Biomedical subjects

Min S Park

Publications and source records attributed to Min S Park.

At least 19 recordsLinked to original sources

PubMed2006

Functional and structural characterization of a thiol peroxidase from Mycobacterium tuberculosis.

A thiol peroxidase (Tpx) from Mycobacterium tuberculosis was functionally analyzed. The enzyme shows NADPH-linked peroxidase activity using a thioredoxin-thioredoxin reductase system as electron donor, and anti-oxidant activity in a thiol-dependent metal-catalyzed oxidation system. It reduces H2O2, t-butyl hydroperoxide, and cumene hydroperoxide, and is inhibited by sulfhydryl reagents. Mutational studies revealed that the peroxidatic (Cys60) and resolving (Cys93) cysteine residues are critical amino acids for catalytic activity. The X-ray structure determined to a resolution of 1.75 A shows a thioredoxin fold similar to that of other peroxiredoxin family members. Superposition with structural homologues in oxidized and reduced forms indicates that the M. tuberculosis Tpx is a member of the atypical two-Cys peroxiredoxin family. In addition, the short distance that separates the Calpha atoms of Cys60 and Cys93 and the location of these cysteine residues in unstructured regions may indicate that the M. tuberculosis enzyme is oxidized, though the side-chain of Cys60 is poorly visible. It is solely in the reduced Streptococcus pneumoniae Tpx structure that both residues are part of two distinct helical segments. The M. tuberculosis Tpx is dimeric both in solution and in the crystal structure. Amino acid residues from both monomers delineate the active site pocket.

Amino Acid Sequence↗

PubMed2006

Hyperoxia increases hepatic arginase expression and ornithine production in mice.

Hyperoxic exposure affects the levels and activities of some hepatic proteins. We tested the hypothesis that hyperoxic exposure would result in greater hepatic .NO concentrations. C3H/HeN mice were exposed to >95% O(2) for 72 or 96 h and compared to room air-breathing controls. In contrast to our working hypothesis, exposure to >95% O(2) for 96 h decreased hepatic nitrite/nitrate NO(X) concentrations (10.9 +/- 2.2 nmol/g liver versus 19.3 +/- 2.4 nmol/g liver in room air, P < 0.05). The hepatic levels of endothelial NO synthase (eNOS) and inducible NOS (iNOS) proteins were not different among the groups. The arginases, which convert L-arginine to urea and L-ornithine, may affect hepatic NOS activities by decreasing L-arginine bioavailability. Hepatic ornithine concentrations were greater in hyperoxic animals than in controls (318 +/- 18 nmol/g liver in room air, and 539 +/- 64, and 475 +/- 40 at 72 and 96 h of hyperoxia, respectively, P < 0.01). Hepatic arginase I protein levels were greater in hyperoxic animals than in controls. Hepatic carbamoyl phosphate synthetase (CPS) protein levels and activities were not different among groups. These results indicate that increases in hepatic levels of arginase I in mice exposed to hyperoxia may diminish .NO production, as reflected by lower liver levels of NO(X). The resultant greater hepatic ornithine concentrations may represent a mechanism to facilitate tissue repair, by favoring the production of polyamines and/or proline.

Animals↗

PubMed2006

Aneurysms in children: review of 15 years experience.

INTRODUCTION: Intracranial aneurysms in children are rare. The location, size, age, and presentation in the young are markedly different from that of adults. The 15-year experience of the senior author in southern California is presented. METHODS: All paediatric patients treated for cerebral aneurysm over a 15-year period were identified. Intraoperative and postoperative data were collected retrospectively from the medical records. The need for additional surgery as well as the incidence of complications including death, hemiparesis, seizures, memory disturbances, and the need for subsequent cerebrospinal fluid (CSF) diversion were identified. RESULTS: Fifty children were identified (54 lesions). Subarachnoid haemorrhage was the most common mode of presentation with the average Hunt-Hess grade being I-II. The locations of the lesions were middle cerebral (10), internal carotid (8), anterior communicating (7), posterior cerebral (6), posterior communicating (5), pericallosal (4), anterior cerebral (3), choroidal (3), posterior inferior cerebellar (3), basilar (2), vertebral (2) and frontopolar (1) arteries. Clinical vasospasm was encountered in eight of our patients, but no cases were observed in those younger than nine years. Long-term outcome was excellent in 22 cases, good in 20 and poor in nine, with one death and two patients lost to follow-up. CONCLUSION: Analysis of our data suggested a predilection for the posterior circulation compared to adults, larger size, more complex architecture, and a decreased incidence of clinical vasospasm in the younger age group. This series and a review of the literature suggest that aneurysmal disease in children may be distinct from that of adults.

Adolescent↗

PubMed2005

Surgical correction of metopic synostosis.

BACKGROUND: Premature closure of the metopic suture results in deformation of the anterior portion of the calvarium, which can vary from mild to severe. In mild forms, there is only prominent ridging of the metopic suture; more severe forms result in a marked narrowing of the frontal and temporal regions that in turn affects the supraorbital rims and produces hypotelorism. METHODS: The authors retrospectively reviewed 39 consecutive cases of metopic synostosis treated over a 12-year period. RESULTS: The average age at referral was 5 months, with surgery performed at an average age of 7.5 months. Fifteen infants had other congenital anomalies, with eight having synostosis of other sutures. Follow-up ranged from 7 months to 6 years, with an average of 29 months. In three mild cases, burring of the metopic ridge was performed with excellent aesthetic results in all cases. The other 36 patients had significant deformity of the supraorbital ridges and temporal regions, with obvious hypotelorism for over 50% of the time. In these cases, the patients underwent craniofacial reconstruction to normalize their appearance. In addition, the lateral aspect of the sphenoid ridges, including the orbital roof and lateral orbital wall to the infraorbital fissure, was removed to free the cranial base. The average blood loss was under 400 ml and the average hospital stay was 3.6 days. Results were considered good to excellent in all except three cases, which had recurrence of a prominent metopic ridge; two required a second operation after 6 months for burring of this ridge, whereas the third was treated conservatively with an orthotic headband. CONCLUSION: Mild forms of metopic synostosis can be successfully treated with burring of the metopic ridge alone. Severe forms require craniofacial reconstruction and may be associated with other congenital abnormalities, additional synostosis, and developmental delay. In all cases, the operative procedure must be tailored to the nature and severity of the deformity.

Child↗

PubMed2004

Initial experience with antibiotic-impregnated silicone catheters for shunting of cerebrospinal fluid in children.

INTRODUCTION: Infection is a major complication of cerebrospinal fluid (CSF) shunting procedures. Recently, rifampin-impregnated and clindamycin-impregnated silicone catheters have been developed in an attempt to prevent and/or reduce the incidence of shunt infections. In vitro and in vivo animal studies have shown their efficacy in reducing bacterial colonization of catheters. However, these shunts are yet to be evaluated in clinical trials and their safety and efficacy in preventing shunt infections is unknown. METHODS: Between April 2002 and April 2003, 31 children (age range 6 months to 17 years, mean 4.5 years) underwent implantation of an antibiotic-impregnated silicone catheter for CSF diversion. All surgeries were performed by a single neurosurgeon (HSM) at a single medical center. The Codman Hakim Bactiseal silicone catheter was used in all children. Thirty-two catheters were implanted in 31 children. All children have been followed since surgery (for an average of 19 months). For comparison, the previous 46 standard implanted shunts over a similar period of time were reviewed (average follow-up 31 months). RESULTS: Of the 32 implanted catheters, 11 involved placement of a new complete shunt system, 8 were distal revisions, and 13 were proximal/ventricular revisions. There were fewer early and late complications than in the standard shunt group (12.5 and 18.8% vs. 23.9 and 34.8%). There was no local reaction from implantation of the catheters. One child contaminated his distal catheter by disrupting his abdominal incision. None of the other patients have developed any evidence of shunt infection to date. CONCLUSION: Rifampin-impregnated and clindamycin-impregnated silicone catheters appear to be safe and well tolerated in children. Preliminary results suggest a low incidence of shunt infection. Longer follow-up and a larger number of patients are needed to more accurately assess the efficacy of these catheters compared with traditional silicone catheters.

Adolescent↗

PubMed2004

Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism.

The structure of Mycobacterium tuberculosis dUTP nucleotidohydrolase (dUTPase) has been determined at 1.3 Angstrom resolution in complex with magnesium ion and the non-hydrolyzable substrate analog, alpha,beta-imido dUTP. dUTPase is an enzyme essential for depleting potentially toxic concentrations of dUTP in the cell. Given the importance of its biological role, it has been proposed that inhibiting M.tuberculosis dUTPase might be an effective means to treat tuberculosis infection in humans. The crystal structure presented here offers some insight into the potential for designing a specific inhibitor of the M.tuberculosis dUTPase enzyme. The structure also offers new insights into the mechanism of dUTP hydrolysis by providing an accurate representation of the enzyme-substrate complex in which both the metal ion and dUTP analog are included. The structure suggests that inclusion of a magnesium ion is important for stabilizing the position of the alpha-phosphorus for an in-line nucleophilic attack. In the absence of magnesium, the alpha-phosphate of dUTP can have either of the two positions which differ by 4.5 Angstrom. A transiently ordered C-terminal loop further assists catalysis by shielding the general base, Asp83, from solvent thus elevating its pK(a) so that it might in turn activate a tightly bound water molecule for nucleophilic attack. The metal ion coordinates alpha, beta, and gamma phosphate groups with tridentate geometry identical with that observed in the crystal structure of DNA polymerase beta complexed with magnesium and dNTP analog, revealing some common features in catalytic mechanism.

Amino Acid Sequence↗

PubMed2004

Mycobacterium tuberculosis RmlC epimerase (Rv3465): a promising drug-target structure in the rhamnose pathway.

The Mycobacterium tuberculosis rmlC gene encodes dTDP-4-keto-6-deoxyglucose epimerase, the third enzyme in the M. tuberculosis dTDP-L-rhamnose pathway which is essential for mycobacterial cell-wall synthesis. Because it is structurally unique, highly substrate-specific and does not require a cofactor, RmlC is considered to be the most promising drug target in the pathway, and the M. tuberculosis rmlC gene was selected in the initial round of TB Structural Genomics Consortium targets for structure determination. The 1.7 A native structure determined by the consortium facilities is reported and implications for in silico screening of ligands for structure-guided drug design are discussed.

Amino Acid Sequence↗

PubMed2004

Human leukocyte antigen A29 subtypes associated with birdshot retinochoroidopathy.

PURPOSE: To determine whether birdshot retinochoroidopathy is associated with subtypes of the human leukocyte antigen (HLA)-A29 other than HLA-A*2902. DESIGN: Experimental study. METHODS: High-resolution DNA typing of HLA-A29 subtypes was performed on blood from 20 subjects with birdshot retinochoroidopathy using polymerase chain reaction-based typing methods. Results were compared with published controls. RESULTS: Four of 20 subjects (20%) had the HLA-A*2901 allele; two were homozygous for HLA-A*29, and both had the HLA-A*2901 and HLA-A*2902 alleles. Among 18 subjects with only one HLA-A*29 allele, the HLA-A*2902 allele was found in 16 (89%) and the HLA-A*2901 allele was found in two (11%). No subject was found to have HLA-A*2903, HLA-A*2904, HLA-A*2905, or HLA-A*2906. CONCLUSIONS: Both HLA-A*2901 and HLA-A*2902 are associated with birdshot retinochoroidopathy. Our data do not support the previous suggestion that the HLA-A29.1 serotype may be protective against development of birdshot retinochoroidopathy. Additional studies will be required to determine whether the other, less common subtypes are associated with the disease. HLA-A29 subtype testing is not required for the clinical evaluation of HLA-A29-positive patients with birdshot retinochoroidopathy.

Chorioretinitis↗

PubMed2004

HLA-DRB1 and -DQB1 alleles in mestizo patients with Vogt-Koyanagi-Harada's disease in Southern California.

We evaluated human leukocyte antigen (HLA)-DRB1 and -DQB1 alleles as genetic markers for Vogt-Koyanagi-Harada (VKH) disease in Mestizo patients in Southern California. Mestizo individuals with VKH disease (n = 29) at two institutions were evaluated. Typing of HLA-DRB1 and DQB1 genes was performed using DNA-based techniques. Gene frequencies were compared to Mestizo individuals living in Southern California. All patients had HLA-DRB1*01, DRB1*04, DQB1*03 or DQB1*05, or a combination of these genes. The gene frequency of combined HLA-DR4 alleles was increased when compared to controls. The frequencies of HLA-DRB1*0404 and DRB1*0407 were increased compared to controls, but were not significant after Bonferroni correction. Three patients had the HLA-DRB1*0410 allele; this allele was not found in controls. All HLA-DRB1*01 positive patients had the DRB1*0102 subtype. No HLA-DQB1 allele was significantly increased compared to controls. This study is the first to identify a possible association between HLA-DRB1*0404 and VKH disease, as well as to find DRB1*0102 and DRB1*0410 in Mestizo patients.

Alleles↗

PubMed2004

Stabilization of anterior cervical spine with bioabsorbable polymer in one- and two-level fusions.

OBJECTIVE: We present our experience using a bioabsorbable polymer in the surgical management of one- and two-level degenerative disc disease of the cervical spine with anterior cervical discectomy and fusion. Twenty-six patients were treated at the University of California, San Diego Medical Center or the Veterans Affairs Medical Center in San Diego, CA. All cases were performed under the direction of a single neurosurgeon (WRT). METHODS: A retrospective review of patients' charts and imaging was performed to determine outcomes after anterior cervical spine operations. Specifically, we looked at the need for additional surgery, local reaction to the bioabsorbable polymer, fusion rate, and complications. Procedures involved the C3-C4, C4-C5, C5-C6, and/or C6-C7 levels, and fibular allograft was used in all but one case. The anterior cervical discectomy and fusion procedures with internal fixation were performed in 26 patients between March 2000 and November 2001. The patients were followed for up to 2 years after surgery (average, 14 mo). RESULTS: Radiographic fusion was achieved in 25 (96.2%) of 26 patients. Only one instance of treatment failure was encountered that required additional surgery and the placement of a titanium plate. There were no clinical signs or symptoms of reaction to the bioabsorbable material. CONCLUSION: The rates of fusion after single-level anterior cervical discectomy and fusion with internal fixation using bioabsorbable polymer and screws in this study match those using metallic implants, as previously reported in the literature, and are superior to those achieved with noninstrumented fusions. Preliminary results suggest that this newly available technology for anterior fusion is as effective in single-level disease as traditional titanium plating systems. The bioabsorbable material seems to be tolerated well by patients. A larger, randomized, controlled study is necessary to bring the results to statistical significance.

Absorbable Implants↗

PubMed2003

Directed evolution approach to a structural genomics project: Rv2002 from Mycobacterium tuberculosis.

One of the serious bottlenecks in structural genomics projects is overexpression of the target proteins in soluble form. We have applied the directed evolution technique and prepared soluble mutants of the Mycobacterium tuberculosis Rv2002 gene product, the wild type of which had been expressed as inclusion bodies in Escherichia coli. A triple mutant I6TV47MT69K (Rv2002-M3) was chosen for structural and functional characterizations. Enzymatic assays indicate that the Rv2002-M3 protein has a high catalytic activity as a NADH-dependent 3alpha, 20beta-hydroxysteroid dehydrogenase. We have determined the crystal structures of a binary complex with NAD(+) and a ternary complex with androsterone and NADH. The structure reveals that Asp-38 determines the cofactor specificity. The catalytic site includes the triad Ser-140Tyr-153Lys-157. Additionally, it has an unusual feature, Glu-142. Enzymatic assays of the E142A mutant of Rv2002-M3 indicate that Glu-142 reverses the effect of Lys-157 in influencing the pKa of Tyr-153. This study suggests that the Rv2002 gene product is a unique member of the SDR family and is likely to be involved in steroid metabolism in M. tuberculosis. Our work demonstrates the power of the directed evolution technique as a general way of overcoming the difficulties in overexpressing the target proteins in soluble form.

Alcohol Oxidoreductases↗

PubMed2003

The crystal structure of the first enzyme in the pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase, from M tuberculosis.

Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate, which is a precursor to coenzyme A and is required for penicillin biosynthesis. The crystal structure of KPHMT from Mycobacterium tuberculosis was determined by the single anomalous substitution (SAS) method at 2.8 A resolution. KPHMT adopts a structure that is a variation on the (beta/alpha) barrel fold, with a metal binding site proximal to the presumed catalytic site. The protein forms a decameric complex, with subunits in opposing pentameric rings held together by a swapping of their C-terminal alpha helices. The structure reveals KPHMT's membership in a small, recently discovered group of (beta/alpha) barrel enzymes that employ domain swapping to form a variety of oligomeric assemblies. The apparent conservation of certain detailed structural characteristics suggests that KPHMT is distantly related by divergent evolution to enzymes in unrelated pathways, including isocitrate lyase and phosphoenolpyruvate mutase.

Binding Sites↗

PubMed2003

Strong associations between specific HLA-DQ and HLA-DR alleles and the tubulointerstitial nephritis and uveitis syndrome.

PURPOSE: To identify genetic markers for the tubulointerstitial nephritis and uveitis (TINU) syndrome by using human leukocyte antigen (HLA) genotyping. METHODS: Eighteen patients who had TINU syndrome were evaluated at three institutions. Typing of class I and II genes was performed by using DNA-based techniques. RESULTS: Significant associations were found with HLA-B14 (6/18 patients, 33.3%; control subjects, 5.5%; P = 0.0003; relative risk [RR] = 8.5), HLA-DQA1*01 (17/18 patients, 94.4%; control subjects, 46.6%, P = 0.0001; RR = 19.5), HLA-DQA1*0101 (14/18 patients, 77.8%; control subjects 22.2%; P < 0.0001; RR = 12.2), HLA-DQB1*05 (14/18 patients, 77.8%; control subjects 17.7%; P < 0.0001; RR = 16.3), HLA-DQB1*0501 (13/18 patients, 72.2%; control subjects 12.9%; P < 0.0001; RR = 17.6), HLA-DRB1*01 (14/18 patients, 77.8%; control subjects, 12.1%; P < 0.0001; RR = 25.5), and HLA-DRB1*0102 (13/18 patients, 72.2%; control subjects, 1.6%; P < 0.0001, RR = 167.1). The HLA haplotype most frequently identified in the study patients was HLA-DQA1*01/DQB1*05/DRB1*01 (13/18 patients, 72.2%). CONCLUSIONS: TINU syndrome is strongly associated with HLA-DQA1*01, HLA-DQB1*05, and HLA-DRB1*01. The association with HLA-DRB1*0102 is one of the highest reported for any disease. Because these genes are in linkage disequilibrium, the role of the individual alleles is difficult to assess. Based on the results of the present study and on previously reported HLA associations in patients with TINU syndrome, the alphabeta dimer encoded by HLA-DQA1*01/DQB1*05 may be particularly important in conferring risk for development of this disease.

Adolescent↗

PubMed2002

Human FEN-1 can process the 5'-flap DNA of CTG/CAG triplet repeat derived from human genetic diseases by length and sequence dependent manner.

Trinucleotide repeat (TNR) instability can cause a variety of human genetic diseases including myotonic dystrophy and Huntington's disease. Recent genetic data show that instability of the CAG/CTG repeat DNA is dependent on its length and replication origin. In yeast, the RAD27 (human FEN-1 homologue) null mutant has a high expansion frequency at the TNR loci. We demonstrate here that FEN-1 processes the 5'-flap DNA of CTG/CAG repeats, which is dependent on the length in vitro. FEN-1 protein can cleave the 5'-flap DNA containing triplet repeating sequence up to 21 repeats, but the activity decreases with increasing size of flap above 11 repeats. In addition, FEN-1 processing of 5'-flap DNA depends on sequence, which play a role in the replication origin-dependent TNR instability. Interestingly, FEN-1 can cleave the 5'-flap DNA of CTG repeats better than CAG repeats possibly through the flap-structure. Our biochemical data of FEN-1's activity with triplet repeat DNA clearly shows length dependence, and aids our understanding on the mechanism of TNR instability.

Base Sequence↗

PubMed2002

Engineering soluble proteins for structural genomics.

Structural genomics has the ambitious goal of delivering three-dimensional structural information on a genome-wide scale. Yet only a small fraction of natural proteins are suitable for structure determination because of bottlenecks such as poor expression, aggregation, and misfolding of proteins, and difficulties in solubilization and crystallization. We propose to overcome these bottlenecks by producing soluble, highly expressed proteins that are derived from and closely related to their natural homologs. Here we demonstrate the utility of this approach by using a green fluorescent protein (GFP) folding reporter assay to evolve an enzymatically active, soluble variant of a hyperthermophilic protein that is normally insoluble when expressed in Escherichia coli, and determining its structure by X-ray crystallography. Analysis of the structure provides insight into the substrate specificity of the enzyme and the improved solubility of the variant.

Evolution, Molecular↗

PubMed2002

Adjuvant immunotherapy of resected, intermediate-thickness, node-negative melanoma with an allogeneic tumor vaccine: impact of HLA class I antigen expression on outcome.

PURPOSE: An association between expression of > or = two of five HLA class I antigens (HLA-A2, HLA-A28, HLA-B44, HLA-B45, and HLA-C3; collectively called M5) and response to an allogeneic melanoma vaccine (Melacine; Corixa Corporation, Seattle, WA) has been described in stage IV melanoma. This study investigated whether class I antigen expression impacted relapse-free survival (RFS) after adjuvant therapy with this vaccine. PATIENTS AND METHODS: We performed class I (HLA-A, HLA-B, and HLA-C) serotyping on patients enrolled onto Southwest Oncology Group Trial 9035, a randomized, observation-controlled, phase III trial of adjuvant Melacine. All patients had clinically node-negative cutaneous melanoma (1.5 to 4.0 mm). Interactions between treatment and class I antigen expression were tested. Analyses involved all serotyped patients and were adjusted for tumor thickness, method of nodal staging, sex, ulceration, and primary tumor site. RESULTS: HLA typing was performed on 553 (80%) of the 689 enrolled patients (294 vaccinated and 259 observed). Expression of > or = two M5 antigens was associated with a superior vaccine treatment effect. Among patients who matched > or = two of the M5, the 97 vaccine-treated patients had improved RFS compared with the 78 observation patients (5-year relapse-free survival, 83% v 59%; P =.0002). The major components of this effect were contributed by HLA-A2 and HLA-C3. Among those who were HLA-A2-positive and/or HLA-C3-positive, the 5-year RFS for vaccinated patients was 77%, compared with 64% for observation (P =.004). There was no impact of HLA-A2 and/or HLA-C3 expression among observation patients. CONCLUSION: This prospective analysis indicates a highly significant benefit of adjuvant therapy with Melacine among patients expressing > or = two of the M5 class I antigens, validating a prior observation in stage IV disease. HLA-A2 and HLA-C3 contributed most to this effect. Processed melanoma peptides found in Melacine may be presented by HLA-A2 and HLA-C3 and play a role in preventing relapse in vaccinated patients.

Adjuvants, Immunologic↗

PubMed2002

Crystallization and preliminary X-ray crystallographic analysis of the Rv2002 gene product from Mycobacterium tuberculosis, a beta-ketoacyl carrier protein reductase homologue.

A 260-residue protein (FabG3) encoded by the Rv2002 gene of Mycobacterium tuberculosis shows amino-acid sequence similarity to beta-ketoacyl carrier protein (ACP) reductase, FabG. A soluble mutant (I6T/V47M/T69M) was produced by the green fluorescent protein-based directed-evolution method. It was crystallized at 296 K using the hanging-drop vapour-diffusion method. The diffraction quality of the crystal improved significantly after annealing/dehydration. X-ray diffraction data were collected to 1.8 A resolution using synchrotron radiation. The crystal belongs to the space group P3(1)21 (or P3(2)21), with unit-cell parameters a = b = 70.38, c = 148.93 A. The asymmetric unit contains two subunits, with a corresponding V(M) of 1.90 A(3) Da(-1) and a solvent content of 35.3%.

3-Oxoacyl-(Acyl-Carrier-Protein) Reductase↗

PubMed2002

The TB structural genomics consortium: providing a structural foundation for drug discovery.

Structural genomics, the large-scale determination of protein structures, promises to provide a broad structural foundation for drug discovery. The tuberculosis (TB) Structural Genomics Consortium is devoted to encouraging, coordinating, and facilitating the determination of structures of proteins from Mycobacterium tuberculosis and hopes to determine 400 TB protein structures over 5 years. The Consortium has determined structures of 28 proteins from TB to date. These protein structures are already providing a basis for drug discovery efforts.

Acyltransferases↗