Biomedical subjects

Do-Hyoung Kim

Publications and source records attributed to Do-Hyoung Kim.

11 recordsLinked to original sources

PubMed2006

Solution structure and membrane interaction mode of an antimicrobial peptide gaegurin 4.

We have applied NMR spectroscopy to determine the high-resolution structure of gaegurin 4, a 37-residue antimicrobial peptide from Rana rugosa, under varying hydrophobic conditions. Even in 100% H2O, gaegurin 4 contains a nascent turn near its C-terminal Rana box. Under a more hydrophobic condition it forms two amphipathic helices, one long encompassing residues 2-23 and the other consisting of residues 25-34, similar to what has been observed in cecropin A. Functional implication of the helix-breaking kink at Gly24 in gaegurin 4 was investigated by preparing several analogs. Based upon the current and previous results, we propose a novel seaanemone-like ion pore-forming model for gaegurin 4.

Amino Acid Sequence↗

PubMed2006

NMR structure determination of alpha-conotoxin BuIA, a novel neuronal nicotinic acetylcholine receptor antagonist with an unusual 4/4 disulfide scaffold.

We have determined a high-resolution three-dimensional structure of alpha-conotoxin BuIA, a 13-residue peptide toxin isolated from Conus bullatus. Despite its unusual 4/4 disulfide bond layout alpha-conotoxin BuIA exhibits strong antagonistic activity at alpha6/alpha3beta2beta3, alpha3beta2, and alpha3beta4 nAChR subtypes like some alpha4/7 conotoxins. alpha-Conotoxin BuIA lacks the C-terminal beta-turn present within the second disulfide loop of alpha4/7 conotoxins, having only a "pseudo omega-shaped" molecular topology. Nevertheless, it contains a functionally critical two-turn helix motif, a feature ubiquitously found in alpha4/7 conotoxins. Such an aspect seems mainly responsible for similarities in the receptor recognition profile of alpha-conotoxin BuIA to alpha4/7 conotoxins. Structural comparison of alpha-conotoxin BuIA with alpha4/7 conotoxins and alpha4/3 conotoxin ImI suggests that presence of the second helical turn portion of the two-turn helix motif in alpha4/7 and alpha4/4 conotoxins may be important for binding to the alpha3 and/or alpha6 subunit of nAChR.

Animals↗

PubMed2006

Solution conformation of an immunodominant epitope in the hepatitis B virus preS2 surface antigen.

We have determined the solution conformation of the major B cell epitope (residues 123-145, adrl23 hereafter) in the preS2 region of hepatitis B virus known to be associated with infection neutralization. The adrl23 shows an "L" shaped helix-turn-helix topology with two beta-turns formed by residues Ala(130)-Asp(133) and Asp(133)-Val(136) intervening the N- and C-terminal helices. The N-terminal alpha-helix consists of residues Ser(124)-Gln(129) whereas the C-terminal 3(10) helix is formed by residues Val(136)-Tyr(140). The beta-turns overlap partially with the putative "conformational" epitope. The overall topology of adrl23 is primarily maintained by hydrophobic interactions involving Phe(127), Leu(131), Leu(132), Val(136), and Tyr(140) that are clustered on one side of the molecule. An additional hydrophobic stabilization comes from Phe(141) that is buried inside the concave side of the molecule. A network of hydrogen bonds formed among Thr(125), His(128), and Arg(137) further contribute to the "boomerang-shaped" architecture of adrl23. The N-terminus of adrl23 is immobile due to a hydrogen bond between the N-terminal amide proton of Asn(123) and the hydroxyl oxygen of Thr(126). The side chains of Asp(133), Arg(135), Val(136), Leu(139), and Tyr(140) that were shown to be important for binding to a monoclonal antibody H8 mAb are surface exposed.

Helix-Turn-Helix Motifs↗

PubMed2006

Solution conformation of a neuronal nicotinic acetylcholine receptor antagonist alpha-conotoxin OmIA that discriminates alpha3 vs. alpha6 nAChR subtypes.

alpha-Conotoxin OmIA from Conus omaria is the only alpha-conotoxin that shows a approximately 20-fold higher affinity to the alpha3beta2 over the alpha6beta2 subtype of nicotinic acetylcholine receptor. We have determined a three-dimensional structure of alpha-conotoxin OmIA by nuclear magnetic resonance spectroscopy. alpha-Conotoxin OmIA has an "omega-shaped" overall topology with His(5)-Asn(12) forming an alpha-helix. Structural features of alpha-conotoxin OmIA responsible for its selectivity are suggested by comparing its surface characteristics with other functionally related alpha4/7 subfamily conotoxins. Reduced size of the hydrophilic area in alpha-conotoxin OmIA seems to be associated with the reduced affinity towards the alpha6beta2 nAChR subtype.

Binding Sites↗

PubMed2006

Assessment of fluid shifts of body compartments using both bioimpedance analysis and blood volume monitoring.

Fluid shifts are commonplace in chronic hemodialysis patients during the intra- and interdialytic periods. In this study, we evaluated fluid shifts of body compartments using both bioimpedance spectroscopy and blood volume monitoring from the start to the end of hemodialysis. 24 stable hemodialysis patients were included on the study. Relative change of blood volume was progressively reduced from the start to the end of hemodialysis (1 hr, -7.22+/-3.23%; 2 hr, -9.78+/-4.69%; 3 hr, -12.88+/-5.65%; 4 hr, -15.41+/-6.54%, respectively). Mean % reduction of intracellular fluid was not significantly different to that of extracellular fluid at the end of hemodialysis (delta ICF, -6.58+/-5.34% vs. delta ECF, -7.07+/-5.12%). Mean % fluid reduction of arms, legs and trunk was -11.98+/-6.76%, -6.43+/-4.37% and -7.47+/-4.56%, respectively at the end of hemodialysis. There were 3 characteristic patterns in blood-volume change. Similar amounts of fluid were removed from the extracellular and intracellular compartments during hemodialysis, with the arms showing the greatest loss in terms of body segments. The pattern of blood volume change measured by blood volume monitoring may be useful for more accurate determination of dry-weight and for correcting volume status in hemodialysis patients.

Adult↗

PubMed2005

Solution structure of alpha-conotoxin PIA, a novel antagonist of alpha6 subunit containing nicotinic acetylcholine receptors.

alpha-Conotoxin PIA is a novel nicotinic acetylcholine receptor (nAChR) antagonist isolated from Conus purpurascens that targets nAChR subtypes containing alpha6 and alpha3 subunits. alpha-conotoxin PIA displays 75-fold higher affinity for rat alpha6/alpha3beta2beta3 nAChRs than for rat alpha3beta2 nAChRs. We have determined the three-dimensional structure of alpha-conotoxin PIA by nuclear magnetic resonance spectroscopy. The alpha-conotoxin PIA has an "omega-shaped" overall topology as other alpha4/7 subfamily conotoxins. Yet, unlike other neuronally targeted alpha4/7-conotoxins, its N-terminal tail Arg1-Asp2-Pro3 protrudes out of its main molecular body because Asp2-Pro3-Cys4-Cys5 forms a stable type I beta-turn. In addition, a kink introduced by Pro15 in the second loop of this toxin provides a distinct steric and electrostatic environment from those in alpha-conotoxins MII and GIC. By comparing the structure of alpha-conotoxin PIA with other functionally related alpha-conotoxins we suggest structural features in alpha-conotoxin PIA that may be associated with its unique receptor recognition profile.

Amino Acid Sequence↗

PubMed2005

Structural details on mdm2-p53 interaction.

Mdm2 is a cellular antagonist of p53 that keeps a balanced cellular level of p53. The two proteins are linked by a negative regulatory feedback loop and physically bind to each other via a putative helix formed by residues 18-26 of p53 transactivation domain (TAD) and its binding pocket located within the N-terminal 100-residue domain of mdm2 (Kussie, P. H., Gorina, S., Marechal, V., Elenbaas, B., Moreau, J., Levine, A. J., and Pavletich, N. P. (1996) Science 274, 948-953). In a previous report we demonstrated that p53 TAD in the mdm2-freee state is mostly unstructured but contains two nascent turns in addition to a "preformed" helix that is the same as the putative helix mediating p53-mdm2 binding. Here, using heteronuclear multidimensional NMR methods, we show that the two nascent turn motifs in p53 TAD, turn I (residues 40-45) and turn II (residues 49-54), are also capable of binding to mdm2. In particular, the turn II motif has a higher mdm2 binding affinity ( approximately 20 mum) than the turn I and targets the same site in mdm2 as the helix. Upon mdm2 binding this motif becomes a well defined full helix turn whose hydrophobic face formed by the side chains of Ile-50, Trp-53, and Phe-54 inserts deeply into the helix binding pocket. Our results suggest that p53-mdm2 binding is subtler than previously thought and involves global contacts such as multiple "non-contiguous" minimally structured motifs instead of being localized to one small helix mini-domain in p53 TAD.

Amino Acid Motifs↗

PubMed2004

Solution conformation of alpha-conotoxin GIC, a novel potent antagonist of alpha3beta2 nicotinic acetylcholine receptors.

Alpha-conotoxin GIC is a 16-residue peptide isolated from the venom of the cone snail Conus geographus. Alpha-conotoxin GIC potently blocks the alpha3beta2 subtype of human nicotinic acetylcholine receptor, showing a high selectivity for neuronal versus muscle subtype [McIntosh, Dowell, Watkins, Garrett, Yoshikami, and Olivera (2002) J. Biol. Chem. 277, 33610-33615]. We have now determined the three-dimensional solution structure of alpha-conotoxin GIC by NMR spectroscopy. The structure of alpha-conotoxin GIC is well defined with backbone and heavy atom root mean square deviations (residues 2-16) of 0.53 A and 0.96 A respectively. Structure and surface comparison of alpha-conotoxin GIC with the other alpha4/7 subfamily conotoxins reveals unique structural aspects of alpha-conotoxin GIC. In particular, the structural comparison between alpha-conotoxins GIC and MII indicates molecular features that may confer their similar receptor specificity profile, as well as those that provide the unique binding characteristics of alpha-conotoxin GIC.

Amino Acid Sequence↗

PubMed2002

Repellent activity of constituents identified in Foeniculum vulgare fruit against Aedes aegypti (Diptera: Culicidae).

The repellent activity of materials derived from the methanol extract of fruits from Foeniculum vulgareagainst hungry Aedes aegypti females was examined using skin and patch tests and compared with that of the commercial N,N-diethyl-m-toluamide (deet) and (Z)-9-octadecenoic acid. The biologically active constituents of the Foeniculum fruits were characterized as (+)-fenchone and (E)-9-octadecenoic acid by spectroscopic analyses. Responses varied according to compound, dose, and exposure time. In a skin test with female mosquitoes, at a dose of 0.4 mg/cm(2), (+)-fenchone and (Z)-9-octadecenoic acid exhibited moderate repellent activity at 30 min after treatment, whereas deet provided >1 h of protection against adult mosquitoes at 0.2 mg/cm(2). (Z)-9-Octadecenoic acid was a more potent repellent agent than (E)-9-octadecenoic acid. (+)-Fenchone and (E)-9-octadecenoic acid merit further study as potential mosquito repellent agents or as lead compounds.

Aedes↗

PubMedDate not supplied

Proteomimetic libraries: design, synthesis, and evaluation of p53-MDM2 interaction inhibitors.

The p53-MDM2 interaction regulates p53-mediated cellular responses to DNA damage, and MDM2 is overexpressed in 7% of all cancers. Structure-based computational design was applied to this system to design libraries centered on a scaffold that projects side chain functionalities with distance and angular relationships equivalent to those seen in the MDM2 interacting motif of p53. A library of 173 such compounds was synthesized using solution phase parallel chemistry. The in vitro competitive ability of the compounds to block p53 peptide binding to MDM2 was determined using a fluorescence polarization competition assay. The most active compound bound with K(d) = 12 microM, and its binding was characterized by (15)N-(1)H HSQC NMR.

Binding Sites↗

PubMedDate not supplied

Association between serum n-terminal pro-brain natriuretic peptide concentration and left ventricular dysfunction and extracellular water in continuous ambulatory peritoneal dialysis patients.

BACKGROUND: This study investigated the association between serum N-terminal pro-brain natriuretic peptide (NT-pro-BNP) levels and extracellular water (ECW%) and left ventricular (LV) dysfunction in continuous ambulatory peritoneal dialysis (CAPD) patients. METHODS: The study involved 30 stable CAPD patients: 14 males, 16 females; mean age 52 +/- 14 years; mean CAPD duration 34 +/- 12 months; 12 with diabetes mellitus (DM) and 18 non-DM. Serum NT-pro-BNP levels were determined using electrochemiluminescence immunoassay. Baseline echocardiography was performed using a Hewlett-Packard Sonos 1000 (Andover, Massachusetts, USA) device equipped with a 2.25-MHz probe, allowing M-mode, two-dimensional, and pulsed Doppler measurements. Left ventricular mass index (LVMI) was calculated according to the Penn formula. A multifrequency bioimpedance analyzer was used; ECW% was calculated as a percentage of total body water and was considered the index of volume load. RESULTS: (1) Serum NT-pro-BNP level, ECW%, LVMI, and LV ejection fraction in CAPD patients were 3924 (240 - 74460) pg/mL, 36.7% +/- 2.2%, 158 +/- 48 g/m2, and 60.5% +/-11.2%, respectively. (2) Patients were divided into three tertiles (10 patients each) according to their serum NT-proBNP concentration [1st tertile 1168 (240 - 2096), 2nd tertile 4856 (2295 - 20088), 3rd tertile 35012 (20539 -74460) pg/mL]. The tertiles did not differ significantly in terms of age, sex, presence of DM, body mass index, or PD duration. Patients in the 3rd tertile (highest serum NT-proBNP concentration) had the highest LVMI (126 +/- 45 vs 160 +/-41 vs 200 +/- 23 g/m2 for 1st, 2nd, 3rd tertiles, respectively) and the lowest LV ejection fraction (66% +/- 11% vs 62% +/-6% vs 55% +/- 9%). ECW% did not differ significantly between tertiles (35.5% +/- 2.0% vs 37.5% +/- 2.0% vs 36.5% +/-2.0%). (3) In CAPD patients, serum NT-pro-BNP levels correlated positively with LVMI (r = 0.628, p = 0.003) and negatively with LV ejection fraction (r = -0.479, p = 0.033). Serum NT-pro-BNP levels did not correlate with ECW% (r = 0.227, p = 0.25). (4) Stepwise regression analysis showed that LV ejection fraction (beta = -0.610, p = 0.015) and LVMI (beta = 0.415, p = 0.007) were independently associated with the serum NT-pro-BNP concentration. CONCLUSIONS: There was no link between ECW% and serum NT-pro-BNP concentration. Thus, serum NT-pro-BNP levels may not provide objective information with respect to pure hydration status in CAPD patients. In contrast, serum NT-pro-BNP levels were linked to LVMI and LV ejection fraction in CAPD patients. Therefore, while the serum NT-proBNP concentration might not be a useful clinical marker for extracellular fluid volume load, it appears useful for evaluating LV hypertrophy and LV dysfunction in CAPD patients.

Adult↗