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Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity.
Wang, H, Feng, L, Webb, GI, Kurgan, L, Song, J, Lin, D
Briefings in bioinformatics. 2018;(5):838-852
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Abstract
X-ray crystallography is the main tool for structural determination of proteins. Yet, the underlying crystallization process is costly, has a high attrition rate and involves a series of trial-and-error attempts to obtain diffraction-quality crystals. The Structural Genomics Consortium aims to systematically solve representative structures of major protein-fold classes using primarily high-throughput X-ray crystallography. The attrition rate of these efforts can be improved by selection of proteins that are potentially easier to be crystallized. In this context, bioinformatics approaches have been developed to predict crystallization propensities based on protein sequences. These approaches are used to facilitate prioritization of the most promising target proteins, search for alternative structural orthologues of the target proteins and suggest designs of constructs capable of potentially enhancing the likelihood of successful crystallization. We reviewed and compared nine predictors of protein crystallization propensity. Moreover, we demonstrated that integrating selected outputs from multiple predictors as candidate input features to build the predictive model results in a significantly higher predictive performance when compared to using these predictors individually. Furthermore, we also introduced a new and accurate predictor of protein crystallization propensity, Crysf, which uses functional features extracted from UniProt as inputs. This comprehensive review will assist structural biologists in selecting the most appropriate predictor, and is also beneficial for bioinformaticians to develop a new generation of predictive algorithms.
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Cyclooxygenase-2 Gly587Arg variant is associated with differential enzymatic activity and risk of esophageal squamous-cell carcinoma.
Zhao, D, Zhang, X, Guo, Y, Tan, W, Lin, D
Molecular carcinogenesis. 2009;(10):934-41
Abstract
Functional SNPs in the COX-2 promoter region have been associated with susceptibility to esophageal squamous-cell carcinoma (ESCC). In this study, we investigated SNPs in the COX-2 coding region and their impact on risk of ESCC. The coding region of COX-2 in DNAs from 30 Han Chinese individuals was sequenced to identify SNPs. Different coding region variants identified were cloned and expressed in MCE-7 cells for the measurement of COX-2 enzymatic activity. Genotypes were determined by PCR-RFLP in 1026 patients with ESCC and 1270 controls and odds ratios (ORs) and 95% confidence intervals (CI) were computed by logistic regression model. A SNP at exon 10 (1759G>A, rs3218625) was identified, which causes (587)Gly to (587)Arg amino acid substitution. Enzymatic assays using different recombinant COX-2 variants showed that COX-2-(587)Arg had significantly higher activity towards arachidonic acid than COX-2-(587)Gly (13.8 +/- 3.2 U/mg vs. 11.2 +/- 2.4 U/mg; P = 0.012). Case-control analysis showed that 10.2% of ESCC patients carried the 1759A allele whereas only 5.4% of controls had this allele (P < 0.0001). No homozygous 1759AA genotype was presented in controls albeit two patients carrying this genotype. Multivariate logistic regression analysis revealed that subjects with at least one 1759A allele had increased risk for the development of ESCC (OR, 1.91; 95% CI, 1.39-2.62) compared with those with the 1759GG genotype. These results extend our previous findings and indicate that inherited variant in arachidonic acid-metabolizing enzyme, which results in heightened enzymatic activity, may confer susceptibility to ESCC.
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Olanzapine versus placebo in the treatment of adolescents with bipolar mania.
Tohen, M, Kryzhanovskaya, L, Carlson, G, Delbello, M, Wozniak, J, Kowatch, R, Wagner, K, Findling, R, Lin, D, Robertson-Plouch, C, et al
The American journal of psychiatry. 2007;(10):1547-56
Abstract
OBJECTIVE The purpose of this study was to evaluate the efficacy and safety of olanzapine for the treatment of acute manic or mixed episodes associated with bipolar disorder in adolescents. METHOD A 3-week multicenter, parallel, double-blind, randomized placebo-controlled trial was conducted at 24 sites in the United States and two sites in Puerto Rico. The participants were outpatient and inpatient male and female adolescents 13-17 years of age with an acute manic or mixed episode. Subjects received either olanzapine (2.5-20 mg/day [N=107]) or placebo (N=54). The mean change from baseline to endpoint in the Young Mania Rating Scale total score was the primary outcome measure. RESULTS The mean baseline-to-endpoint change in the Young Mania Rating Scale total score was significantly greater for patients receiving olanzapine relative to patients receiving placebo, and a greater proportion of olanzapine-treated patients met response and remission criteria (44.8% versus 18.5% and 35.2% versus 11.1%, respectively). The mean baseline-to-endpoint weight change was significantly greater for patients receiving olanzapine relative to patients receiving placebo (3.7 kg versus 0.3 kg), and the incidence of treatment-emergent weight gain > or =7% of baseline was higher for olanzapine-treated patients (41.9% versus 1.9%). The mean baseline-to-endpoint changes in prolactin, fasting glucose, fasting total cholesterol, uric acid, and the hepatic enzymes aspartate transaminase and alanine transaminase were significantly greater in patients treated with olanzapine relative to patients receiving placebo. CONCLUSIONS Olanzapine was effective in the treatment of bipolar mania in adolescent patients. Patients treated with olanzapine, however, had significantly greater weight gain and increases in the levels of hepatic enzymes, prolactin, fasting glucose, fasting total cholesterol, and uric acid.
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Role of sequence variations in the human ether-a-go-go-related gene (HERG, KCNH2) in the Brugada syndrome.
Verkerk, AO, Wilders, R, Schulze-Bahr, E, Beekman, L, Bhuiyan, ZA, Bertrand, J, Eckardt, L, Lin, D, Borggrefe, M, Breithardt, G, et al
Cardiovascular research. 2005;(3):441-53
Abstract
BACKGROUND Brugada syndrome (BrS) is an inherited electrical disorder associated with a high incidence of sudden death. In a minority of patients, it has been linked to mutations in SCN5A, the gene encoding the pore-forming alpha-subunit of the cardiac Na(+) channel. Other causally related genes still await identification. We evaluated the role of HERG (KCNH2), which encodes the alpha-subunit of the rapid delayed rectifier K(+) channel (I(Kr)), in BrS. METHODS AND RESULTS In two unrelated SCN5A mutation-negative patients, different amino acid changes in the C-terminal domain of the HERG channel (G873S and N985S) were identified. Voltage-clamp experiments on transfected HEK-293 cells show that these changes increase I(Kr) density and cause a negative shift of voltage-dependent inactivation, resulting in increased rectification. Action potential (AP) clamp experiments reveal increased transient HERG peak currents (I(peak)) during phase-0 and phase-1 of the ventricular AP, particularly at short cycle length. Computer simulations demonstrate that the increased I(peak) enhances the susceptibility to loss of the AP-dome typically in right ventricular subepicardial myocytes, thereby contributing to the BrS phenotype. CONCLUSION Our study reveals a modulatory role of I(Kr) in BrS. These findings may provide better understanding of BrS and have implications for diagnosis and therapy.
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A functional polymorphism in the SULT1A1 gene (G638A) is associated with risk of lung cancer in relation to tobacco smoking.
Liang, G, Miao, X, Zhou, Y, Tan, W, Lin, D
Carcinogenesis. 2004;(5):773-8
Abstract
Sulfotransferase 1A1, an important member of sulfotransferase superfamily, is involved in the biotransformation of many compounds including tobacco carcinogens. A single nucleotide polymorphism (G638A) in the sulfotransferase 1A1 (SULT1A1) gene causes Arg213His amino acid change and consequently results in significantly reduced enzyme activity and thermostability. We thus hypothesized that the variant SULT1A1 allele may protect against the risk of lung cancer related to tobacco smoking. To examine this hypothesis, we analyzed 805 patients with lung cancer and 809 controls for this polymorphism in a hospital-based, case-control study. We observed that, compared with the GG genotype, the variant SULT1A1 genotype (638GA or AA) was associated with a significantly increased risk for overall lung cancer [odds ratio (OR) 1.85; 95% confidence interval (CI) 1.44-2.37]. Stratification analysis showed that the increased risk of lung cancer related to the variant SULT1A1 genotypes was more pronounced in younger subjects and limited to smokers but not non-smokers [OR 2.28 (95% CI 1.66-3.13) versus OR 1.35 (95% CI 0.91-1.99); P for homogeneity = 0.000]. Furthermore, the risk of lung cancer for the variant genotypes was increased consistently with cumulative smoking dose, with the ORs being 1.66 (95% CI, 0.75-3.68), 2.28 (95% CI, 1.47-3.54) and 3.35 (95% CI, 1.71-6.57) for those who smoked <15 pack-years, 15-36 pack-years and >36 pack-years, respectively (P for trend = 0.000). When analysis was stratified by histological subtypes of lung cancer, consistent results were observed for all three major types of the cancer, i.e. squamous cell carcinoma, adenocarcinoma and other types. Our results, which are against the original hypothesis, demonstrate that the variant SULT1A1 638A allele is associated with susceptibility to lung cancer in relation to tobacco smoking.