furthermore, about 1/2 of the structures of 'unique' protein sequences revealed new and novel folds, and over 2/3 of the structures of previously annotated 'hypothetical proteins' inferred their molecular functions.

Bacterial Proteins↗

PubMed2005

[Effects of a drug misuse and abuse prevention program on knowledge, attitude, and preventive behaviors related to drug misuse and abuse, and depression in low-income elderly women].

PURPOSE: This study was conducted to determine the effects of a drug misuse and abuse prevention program on knowledge, attitude, and preventive behaviors related to drug misuse and abuse, and depression in low-income elderly women in the urban area. METHOD: The design of this study was a nonequivalent control group pretest-posttest design. The subjects consisted of 26 in the experimental group and 23 in the control group. The program was performed for about 1 hour, once a week for 5 weeks. Data was analyzed by the SAS(ver.8.02) computer program, and it included descriptive statistics, Fisher's exact test, Mann-Whitney U test, Wilcoxon signed ranks test, and ANCOVA. RESULT: There were statistically significant differences in knowledge, attitude, and preventive behaviors related to drug misuse and abuse, and depression between the experimental group and the control group. CONCLUSION: This study showed that this prevention program of drug misuse and abuse is appropriate for low-income elderly women, Therefore this program is recommended as a nursing intervention strategy for the elderly.

Aged↗

PubMed2004

Crystal structure of fervidolysin from Fervidobacterium pennivorans, a keratinolytic enzyme related to subtilisin.

Structure-forming fibrous proteins like keratins, gelatins and collagens are degraded only by a few proteases as their tight packing limits access to the potential cleavage sites. To understand the keratin degradation in detail, we describe the first crystal structure of a keratin-degrading enzyme (keratinase), fervidolysin, from Fervidobacterium pennivorans as an immature form with propeptide (PD)-bound. The 1.7A resolution crystal structure shows that the protease is composed of four domains: a catalytic domain (CD), two beta-sandwich domains (SDs), and the PD domain. A structural alignment shows a distant relationship between the PD-CD substructure of fervidolysin and pro-subtilisin E. Tight binding of PD to the remaining part of the protease is mediated by hydrogen bonds along the domain surfaces and around the active cleft, and by the clamps to SD1 and SD2. The crystal structure of this multi-domain protein fervidolysin provides insights into proenzyme activation and the role of non-catalytic domains, suggesting a functional relationship to the fibronectin (FN)-like domains of the human promatrix metalloprotease-2 (proMMP-2) that degrades the fibrous polymeric substrate gelatin.

Bacterial Proteins↗

PubMed2004

Uncertainty and its antecedents in patients with atrial fibrillation.

The aim of this descriptive, correlational, and cross-sectional survey was to explore uncertainty in patients with atrial fibrillation and to examine the relationships between uncertainty and its antecedents, including education, social support, and perceived seriousness of illness in patients newly diagnosed with atrial fibrillation. The theoretical framework of the study was Mishel's middle-range nursing theory of uncertainty in illness. A convenience sample of 81 participants recruited from two academic medical centers over 10 months was interviewed. Uncertainty was moderately high in patients with atrial fibrillation compared to other clinical populations. Among antecedents of uncertainty, higher education was significantly associated with less uncertainty (beta = -.21 to -.25). Except for tangible support, persons with greater social supports perceived less uncertainty (beta= -.25 to -.27), and individuals with greater perceived seriousness of illness reported greater uncertainty (beta= .30 to .33).

Academic Medical Centers↗

PubMed2004

[A study on depression, stress, and social support in adult women].

PURPOSE: This study was conducted to examine the relationship among Depression, Stress, and Social support in Korean Adult Women. METHOD: The subjects of this study consisted of 2,503 Korean Adult Women from 20 to 64 years. The data was collected through personal interviews from March to May of 2001 using questionnaires. The data was analyzed by the SPSS(ver.10.0) computer program, and it included descriptive statistics, t-test, one way ANOVA, the pearson correlation coefficient, and Stepwise multiple regression. RESULT: The level of depression, stress, and social support were 16.22 for depression, 27.43 for stress, and 87.48 for social support. There was a significant difference in social support according to residence area, age, level of education, marital status, type of family, religion, income, and job. There was a significant positive correlation between stress and depression, a significant negative correlation between stress and social support, and social support and depression. Stress and social support were significant predictors (29.6%) of depression. CONCLUSION: This study showed that thorough nursing assessment of variables related to social support is needed for development of nursing intervention strategies. Further studies need to be conducted for group comparisons according to the life cycle of Korean women.

Adult↗

PubMed2004

[A study on health concern, self-rated health, health status, and health promotion behavior of elderly women in urban area].

PURPOSE: This study was conducted to examine the relationship among health concern, self-rated health, health status, and health promotion behavior of elderly women in urban areas. METHOD: The subjects of this study consisted of 271 Korean elderly women over 65 years. The data was collected through personal interviews using questionnaires from March to May of 2003. The data was analyzed by the SPSS (ver.10.0) computer program, and it included descriptive statistics, t-test, one way ANOVA, and the pearson correlation coefficient. RESULT: There was a significant positive correlation between self-rated health and health status. Health promotion behavior related to all health concerns, self-rated health, and health status. CONCLUSION: This study showed that strategies of elderly care intervention to put in practice health promoting behavior is needed to improve quality of life in elderly women. In addition, health education appropriate for health maintenance and health promotion must be done for daily living to maintain well-being for the rest of their lives.

Aged↗

PubMed2002

Structures of the tricorn-interacting aminopeptidase F1 with different ligands explain its catalytic mechanism.

F1 is a 33.5 kDa serine peptidase of the alpha/beta-hydrolase family from the archaeon Thermoplasma acidophilum. Subsequent to proteasomal protein degradation, tricorn generates small peptides, which are cleaved by F1 to yield single amino acids. We have solved the crystal structure of F1 with multiwavelength anomalous dispersion (MAD) phasing at 1.8 A resolution. In addition to the conserved catalytic domain, the structure reveals a chiefly alpha-helical domain capping the catalytic triad. Thus, the active site is accessible only through a narrow opening from the protein surface. Two structures with molecules bound to the active serine, including the inhibitor phenylalanyl chloromethylketone, elucidate the N-terminal recognition of substrates and the catalytic activation switch mechanism of F1. The cap domain mainly confers the specificity for hydrophobic side chains by a novel cavity system, which, analogously to the tricorn protease, guides substrates to the buried active site and products away from it. Finally, the structure of F1 suggests a possible functional complex with tricorn that allows efficient processive degradation to free amino acids for cellular recycling.

Amino Acid Sequence↗

PubMedDate not supplied

Structural basis for the processive protein degradation by tricorn protease.

Cell survival critically depends on the efficient use of available resources. This includes both the clearance and the recycling of those protein components that have become futile or defective. Several proteins sequentially accomplish this complex task. The proteasome serves as an initial protein shredder and generates peptides of 7-12 amino acids in length. In general, these products are useless burden to the cell and need further processing. A few years ago, a proteolytic system was identified in the model organism Thermoplasma acidophilum which indeed performs this processing [Tamura et al., Science 274 (1996), 1385-1389]. The hexameric core protein of this modular system, referred to as tricorn protease, is a 720 kDa protease which is able to assemble further into a giant icosahedral capsid, as determined by electron microscopy. Recently, we determined the crystal structure of the tricorn core particle at 2.0 A resolution [Brandstetter et al., Nature 414 (2001), 466-469]. Here we describe the structural and mechanistic basis for tricorn's processive degradation mode, including a novel electrostatic substrate-to-product sink, and suggest how further components might interact with the tricorn protease to complete the cellular waste recycling process.

Archaeal Proteins↗