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Chen YC, Liaw YC, Nfor ON, Hsiao CH, Zhong JH, Wu SL, Liaw YP. Epigenetic regulation of Parkinson's disease risk variant GPNMB cg17274742 methylation by sex and exercise from Taiwan Biobank. Front Aging Neurosci 2023; 15:1235840. [PMID: 37744396 PMCID: PMC10513104 DOI: 10.3389/fnagi.2023.1235840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
Background Parkinson's disease (PD) is a complex neurodegenerative disease with an elusive etiology that involves the interaction between genetic, behavioral, and environmental factors. Recently, epigenetic modifications, particularly DNA methylation, have been recognized to play an important role in the onset of PD. Glycoprotein non-metastatic melanoma protein B (GPNMB), a type I transmembrane protein crucial for immune cell activation and maturation, has emerged as a potential biomarker for the risk of PD. This research aims to investigate the influence of exercise and gender on the regulation of methylation levels of GPNMB cg17274742 in individuals. Methods We analyze data from 2,474 participants in the Taiwan Biobank, collected from 2008 and 2016. Methylation levels at the GPNMB cg17274742 CpG site were measured using Illumina Infinium MethylationEPIC beads. After excluding individuals with incomplete data or missing information on possible risk factors, our final analysis included 1,442 participants. We used multiple linear regression models to assess the association between sex and exercise with adjusted levels of GPNMB cg17274742 for age, BMI, smoking, drinking, coffee consumption, serum uric acid levels, and hypertension. Results Our results demonstrated that exercise significantly influenced the methylation levels of GPNMB cg17274742 in males (β = -0.00242; p = 0.0026), but not in females (β = -0.00002362; p = 0.9785). Furthermore, male participants who exercised showed significantly lower levels of methylation compared to the reference groups of the female and non-exercising reference groups (β = -0.00357; p = 0.0079). The effect of the interaction between gender and exercise on the methylation of GPNMB cg17274742 was statistically significant (p = 0.0078). Conclusion This study suggests that gender and exercise can modulate GPNMB cg17274742, with hypomethylation observed in exercise men. More research is needed to understand the underlying mechanisms and implications of these epigenetic changes in the context of risk and prevention strategies.
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Affiliation(s)
- Yen-Chung Chen
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
- Department of Neurology, Changhua Christian Hospital, Changhua, Taiwan
| | - Yi-Chia Liaw
- Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Oswald Ndi Nfor
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Chih-Hsuan Hsiao
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Ji-Han Zhong
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Shey-Lin Wu
- Department of Neurology, Changhua Christian Hospital, Changhua, Taiwan
- Department of Electrical Engineering, Changhua National University of Education, Changhua, Taiwan
| | - Yung-Po Liaw
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Imaging, Chung Shan Medical University Hospital, Taichung, Taiwan
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
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2
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Liaw YC, Wang YF, Chen WT, Chen SP, Wu JW, Chen ST, Lai KL, Fuh JL, Wang SJ. Sex-related differences in cluster headache: A hospital-based study in Taiwan. Cephalalgia 2022; 42:1532-1542. [PMID: 36003003 DOI: 10.1177/03331024221120054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVES To compare the clinical profiles between male and female cluster headache patients from a large cohort. METHODS This hospital-based study enrolled patients diagnosed with cluster headache between 1997 to 2021. Participants completed structured questionnaires collecting information on demographics, clinical profiles, and quality of life. Treatment regimens and effectiveness were determined through medical chart review. All variables were compared between the sexes. RESULTS In total, 798 patients (M/F:659/139) were enrolled. The male-to-female ratio was 4.7:1 for the full study period, but it declined from 5.2:1 to 4.3:1 for patients enrolled before and after 2010, respectively. The frequencies of chronic cluster headache (M:1.2%, F:1.4%) and aura (M:0.3%, F:0.7%) were low but similar between the sexes. Most headache features showed no difference between men and women. Female patients had significantly longer attack duration, shorter inter-bout duration, higher frequencies for eyelid edema, nausea and vomiting and lower frequencies for conjunctival injection and pacing. Sex difference did not influence headache-associated disability, anxiety, or depression, but poor sleep quality was significantly more common in women. Among menstruating women, 22/122 (18.0%) reported worsening headaches during menses. The effectiveness of treatment was similar between the sexes. CONCLUSIONS Despite a decline of male-to-female ratio in the past two decades, most clinical profiles were similar between the sexes.
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Affiliation(s)
- Yi-Chia Liaw
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yen-Feng Wang
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Wei-Ta Chen
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Department of Neurology, Keelung Hospital, Ministry of Health and Welfare, Keelung, Taiwan
| | - Shih-Pin Chen
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Division of Translational Research, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jr-Wei Wu
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shu-Ting Chen
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Department of Radiology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Kuan-Lin Lai
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Jong-Ling Fuh
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shuu-Jiun Wang
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
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3
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Lin CH, Nfor ON, Ho CC, Hsu SY, Tantoh DM, Liaw YC, Daria MR, Chen CH, Liaw YP. Association of ADH1B polymorphism and alcohol consumption with increased risk of intracerebral hemorrhagic stroke. J Transl Med 2021; 19:227. [PMID: 34051793 PMCID: PMC8164791 DOI: 10.1186/s12967-021-02904-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/22/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Alcohol consumption is one of the modifiable risk factors for intracerebral hemorrhage, which accounts for approximately 10-20% of all strokes worldwide. We evaluated the association of stroke with genetic polymorphisms in the alcohol metabolizing genes, alcohol dehydrogenase 1B (ADH1B, rs1229984) and aldehyde dehydrogenase 2 (ALDH2, rs671) genes based on alcohol consumption. METHODS Data were available for 19,500 Taiwan Biobank (TWB) participants. We used logistic regression models to test for associations between genetic variants and stroke. Overall, there were 890 individuals with ischemic stroke, 70 with hemorrhagic stroke, and 16,837 control individuals. Participants with ischemic but not hemorrhagic stroke were older than their control individuals (mean ± SE, 58.47 ± 8.17 vs. 48.33 ± 10.90 years, p < 0.0001). ALDH2 rs671 was not associated with either hemorrhagic or ischemic stroke among alcohol drinkers. However, the risk of developing hemorrhagic stroke was significantly higher among ADH1B rs1229984 TC + CC individuals who drank alcohol (odds ratio (OR), 4.85; 95% confidence interval (CI) 1.92-12.21). We found that the test for interaction was significant for alcohol exposure and rs1229984 genotypes (p for interaction = 0.016). Stratification by alcohol exposure and ADH1B rs1229984 genotypes showed that the risk of developing hemorrhagic stroke remained significantly higher among alcohol drinkers with TC + CC genotype relative to those with the TT genotype (OR, 4.43, 95% CI 1.19-16.52). CONCLUSIONS Our study suggests that the ADH1B rs1229984 TC + CC genotype and alcohol exposure of at least 150 ml/week may increase the risk of developing hemorrhagic stroke among Taiwanese adults.
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Affiliation(s)
- Chun-Hsiang Lin
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung, 40201, Taiwan
- Department of Neurology, Yuanlin Christian Hospital, Yuanlin, Changhua County, 510, Taiwan
| | - Oswald Ndi Nfor
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung, 40201, Taiwan
| | - Chien-Chang Ho
- Department of Physical Education, Fu Jen Catholic University, New Taipei City, 24205, Taiwan
- Research and Development Center for Physical Education, Health and Information Technology, Fu Jen Catholic University, New Taipei City, 24205, Taiwan
| | - Shu-Yi Hsu
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung, 40201, Taiwan
| | - Disline Manli Tantoh
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung, 40201, Taiwan
- Department of Medical Imaging, Chung Shan Medical University Hospital, Taichung City, 40201, Taiwan
| | - Yi-Chia Liaw
- Department of Medical Education, Taipei Veterans General Hospital, Taipei, 11217, Taiwan
| | - Mochly-Rosen Daria
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Che-Hong Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Yung-Po Liaw
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung, 40201, Taiwan.
- Department of Medical Imaging, Chung Shan Medical University Hospital, Taichung City, 40201, Taiwan.
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Lin CJ, Chang FC, Lin CJ, Liaw YC, Tu PC, Wang PN, Saver JL, Lee IH. Long-term cognitive and multimodal imaging outcomes after carotid artery stenting vs intensive medication alone for severe asymptomatic carotid stenosis. J Formos Med Assoc 2021; 121:134-143. [PMID: 33674231 DOI: 10.1016/j.jfma.2021.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/04/2021] [Accepted: 02/07/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Severe carotid stenosis is associated with cognitive impairment, which may be attributed to asymptomatic microembolism and/or chronic hypoperfusion. We aim to evaluate the long-term cognitive and brain connectivity outcomes of carotid artery stenting (CAS) for asymptomatic ≥70% stenosis of the extracranial internal carotid artery (ICA). METHODS We conducted a non-randomized controlled study to compare intensive medical therapy alone (Med) or in combination with carotid artery stenting for the composite vascular events, neuropsychological, and multimodal magnetic resonance perfusion imaging and diffusion tensor imaging outcomes. RESULTS Sixty-nine patients were followed for a mean of 2.3 years (31 Med, 38 CAS) and 11 patients had composite vascular events of all-cause death, ischemic stroke, or myocardial infarction (6 Med vs 5 CAS). Forty-six asymptomatic subjects completed neuropsychological and multimodality imaging follow-ups (23 Med, 23 CAS). Compared to the Med group, the CAS group had a modest improvement of 12-item delayed verbal memory (8.9 ± 2.4 to 9.8 ± 2.7 vs 9.0 ± 2.1 to 8.9 ± 2.3, p = 0.04), but not in global cognition, attention or executive function, which was associated with increased structural connectivity of fractional anisotropy at the ipsilateral deep white matter. Importantly, the memory improvement was correlated with the perfusion increment at the ipsilateral middle cerebral artery territory. CONCLUSION For asymptomatic extracranial carotid steno-occlusion, successful carotid revascularization in addition to intensive medical treatment may potentially benefit cognitive reserve and connectivity strength which are partly attributed to restoration of non-critical hypoperfusion.
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Affiliation(s)
- Chun-Jen Lin
- Division of Cerebrovascular Diseases, Neurological Institute, Taipei Veterans General Hospital, Taiwan; School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Feng-Chi Chang
- School of Medicine, National Yang-Ming University, Taipei, Taiwan; Department of Radiology, Taipei Veterans General Hospital, Taiwan
| | - Chung-Jung Lin
- School of Medicine, National Yang-Ming University, Taipei, Taiwan; Department of Radiology, Taipei Veterans General Hospital, Taiwan
| | - Yi-Chia Liaw
- Division of Cerebrovascular Diseases, Neurological Institute, Taipei Veterans General Hospital, Taiwan
| | - Pei-Chi Tu
- Department of Medical Research, Taipei Veterans General Hospital, Taiwan; Institute of Philosophy of Mind and Cognition, National Yang-Ming University, Taipei, Taiwan
| | - Pei-Ning Wang
- Division of Cerebrovascular Diseases, Neurological Institute, Taipei Veterans General Hospital, Taiwan; School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | | | - I-Hui Lee
- Division of Cerebrovascular Diseases, Neurological Institute, Taipei Veterans General Hospital, Taiwan; Institute of Brain Science, Brain Research Center, National Yang-Ming University, Taipei, Taiwan.
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Tantoh DM, Lee KJ, Nfor ON, Liaw YC, Lin C, Chu HW, Chen PH, Hsu SY, Liu WH, Ho CC, Lung CC, Wu MF, Liaw YC, Debnath T, Liaw YP. Methylation at cg05575921 of a smoking-related gene (AHRR) in non-smoking Taiwanese adults residing in areas with different PM 2.5 concentrations. Clin Epigenetics 2019; 11:69. [PMID: 31060609 PMCID: PMC6503351 DOI: 10.1186/s13148-019-0662-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/08/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND DNA methylation is associated with cancer, metabolic, neurological, and autoimmune disorders. Hypomethylation of aryl hydrocarbon receptor repressor (AHRR) especially at cg05575921 is associated with smoking and lung cancer. Studies on the association between AHRR methylation at cg05575921 and sources of polycyclic aromatic hydrocarbon (PAH) other than smoking are limited. The aim of our study was to assess the pattern of blood DNA methylation at cg05575921 in non-smoking Taiwanese adults living in areas with different PM2.5 levels. METHODS Data on blood DNA methylation, smoking, and residence were retrieved from the Taiwan Biobank dataset (2008-2015). Current and former smokers, as well as individuals with incomplete information were excluded from the current study. The final analysis included 708 participants (279 men and 429 women) aged 30-70 years. PM2.5 levels have been shown to increase as one moves from the northern through central towards southern Taiwan. Based on this trend, the study areas were categorized into northern, north-central, central, and southern regions. RESULTS Living in PM2.5 areas was associated with lower methylation levels: compared with the northern area (reference area), living in north-central, central, and southern areas was associated with lower methylation levels at cg05575921. However, only methylation levels in those living in central and southern areas were significant (β = - 0.01003, P = 0.009 and β = - 0.01480, P < 0.001, respectively. Even though methylation levels in those living in the north-central area were not statistically significant, the test for linear trend was significant (P < 0.001). When PM2.5 was included in the regression model, a unit increase in PM2.5 was associated with 0.00115 (P < 0.001) lower cg05575921 methylation levels. CONCLUSION Living in PM2.5 areas was inversely associated with blood AHRR methylation levels at cg05575921. The methylation levels were lowest in participants residing in southern followed by central and north-central areas. Moreover, when PM2.5 was included in the regression model, it was inversely associated with methylation levels at cg05575921. Blood methylation at cg05575921 (AHRR) in non-smokers might indicate different exposures to PM2.5 and lung cancer which is a PM2.5-related disease.
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Affiliation(s)
- Disline Manli Tantoh
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Kuan-Jung Lee
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Oswald Ndi Nfor
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Yi-Chia Liaw
- Department of Medical Education, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chin Lin
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Hou-Wei Chu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Pei-Hsin Chen
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Shu-Yi Hsu
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Wen-Hsiu Liu
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Chen-Chang Ho
- Department of Physical Education, Fu-Jen Catholic University, New Taipei City, Taiwan
| | - Chia-Chi Lung
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Ming-Fang Wu
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung City, Taiwan
| | - Yi-Ching Liaw
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Tonmoy Debnath
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Yung-Po Liaw
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan. .,Department of Family and Community Medicine, Chung Shan Medical University Hospital, Taichung City, Taiwan.
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Tantoh DM, Wu MF, Ho CC, Lung CC, Lee KJ, Nfor ON, Liaw YC, Hsu SY, Chen PH, Lin C, Chu HW, Liaw YC, Liaw YP. SOX2 promoter hypermethylation in non-smoking Taiwanese adults residing in air pollution areas. Clin Epigenetics 2019; 11:46. [PMID: 30867047 PMCID: PMC6416982 DOI: 10.1186/s13148-019-0647-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 03/03/2019] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Both SOX2 promoter methylation and air pollution have been associated with lung cancer risk. However, little has been done to assess SOX2 promoter methylation in individuals living in air pollution areas. The aim of this study was to investigate SOX2 promoter methylation in non-smoking Taiwanese adults living in areas with different levels of air pollution especially particulate matter with diameter < 2.5 μm (PM2.5). METHODS A total of 1142 individuals aged 30-70 years were recruited. Data on SOX2 methylation, residence, age, and exposure to second-hand smoke (SHS) among others were extracted from the Taiwan Biobank dataset (2008-2015). After excluding former and current smokers, alongside those with incomplete information, a total of 461 non-smokers comprising 176 men and 285 women were included in the study. Participants' residences were grouped under northern and central/southern areas because air pollution (PM2.5) is lower in northern compared to central and southern areas. RESULTS The methylation levels in men (0.16310 ± 0.01230) and women (0.15740 ± 0.01240) were significantly different (P < .0001). In both sexes, the SOX2 promoter region was shown to be significantly hypermethylated in central and southern areas compared with the northern areas. The regression coefficient (β) was 0.00331 (P = 0.0257) in men and 0.00514 (P < .0001) in women. CONCLUSION SOX2 was significantly hypermethylated in both men and women residing in central and southern areas. The consistency in the results for both sexes shows that SOX2 promoter methylation could serve as a potential biomarker for industrial air pollution exposure. Moreover, it might reflect predisposition to cancer. Hence, healthy non-smokers at precancerous stages who have not been clinically diagnosed could be identified.
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Affiliation(s)
- Disline Manli Tantoh
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Ming-Fang Wu
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung City, Taiwan
| | - Chien-Chang Ho
- Department of Physical Education, Fu-Jen Catholic University, New Taipei City, Taiwan
| | - Chia-Chi Lung
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Kuan-Jung Lee
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Oswald Ndi Nfor
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Yi-Chia Liaw
- Department of Medical Education, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Shu-Yi Hsu
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Pei-Hsin Chen
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Chin Lin
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Hou-Wei Chu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Ching Liaw
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yung-Po Liaw
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan.
- Department of Family and Community Medicine, Chung Shan Medical University Hospital, Taichung City, Taiwan.
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Leung KW, Liaw YC, Chan SC, Lo HY, Musayev FN, Chen JZ, Fang HJ, Chen HM. Significance of local electrostatic interactions in staphylococcal nuclease studied by site-directed mutagenesis. J Biol Chem 2001; 276:46039-45. [PMID: 11598114 DOI: 10.1074/jbc.m106620200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this paper, we show that amino acids Glu(73) and Asp(77) of staphylococcal nuclease cooperate unequally with Glu(75) to stabilize its structure located between the C-terminal helix and beta-barrel of the protein. Amino acid substitutions E73G and D77G cause losses of the catalytic efficiency of 24 and 16% and cause thermal stability losses of 22 and 26%, respectively, in comparison with the wild type (WT) protein. However, these changes do not significantly change global and local secondary structures, based on measurements of fluorescence and CD(222 nm). Furthermore, x-ray diffraction analysis of the E75G protein shows that the overall structure of mutant and WT proteins is similar. However, this mutation does cause a loss of essential hydrogen bonding and charge interactions between Glu(75) and Lys(9), Tyr(93), and His(121). In experiments using double point mutations, E73G/D77G, E73G/E75G, and E75G/D77G, significant changes are seen in all mutants in comparison with WT protein as measured by fluorescence and CD spectroscopy. The losses of thermal stability are 47, 59, and 58%, for E73G/D77G, E73G/E75G, and E75G/D77G, respectively. The triple mutant, E73G/E75G/D77G, results in fluorescence intensity and CD(222 nm) close to those of the denatured state and in a thermal stability loss of 65% relative to the WT protein. Based on these results, we propose a model in which significant electrostatic interactions result in the formation of a locally stable structure in staphylococcal nuclease.
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Affiliation(s)
- K W Leung
- Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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Huang YT, Liaw YC, Gorbatyuk VY, Huang TH. Backbone dynamics of Escherichia coli thioesterase/protease I: evidence of a flexible active-site environment for a serine protease. J Mol Biol 2001; 307:1075-90. [PMID: 11286557 DOI: 10.1006/jmbi.2001.4539] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Escherichia coli thioesterase/protease I (TEP-I) is a member of a novel subclass of the lipolytic enzymes with a distinctive GDSLS motif. In addition to possessing thioesterase and protease activities, TEP-I also exhibits arylesterase activity. We have determined the (15)N nuclear magnetic spin relaxation rates, R(1) and R(2), and the steady state (1)H-(15)N heteronuclear Overhauser effect, measured at both 11.74 T and 14.09 T, of (u-(15)N) TEP-I. These data were analyzed using model-free formalism (with axially symmetric rotational diffusion anisotropy) to extract the backbone dynamics of TEP-I. The results reveal that the core structure of the central beta-sheet and the long alpha-helices are rigid, while the binding pocket appears to be rather flexible. The rigid core serves as a scaffold to anchor the essential loops, which form the binding pocket. The most flexible residues display large amplitude fast (ps/ns time-scale) motion and lie on one stripe whose orientation is presumed to be the ligand-binding orientation. We also detected the presence of several residues displaying slow (microseconds/ms time-scale) conformational exchanging processes. These residues lie around the binding pocket and are oriented perpendicularly to the orientation of the flexible stripe. Two of the putative catalytic triads, Ser10 and His157, and their neighbors show motion on the microseconds/ms time-scale, suggesting that their slow motion may have a role in catalysis, in addition to their possible roles in ligand binding. The presence of a flexible substrate-binding pocket may also facilitate binding to a wide range of substrates and confer the versatile functional property of this protein.
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Affiliation(s)
- Y T Huang
- Institute of Biomedical Sciences, Nankang Taipei, Taiwan, 11529, Rupublic of China
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9
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Su S, Gao YG, Robinson H, Liaw YC, Edmondson SP, Shriver JW, Wang AH. Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs. J Mol Biol 2000; 303:395-403. [PMID: 11031116 DOI: 10.1006/jmbi.2000.4112] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sso7d and Sac7d are two small chromatin proteins from the hyperthermophilic archaeabacterium Sulfolobus solfataricus and Sulfolobus acidocaldarius, respectively. The crystal structures of Sso7d-GTGATCGC, Sac7d-GTGATCGC and Sac7d-GTGATCAC have been determined and refined at 1.45 A, 2.2 A and 2.2 A, respectively, to investigate the DNA binding property of Sso7d/Sac7d in the presence of a T-G mismatch base-pair. Detailed structural analysis revealed that the intercalation site includes the T-G mismatch base-pair and Sso7d/Sac7d bind to that mismatch base-pair in a manner similar to regular DNA. In the Sso7d-GTGATCGC complex, a new inter-strand hydrogen bond between T2O4 and C14N4 is formed and well-order bridging water molecules are found. The results suggest that the less stable DNA stacking site involving a T-G mismatch may be a preferred site for protein side-chain intercalation.
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Affiliation(s)
- S Su
- Center for Biophysics and COmputational BIology, University of Illinois at Urbana-Champaign, 61801, USA
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10
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Tsai YW, Chia JS, Shiau YY, Chou HC, Liaw YC, Lou KL. Three-dimensional modelling of the catalytic domain of Streptococcus mutans glucosyltransferase GtfB. FEMS Microbiol Lett 2000; 188:75-9. [PMID: 10867237 DOI: 10.1111/j.1574-6968.2000.tb09171.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Glucosyltransferases (GtfB/C/D) of Streptococcus mutans, a pathogen for human dental caries, synthesize water-insoluble glucan through the hydrolysis of sucrose. Genetic and biochemical approaches have identified several active sites of these enzymes, but no three-dimensional (3D) structural evidence is yet available to elucidate the subdomain arrangement and molecular mechanism of catalysis. Based on a combined sequence and secondary structure alignment against known crystal structures of segments from closely related proteins, we propose here the 3D model of an N-terminal domain essential for the sucrose binding and splitting in GtfB. A Tim-barrel of (alpha/beta)(8) structural characteristics is revealed and the structural correlation for two peptides is described.
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Affiliation(s)
- Y W Tsai
- Graduate Institute of Oral Biology, College of Medicine, National Taiwan University, Taipei
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11
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Panneerselvam K, Lin SC, Liu CL, Liaw YC, Lin JY, Lu TH. Crystallization of agglutinin from the seeds of Abrus precatorius. Acta Crystallogr D Biol Crystallogr 2000; 56:898-9. [PMID: 10930837 DOI: 10.1107/s0907444900005047] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/1999] [Accepted: 03/21/2000] [Indexed: 11/10/2022]
Abstract
Agglutinin protein purified from the seeds of Abrus precatorius has a high antitumour activity and was crystallized at room temperature with polyethylene glycol 8000 as the precipitant. The agglutinin crystal diffracted to 3.45 A and belongs to one of two possible tetragonal space groups, P4(1)2(1)2 or P4(3)2(1)2, with unit-cell parameters a = b = 141.91, c = 105.63 A. The asymmetric unit contains a heterotetrameric protein molecule of molecular weight 134 kDa and has a solvent content of approximately 38%.
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Affiliation(s)
- K Panneerselvam
- Department of Physics, National Tsing Hua University, Hsinchu 30055, Taiwan
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12
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Lo YC, Lee YL, Shaw JF, Liaw YC. Crystallization and preliminary X-ray crystallographic analysis of thioesterase I from Escherichia coli. Acta Crystallogr D Biol Crystallogr 2000; 56:756-7. [PMID: 10818355 DOI: 10.1107/s0907444900004339] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Escherichia coli thioesterase I specifically catalyzes the deacylation of fatty acyl-CoA thioesters, especially those with long acyl groups (C(12)-C(18)). Single crystals of thioesterase I (E.C. 3. 1.2.2) from E. coli have been obtained using methoxypolyethylene glycol 5000 (PEG-MME 5K) as a precipitant at room temperature in 21 d. The crystals belong to the tetragonal space group P4(1)2(1)2 or its enantiomorph P4(3)2(1)2, with unit-cell parameters a = b = 50.85 (7), c = 171.5 (1) A. The crystals diffract to beyond 2.4 A resolution. There is one molecule of molecular weight 20.5 kDa in the asymmetric unit, with a solvent content of 55%.
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Affiliation(s)
- Y C Lo
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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13
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Abstract
To investigate a potential candidate material for making artificial red blood cells to supplement blood transfusion, the X-ray structure of porcine haemoglobin at 1.8 A resolution was determined as part of research towards synthesizing human blood. Porcine haemoglobin was crystallized by the vapor-diffusion method, producing crystals of dimensions 0.3-0.5 mm after successive seeding. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 68.10, b = 72.27, c = 114.85 A. The initial phase was determined by the molecular-replacement method, using human oxyhaemoglobin as a model. The final R factor was 21.1% for 36 820 reflections after validation of 574 water molecules. The r.m.s. deviations of bond lengths, angles, torsion angles and improper angles from their ideal values are 0.017 A, 3.0, 20.6 and 1.8 degrees, respectively. The average B factor is 33.63 A(2) for the haemoglobin molecule and 50.53 A(2) for the water molecules. The structure could be superimposed on a 2.8 A resolution structure with an r.m.s. difference of 0.59 A in main-chain atomic positions and 1. 27 A in side-chain atomic positions. Porcine and human haemoglobins are compared. A tentative model for artificial blood is proposed based on the complementarity relationship of the surface charges between haemoglobin and the surrounding cell membrane.
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Affiliation(s)
- T H Lu
- Department of Physics, National Tsing-Hua University, Hsinchu 30043, Taiwan.
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14
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Gao YG, Robinson H, Guan Y, Liaw YC, van Boom JH, van der Marel GA, Wang AH. Molecular structure of two crystal forms of cyclic triadenylic acid at 1A resolution. J Biomol Struct Dyn 1998; 16:69-76. [PMID: 9745896 DOI: 10.1080/07391102.1998.10508228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The three dimensional structures of cyclic deoxytriadenylic acid, c-d(ApApAp), from two different trigonal crystal forms (space groups P3 and R32) have been determined by x-ray diffraction analysis at 1A resolution. Both structures were solved by direct methods and refined by anisotropic least squares refinement to R-factors of 0.109 and 0.137 for the P3 and R32 forms, respectively. In both crystal forms, each of the two independent c-d(ApApAp) molecules sits on the crystallographic 3-fold axis. All four independent c-d(ApApAp) molecules have similar backbone conformations. The deoxyriboses are in the S-type pucker with pseudorotation angles ranging from 156.7 degrees to 168.6 degrees and the bases have anti glycosyl torsion angles (chi falling in two ranges, one at -104.3 degrees and the other ranging from -141.0 degrees to -143.8 degrees). In the R32 form, a hexahydrated cobalt(II) ion is found to coordinate through bridging water molecules to N1, N3, and N7 atoms of three adjacent adenines and oxygen atoms of phosphates. Comparison with other structures of cyclic oligonucleotides indicates that the sugar adopts N-type pucker in cyclic dinucleotides and S-type pucker in cyclic trinucleotides, regardless whether the sugar is a ribose or a deoxyribose.
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Affiliation(s)
- Y G Gao
- Department of Cell & Structural Biology, University of Illinois at Urbana-Champaign, Urbana 61801, USA
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15
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Mei HC, Liaw YC, Li YC, Wang DC, Takagi H, Tsai YC. Engineering subtilisin YaB: restriction of substrate specificity by the substitution of Gly124 and Gly151 with Ala. Protein Eng 1998; 11:109-17. [PMID: 9605545 DOI: 10.1093/protein/11.2.109] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The 3-D structure of subtilisin YaB was computer modelled using the structures of subtilisin BPN', subtilisin Carlsberg and thermitase as templates. Gly124 and Gly151 located on both sides of the waist of the S1 pocket were selected for site-directed mutagenesis based on the modelled structure. The mutated ale genes coding for the mutant subtilisin YaB were expressed in Bacillus subtilis DB104. All of the G124 and G151 series of mutants exhibited an increase of relative catalytic activity for elastin-orcein against casein and myofibrillar proteins. The S1 substrate specificity of G124A, G124V and G151A mutants were assessed using various carbobenzoxy-amino acid-nitrophenyl esters and succinyl-Ala-Ala-(Pro or Val)-(Ala, Phe or Leu)-p-nitroanilide [AA(P/V) (A/F/L)]. While G124A and G124V mutants hydrolyzed only Ala and Gly esters, G151A mutant hydrolyzed Ala, Leu and Gly esters. The G124A and G124V mutants did not hydrolyze AAPF and AAPL. However, these two mutants hydrolyzed AAPA and AAVA with kcat/Km values approximately 3-10-fold higher than those of the wild-type enzyme. The G151A mutant did not hydrolyze AAPF, but hydrolyzed AAPL, AAPA and AAVA with kcat/Km values approximately 1-4-fold higher than those of the wild-type enzyme. These results clearly indicate that the S1 substrate specificity of G124A and G124V mutants was restricted to Ala and Gly, and G151A mutant to Ala, Gly and Leu.
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Affiliation(s)
- H C Mei
- Institute of Biochemistry, National Yang-Ming University, Taipei, Taiwan, Republic of China
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16
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Liu LF, Liaw YC, Tam MF. Characterization of chicken-liver glutathione S-transferase (GST) A1-1 and A2-2 isoenzymes and their site-directed mutants heterologously expressed in Escherichia coli: identification of Lys-15 and Ser-208 on cGSTA1-1 as residues interacting with ethacrynic acid. Biochem J 1997; 327 ( Pt 2):593-600. [PMID: 9359434 PMCID: PMC1218834 DOI: 10.1042/bj3270593] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Escherichia coli-expressed chicken-liver glutathione S-transferase, cGSTA1-1, displays high ethacrynic acid (EA)-conjugating activity. Molecular modelling of cGSTA1-1 with EA in the substrate binding site reveals that the side chain of Phe-111 protrudes into the substrate binding site and possibly interacts with EA. Replacement of Phe-111 with alanine resulted in an enzyme (F111A mutant) with a 4.5-fold increase in EA-conjugating activity (9.2 mmol/min per mg), and an incremental Gibbs free energy (DeltaDeltaG) of 4.0 kJ/mol lower than that of the wild-type cGSTA1-1. Two other amino acid residues that possibly interact with EA are Ser-208 and Lys-15. Substitution of Ser-208 with methionine generated a cGSTA1-1(F111AS208M) double mutant that has low EA-conjugating activity (2.0 mmol/min per mg) and an incremental Gibbs free energy of +3.9 kJ/mol greater than the cGSTA1-1(F111A) single mutant. The cGSTA1-1(F111A) mutant, with an additional Lys-15-to-leucine substitution, lost 90% of the EA-conjugating activity (0.55 mmol/min per mg). The Km values of the cGSTA1-1(F111A) and cGSTA1-1(F111AK15L) mutants for EA are nearly identical. The wild-type cGSTA2-2 isoenzyme has a low EA-conjugating activity (0.56 mmol/min per mg). The kcat of this reaction can be increased 2. 5-fold by substituting Arg-15 and Glu-104 with lysine and glycine respectively. The KmEA of the cGSTA2-2(R15KE104G) double mutant is nearly identical with that of the wild-type enzyme. Another double mutant, cGSTA2-2(E104GL208S), has a KmEA that is 3.3-fold lower and a kcat that is 1.8-fold higher than that of the wild-type enzyme. These results, taken together, illustrate the interactions of Lys-15 and Ser-208 on cGSTA1-1 with EA.
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Affiliation(s)
- L F Liu
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan, Republic of China
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17
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Chern JW, Leu YL, Wang SS, Jou R, Lee CF, Tsou PC, Hsu SC, Liaw YC, Lin HM. Synthesis and cytotoxic evaluation of substituted sulfonyl-N-hydroxyguanidine derivatives as potential antitumor agents. J Med Chem 1997; 40:2276-86. [PMID: 9216847 DOI: 10.1021/jm9607818] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A series of sulfonyl-N-hydroxyguanidine derivatives was designed and synthesized for cytotoxic evaluation as potential anticancer agents on the basis of the lead compound LY-181984. Replacement of the ureido moiety of the lead compound with hydroxyguanidine provided a stable cytotoxic agent. The conformation of sulfonyl-N-hydroxyguanidine derivatives, such as N-(4-chlorophenyl)-N'-[(benzo[2,1,3]thiadiazol-4-yl)sulfonyl]-N"- hydroxyguanidine (4g), investigated utilizing HMBC NMR, theoretical calculations, and X-ray crystallography, indicated stacking of the two aromatic rings. The derivatives were evaluated for in vitro cytoxicity against five human tumor cell lines, including HepG2, TSGH 8302, COLO 205, KB, and MOLT-4. The cytotoxic activities of the derived compounds against the human tumor cell lines were equal to or greater than that of the lead compound. N-(4-Chlorophenyl)-N'-[[3,5-dichloro-4-(4-nitrophenoxy)phenyl]sulfonyl]- N"- hydroxyguanidine (4n) and N-(4-chlorophenyl)-N'-[[3,5-dichloro-4-(2-chloro-4-nitrophenoxy)phenyl] sulfonyl]-N"-hydroxyguanidine (4o) exhibited the greatest growth inhibition of solid tumor cell lines. Compound 4o was found to possess antitumor activity against murine K1735/M2 melanoma xenografts.
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Affiliation(s)
- J W Chern
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei, Republic of China.
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18
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Chen JK, Hung CH, Liaw YC, Lin JY. Identification of amino acid residues of abrin-a A chain is essential for catalysis and reassociation with abrin-a B chain by site-directed mutagenesis. Protein Eng 1997; 10:827-33. [PMID: 9342148 DOI: 10.1093/protein/10.7.827] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Abrin is a toxic protein consisting of two subunits, an enzymatic A chain (ABRaA) and a lectin-active B chain (ABRaB), linked by a disulfide bond. Site-directed mutagenesis was performed using PCR to study how the conserved amino acid residues, Tyr74, Tyr113, Glu164 and Trp198, around the active site of ABRaA are involved in enzyme catalysis, enzyme-substrate recognition and reassociation of ABRaA with ABRaB. The protein biosynthesis inhibitory activities of Y74F, Y113F and W198F were decreased moderately to that of wild type reABRaA, while that of E164Q decreased dramatically. Kinetic analysis showed that the kat of Y74F, Y113F and W198F resembled that of wild type, while the Km increased significantly. W198F did not reassociate with ABRaB to form heterodimers, while Y74F, Y113F and E164Q did. SDS-PAGE analysis of ABRaA treated with trypsin showed that reABRaA, Y74F, Y113F and E164Q survived digestion, whereas W198F was not protected from digestion. CD spectra revealed that W198F showed significant conformational changes. These observations suggest that E164 is directly involved in catalysis, and Tyr74, Tyr113 and Trp198 in substrate binding, while Trp198 also plays an important role in maintaining the conformation of ABRaA required for its reassociation with ABRaB.
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Affiliation(s)
- J K Chen
- Institute of Biochemistry, College of Medicine, National Taiwan University, Taipei, Republic of China
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19
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Abstract
Abrin-a is a potent plant toxin that consists of A and B chains linked by a disulfide bond. The abrin-a A chain (AaTA) has N-glycosidase activity while the abrin-a B chain (AaTB) has galactose-binding activity. By partial tryptic digestion, the domain structure of abrin-a was investigated. Seven tryptic fragments with molecular masses greater than 3500 Da were isolated and characterized. One fragment, designated T-21 and consisting of 153 amino acid residues, contained the major part of the second domain of AaTB and, after cross-linking of T-21 with glutaraldehyde, the reaction product had the same level of hemagglutinating activity as native abrin. When the T-21 fragment was conjugated with AaTA, the conjugate inhibited protein biosynthesis in HeLa cells. This suggests that the T-21 fragment is able to bind specifically to cells; its conjugate facilitates membrane translocation of AaTA into cells and consequently inhibits protein biosynthesis. T-21, with a molecular mass less than AaTB, is therefore a potentially useful substance for the preparation of immunotoxins.
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Affiliation(s)
- S H Lin
- Institute of Biochemistry, College of Medicine, National Taiwan University, Taipei, Taiwan, Republic of China
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20
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Lin SC, Yu HH, Liu LF, Lee JY, Huang A, Tam MF, Liaw YC. Crystallization and preliminary X-ray analysis of chicken-liver glutathione S-transferase CL 3-3. Acta Crystallogr D Biol Crystallogr 1996; 52:601-3. [PMID: 15299692 DOI: 10.1107/s0907444995016866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Five different crystal forms of recombinant chicken-liver glutathione S-transferase CL 3-3 have been obtained by the vapor-diffusion method. The form A crystals are monoclinic C2, a = 125.56, b = 85.81, c = 52.71 A and beta = 114.64 degrees, and diffract to 4 A resolution. The form B crystals are monoclinic P2(1), a = 105.13, b = 118.54, c = 62.62 A and beta = 124.74 degrees, and diffract to 2.8 A resolution. The form C crystals are orthorhombic C222(l), a = 101.69, b = 115.46, c = 95.40 A, and diffract to 2.8 A resolution. The form D crystals are tetragonal, P4(1)2(1)2 or P4(3)2(1)2, a = b = 115.31, c = 171.20 A and diffract to 3.5 A resolution. The form E crystals are hexagonal, P6(1) or P6(5), a = b = 104.23, c = 114.35 A, diffract to 3.5 A resolution. Forms A, C and E have one dimer of molecular weight 50 kDa, while forms B and D have two dimers per asymmetric unit, respectively.
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Affiliation(s)
- S C Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, China
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21
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Lee KF, Liaw YC, Shaw PC. Overproduction, purification and characterization of M.EcoHK31I, a bacterial methyltransferase with two polypeptides. Biochem J 1996; 314 ( Pt 1):321-6. [PMID: 8660301 PMCID: PMC1217043 DOI: 10.1042/bj3140321] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The two overlapping genes coding for EcoHK31I methyltransferase have previously been cloned, sequenced and expressed [Lee, Kam and Shaw (1995) Nucleic Acids Res. 23, 103-108]. Here we describe protocols developed to purify polypeptides alpha and beta together or separately, to apparent homogeneity by various chromatographic media. M.EcoHK31I is a heterodimer with a native molecular mass of 61 kDa. Its specific activity towards non-methylated lambda DNA was 3.0 x 10(5) units per mg of protein. The respective denatured molecular masses of polypeptides alpha and beta were 38 and 23 kDa, and their pI values were 8.7 and 6.8. Initial rate kinetic parameters of the native enzyme were 2.0 nM, 0.58 microM and 3 min-1 for KmDNA, KmAdoMet and kcat. respectively, where AdoMet stands for S-adenosyl-L-methionine. Fully active enzyme was reconstituted by co-purifying the two separately synthesized polypeptides, and activity assays confirmed our previous finding that two polypeptides were needed to methylate substrate DNA.
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Affiliation(s)
- K F Lee
- Department of Biochemistry, The Chinese University of Hong Kong
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22
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Abstract
Volvatoxin A2, an ion channel disturbed cardiotoxic and hemolytic protein from the edible mushroom, Volvarilla volvacea, has been crystallized by the vapor diffusion method using polyethylene glycol 4000 and ammonium sulfate in sodium acetate buffer pH 4.6. The best crystals belong to the monoclinic space group C2 with unit cell dimensions a = 155.25 angstroms, b = 58.06 angstroms, c = 116.92 angstroms, and beta = 119.5 degrees. These crystals diffract to at least 2.2 angstroms and there are four molecules of molecular weight 24 kDa per asymmetric unit with a solvent content of 48%.
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Affiliation(s)
- S C Lin
- Institute of Molecular Biology, Taipei, Taiwan, Republic of China
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23
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Abstract
Recent structural analysis of the peptide-MHC complex reveals that an antigenic peptide binds to MHC in only one conformation and that side chains anchoring in the binding pocket would not contact TCR. The identification of all the MHC-anchoring residues on an antigenic peptide is a prerequisite to understand how a given peptide interacts with the TCR. In a combination of binding analysis and model simulation, model peptide lambda repressor cl 16-26 was shown to bind to I-Ek through four anchor residues (Leu18, IIe21, Glu23 and Lys26), a pattern found in many I-Ek-binding peptides. TCR reactivity analysis clearly indicates a great variation in the interaction with cl 16-26 by T cells generated from different strains of I-Ek-bearing mice. Most of the T cell generated from A/J mice reacted with the central regions of cl 16-26, while there is a great diversity on the recognition of cl 16-26 by T cells from C3H and B10.BR mice. Despite the diverse interactions with antigenic peptide by these T cells, most TCR-E-k contacts are limited to the central region of the I-Ek beta-chain. T cells recognizing only the N-terminal part of cl 16-26 were found to contact I-Ek at nearly the same residues as T cells interacting with the C-terminal of cl 16-26. TCR-I-Ek recognition was apparently independent of TCR-cl 16-26 contact. The discordant TCR-peptide and TCR-MHC interaction may represent a unique feature of TCR recognition.
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Affiliation(s)
- M H Feng
- Graduate Institute of Microbiology and Immunology, National Yang-Ming Medical School, Taipei, Taiwan, ROC
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24
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Abstract
Single crystals of arylesterase (EC 3.1.1.2) from Vibrio mimicus have been obtained from ammonium sulfate as a precipitant at room temperature for 2 months. The present crystals diffract up to 2.2 A resolution and belong to monoclinic space group P2(1). The cell dimensions are a = 55.65(1) A, b = 53.46(1) A, c = 65.79(1) A, and beta = 106.54(1) degrees. There are two molecules of molecular weight 22 kDa in an asymmetric unit with a solvent content of 43%.
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Affiliation(s)
- F N Musayev
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
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25
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Abstract
The crystal structure of abrin-a, a type II ribosome-inactivating protein from the seeds of Abrus precatorius, has been determined from a novel crystalline form by the molecular replacement method using the coordinates of ricin. The structure has been refined at 2.14 A to a R-factor of 18.9%. The root-mean-square deviations of bond lengths and angles from the standard values are 0.013 A and 1.82 degrees, respectively. The overall protein folding is similar to that of ricin, but there are differences in the secondary structure, mostly of the A-chain. Several parts of the molecular surface differ significantly; some of them are quite near the active site cleft, and probably influence ribosome recognition. The positions of invariant active site residues remain the same, except the position of Tyr74. Two water molecules of hydrogen-bonded active site residues have been located in the active site cleft. Both of them may be responsible for hydrolyzing the N-C glycosidic bond. The current abrin-a structure is lactose free; this is probably essential for abrin-a crystallization. The B-chain is a glycoprotein, and the positions of several sugar residues of two sugar chains linked to earlier predicted glycosylation sites were determined. One of the sugar chains is a bridge between two neighboring molecules, since one of its mannose residues is connected to the galactose binding site of the neighboring molecule. Another sugar chain covers the surface of the B-chain.
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Affiliation(s)
- T H Tahirov
- Department of Physics, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
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26
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Lee-Huang S, Kung HF, Chen HC, Huang PL, Rybak SM, Huang PL, Bourinbaiar AS, Musayev F, Liaw YC. Crystallization and preliminary X-ray analysis of GAP 31. A protein which inhibits the life cycle of HIV-1. J Mol Biol 1994; 240:92-4. [PMID: 8021945 DOI: 10.1006/jmbi.1994.1421] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
GAP 31 is an anti-HIV plant protein that we have identified and purified to homogeneity from Gelonium multiflorum. It is the first reported example of an anti-HIV agent capable of acting against multiple stages of the viral life cycle, on viral infection and viral replication. GAP 31 is a unique paragon of multi-functional protein. In addition to anti-HIV activity, it also exhibits anti-tumor action, DNA binding, RNA binding and ribosome inactivation. The present crystals diffract up to 2.0 A resolution and belong to monoclinic space group P2(1). The cell dimensions are a = 49.30(2) A, b = 44.57(2) A, c = 137.78(7) A and beta = 98.32(3) degrees. There are two molecules of molecular weight 31 kDa in an asymmetric unit with a solvent content of 49%.
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Affiliation(s)
- S Lee-Huang
- Department of Biochemistry, New York University School of Medicine, NY 10016
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27
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Abstract
The title molecule, C12H14N4O5S.H2O (I), has a syn-XCN glycosyl torsion angle, which is stabilized by an intramolecular hydrogen bond between N3 of the tricylic base and O5' of the ribose (in a C2'-endo pucker). [The purine base, including atoms S and O6, of the molecule is planar to within 0.043 (2) A.] The tricyclic bases are stacked along a with an interplanar distance of 3.602 (3) A.
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Affiliation(s)
- Y C Liaw
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan, ROC
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28
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Abstract
A new crystal form of abrin-a from the seeds of Abrus precatorius has been obtained by vapor diffusion method. The abrin-a crystals belong to monoclinic space group P2(1) with cell dimensions a = 84.58 A, b = 73.07 A, c = 48.23 A, beta = 96.20 degrees. An asymmetric unit contains one protein molecule of molecular weight 65 kDa and has a solvent content of approximately 46%.
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Affiliation(s)
- T H Tahirov
- Department of Physics, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
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29
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Guan Y, Gao YG, Liaw YC, Robinson H, Wang AH. Molecular structure of cyclic diguanylic acid at 1 A resolution of two crystal forms: self-association, interactions with metal ion/planar dyes and modeling studies. J Biomol Struct Dyn 1993; 11:253-76. [PMID: 8286055 DOI: 10.1080/07391102.1993.10508725] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Cyclic ribodiguanylic acid, c-(GpGp), is the endogenous effector regulator of cellulose synthase. Its three dimensional structure from two different crystal forms (tetragonal and trigonal) has been determined by x-ray diffraction analysis at 1 A resolution. Both structures were solved by direct methods and refined by block-matrix least squares refinement to R-factors of 0.112 (tetragonal) and 0.119 (trigonal). In both crystal forms, two independent c-(GpGp) molecules associate with each other to form a self-intercalated dimer. All four c-(GpGp) molecules have very similar backbone conformation. The riboses are in the C3'-endo pucker with pseudorotation angles ranging from -7.2 degrees to 16.5 degrees and the bases have anti glycosyl chi angles (-175.5 degrees to 179.7 degrees). In the tetragonal form, a hydrated cobalt ion is found to coordinate to two N7 atoms of adjacent guanines, forcing these two guanines to destack with a large dihedral angle (33 degrees). This metal coordination mechanism has been noted previously in other Pt- or Co-GMP complexes and may be relevant to the binding of the anticancer drug cisplatin to a GpG sequence in DNA. A model of the adduct between cisplatin and a d(CAATGGATTG) duplex has been constructed in which the induced bending of the DNA helix at the Pt crosslinking site is 33 degrees, consistent with earlier electrophoretic analyses. Moreover, c-(GpGp) exhibits unusual spectral properties not seen in other cyclic dinucleotides. It interacts with planar organic intercalator molecules in ways similar to double helical DNA. We propose a cage-like model consisting of a tetrameric c-(GpGp) aggregate in which a large cavity (host molecule) is generated to afford a binding site for certain planar intercalators (guests molecules). The aggregate likely uses a hydrogen bonding scheme the same as that found in the G-quartet molecules, e.g., telomere DNA. The conformation of c-(GpGp) also suggests that certain nearest-neighbor intercalators may be synthesized on the basis of its unique molecular framework. Modeling studies have been carried out to test this hypothesis.
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Affiliation(s)
- Y Guan
- Division of Biophysics, University of Illinois at Urbana-Champaign 61801
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30
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Liaw YC, Chiou SH, Chang T, Chang WC. Predicted secondary and tertiary structures of carp gamma-crystallins with high methionine content: role of methionine residues in the protein stability. J Biochem 1992; 112:341-5. [PMID: 1429521 DOI: 10.1093/oxfordjournals.jbchem.a123902] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A systematic structural comparison of several carp gamma-crystallins with high methionine contents was made by the secondary-structure prediction together with computer model-building based on the established X-ray structure of calf gamma-II crystallin. The overall surface hydrophilicity profile and the distribution of helices, beta-sheets, and beta-turns along the polypeptide chains are very similar among these carp gamma-crystallins. In addition, their general polypeptide packing is close to the characteristic 2 domain/4 motif Greek key three-dimensional conformation depicted for the calf gamma-II crystallin. Interestingly, most hydrophobic methionine residues are located on the protein surface with only a few buried inside the protein surface or in the interface between two motifs of each domain. The exposed hydrophobic and polarizable methionine cluster on the protein surface may have a bearing on the crystallin stability and dense packing in the piscine species, and probably also provides a malleable nonpolar surface for the interaction with other crystallin components for the maintenance of a clear and transparent lens.
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Affiliation(s)
- Y C Liaw
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
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31
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Liaw YC, Gao YG, Marquez VE, Wang AH. Molecular structures of two new anti-HIV nucleoside analogs: 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl)adenine and 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl)hypoxanthine. Nucleic Acids Res 1992; 20:459-65. [PMID: 1741280 PMCID: PMC310408 DOI: 10.1093/nar/20.3.459] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The x-ray crystal structures of two new anti-HIV compounds, 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl)adenine (2'-F-dd-araA) and 9-(2,3-dideoxy-2-fluoro-beta-D-threo- pentofuranosyl)hypoxanthine (2'-F-dd-aral), have been determined at two temperatures. Both crystals are in the space group P2(1)2(1)2(1), and their structures were solved by direct methods. Least-squares refinement produced final R-factors of 0.027 for the 2'-F-dd-araA structure and of 0.044 for the 2'-F-dd-aral structure, respectively. The latter structure contains a two-fold disordered conformation of the sugar moiety. All three conformers (one for 2'-F-dd-araA and two for 2'-F-dd-aral) adopt an anti chi CN glycosyl torsion angle. The sugar in the 2'-F-dd-araA structure has a C2'-endo pucker conformation, whereas the sugar in the 2'-F-dd-aral structure has a mixture of C2'-endo and C3'-endo pucker conformations. When the sugar adopts the C2'-endo conformation, the torsion angle about the C4'-C5' bond is in a transgauche+ conformation. In contrast, when the sugar adopts the C3'-endo conformation, the torsion angle about the C4'-C5' bond is in a gauche(+)-gauche- conformation. The C2'-F bond distance is 1.406(3) A, similar to that found in other aliphatic C-F bonds. The results suggest that the 2'-fluoro-2',3'-dideoxyarabinosyl nucleosides do not have a strong preference for either C2'-endo or C3'-endo sugar pucker.
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Affiliation(s)
- Y C Liaw
- Department of Physiology & Biophysics, University of Illinois, Urbana 61801
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32
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Liaw YC, Chern JW, Lin GS, Wang AH. Unusual conformational flexibility in N1-substituted uncommon purine nucleosides. Crystal structure of 1-allyl-isoguanosine and 1-allyl-xanthosine. FEBS Lett 1992; 297:4-8. [PMID: 1551434 DOI: 10.1016/0014-5793(92)80315-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Several new N1-substituted uncommon purine nucleosides, including doridosine (1-methyl-isoguanosine; m-iG), 1-allyl-isoguanosine (a-iG) and 1-allyl-xanthosine (a-X), have been synthesized and tested as agonists for the adenosine receptors. Some have smooth muscle relaxant or negative chronotropic activities. The X-ray crystal structure of these compounds has been determined at atomic resolution in order to understand the structure-activity relationship. The structures were solved by direct methods and refined by full-matrix least-squares refinement procedure. The crystallographic parameters are: a-iG, space group P2(1), a = 10.573 (1) A, b = 21.955 (2) A, c = 14.360 (1) A, beta = 110.65 (1) degree, no. of 3 sigma Fo's = 4585, R = 0.047; a-X, space group P2(1)2(1)2(1), a = 16.015 (2) A, b = 16.239 (1) A, (1) A, c = 5.3723 (5) A, no. of 3 sigma Fo's = 1169, R = 0.031. In the a-iG crystal, there are 4 independent molecules (with different conformation) per asymmetric unit. While all 4 molecules adopt anti chi CN glycosyl torsion angle, their riboses have 3 distinct puckers (C2'-exo, C2'-endo and C1'-exo). In contrast, the a-X structure adopts a syn chi CN glycosyl torsion angle, which is stabilized by an intramolecular hydrogen bond between the N3 of purine base and the O5' of the ribose (in C2'-endo pucker). Both purine bases (a-iG and a-X) are mainly in the keto tautomer form. For the isoguanine base, the averaged N1-C2 bond distance (1.42 A) is significantly longer than that (1.375 A) of the guanine base. For the xanthine base, N3 nitrogen has an imino proton attached which is unambiguously located in the electron density map. The surprising flexibility in the ribose ring of these N1-substituted uncommon purine nucleosides suggests that the ribose moiety may not participate in the binding of nucleoside to the adenosine receptors.
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Affiliation(s)
- Y C Liaw
- Laboratory of Structural Biology, Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
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33
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Abstract
The molecular and crystal structure of steffimycin have been determined by single crystal X-ray diffraction to 0.9 angstrom resolution. The triclinic crystals are in the space group P1, with the unit cell dimensions of a = 8.606(3) angstrom, b = 22.168(7) angstrom, c = 8.448(2) angstrom, alpha = 97.56(3) degrees, beta = 95.97(2) degrees, gamma = 87.94(3) degrees, Z = 2. The structure was solved by direct methods and refined by the full-matrix least-squares method to a final R value of 0.065 with 3405 (Inet greater than 2.0 sigma (Inet] observed reflections using the NRCVAX software package. The crystal lattice includes 2 independent steffimycin, 3 water and one 2-methyl-2,4-pentanediol molecules. The conformation of steffimycin is grossly similar to other anthracycline antibiotics including daunorubicin. The crystal packing interactions of steffimycin suggest a preferred stacking of the aglycone chromophore of the antibiotic which resembles the intercalative interactions seen in the daunorubicin-d(CGTACG) (Wang et al., Biochemistry 26, 1152 (1987] and nogalamycin-d(CGT(pS)ACG) (Liaw et al., Biochemistry 28, 9913 (1989] complexes. The atomic coordinates data from these complexes were used to model the intercalative binding of steffimycin to DNA. The models were then stereochemically idealized by the constraint refinement program NUCLSQ. Subsequently XPLOR software package was used for energy minimization of these models in vacuo. The model building studies suggest that steffimycin has a higher CpG base sequence specificity over the TpA step, similar to that of daunorubicin and nogalamycin.
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Affiliation(s)
- M Sriram
- Department of Physiology and Biophysics, University of Illinois, Urbana-Champaign 61801
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34
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Gao YG, Liaw YC, Li YK, van der Marel GA, van Boom JH, Wang AH. Facile formation of a crosslinked adduct between DNA and the daunorubicin derivative MAR70 mediated by formaldehyde: molecular structure of the MAR70-d(CGTnACG) covalent adduct. Proc Natl Acad Sci U S A 1991; 88:4845-9. [PMID: 2052564 PMCID: PMC51763 DOI: 10.1073/pnas.88.11.4845] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
MAR70 is a synthetic derivative of the anticancer drug daunorubicin that contains an additional sugar, attached to the O4' of daunosamine. When MAR70 was crystallized with the DNA hexamer d(CGTnACG), where nA is 2-aminoadenine, a covalent methylene bridge was formed between the N3' of daunosamine and the N2 of 2-aminoadenine. This spontaneous reaction occurred through the crosslinking action of formaldehyde. The crosslink was demonstrated by the three-dimensional structure of the 2:1 adduct between MAR70 and d(CGTnACG) solved at 1.3-A resolution by x-ray diffraction analysis. The perfect juxtaposition of the two amino groups in the complex provides a template for efficient addition of formaldehyde. This adduct structure is compared with the analogous structure at 1.5-A resolution of the complex of MAR70-d(CGTACG), in which no formaldehyde addition was observed. In both complexes, two MAR70 molecules bind to the DNA hexamer double helix; the elongated aglycon chromophore is intercalated between the CpG steps and spans the G.C Watson-Crick base pairs. The disaccharides occupy nearly the entire minor groove of the distorted B-DNA hexamer double helix. The second sugar is in contact with the sugar-phosphate backbone and does not affect the binding interactions of the daunorubicin portion to DNA. The structure allows us to model the binding to DNA of drugs having more extensive oligosaccharides. In addition, it suggests that placing a reactive (e.g., alkylating) functional group at the N3' amino position of daunorubicin might be a fruitful route for designing anticancer drugs.
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Affiliation(s)
- Y G Gao
- Department of Physiology and Biophysics, University of Illinois, Urbana-Champaign 61801
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35
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Abstract
Formaldehyde (HCHO) cross-links the anticancer drug daunorubicin (DAU) to DNA efficiently. When DAU is mixed with DNA hexamers, d(CGCGCG) and d(CGTDCG), in the presence of HCHO, stable covalent adducts of DNA are formed, as shown by the HPLC analyses. The major adducts are identical with the materials in the respective crystals which can be readily obtained from the 1:1 mixture of DAU-d(CGCGCG) and DAU-d(CGTDCG) plus HCHO, but not from the solution without HCHO. The high-resolution (1.5 A) X-ray crystal structure of those adducts shows unambiguously that they contain a covalent methylene bridge between the N3' of daunosamine and the N2 of the guanine or 2-aminoadenine. The perfect juxtaposition of the two amino groups in the minor groove of the complex provides a template for an efficient addition of HCHO. The methylene bridge does not perturb the conformation of the drug-DNA complex, when compared to the structure of DAU-d(CGTACG). The results suggest new approaches for synthesizing a new type of potential anticancer drug by attaching a reactive (e.g., alkylating) functional group at the N3' amino position of daunorubicin/doxorubicin. The stable drug-DNA adduct may be useful as probes for other biological studies.
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Affiliation(s)
- A H Wang
- Department of Physiology and Biophysics, University of Illinois, Urbana-Champaign 61801
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36
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Abstract
The crystal and molecular structure of a decahydrated form of the sodium salt of inosine 5'-monophosphate (C10H12N4O8P-.Na+.10H2O) was solved to study the effect of hydration on the conformation of nucleic acids. Monoclinic, space group P2(1), a = 8.730 (3), b = 22.349 (7), c = 12.282 (4) A, beta = 109.68 (3) degrees, V = 2256.52 A3, Mr = 550.34, Z = 4, F(000) = 1196, Dx = 1.62 g cm-3, mu = 21.7 cm-1, lambda(Cu K alpha) = 1.54056 A, R = 0.070, wR = 0.102 for 3404 unique [Inet greater than 2 sigma (Inet)] observed reflections out of 3457 unique reflections. The two molecules (A and B) in the asymmetric unit differ in the arrangement of the first shell of hydration and in the torsion angles of the ribose and phosphate. The bond lengths and angles are similar to those of the structure of a less hydrated ('dry') form of the same nucleotide (C10H12N4O8P-.Na+.8H2O) determined previously in space group C222(1) [Rao & Sundaraligam (1969). J. Am. Chem. Soc. 91, 1210-1217]. The twofold symmetry in the 'dry' form is destroyed in the present crystal structure due to the relative displacement of the two independent molecules and reorganization of the hydration shell. Molecule A is different from (r.m.s. = 0.190 A) while molecule B is similar to (r.m.s. = 0.093 A) that of the 'dry' form. The conformation adopted is influenced mainly by the differences in the endocyclic torsion angles of the ribose.
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Affiliation(s)
- M Sriram
- Department of Physiology and Biophysics, University of Illinois at Urbana-Champaign 61801
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37
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Abstract
The three-dimensional molecular structures of the complexes between a novel antitumor drug nogalamycin and its derivative U-58872 with a modified DNA hexamer d[m5CGT(pS)Am5CG] have been determined at 1.7- and 1.8-A resolution, respectively, by X-ray diffraction analyses. Both structures (in space group P6(1)) have been refined with constrained refinement procedure to final R factors of 0.208 (3386 reflections) and 0.196 (2143 reflections). In both complexes, two nogalamycins bind to the DNA hexamer double helix in a 2:1 ratio with the elongated aglycon chromophore intercalated between the CpG steps at both ends of the helix. The aglycon chromophore spans across the GC Watson-Crick base pairs with its nogalose lying in the minor groove and the aminoglucose lying in the major groove of the distorted B-DNA double helix. Most of the sugars remain in the C2'-endo pucker family, except three deoxycytidine residues (terminal C1, C7, and internal C5). All nucleotides are in the anti conformation. Specific hydrogen bonds are found in the complex between the drug and guanine-cytosine bases in both grooves of the helix. One hydroxyl group of the aminoglucose donates a hydrogen bond to the N7 of guanine, while the other receives a hydrogen bond from the N4 amino group of cytosine. The orientation of these two hydrogen bonds suggests that nogalamycin prefers a GC base pair with its aglycon chromophore intercalating at the 5'-side of a guanine (between NpG), or at the 3'-side of a cytosine (between CpN) with the sugars pointing toward the GC base pair. The binding of nogalamycin to DNA requires that the base pairs in DNA open up transiently to allow the bulky sugars to go through, suggesting that nogalamycin prefers GC sequences embedded in a stretch of AT sequences.
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Affiliation(s)
- Y G Gao
- Department of Physiology and Biophysics, University of Illinois, Urbana 61801
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38
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Robinson H, Liaw YC, van der Marel GA, van Boom JH, Wang AH. NMR studies on the binding of antitumor drug nogalamycin to DNA hexamer d(CGTACG). Nucleic Acids Res 1990; 18:4851-8. [PMID: 2395646 PMCID: PMC331962 DOI: 10.1093/nar/18.16.4851] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The interactions between a novel antitumor drug nogalamycin with the self-complementary DNA hexamer d(CGTACG) have been studied by 500 MHz two dimensional proton nuclear magnetic resonance spectroscopy. When two nogalamycins are mixed with the DNA hexamer duplex in a 2:1 ratio, a symmetrical complex is formed. All non-exchangeable proton resonances (except H5' & H5") of this complex have been assigned using 2D-COSY and 2D-NOESY methods at pH 7.0. The observed NOE cross peaks are fully consistent with the 1.3 A resolution x-ray crystal structure (Liaw et al., Biochemistry 28, 9913-9918, 1989) in which the elongated aglycone chromophore is intercalated between the CpG steps at both ends of the helix. The aglycone chromophore spans across the GC Watson-Crick base pairs with its nogalose lying in the minor groove and the aminoglucose lying in the major groove of the distorted B-DNA double helix. The binding conformation suggests that specific hydrogen bonds exist in the complex between the drug and guanine-cytosine bases in both grooves of the helix. When only one drug per DNA duplex is present in solution, there are three molecular species (free DNA, 1:1 complex and 2:1 complex) in slow exchange on the NMR time scale. This equilibrium is temperature dependent. At high temperature the free DNA hexamer duplex and the 1:1 complex are completely destabilized such that at 65 degrees C only free single-stranded DNA and the 2:1 complex co-exist. At 35 degrees C the equilibrium between free DNA and the 1:1 complex is relatively fast, while that between the 1:1 complex and the 2:1 complex is slow. This may be rationalized by the fact that the binding of nogalamycin to DNA requires that the base pairs in DNA open up transiently to allow the bulky sugars to go through. A separate study of the 2:1 complex at low pH showed that the terminal GC base pair is destabilized.
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Affiliation(s)
- H Robinson
- Department of Physiology/Biophysics, University of Illinois, Urbana-Champaign 61801
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39
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Liaw YC, Gao YG, Robinson H, Sheldrick GM, Sliedregt LA, van der Marel GA, van Boom JH, Wang AH. Cyclic diguanylic acid behaves as a host molecule for planar intercalators. FEBS Lett 1990; 264:223-7. [PMID: 2162785 DOI: 10.1016/0014-5793(90)80253-f] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cyclic ribodiguanylic acid, c-(GpGp), is the endogenous effector regulator of cellulose synthase. Its three-dimensional structure from two different crystal forms (tetragonal and trigonal) has been determined by X-ray diffraction analysis at 1 A resolution. In both crystal forms, two independent c-(GpGp) molecules associate with each other to form a self-intercalated dimer. A hydrated cobalt ion is found to coordinate to two N7 atoms of adjacent guanines, forcing these two guanines to destack with a large dihedral angle (32 degrees), in the dimer of the tetragonal form. This metal coordination mechanism may be relevant to that of the anticancer drug cisplatin. Moreover, c-(GpGp) exhibits unusual spectral properties not seen in any other cyclic dinucleotide. It interacts with planar organic intercalator molecules in ways similar to double helical DNA. We propose a cage-like model consisting of a tetrameric c-(GpGp) aggregate in which a large cavity ('host') is generated to afford a binding site for certain planar intercalators ('guests').
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Affiliation(s)
- Y C Liaw
- Department of Physiology and Biophysics, University of Illinois, Urbana 61801
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40
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Liaw YC, Gao YG, Robinson H, van der Marel GA, van Boom JH, Wang AH. Antitumor drug nogalamycin binds DNA in both grooves simultaneously: molecular structure of nogalamycin-DNA complex. Biochemistry 1989; 28:9913-8. [PMID: 2620066 DOI: 10.1021/bi00452a006] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The three-dimensional molecular structures of the complexes between an interesting antitumor drug, nogalamycin, and two DNA hexamers, d[CGT(pS)ACG] and d[m5CGT(pS)Am5CG], were determined at high resolution by X-ray diffraction analyses. Two nogalamycins bind to the DNA double helix in a 2:1 ratio with the aglycon chromophore intercalated between the CpG steps at both ends of the helix. The nogalose and aminoglucose sugars lie in the minor and major grooves, respectively, of the distorted B-DNA double helix. The binding of nogalamycin to DNA requires that the base pairs in DNA open up transiently to allow the bulky sugars to go through. Specific hydrogen bonds are found in the complex between the drug and guanine bases. We suggest that nogalamycin may prefer GC sequences embedded in a stretch of AT sequences.
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Affiliation(s)
- Y C Liaw
- Department of Physiology and Biophysics, University of Illinois at Urbana-Champaign 61801
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41
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Teng MK, Liaw YC, van der Marel GA, van Boom JH, Wang AH. Effects of the O2' hydroxyl group on Z-DNA conformation: structure of Z-RNA and (araC)-[Z-DNA]. Biochemistry 1989; 28:4923-8. [PMID: 2475172 DOI: 10.1021/bi00438a001] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The left-handed Z structures of two hexamers [d(CG)r(CG)d(CG) and d(CG)(araC)d(GCG)] containing ribose and arabinose residues have been solved by X-ray diffraction analysis at 1.5-A resolution. Their conformations closely resemble that of the canonical Z-DNA. The O2' hydroxyl groups of both rC and araC residues form intramolecular hydrogen bonds with N2 of the 5' guanine residue and replace the bridging water molecules in the deep groove of Z-DNA, which stabilize the guanine in the syn conformation. The araC residue can be incorporated into the Z structure readily and facilitates B to Z transition, as supported by UV absorption spectroscopic studies. In contrast, in Z-RNA the ribose of the cytidine residue is twisted in order to form the respective hydrogen bond. The potential biological roles of the modified Z-DNA containing anticancer nucleoside araC and of Z-RNA are discussed.
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Affiliation(s)
- M K Teng
- Department of Physiology and Biophysics, University of Illinois, Urbana-Champaign 61801
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