Biomedical subjects

Sangho Lee

Publications and source records attributed to Sangho Lee.

14 recordsLinked to original sources

PubMed2006

Ubiquitin-binding domains.

The covalent modification of proteins by ubiquitination is a major regulatory mechanism of protein degradation and quality control, endocytosis, vesicular trafficking, cell-cycle control, stress response, DNA repair, growth-factor signalling, transcription, gene silencing and other areas of biology. A class of specific ubiquitin-binding domains mediates most of the effects of protein ubiquitination. The known membership of this group has expanded rapidly and now includes at least sixteen domains: UBA, UIM, MIU, DUIM, CUE, GAT, NZF, A20 ZnF, UBP ZnF, UBZ, Ubc, UEV, UBM, GLUE, Jab1/MPN and PFU. The structures of many of the complexes with mono-ubiquitin have been determined, revealing interactions with multiple surfaces on ubiquitin. Inroads into understanding polyubiquitin specificity have been made for two UBA domains, whose structures have been characterized in complex with Lys48-linked di-ubiquitin. Several ubiquitin-binding domains, including the UIM, CUE and A20 ZnF (zinc finger) domains, promote auto-ubiquitination, which regulates the activity of proteins that contain them. At least one of these domains, the A20 ZnF, acts as a ubiquitin ligase by recruiting a ubiquitin-ubiquitin-conjugating enzyme thiolester adduct in a process that depends on the ubiquitin-binding activity of the A20 ZnF. The affinities of the mono-ubiquitin-binding interactions of these domains span a wide range, but are most commonly weak, with Kd>100 microM. The weak interactions between individual domains and mono-ubiquitin are leveraged into physiologically relevant high-affinity interactions via several mechanisms: ubiquitin polymerization, modification multiplicity, oligomerization of ubiquitinated proteins and binding domain proteins, tandem-binding domains, binding domains with multiple ubiquitin-binding sites and co-operativity between ubiquitin binding and binding through other domains to phospholipids and small G-proteins.

Animals↗

PubMed2006

Permeability of collapsed cakes formed by deposition of fractal aggregates upon membrane filtration.

We have investigated, theoretically, the physical properties of cake layers formed from aggregates to obtain a better understanding of membrane systems used in conjunction with coagulation/flocculation pretreatment. We developed a model based on fractal theory and incorporated a cake collapse effect to predict the porosity and permeability of the cake layers. The floc size, fractal dimension, and transmembrane pressure were main parameters that we used in these model calculations. We performed experiments using a batch cell device and a confocal laser-scanning microscope to verify the predicted specific cake resistances and porosities under various conditions. Based on the results of the model, the reduction in inter-aggregate porosity is more important than that in intra-aggregate porosity during the cake collapsing process. The specific cake resistance decreases upon increasing the aggregate size and decreasing the fractal dimensions. The modeled porosities and specific cake resistances of the collapsed cake layer agreed reasonably well with those obtained experimentally.

Filtration↗

PubMed2006

Structural and functional organization of the ESCRT-I trafficking complex.

The endosomal sorting complex required for transport (ESCRT) complexes are central to receptor downregulation, lysosome biogenesis, and budding of HIV. The yeast ESCRT-I complex contains the Vps23, Vps28, and Vps37 proteins, and its assembly is directed by the C-terminal steadiness box of Vps23, the N-terminal half of Vps28, and the C-terminal half of Vps37. The crystal structures of a Vps23:Vps28 core subcomplex and the Vps23:Vps28:Vps37 core were solved at 2.1 and 2.8 A resolution. Each subunit contains a structurally similar pair of helices that form the core. The N-terminal domain of Vps28 has a hydrophobic binding site on its surface that is conformationally dynamic. The C-terminal domain of Vps28 binds the ESCRT-II complex. The structure shows how ESCRT-I is assembled by a compact core from which the Vps23 UEV domain, the Vps28 C domain, and other domains project to bind their partners.

Amino Acid Motifs↗

PubMed2006

Structural basis for ubiquitin recognition and autoubiquitination by Rabex-5.

Rabex-5 is an exchange factor for Rab5, a master regulator of endosomal trafficking. Rabex-5 binds monoubiquitin, undergoes covalent ubiquitination and contains an intrinsic ubiquitin ligase activity, all of which require an N-terminal A20 zinc finger followed immediately by a helix. The structure of the N-terminal portion of Rabex-5 bound to ubiquitin at 2.5-A resolution shows that Rabex-5-ubiquitin interactions occur at two sites. The first site is a new type of ubiquitin-binding domain, an inverted ubiquitin-interacting motif, which binds with approximately 29-microM affinity to the canonical Ile44 hydrophobic patch on ubiquitin. The second is a diaromatic patch on the A20 zinc finger, which binds with approximately 22-microM affinity to a polar region centered on Asp58 of ubiquitin. The A20 zinc-finger diaromatic patch mediates ubiquitin-ligase activity by directly recruiting a ubiquitin-loaded ubiquitin-conjugating enzyme.

Amino Acid Sequence↗

PubMed2005

Multiple mutations contribute to repression by the v-Erb A oncoprotein.

The v-Erb A oncoprotein of avian erythroblastosis virus is derived from c-Erb A, a hormone-activated transcription factor. Notably, v-Erb A has sustained multiple mutations relative to c-Erb A and functions as a constitutive transcriptional repressor. We report here an analysis of the contributions of these different mutations to v-Erb A function. Our experiments demonstrate that two amino-acid differences between v-Erb A and c-Erb A, located in the 'I-box,' alter the dimerization properties of the viral protein, resulting in more stable homodimer formation, increased corepressor binding, and increased target gene repression. An additional amino-acid difference between v- and c-Erb A, located in helix 3 of the hormone binding domain, renders corepressor binding by the viral protein more resistant to release by thyroid hormone. Finally, we report that a C-terminal truncation in v-Erb A not only inhibits exchange of corepressor and coactivator, as previously noted, but also permits v-Erb A to recruit both SMRT and N-CoR corepressors, whereas c-Erb A is selective for N-CoR. The latter two mutations in v-Erb A also impair its ability to suppress c-Jun function in response to T3 hormone. We propose that the acquisition of oncogenic potential by the v-Erb A protein was a multistep process involving a series of mutations that alter the transcriptional repressive properties of the viral protein through multiple mechanisms.

Animals↗

PubMed2005

Structural mechanism for ubiquitinated-cargo recognition by the Golgi-localized, gamma-ear-containing, ADP-ribosylation-factor-binding proteins.

The Golgi-localized, gamma-ear-containing, Arf (ADP-ribosylation factor)-binding (GGA) proteins are clathrin adaptors that mediate the sorting of transmembrane-cargo molecules at the trans-Golgi network and endosomes. Cargo proteins can be directed into the GGA pathway by at least two different types of sorting signals: acidic cluster-dileucine motifs and covalent modification by ubiquitin. The latter modification is recognized by the GGAs through binding to their GAT [GGA and TOM (target of Myb)] domain. Here we report the crystal structure of the GAT domain of human GGA3 in a 1:1 complex with ubiquitin at 2.8-A resolution. Ubiquitin binds to a hydrophobic and acidic patch on helices alpha1 and alpha2 of the GAT three-helix bundle that includes Asn-223, Leu-227, Glu-230, Met-231, Asp-244, Glu-246, Leu-247, Glu-250, and Leu-251. The GAT-binding surface on ubiquitin is a hydrophobic patch centered on Ile-44 that is also responsible for binding most other ubiquitin effectors. The ubiquitin-binding site observed in the crystal is distinct from the Rabaptin-5-binding site on helices alpha2 and alpha3 of the GAT domain. Mutational analysis and modeling of the ubiquitin-Rabaptin-5-GAT ternary complex indicates that ubiquitin and Rabaptin-5 can bind to the GAT domain at two different sites without any steric conflict. This ability highlights the GAT domain as a hub for interactions with multiple partners in trafficking.

ADP-Ribosylation Factors↗

PubMed2005

Heterodimers of retinoic acid receptors and thyroid hormone receptors display unique combinatorial regulatory properties.

Nuclear receptors are ligand-regulated transcription factors that regulate key aspects of metazoan development, differentiation, and homeostasis. Nuclear receptors recognize target genes by binding to specific DNA recognition sequences, denoted hormone response elements (HREs). Many nuclear receptors can recognize HREs as either homodimers or heterodimers. Retinoid X receptors (RXRs), in particular, serve as important heterodimer partners for many other nuclear receptors, including thyroid hormone receptors (TRs), and RXR/TR heterodimers have been proposed to be the primary mediators of target gene regulation by T3 hormone. Here, we report that the retinoic acid receptors (RARs), a distinct class of nuclear receptors, are also efficient heterodimer partners for TRs. These RAR/TR heterodimers form with similar affinities as RXR/TR heterodimers on an assortment of consensus and natural HREs, and preferentially assemble with the RAR partner 5' of the TR moiety. The corepressor and coactivator recruitment properties of these RAR/TR heterodimers and their transcriptional activities in vivo are distinct from those observed with the corresponding RXR heterodimers. Our studies indicate that RXRs are not unique in their ability to partner with TRs, and that RARs can also serve as robust heterodimer partners and combinatorial regulators of T3-modulated gene expression.

Animals↗

PubMed2005

Critical operational parameters for zero sludge production in biological wastewater treatment processes combined with sludge disintegration.

Mathematical models were developed to elucidate the relationships among process control parameters and the effect of these parameters on the performance of anoxic/oxic biological wastewater processes combined with sludge disintegrators (A/O-SD). The model equations were also applied for analyses of activated sludge processes hybrid with sludge disintegrators (AS-SD). Solubilization ratio of sludge in the sludge disintegrator, alpha, hardly affected sludge reduction efficiencies if the biomass was completely destructed to smaller particulates. On the other hand, conversion efficiency of non-biodegradable particulates to biodegradable particulates, beta, significantly affected sludge reduction efficiencies because beta was directly related to the accumulation of non-biodegradable particulates in bioreactors. When 30% of sludge in the oxic tank was disintegrated everyday and beta was 0.5, sludge reduction was expected to be 78% and 69% for the A/O-SD and AS-SD processes, respectively. Under this condition, the sludge disintegration number (SDN), which is the amount of sludge disintegrated divided by the reduced sludge, was calculated to be around 4. Due to the sludge disintegration, live biomass concentration decreased while other non-biodegradable particulates concentration increased. As a consequence, the real F/M ratio was expected to be much higher than the apparent F/M. The effluent COD was maintained almost constant for the range of sludge disintegration rate considered in this study. Nitrogen removal efficiencies of the A/O-SD process was hardly affected by the sludge disintegration until daily sludge disintegration reaches 40% of sludge in the oxic tank. Above this level of sludge disintegration, autotrophic biomass concentration decreases overly and TKN in the effluent increases abruptly in both the A/O-SD and AS-SD processes. Overall, the trends of sludge reduction and effluent quality according to operation parameters matched well with experimental results found in literatures.

Biodegradation, Environmental↗

PubMed2005

Association between the GNB3 polymorphism and blood pressure in young Korean men.

PURPOSE: The purpose of the current study was to investigate the associations between the GNB3 C825T polymorphism, body fatness and fitness, and blood pressure in a sample of young Korean men. METHODS: A total of 282 apparently healthy Korean men (nonobese N = 152, obese N = 130) aged 19-33 yr participated in the study. Body fatness and blood pressure were measured by using standardized protocols. The GNB3 C825T was genotyped by using polymerase chain reaction with restriction fragment length polymorphism. RESULTS: Univariate analyses of variance and Bonferroni post hoc tests showed that in the obese group only, TT homozygotes had a lower VO2max (P = 0.015 and 0.043, respectively) but higher resting systolic (P = 0.025 and < 0.001, respectively) and mean arterial blood pressures (P = 0.049 and 0.002, respectively) than CC homozygotes or CT heterozygotes. We further investigated possible interactions between group and genotype and found a significant interaction in SBP only (P = 0.037) between the group and genotype, even when controlling for age, BMI, and VO2max as potential confounding factors. Stepwise regression analyses showed that body mass index and GNB3 genotype were two independent predictors for the variations in systolic blood pressure and heart rate up to by 14.3 and 14.5%, respectively. In addition, waist-to-hip ratio explained an individual variation in mean arterial pressure (MAP) up to by 11.2%. CONCLUSION: The current findings of the study suggest that increased body fatness along with low cardiorespiratory fitness may magnify the genetic susceptibility of the GNB3 825T allele to elevated blood pressure in this study population.

Adult↗

PubMed2004

Effects of bone morphogenetic protein-7 (BMP-7) on primordial follicular growth in the mouse ovary.

Previously, bone morphogenetic protein-7 (BMP-7) was suggested as a factor that may act to facilitate the transition of follicles from primordial stage to the pool of developed primary, preantral, and antral follicles (Lee et al. 2001: Biol Reprod 65:994-999.). Thus, aim of the present study was to evaluate effect(s) of BMP-7 on the primordial-primary follicle transition. Neonatal mouse ovaries were cultured in the presence or absence of 100 mIU/ml FSH with various doses of BMP-7 (0, 10, and 100 ng/ml). After 4-day culture period, number of follicles was counted and the expression of transcripts for FSH receptor (FSHR), kit ligand (KL), and c-kit was measured by RT-PCR. BMP-7 alone at 100 ng/ml concentration stimulated follicle development with concurrent increase of mRNA for FSHR. BMP-7 alone down-regulated KL expression however, the ratio between KL1 and KL2 was increased. There was no change in the c-kit mRNA expression. Results of the present study suggest that the BMP-7 is one of the factors involved in primordial-primary follicle transition in the mouse ovary and it may play a role in expression of FSHR for further follicular development.

Animals↗

PubMed2004

Fanconi's syndrome and subsequent progressive renal failure caused by a Chinese herb containing aristolochic acid.

Chinese herb nephropathy contains a variety of clinical features of progressive renal failure (indicated by studies conducted in Belgium) to the variant type of Fanconi's syndrome. Fanconi's syndrome has mostly been reported in Asian countries, and is characterized by proximal tubular dysfunction and slower progression to end-stage renal disease (ESRD); it also often revealed a reversible clinical course. We describe a 43-year-old woman who presented with polyuria and polydipsia caused by Fanconi's syndrome. The cause of Fanconi's syndrome was not identified because the patient denied the intake of the Chinese herbal mixture at first. Fanconi's syndrome seemed to be reversible in its early stage, but it rapidly progressed to renal failure after 3 months, despite the interruption of Chinese mixture use. A renal biopsy revealed typical findings of aristolochic acid-induced nephropathy. Aristolochic acids were also detected in the Chinese herbs that were consumed. This case highlights the variety of the clinical spectrum of aristolochic acid induced nephropathy (AAN). We emphasize that AAN should be suspected in all patients with Fanconi's syndrome, even if patients deny the intake of any Chinese herbal preparation.

Adult↗

PubMed2003

Structure of superoxide dismutase from Pyrobaculum aerophilum presents a challenging case in molecular replacement with multiple molecules, pseudo-symmetry and twinning.

The crystal structure of superoxide dismutase from the hyperthermophilic crenarchaeon Pyrobaculum aerophilum was determined by molecular replacement at 1.8 A resolution. The structure determination was made especially challenging by the large number of molecules (24) in the asymmetric unit, the presence of a pseudo-crystallographic twofold operator close to a twinning operator and the inability to detect twinning by conventional means. Molecular replacement proceeded at low resolution in pseudo (apparent) space group P3(2)12 and was facilitated by examination of the self-rotation function and native Patterson map. Refinement, however, stalled at an R factor of 40% when high-resolution data were included. Expanding to the lower symmetry space group P3(2) decreased R (to 22%) and R(free) (to 26%), but not by as much as expected for the quality of data. Finally, despite the apparent lack of evidence from conventional twinning tests [i.e. plots of the second moment of I and N(Z) distributions], a twinning operator was included in the refinement, lowering R and R(free) to 16.2 and 21.7%, respectively. The early detection of twinning appears to have been masked by a deviation in the expected intensity distribution caused by the presence of non-crystallographic translational symmetry. These findings suggest the importance of testing twinning operators in cases where pseudo-translational symmetry can explain negative results from conventional twinning tests. The structure reveals a tetrameric assembly with 222 symmetry, similar to superoxide dismutase structures from other organisms. The current structural model represents the metal-free state of the enzyme.

Archaeal Proteins↗

PubMed2003

Seeded conversion of recombinant prion protein to a disulfide-bonded oligomer by a reduction-oxidation process.

The infectious form of prion protein, PrP(Sc), self-propagates by its conversion of the normal, cellular prion protein molecule PrP(C) to another PrP(Sc) molecule. It has not yet been demonstrated that recombinant prion protein can convert prion protein molecules from PrP(C) to PrP(Sc). Here we show that recombinant hamster prion protein is converted to a second form, PrP(RDX), by a redox process in vitro and that this PrP(RDX) form seeds the conversion of other PrP(C) molecules to the PrP(RDX) form. The converted form shows properties of oligomerization and seeded conversion that are characteristic of PrP(Sc). We also find that the oligomerization can be reversed in vitro. X-ray fiber diffraction suggests an amyloid-like structure for the oligomerized prion protein. A domain-swapping model involving intermolecular disulfide bonds can account for the stability and coexistence of two molecular forms of prion protein and the capacity of the second form for self-propagation.

Animals↗

PubMed2002

Alpha-synuclein regulates neuronal survival via Bcl-2 family expression and PI3/Akt kinase pathway.

Alpha-synuclein (alpha-SN) is a ubiquitous protein that is especially abundant in the brain and has been postulated to play a central role in the pathogenesis of Parkinson's disease, Alzheimer's disease, and other neurodegenerative disorders. However, little is known about the neuronal functions of alpha-SN and the molecular and cellular mechanisms underlying neuronal loss. Here, we show that alpha-SN plays dual roles of neuroprotection and neurotoxicity depending on its concentration or level of expression. At nanomolar concentrations, a-SN protected neurons against serum deprivation, oxidative stress, and excitotoxicity through the PI3/Akt signaling pathway, and its protective effect was increased by Bcl-2 overexpression. Conversely, at both low micromolar and overexpressed levels in the cell, alpha-SN resulted in cytotoxicity. This might be related to decreased Bcl-xL expression and increased bax expression, which is subsequently followed by cytochrome c release and caspase activation and also by microglia-mediated inflammatory responses via the NFkappaB and mitogen-activated protein kinase pathways.

Animals↗