124 results on '"Nham T"'
Search Results
2. Ivermectin inhibits HSP27 and potentiates efficacy of oncogene targeting in tumor models
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Nappi, Lucia, Aguda, Adeleke H., Nakouzi, Nader Al, Lelj-Garolla, Barbara, Beraldi, Eliana, Lallous, Nada, Thi, Marisa, Moore, Susan, Fazli, Ladan, Battsogt, Dulguun, Stief, Sophie, Ban, Fuqiang, Nguyen, Nham T., Saxena, Neetu, Dueva, Evgenia, Zhang, Fan, Yamazaki, Takeshi, Zoubeidi, Amina, Cherkasov, Artem, Brayer, Gary D., and Gleave, Martin
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Enzalutamide -- Analysis ,Ivermectin -- Analysis ,Tumors -- Genetic aspects -- Analysis ,Heat shock proteins -- Analysis ,Drug discovery -- Analysis ,Biochemistry ,Cancer ,Serine ,Health care industry - Abstract
HSP27 is highly expressed in, and supports oncogene addiction of, many cancers. HSP27 phosphorylation is a limiting step for activation of this protein and a target for inhibition, but its highly disordered structure challenges rational structure-guided drug discovery. We performed multistep biochemical, structural, and computational experiments to define a spherical 24-monomer complex composed of 12 HSP27 dimers with a phosphorylation pocket flanked by serine residues between their N-terminal domains. Ivermectin directly binds this pocket to inhibit MAPKAP2-mediated HSP27 phosphorylation and depolymerization, thereby blocking HSP27-regulated survival signaling and client-oncoprotein interactions. Ivermectin potentiated activity of anti-androgen receptor and anti-EGFR drugs in prostate and EGFR/HER2-driven tumor models, respectively, identifying a repurposing approach for cotargeting stress-adaptive responses to overcome resistance to inhibitors of oncogenic pathway signaling., Introduction Small heat shock proteins (sHSPs) are ATP-independent molecular chaperones characterized by a conserved [alpha]-crystallin domain located between a highly flexible, variable C-terminal region and a poorly conserved, disorganized N-terminal [...]
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- 2020
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3. Circulating Tumour Cell Associated MicroRNA Profiles Change during Chemoradiation and Are Predictive of Response in Locally Advanced Rectal Cancer
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Lim, Stephanie H., primary, Chua, Wei, additional, Ng, Weng, additional, Ip, Emilia, additional, Marques, Tania M., additional, Tran, Nham T., additional, Gama-Carvalho, Margarida, additional, Asghari, Ray, additional, Henderson, Christopher, additional, Ma, Yafeng, additional, de Souza, Paul, additional, and Spring, Kevin J., additional
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- 2023
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4. Structural basis of collagen fiber degradation by cathepsin K
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Aguda, Adeleke H., Panwar, Preety, Du, Xin, Nguyen, Nham T., Brayer, Gary D., and Brömme, Dieter
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- 2014
5. Both host and parasite non-coding RNAs co-ordinate the regulation of macrophage gene expression to reduce pro-inflammatory immune responses and promote tissue repair pathways during infection with fasciola hepatica
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Dayna Sais, Sumaiya Chowdhury, John. P. Dalton, Nham Tran, and Sheila Donnelly
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Fasciola hepatica ,helminth ,non-coding miRNAs ,miRNA ,lncRNA ,macrophages ,Genetics ,QH426-470 - Abstract
Parasitic worms (helminths) establish chronic infection within mammalian hosts by strategically regulating their host’s immune responses. Deciphering the mechanisms by which host non-coding RNAs (ncRNA) co-ordinate the activation and regulation of immune cells is essential to understanding host immunity and immune-related pathology. It is also important to comprehend how pathogens secrete specific ncRNAs to manipulate gene expression of host immune cells and influence their response to infection. To investigate the contribution of both host and helminth derived ncRNAs to the activation and/or regulation of innate immune responses during a parasite infection, we examined ncRNA expression in the peritoneal macrophages from mice infected with Fasciola hepatica. We discovered the presence of several parasitic-derived miRNAs within host macrophages at 6 hrs and 18 hrs post infection. Target prediction analysis showed that these Fasciola miRNAs regulate host genes associated with the activation of host pro-inflammatory macrophages. Concomitantly, there was a distinct shift in host ncRNA expression, which was significant at 5 days post-infection. Prediction analysis suggested that these host ncRNAs target a different cohort of host genes compared to the parasite miRNAs, although the functional outcome was predicted to be similar i.e. reduced pro-inflammatory response and the promotion of a reparative/tolerant phenotype. Taken together, these observations uncover the interplay between host and parasitic ncRNAs and reveal a complementary regulation of the immune response that allows the parasite to evade immune detection and promote tissue repair for the host. These findings will provide a new understanding of the molecular interaction between parasites and host.
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- 2024
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6. Enzyme–substrate complexes of allosteric citrate synthase: Evidence for a novel intermediate in substrate binding
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Duckworth, Harry W., Nguyen, Nham T., Gao, Yin, Donald, Lynda J., Maurus, Robert, Ayed, Ayeda, Bruneau, Brigitte, and Brayer, Gary D.
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- 2013
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7. P1523: DEMOGRAPHICS, CLINICAL CHARACTERISTICS, AND REAL-WORLD TREATMENT PATTERNS AMONG PATIENTS WITH BETA-THALASSEMIA: A RETROSPECTIVE MEDICAL RECORD ABSTRACTION STUDY
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Cappellini, M. D., primary, Yucel, A., additional, Meyers, J., additional, Jimenez, M., additional, Nham, T., additional, Glassberg, M. B., additional, and Alashkar, F., additional
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- 2022
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8. Biplex quantitative PCR to detect transcriptionally active human papillomavirus 16 from patient saliva
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Fiona Deutsch, Dayna Sais, Ni Keatinge, Meredith Hill, Ngoc Ha Tran, Michael Elliott, and Nham Tran
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HPV16 ,Oropharyngeal cancers ,Saliva ,Biplex Quantitative PCR ,Viral diagnosis ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Head and neck cancers, particularly oropharyngeal cancers (OPC), have been increasingly associated with human papillomavirus (HPV) infections, specifically HPV16. The current methods for HPV16 detection primarily rely on p16 staining or PCR techniques. However, it is important to note the limitations of conventional PCR, as the presence of viral DNA does not always indicate an ongoing viral infection. Moreover, these tests heavily rely on the availability of tissue samples, which can present challenges in certain situations. In this study, we developed a RT-qPCR biplex approach to detect HPV16 oncogenes E6 and E7 RNA in saliva samples from OPC patients. Salivary supernatant was used as the liquid biopsy source. We successfully obtained RNA from salivary supernatant, preserving its integrity as indicated by the detection of several housekeeping genes. Our biplex approach accurately detected E6 and E7 RNA in HPV16-positive cell lines, tissues, and finally in OPC salivary samples. Importantly, the assay specifically targeted HPV16 and not HPV18. This biplexing technique allowed for reduced sample input without compromising specificity. In summary, our approach demonstrates the potential to detect viable HPV16 in saliva from OPC patients. Since the assay measures HPV16 RNA, it provides insights into the transcriptional activity of the virus. This could guide clinical decision-making and treatment planning for individuals with HPV-related OPC.
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- 2024
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9. Exploring the utility of circulating miRNAs as diagnostic biomarkers of fasciolosis
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Sumaiya Chowdhury, Alison Ricafrente, Krystyna Cwiklinski, Dayna Sais, John P. Dalton, Nham Tran, and Sheila Donnelly
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Medicine ,Science - Abstract
Abstract Effective management and control of parasitic infections on farms depends on their early detection. Traditional serological diagnostic methods for Fasciola hepatica infection in livestock are specific and sensitive, but currently the earliest detection of the parasite only occurs at approximately three weeks post-infection. At this timepoint, parasites have already entered the liver and caused the tissue damage and immunopathology that results in reduced body weight and loss in productivity. Here, we investigated whether the differential abundance of micro(mi)miRNAs in sera of F. hepatica-infected sheep has potential as a tool for the early diagnosis of infection. Using miRNA sequencing analysis, we discovered specific profiles of sheep miRNAs at both the pre-hepatic and hepatic infection phases in comparison to non-infected sheep. In addition, six F. hepatica-derived miRNAs were specifically identified in sera from infected sheep. Thus, a panel of differentially expressed miRNAs comprising four sheep (miR-3231-3p; miR133-5p; 3957-5p; 1197-3p) and two parasite miRNAs (miR-124-3p; miR-Novel-11-5p) were selected as potential biomarkers. The expression of these candidates in sera samples from longitudinal sheep infection studies collected between 7 days and 23 weeks was quantified using RT-qPCR and compared to samples from age-matched non-infected sheep. We identified oar-miR-133-5p and oar-miR-3957-5p as promising biomarkers of fasciolosis, detecting infection as early as 7 days. The differential expression of the other selected miRNAs was not sufficient to diagnose infection; however, our analysis found that the most abundant forms of fhe-miR-124-3p in sera were sequence variants (IsomiRs) of the canonical miRNA, highlighting the critical importance of primer design for accurate diagnostic RT-qPCR. Accordingly, this investigative study suggests that certain miRNAs are biomarkers of F. hepatica infection and validates miRNA-based diagnostics for the detection of fasciolosis in sheep.
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- 2024
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10. Editorial: Non-coding RNA elements as regulators of host–pathogen interactions
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Margarida Gama-Carvalho and Nham Tran
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ncRNA ,host–pathogen interaction ,gene expression ,virus ,parasites ,RNA modifications ,Genetics ,QH426-470 - Published
- 2024
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11. Comparative analysis of folding and substrate binding sites between regulated hexameric type II citrate synthases and unregulated dimeric type I enzymes
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Nguyen, Nham T., Maurus, Robert, Stokell, David J., Ayed, Ayeda, Duckworth, Harry W., and Brayer, Gary D.
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Proteins -- Structure ,Enzymes -- Structure-activity relationship ,Protein folding -- Analysis ,Binding sites (Biochemistry) -- Analysis ,Allosteric enzymes -- Research ,Biological sciences ,Chemistry - Abstract
Research brings out the differences between dimeric type I and hexameric type II citrate synthase enzymes. Data suggest that development of hexameric association, N-terrminal domain elaboration, NADH binding site, refolding of the substrate binding site confer an allosteric control of catalysis on type II citrate synthases.
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- 2001
12. Subsite mapping of the human pancreatic alpha-amylase active site through structural, kinetic, and mutagenesis techniques
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Brayer, Gary D., Sidhu, Gary, Maurus, Robert, Rydberg, Edwin H., Braun, Curtis, Wang, Yili, Nguyen, Nham T., Overall, Christopher M., and Withers, Stephen G.
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Biochemistry -- Research ,Amylases -- Analysis ,Mutagenesis -- Analysis ,Oligosaccharides -- Research ,Fluorides -- Research ,Biological sciences ,Chemistry - Abstract
Research has been conducted on the human pancreatic alpha-amylase active site region. The use of malto-oligosaccharides and malto-oligosaccharyl fluorides in developing cleavage action pattern is discussed.
- Published
- 2000
13. Ivermectin inhibits HSP27 and potentiates efficacy of oncogene targeting in tumor models
- Author
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Nappi, Lucia, primary, Aguda, Adeleke H., additional, Nakouzi, Nader Al, additional, Lelj-Garolla, Barbara, additional, Beraldi, Eliana, additional, Lallous, Nada, additional, Thi, Marisa, additional, Moore, Susan, additional, Fazli, Ladan, additional, Battsogt, Dulguun, additional, Stief, Sophie, additional, Ban, Fuqiang, additional, Nguyen, Nham T., additional, Saxena, Neetu, additional, Dueva, Evgenia, additional, Zhang, Fan, additional, Yamazaki, Takeshi, additional, Zoubeidi, Amina, additional, Cherkasov, Artem, additional, Brayer, Gary D., additional, and Gleave, Martin, additional
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- 2019
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14. Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase
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Sidhu, Gary, Withers, Stephen G., Nguyen, Nham T., McIntosh, Lawrence P., Ziser, Lothar, and Brayer, Gary D.
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Glycosylation -- Research ,Enzymes -- Research ,Bacillus (Bacteria) -- Research ,Hydrolysis -- Research ,Sugar -- Inversion ,Proteins -- Conformation ,Biological sciences ,Chemistry - Abstract
The resolution structure of the glycosyl-enzyme intermediate is formed on the retaining beta-1,4-xylanase from Bacillus circulans. An analysis of the 1.8 Angstroms resolution structure of the intermediate shows that atoms C5, O5, C1 and C2 of the sugar attains coplanarity as required at the oxocarbenium ion-like transition phases of the double-displacement catalytic mechanism. Several differences beyond the distortion of the sugar moiety are observed following X-ray crystallographic analysis.
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- 1999
15. Ivermectin inhibits HSP27 and potentiates efficacy of oncogene targeting in tumor models
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Fuqiang Ban, Evgenia V. Dueva, Takeshi Yamazaki, Nada Lallous, Nader Al Nakouzi, Martin E. Gleave, Amina Zoubeidi, Susan C. Moore, Nham T. Nguyen, Fan Zhang, Neetu Saxena, Sophie M. Stief, Lucia Nappi, Dulguun Battsogt, Eliana Beraldi, Marisa Thi, Barbara Lelj-Garolla, Artem Cherkasov, Adeleke H Aguda, Gary D. Brayer, and Ladan Fazli
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0301 basic medicine ,animal structures ,Receptor, ErbB-2 ,Protein Serine-Threonine Kinases ,Serine ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Ivermectin ,Hsp27 ,Protein Domains ,medicine ,Animals ,Humans ,Receptor ,Heat-Shock Proteins ,Oncogene ,biology ,Drug discovery ,Chemistry ,Intracellular Signaling Peptides and Proteins ,General Medicine ,Neoplasms, Experimental ,Oncogene Addiction ,3. Good health ,030104 developmental biology ,A549 Cells ,030220 oncology & carcinogenesis ,Cancer research ,biology.protein ,Phosphorylation ,Protein Multimerization ,medicine.drug ,Molecular Chaperones ,Research Article - Abstract
HSP27 is highly expressed in, and supports oncogene addiction of, many cancers. HSP27 phosphorylation is a limiting step for activation of this protein and a target for inhibition, but its highly disordered structure challenges rational structure-guided drug discovery. We performed multistep biochemical, structural, and computational experiments to define a spherical 24-monomer complex composed of 12 HSP27 dimers with a phosphorylation pocket flanked by serine residues between their N-terminal domains. Ivermectin directly binds this pocket to inhibit MAPKAP2-mediated HSP27 phosphorylation and depolymerization, thereby blocking HSP27-regulated survival signaling and client-oncoprotein interactions. Ivermectin potentiated activity of anti-androgen receptor and anti-EGFR drugs in prostate and EGFR/HER2-driven tumor models, respectively, identifying a repurposing approach for cotargeting stress-adaptive responses to overcome resistance to inhibitors of oncogenic pathway signaling.
- Published
- 2019
16. The Parasite-Derived Peptide, FhHDM-1, Selectively Modulates miRNA Expression in β-Cells to Prevent Apoptotic Pathways Induced by Proinflammatory Cytokines
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Inah Camaya, Meredith Hill, Dayna Sais, Nham Tran, Bronwyn O’Brien, and Sheila Donnelly
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Diseases of the endocrine glands. Clinical endocrinology ,RC648-665 - Abstract
We have previously identified a parasite-derived peptide, FhHDM-1, that prevented the progression of diabetes in nonobese diabetic (NOD) mice. Disease prevention was mediated by the activation of the PI3K/Akt pathway to promote β-cell survival and metabolism without inducing proliferation. To determine the molecular mechanisms driving the antidiabetogenic effects of FhHDM-1, miRNA:mRNA interactions and in silico predictions of the gene networks were characterised in β-cells, which were exposed to the proinflammatory cytokines that mediate β-cell destruction in Type 1 diabetes (T1D), in the presence and absence of FhHDM-1. The predicted gene targets of miRNAs differentially regulated by FhHDM-1 mapped to the biological pathways that regulate β-cell biology. Six miRNAs were identified as important nodes in the regulation of PI3K/Akt signaling. Additionally, IGF-2 was identified as a miRNA gene target that mediated the beneficial effects of FhHDM-1 on β-cells. The findings provide a putative mechanism by which FhHDM-1 positively impacts β-cells to permanently prevent diabetes. As β-cell death/dysfunction underlies diabetes development, FhHDM-1 opens new therapeutic avenues.
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- 2024
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17. Potent Human α-Amylase Inhibition by the β-Defensin-like Protein Helianthamide
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Adeleke Aguda, Leonard J. Foster, Jacqueline Wicki, Ethan D. Goddard-Borger, Gary D. Brayer, Christina Tysoe, Robert A. Keyzers, Stephen G. Withers, Leslie K. Williams, Nham T. Nguyen, Raymond J. Andersen, Suzanne Perry, and Chris A. Tarling
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0301 basic medicine ,Barnase ,030102 biochemistry & molecular biology ,Stichodactyla helianthus ,General Chemical Engineering ,Antimicrobial peptides ,Active site ,General Chemistry ,Biology ,medicine.disease_cause ,biology.organism_classification ,Fusion protein ,3. Good health ,lcsh:Chemistry ,03 medical and health sciences ,030104 developmental biology ,lcsh:QD1-999 ,Biochemistry ,biology.protein ,medicine ,Glycoside hydrolase ,Amylase ,Escherichia coli ,Research Article - Abstract
Selective inhibitors of human pancreatic α-amylase (HPA) are an effective means of controlling blood sugar levels in the management of diabetes. A high-throughput screen of marine natural product extracts led to the identification of a potent (Ki = 10 pM) peptidic HPA inhibitor, helianthamide, from the Caribbean sea anemone Stichodactyla helianthus. Active helianthamide was produced in Escherichia coli via secretion as a barnase fusion protein. X-ray crystallographic analysis of the complex of helianthamide with porcine pancreatic α-amylase revealed that helianthamide adopts a β-defensin fold and binds into and across the amylase active site, utilizing a contiguous YIYH inhibitory motif. Helianthamide represents the first of a novel class of glycosidase inhibitors and provides an unusual example of functional malleability of the β-defensin fold, which is rarely seen outside of its traditional role in antimicrobial peptides., We describe the discovery and structural characterization of helianthamide, a peptide with highly potent and selective inhibitory activity against human pancreatic α-amylase.
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- 2016
18. The amylase inhibitor montbretin A reveals a new glycosidase inhibition motif
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David E. Williams, Jacqueline Wicki, Gary D. Brayer, Coleman John, Leslie K. Williams, Stephen G. Withers, Nham T. Nguyen, Raymond J. Andersen, Violet G. Yuen, Xiaohua Zhang, Sami Caner, John H. McNeill, and Christina Tysoe
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Models, Molecular ,Flavonols ,Stereochemistry ,Molecular Sequence Data ,Disaccharide ,Gene Expression ,Plasma protein binding ,Ligands ,Pichia ,chemistry.chemical_compound ,Caffeic Acids ,Caffeic acid ,Humans ,Glycoside hydrolase ,Glycosides ,Enzyme Inhibitors ,Binding site ,Molecular Biology ,Flavonoids ,chemistry.chemical_classification ,Binding Sites ,Hydrolysis ,Glycoside ,Hydrogen Bonding ,Cell Biology ,Flavones ,Recombinant Proteins ,Enzyme ,Carbohydrate Sequence ,chemistry ,Biochemistry ,Drug Design ,Myricetin ,alpha-Amylases ,Trisaccharides ,Protein Binding - Abstract
The complex plant flavonol glycoside montbretin A is a potent (Ki = 8 nM) and specific inhibitor of human pancreatic α-amylase with potential as a therapeutic for diabetes and obesity. Controlled degradation studies on montbretin A, coupled with inhibition analyses, identified an essential high-affinity core structure comprising the myricetin and caffeic acid moieties linked via a disaccharide. X-ray structural analyses of the montbretin A-human α-amylase complex confirmed the importance of this core structure and revealed a novel mode of glycosidase inhibition wherein internal π-stacking interactions between the myricetin and caffeic acid organize their ring hydroxyls for optimal hydrogen bonding to the α-amylase catalytic residues D197 and E233. This novel inhibitory motif can be reproduced in a greatly simplified analog, offering potential for new strategies for glycosidase inhibition and therapeutic development.
- Published
- 2015
19. Associations between methamphetamine use and lack of viral suppression among a cohort of HIV-positive persons who inject drugs in Hai Phong, Vietnam.
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Feelemyer, Jonathan, Arasteh, Kamyar, Huong, Duong T., Oanh, Khuat T. H., Khue, Pham M., Giang, Hoang T., Thanh, Nham T. T., Moles, Jean Pierre, Vinh, Vu H., Vallo, Roselyne, Quillet, Catherine, Rapoud, Delphine, Le, Sao M., Michel, Laurent, Laureillard, Didier, Nagot, Nicolas, Des Jarlais, Don C., Thi, Huong Duong, Hai, Oanh Khuat Thi, and Minh, Khue Pham
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- 2020
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20. Establishment of cancer cell line originating from a patient with high-grade serous ovarian carcinoma
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Nguyen Thuy Linh, Ngo Thu Hang, Bui Khac Cuong, Dang Thuy Linh, Nham Thi Phuong Linh, Do Nguyen-Van, Tran Ngoc Dzung, Can Van Mao, Dang Thanh Chung, Le Tri Chinh, Nguyen Phu Hung, Hoang Van Tong, and Nguyen Linh Toan
- Subjects
CD46 ,cell line ,high-grade serous carcinoma ,immunohistochemistry ,ovarian cancer ,Medicine ,Medicine (General) ,R5-920 - Abstract
Aim: Ovarian cancer is a serious malignancy with high prevalence and mortality. Methods: We isolated and characterized an ovarian high-grade serous cancer cell line (M4) from a tumor of a Vietnamese patient with ovarian carcinoma. Results: The M4 cancer cell line showed good proliferation and stability in culture. Morphologically, the M4 cells showed similar characteristics to tumor cells such as a polyhedral shape, large irregular nuclei, high nuclear/cytoplasmic ratio, high nuclear density and expressing cancer markers like CA125, p53 and Ki67 markers. Conclusion: We have successfully isolated and characterized the M4 cell line from a Vietnamese patient with ovarian carcinoma.
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- 2023
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21. Identification of mouse cathepsin K structural elements that regulate the potency of odanacatib
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Natasha Kruglyak, Simon Law, Nham T. Nguyen, Pierre-Marie Andrault, Adeleke Aguda, Gary D. Brayer, and Dieter Brömme
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0301 basic medicine ,medicine.medical_treatment ,Transgene ,Cathepsin K ,Gene Expression ,Pharmacology ,Biology ,Crystallography, X-Ray ,Ligands ,Biochemistry ,Piperazines ,Protein Structure, Secondary ,03 medical and health sciences ,chemistry.chemical_compound ,Mice ,0302 clinical medicine ,medicine ,Escherichia coli ,Potency ,Animals ,Humans ,Protease Inhibitors ,Protein Interaction Domains and Motifs ,Amino Acid Sequence ,Cloning, Molecular ,Molecular Biology ,Protease ,Binding Sites ,Protease inhibitor complex ,Bone Density Conservation Agents ,Biphenyl Compounds ,Cell Biology ,Recombinant Proteins ,Mutational analysis ,Kinetics ,030104 developmental biology ,chemistry ,Drug development ,Structural Homology, Protein ,030220 oncology & carcinogenesis ,Benzamides ,Mutagenesis, Site-Directed ,Sequence Alignment ,Odanacatib ,Protein Binding - Abstract
Cathepsin K (CatK) is the predominant mammalian bone-degrading protease and thus an ideal target for antiosteoporotic drug development. Rodent models of osteoporosis are preferred due to their close reflection of the human disease and their ease of handling, genetic manipulation and economic affordability. However, large differences in the potency of CatK inhibitors for the mouse/rat vs. the human protease orthologs have made it impossible to use rodent models. This is even more of a problem considering that the most advanced CatK inhibitors, including odanacatib (ODN) and balicatib, failed in human clinical trials due to side effects and rodent models are not available to investigate the mechanism of these failures. Here, we elucidated the structural elements of the potency differences between mouse and human CatK (hCatK) using ODN. We determined and compared the structures of inhibitor-free mouse CatK (mCatK), hCatK and ODN bound to hCatK. Two structural differences were identified and investigated by mutational analysis. Humanizing subsite 2 in mCatK led to a 5-fold improvement of ODN binding, whereas the replacement of Tyr61 in mCatK with Asp resulted in an hCatK with comparable ODN potency. Combining both sites further improved the inhibition of the mCatK variant. Similar results were obtained for balicatib. These findings will allow the generation of transgenic CatK mice that will facilitate the evaluation of CatK inhibitor adverse effects and to explore routes to avoid them.
- Published
- 2016
22. Enzyme–substrate complexes of allosteric citrate synthase: Evidence for a novel intermediate in substrate binding
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Harry W. Duckworth, Ayeda Ayed, Lynda J. Donald, Brigitte Bruneau, Yin Gao, Nham T. Nguyen, Gary D. Brayer, and Robert Maurus
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Swine ,Stereochemistry ,Allosteric regulation ,Biophysics ,Citrate (si)-Synthase ,Substrate analog ,Biochemistry ,Analytical Chemistry ,chemistry.chemical_compound ,Allosteric Regulation ,Acetyl Coenzyme A ,Catalytic Domain ,Escherichia coli ,Acetobacter ,Animals ,Citrate synthase ,Transferase ,Molecular Biology ,chemistry.chemical_classification ,biology ,Escherichia coli Proteins ,Active site ,Substrate (chemistry) ,Enzyme structure ,Enzyme ,chemistry ,biology.protein ,NADP ,Protein Binding - Abstract
The citrate synthase (CS) of Escherichia coli is an allosteric hexameric enzyme specifically inhibited by NADH. The crystal structure of wild type (WT) E. coli CS, determined by us previously, has no substrates bound, and part of the active site is in a highly mobile region that is shifted from the position needed for catalysis. The CS of Acetobacter aceti has a similar structure, but has been successfully crystallized with bound substrates: both oxaloacetic acid (OAA) and an analog of acetyl coenzyme A (AcCoA). We engineered a variant of E. coli CS wherein five amino acids in the mobile region have been replaced by those in the A. aceti sequence. The purified enzyme shows unusual kinetics with a low affinity for both substrates. Although the crystal structure without ligands is very similar to that of the WT enzyme (except in the mutated region), complexes are formed with both substrates and the allosteric inhibitor NADH. The complex with OAA in the active site identifies a novel OAA-binding residue, Arg306, which has no functional counterpart in other known CS-OAA complexes. This structure may represent an intermediate in a multi-step substrate binding process where Arg306 changes roles from OAA binding to AcCoA binding. The second complex has the substrate analog, S-carboxymethyl-coenzyme A, in the allosteric NADH-binding site and the AcCoA site is not formed. Additional CS variants unable to bind adenylates at the allosteric site show that this second complex is not a factor in positive allosteric activation of AcCoA binding.
- Published
- 2013
23. Application of salivary noncoding microRNAs for the diagnosis of oral cancers.
- Author
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Deutsch, Fiona T., Khoury, Samantha J., Sunwoo, John B., Elliott, Michael S., and Tran, Nham T.
- Subjects
MICRORNA ,MOUTH ,CANCER diagnosis ,ORAL cancer ,INSPECTION & review - Abstract
Oral cancer is on the rise globally and survival rates, despite improvements in clinical care, have not significantly improved. Early detection followed by immediate intervention is key to improving patient outcomes. The use of biomarkers has changed the diagnostic landscape for many cancers. For oral cancers, visual inspection followed by a tissue biopsy is standard practice. The discovery of microRNAs as potential biomarkers has attracted clinical interest but several challenges remain. These microRNAs can be found in bodily fluids such as blood and saliva which have been investigated as potential sources of biomarker discovery. As oral cancer is localized within the oral cavity, saliva may contain clinically relevant molecular markers for disease detection. Our review provides an outline of the current advances for the application of salivary microRNAs in oral cancer. We also provide a technical guide for the processing of salivary RNAs to ensure accurate clinical measurement and validation. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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24. Affinity Crystallography: A New Approach to Extracting High-Affinity Enzyme Inhibitors from Natural Extracts
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Gary D. Brayer, Labros G. Meimetis, Ping Cheng, Ivan Villanueva, Tina M. Bott, Simon Law, Dieter Brömme, Adeleke Aguda, Vincent Lavallee, Nham T. Nguyen, Jadwiga Kaleta, David E. Williams, Julian Davies, and Raymond J. Andersen
- Subjects
0301 basic medicine ,Lichens ,Chemical structure ,Cathepsin K ,Pharmaceutical Science ,Biology ,Crystallography, X-Ray ,01 natural sciences ,Analytical Chemistry ,03 medical and health sciences ,chemistry.chemical_compound ,Drug Discovery ,Hydrolase ,Potency ,Antipain ,Nuclear Magnetic Resonance, Biomolecular ,Pharmacology ,chemistry.chemical_classification ,Biological Products ,Natural product ,British Columbia ,Molecular Structure ,010405 organic chemistry ,Drug discovery ,Organic Chemistry ,Combinatorial chemistry ,0104 chemical sciences ,Crystallography ,030104 developmental biology ,Enzyme ,Complementary and alternative medicine ,chemistry ,Biochemistry ,Molecular Medicine ,Peptides - Abstract
Natural products are an important source of novel drug scaffolds. The highly variable and unpredictable timelines associated with isolating novel compounds and elucidating their structures have led to the demise of exploring natural product extract libraries in drug discovery programs. Here we introduce affinity crystallography as a new methodology that significantly shortens the time of the hit to active structure cycle in bioactive natural product discovery research. This affinity crystallography approach is illustrated by using semipure fractions of an actinomycetes culture extract to isolate and identify a cathepsin K inhibitor and to compare the outcome with the traditional assay-guided purification/structural analysis approach. The traditional approach resulted in the identification of the known inhibitor antipain (1) and its new but lower potency dehydration product 2, while the affinity crystallography approach led to the identification of a new high-affinity inhibitor named lichostatinal (3). The structure and potency of lichostatinal (3) was verified by total synthesis and kinetic characterization. To the best of our knowledge, this is the first example of isolating and characterizing a potent enzyme inhibitor from a partially purified crude natural product extract using a protein crystallographic approach.
- Published
- 2016
25. Glucosyl epi-cyclophellitol allows mechanism-based inactivation and structural analysis of human pancreatic α-amylase
- Author
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Xiaohua Zhang, Sami Caner, Gary D. Brayer, Jianbing Jiang, Stephen G. Withers, Nham T. Nguyen, Hermen S. Overkleeft, and Hong-Ming Chen
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glycosyl enzyme ,Models, Molecular ,amylase ,Stereochemistry ,activity-based probes ,Kinetics ,Biophysics ,Disaccharide ,Pancreatic alpha-Amylases ,010402 general chemistry ,Disaccharides ,01 natural sciences ,Biochemistry ,conduritol epoxide ,Mass Spectrometry ,chemistry.chemical_compound ,Nucleophile ,X-Ray Diffraction ,Structural Biology ,GH13 structure ,Catalytic Domain ,Genetics ,Humans ,Computer Simulation ,Amylase ,Molecular Biology ,mechanism-based inhibition ,biology ,010405 organic chemistry ,Hydrogen bond ,Active site ,Water ,Hydrogen Bonding ,Cell Biology ,Cyclohexanols ,0104 chemical sciences ,chemistry ,Covalent bond ,biology.protein ,Epoxy Compounds ,Derivative (chemistry) ,Inositol - Abstract
As part of a search for selective, mechanism-based covalent inhibitors of human pancreatic α-amylase we describe the chemoenzymatic synthesis of the disaccharide analog α-glucosyl epi-cyclophellitol, demonstrate its stoichiometric reaction with human pancreatic α-amylase and evaluate the time dependence of its inhibition. X-ray crystallographic analysis of the covalent derivative so formed confirms its reaction at the active site with formation of a covalent bond to the catalytic nucleophile D197. The structure illuminates the interactions with the active site and confirms OH4' on the nonreducing end sugar as a good site for attachment of fluorescent tags in generating probes for localization and quantitation of amylase in vivo.
- Published
- 2015
26. Stage-specific miRNAs regulate gene expression associated with growth, development and parasite-host interaction during the intra-mammalian migration of the zoonotic helminth parasite Fasciola hepatica
- Author
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Alison Ricafrente, Krystyna Cwiklinski, Hieu Nguyen, John P. Dalton, Nham Tran, and Sheila Donnelly
- Subjects
Fasciola hepatica ,Helminth ,microRNAs ,Newly excysted juvenile ,Cathepsin L3 ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background MiRNAs are small non-coding RNAs that post-transcriptionally regulate gene expression in organisms ranging from viruses to mammals. There is great relevance in understanding how miRNAs regulate genes involved in the growth, development, and maturation of the many parasitic worms (helminths) that together afflict more than 2 billion people. Results Here, we describe the miRNAs expressed by each of the predominant intra-mammalian development stages of Fasciola hepatica, a foodborne flatworm that infects a wide range of mammals worldwide, most importantly humans and their livestock. A total of 124 miRNAs were profiled, 72 of which had been previously reported and three of which were conserved miRNA sequences described here for the first time. The remaining 49 miRNAs were novel sequences of which, 31 were conserved with F. gigantica and the remaining 18 were specific to F. hepatica. The newly excysted juveniles express 22 unique miRNAs while the immature liver and mature bile duct stages each express 16 unique miRNAs. We discovered several sequence variant miRNAs (IsomiRs) as well as miRNA clusters that exhibit strict temporal expression paralleling parasite development. Target analysis revealed the close association between miRNA expression and stage-specific changes in the transcriptome; for example, we identified specific miRNAs that target parasite proteases known to be essential for intestinal wall penetration (cathepsin L3). Moreover, we demonstrate that miRNAs fine-tune the expression of genes involved in the metabolic pathways that allow the parasites to move from an aerobic external environment to the anerobic environment of the host. Conclusions These results provide novel insight into the regulation of helminth parasite development and identifies new genes and miRNAs for therapeutic development to limit the virulence and pathogenesis caused by F. hepatica.
- Published
- 2022
- Full Text
- View/download PDF
27. Structure, Binding, and Activity of Syd, a SecY-interacting Protein
- Author
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Robert Maurus, Meriem Alami, Jennifer Tan, Franck Duong, Stephen S. Sligar, Woo Cheol Lee, Nham T. Nguyen, Gary D. Brayer, Kush Dalal, and Trevor F. Moraes
- Subjects
Protein subunit ,Static Electricity ,Plasma protein binding ,Biology ,Crystallography, X-Ray ,Biochemistry ,Protein Structure, Secondary ,Heterotrimeric G protein ,Escherichia coli ,Protein Structure, Quaternary ,Molecular Biology ,Escherichia coli Proteins ,Cell Membrane ,Membrane Proteins ,Cell Biology ,Translocon ,Transport protein ,Protein Subunits ,Protein Transport ,Membrane Transport, Structure, Function, and Biogenesis ,Membrane protein ,Biophysics ,SEC Translocation Channels ,Biogenesis ,Protein Binding - Abstract
The Syd protein has been implicated in the Sec-dependent transport of polypeptides across the bacterial inner membrane. Using Nanodiscs, we here provide direct evidence that Syd binds the SecY complex, and we demonstrate that interaction involves the two electropositive and cytosolic loops of the SecY subunit. We solve the crystal structure of Syd and together with cysteine cross-link analysis, we show that a conserved concave and electronegative groove constitutes the SecY-binding site. At the membrane, Syd decreases the activity of the translocon containing loosely associated SecY-SecE subunits, whereas in detergent solution Syd disrupts the SecYEG heterotrimeric associations. These results support the role of Syd in proofreading the SecY complex biogenesis and point to the electrostatic nature of the Sec channel interaction with its cytosolic partners.
- Published
- 2009
28. Identification of mouse cathepsin K structural elements that regulate the potency of odanacatib
- Author
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Law, Simon, primary, Andrault, Pierre-Marie, additional, Aguda, Adeleke H., additional, Nguyen, Nham T., additional, Kruglyak, Natasha, additional, Brayer, Gary D., additional, and Brömme, Dieter, additional
- Published
- 2017
- Full Text
- View/download PDF
29. Insights into the evolution of allosteric properties. the NADH binding site of hexameric type II citrate synthases
- Author
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Maurus, Robert, Nguyen, Nham T., Stokell, David J., Ayed, Ayeda, Hultin, Philip G., Duckworth, Harry W., and Brayer, Gary D.
- Subjects
Enzymes -- Structure-activity relationship ,Protein binding -- Analysis ,Allosteric enzymes -- Analysis ,Biological sciences ,Chemistry - Abstract
Structural analyses demonstrate that the six NADH binding sites of the hexameric type II citrate synthases are situated at the interfaces between dimer units, suggesting that each site is formed by one subunit with a sharing of key amino acid residues from the adjacent dimer. Data indicate that the NADH-binding residues are conserved and the above arrangement confers NADH allosteric regulation on the hexameric type II citrate synthases.
- Published
- 2003
30. Structural basis of collagen fiber degradation by cathepsin K
- Author
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Dieter Brömme, Adeleke Aguda, Gary D. Brayer, Preety Panwar, Xin Du, and Nham T. Nguyen
- Subjects
Models, Molecular ,Pathology ,medicine.medical_specialty ,Protein Denaturation ,Protein Folding ,Materials science ,medicine.medical_treatment ,Dimer ,Cathepsin K ,Protein dimer ,Cleavage (embryo) ,Crystallography, X-Ray ,Bone and Bones ,Pichia ,Substrate Specificity ,Glycosaminoglycan ,chemistry.chemical_compound ,medicine ,Humans ,Amino Acids ,Glycosaminoglycans ,Glycosaminoglycan binding ,Multidisciplinary ,Protease ,Binding Sites ,Edman degradation ,Hydrolysis ,Biological Sciences ,Protein Structure, Tertiary ,Microscopy, Electron ,chemistry ,Mutagenesis ,Biophysics ,Osteoporosis ,Bone Remodeling ,Collagen ,Protein Multimerization ,Peptide Hydrolases - Abstract
Cathepsin K is the major collagenolytic protease in bone that facilitates physiological as well as pathological bone degradation. Despite its key role in bone remodeling and for being a highly sought-after drug target for the treatment of osteoporosis, the mechanism of collagen fiber degradation by cathepsin K remained elusive. Here, we report the structure of a collagenolytically active cathepsin K protein dimer. Cathepsin K is organized into elongated C-shaped protease dimers that reveal a putative collagen-binding interface aided by glycosaminoglycans. Molecular modeling of collagen binding to the dimer indicates the participation of nonactive site amino acid residues, Q21 and Q92, in collagen unfolding. Mutations at these sites as well as perturbation of the dimer protein–protein interface completely inhibit cathepsin-K–mediated fiber degradation without affecting the hydrolysis of gelatin or synthetic peptide. Using scanning electron microscopy, we demonstrate the specific binding of cathepsin K at the edge of the fibrillar gap region of collagen fibers, which suggest initial cleavage events at the N - and C -terminal ends of tropocollagen molecules. Edman degradation analysis of collagen fiber degradation products revealed those initial cleavage sites. We propose that one cathepsin K molecule binds to collagen-bound glycosaminoglycans at the gap region and recruits a second protease molecule that provides an unfolding and cleavage mechanism for triple helical collagen. Removal of collagen-associated glycosaminoglycans prevents cathepsin K binding and subsequently fiber hydrolysis. Cathepsin K dimer and glycosaminoglycan binding sites represent novel targeting sites for the development of nonactive site-directed second-generation inhibitors of this important drug target.
- Published
- 2014
31. Probing the Roles of Key Residues in the Unique Regulatory NADH Binding Site of Type II Citrate Synthase of Escherichia coli
- Author
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David J. Stokell, Philip G. Hultin, Nham T. Nguyen, Robert Maurus, Harry W. Duckworth, Gary D. Brayer, Gillian Sadler, Lynda J. Donald, and Kajal Choudhary
- Subjects
Models, Molecular ,Conformational change ,Protein Conformation ,NADH binding ,Stereochemistry ,Static Electricity ,Allosteric regulation ,Citrate (si)-Synthase ,Random hexamer ,Crystallography, X-Ray ,medicine.disease_cause ,Biochemistry ,Escherichia coli ,medicine ,Citrate synthase ,Transferase ,Molecular Biology ,Binding Sites ,biology ,Chemistry ,Wild type ,Genetic Variation ,Hydrogen Bonding ,Cell Biology ,NAD ,Recombinant Proteins ,Kinetics ,Amino Acid Substitution ,Mutagenesis, Site-Directed ,biology.protein ,Thermodynamics - Abstract
The citrate synthase of Escherichia coli is an example of a Type II citrate synthase, a hexamer that is subject to allosteric inhibition by NADH. In previous crystallographic work, we defined the NADH binding sites, identifying nine amino acids whose side chains were proposed to make hydrogen bonds with the NADH molecule. Here, we describe the functional properties of nine sequence variants, in which these have been replaced by nonbonding residues. All of the variants show some changes in NADH binding and inhibition and small but significant changes in kinetic parameters for catalysis. In three cases, Y145A, R163L, and K167A, NADH inhibition has become extremely weak. We have used nanospray/time-of-flight mass spectrometry, under non-denaturing conditions, to show that two of these, R163L and K167A, do not form hexamers in response to NADH binding, unlike the wild type enzyme. One variant, R109L, shows tighter NADH binding. We have crystallized this variant and determined its structure, with and without bound NADH. Unexpectedly, the greatest structural changes in the R109L variant are in two regions outside the NADH binding site, both of which, in wild type citrate synthase, have unusually high mobilities as measured by crystallographic thermal factors. In the R109L variant, both regions (residues 260 -311 and 316-342) are much less mobile and have rearranged significantly. We argue that these two regions are elements in the path of communication between the NADH binding sites and the active sites and are centrally involved in the regulatory conformational change in E. coli citrate synthase.
- Published
- 2003
32. Introduction and characterization of a functionally linked metal ion binding site at the exposed heme edge of myoglobin
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Harry Tong, Robert Maurus, Gary D. Brayer, Nham T. Nguyen, A. Grant Mauk, Emma Lloyd Raven, H. Lee, Michael J. Smith, Christie L. Hunter, and Marcia R. Mauk
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inorganic chemicals ,Models, Molecular ,Metal ions in aqueous solution ,Inorganic chemistry ,Heme ,Crystallography, X-Ray ,chemistry.chemical_compound ,Chlorides ,Electrochemistry ,Animals ,Horses ,Binding site ,Binding Sites ,Multidisciplinary ,Myoglobin ,Hexacoordinate ,Recombinant Proteins ,Kinetics ,Crystallography ,Manganese Compounds ,chemistry ,Metmyoglobin ,Metals ,Mutagenesis ,Spectrophotometry ,Ionic strength ,Physical Sciences ,Azide - Abstract
A binding site for metal ions has been created on the surface of horse heart myoglobin (Mb) near the heme 6-propionate group by replacing K45 and K63 with glutamyl residues. One-dimensional 1 H NMR spectroscopy indicates that Mn 2+ binds in the vicinity of the heme 6-propionate as anticipated, and potentiometric titrations establish that the affinity of the new site for Mn 2+ is 1.28(4) × 10 4 M −1 (pH 6.96, ionic strength I = 17.2 μM, 25°C). In addition, these substitutions lower the reduction potential of the protein and increase the pK a for the water molecule coordinated to the heme iron of metmyoglobin. The peroxidase [2,2′-azinobis(3-ethylbenzthiazoline-6-sulfonic acid), ABTS, as substrate] and the Mn 2+ -peroxidase activity of the variant are both increased ≈3-fold. In contrast to wild-type Mb, both the affinity for azide and the midpoint potential of the variant are significantly influenced by the addition of Mn 2+ . The structure of the variant has been determined by x-ray crystallography to define the coordination environment of bound Mn 2+ and Cd 2+ . Although slight differences are observed between the geometry of the binding of the two metal ions, both are hexacoordinate, and neither involves coordination by E63.
- Published
- 2003
33. Affinity Crystallography: A New Approach to Extracting High-Affinity Enzyme Inhibitors from Natural Extracts
- Author
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Aguda, Adeleke H., primary, Lavallee, Vincent, additional, Cheng, Ping, additional, Bott, Tina M., additional, Meimetis, Labros G., additional, Law, Simon, additional, Nguyen, Nham T., additional, Williams, David E., additional, Kaleta, Jadwiga, additional, Villanueva, Ivan, additional, Davies, Julian, additional, Andersen, Raymond J., additional, Brayer, Gary D., additional, and Brömme, Dieter, additional
- Published
- 2016
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- View/download PDF
34. Glucosyl epi‐cyclophellitol allows mechanism‐based inactivation and structural analysis of human pancreatic α‐amylase
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Caner, Sami, primary, Zhang, Xiaohua, additional, Jiang, Jianbing, additional, Chen, Hong‐Ming, additional, Nguyen, Nham T., additional, Overkleeft, Hermen, additional, Brayer, Gary D., additional, and Withers, Stephen G., additional
- Published
- 2016
- Full Text
- View/download PDF
35. Potent Human α-Amylase Inhibition by the β-Defensin-like Protein Helianthamide
- Author
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Tysoe, Christina, primary, Williams, Leslie K., additional, Keyzers, Robert, additional, Nguyen, Nham T., additional, Tarling, Chris, additional, Wicki, Jacqueline, additional, Goddard-Borger, Ethan D., additional, Aguda, Adeleke H., additional, Perry, Suzanne, additional, Foster, Leonard J., additional, Andersen, Raymond J., additional, Brayer, Gary D., additional, and Withers, Stephen G., additional
- Published
- 2016
- Full Text
- View/download PDF
36. The structure of the Mycobacterium smegmatis trehalose synthase reveals an unusual active site configuration and acarbose-binding mode†
- Author
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Stephen G. Withers, Gary D. Brayer, Nham T. Nguyen, Sami Caner, Adeleke Aguda, Yuan T. Pan, and Ran Zhang
- Subjects
Protein Conformation ,Molecular Sequence Data ,Mycobacterium smegmatis ,Disaccharide ,Biochemistry ,chemistry.chemical_compound ,Structure-Activity Relationship ,Catalytic Domain ,Hydrolase ,Amino Acid Sequence ,chemistry.chemical_classification ,biology ,Glycogen ,Active site ,Maltose ,Original Articles ,biology.organism_classification ,Trehalose ,Enzyme ,chemistry ,Glucosyltransferases ,biology.protein ,Biocatalysis ,Acarbose ,Sequence Alignment ,Protein Binding - Abstract
Trehalose synthase (TreS) catalyzes the reversible conversion of maltose into trehalose in mycobacteria as one of three biosynthetic pathways to this nonreducing disaccharide. Given the importance of trehalose to survival of mycobacteria, there has been considerable interest in understanding the enzymes involved in its production; indeed the structures of the key enzymes in the other two pathways have already been determined. Herein, we present the first structure of TreS from Mycobacterium smegmatis, thereby providing insights into the catalytic machinery involved in this intriguing intramolecular reaction. This structure, which is of interest both mechanistically and as a potential pharmaceutical target, reveals a narrow and enclosed active site pocket within which intramolecular substrate rearrangements can occur. We also present the structure of a complex of TreS with acarbose, revealing a hitherto unsuspected oligosaccharide-binding site within the C-terminal domain. This may well provide an anchor point for the association of TreS with glycogen, thereby enhancing its role in glycogen biosynthesis and degradation.
- Published
- 2013
37. Mental Disorders Are Associated With Leukocytes Telomere Shortening Among People Who Inject Drugs
- Author
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Mélusine Durand, Nicolas Nagot, Laurent Michel, Sao Mai Le, Huong Thi Duong, Roselyne Vallo, Amélie Vizeneux, Delphine Rapoud, Hoang Thi Giang, Catherine Quillet, Nham Thi Tuyet Thanh, Khuat Thi Hai Oanh, Vu Hai Vinh, Jonathan Feelemyer, Philippe Vande Perre, Khue Pham Minh, Didier Laureillard, Don Des Jarlais, and Jean-Pierre Molès
- Subjects
drug use ,depression ,psychotic syndrome ,telomere shortening ,mitochondrial DNA ,hepatitis C virus ,Psychiatry ,RC435-571 - Abstract
Premature biological aging, assessed by shorter telomere length (TL) and mitochondrial DNA (mtDNA) alterations, has been reported among people with major depressive disorders or psychotic disorders. However, these markers have never been assessed together among people who inject drugs (PWIDs), although mental disorders are highly prevalent in this population, which, in addition, is subject to other aggravating exposures. Diagnosis of mental disorders was performed by a psychiatrist using the Mini International Neuropsychiatric Interview test among active PWIDs in Haiphong, Vietnam. mtDNA copy number (MCN), mtDNA deletion, and TL were assessed by quantitative PCR and compared to those without any mental disorder. We next performed a multivariate analysis to identify risk factors associated with being diagnosed with a major depressive episode (MDE) or a psychotic syndrome (PS). In total, 130 and 136 PWIDs with and without psychiatric conditions were analyzed. Among PWIDs with mental disorders, 110 and 74 were diagnosed with MDE and PS, respectively. TL attrition was significantly associated with hepatitis C virus-infected PWIDs with MDE or PS (adjusted odds ratio [OR]: 0.53 [0.36; 0.80] and 0.59 [0.39; 0.88], respectively). TL attrition was even stronger when PWIDs cumulated at least two episodes of major depressive disorders. On the other hand, no difference was observed in mtDNA alterations between groups. The telomeric age difference with drug users without a diagnosis of psychiatric condition was estimated during 4.2–12.8 years according to the number of MDEs, making this group more prone to age-related diseases.
- Published
- 2022
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38. The amylase inhibitor montbretin A reveals a new glycosidase inhibition motif
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Williams, Leslie K, primary, Zhang, Xiaohua, additional, Caner, Sami, additional, Tysoe, Christina, additional, Nguyen, Nham T, additional, Wicki, Jacqueline, additional, Williams, David E, additional, Coleman, John, additional, McNeill, John H, additional, Yuen, Violet, additional, Andersen, Raymond J, additional, Withers, Stephen G, additional, and Brayer, Gary D, additional
- Published
- 2015
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39. The functional architecture of a cationic pore that modulates citrate synthase quaternary structure and allostery
- Author
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Gary D. Brayer, Nham T. Nguyen, Harry W. Duckworth, David John Stokell, Robert Maurus, and Lynda J. Donald
- Subjects
0303 health sciences ,biology ,Chemistry ,Stereochemistry ,Allosteric regulation ,Cationic polymerization ,Biochemistry ,03 medical and health sciences ,0302 clinical medicine ,Genetics ,biology.protein ,Citrate synthase ,Protein quaternary structure ,Molecular Biology ,030217 neurology & neurosurgery ,030304 developmental biology ,Biotechnology - Published
- 2010
40. Crystallographic characterization of the passenger domain of the Bordetella autotransporter BrkA
- Author
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Nham T. Nguyen, Li Zhao, Rachel C. Fernandez, and Michael E. P. Murphy
- Subjects
Bordetella pertussis ,Protein Folding ,Molecular Sequence Data ,Statistics as Topic ,Biophysics ,Protein Sorting Signals ,medicine.disease_cause ,Biochemistry ,Gene product ,X-Ray Diffraction ,Structural Biology ,Genetics ,medicine ,Escherichia coli ,Secretion ,Amino Acid Sequence ,Cloning, Molecular ,Peptide sequence ,Inclusion Bodies ,Secretory Pathway ,biology ,Sequence Homology, Amino Acid ,Circular Dichroism ,Data Collection ,Temperature ,Membrane Transport Proteins ,Proteins ,Condensed Matter Physics ,biology.organism_classification ,Protein Structure, Tertiary ,Bordetella ,Crystallography ,Crystallization Communications ,Autotransporter domain ,Crystallization ,Autotransporters ,Bacterial Outer Membrane Proteins - Abstract
Autotransporters (ATs) are proteins that deliver effectors (the passenger domain) to the surface of Gram-negative bacteria by the type V secretion pathway. The passenger domain of BrkA, a Bordetella pertussis autotransporter mediating serum resistance and adherence, was cloned in a pET expression system and overexpressed in Escherichia coli. The gene product was correctly refolded, purified to homogeneity and crystallized. The crystals diffracted to 2.8 A resolution. The space group was assumed to be P4(1)2(1)2, with unit-cell parameters a = b = 108.19, c = 115.35 A.
- Published
- 2009
41. Fasciola hepatica hijacks host macrophage miRNA machinery to modulate early innate immune responses
- Author
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Nham Tran, Alison Ricafrente, Joyce To, Maria Lund, Tania M. Marques, Margarida Gama-Carvalho, Krystyna Cwiklinski, John P. Dalton, and Sheila Donnelly
- Subjects
Medicine ,Science - Abstract
Abstract Fasciola hepatica, a global worm parasite of humans and their livestock, regulates host innate immune responses within hours of infection. Host macrophages, essential to the first-line defence mechanisms, are quickly restricted in their ability to initiate a classic protective pro-inflammatory immune response. We found that macrophages from infected animals are enriched with parasite-derived micro(mi)RNAs. The most abundant of these miRNAs, fhe-miR-125b, is released by the parasite via exosomes and is homologous to a mammalian miRNA, hsa-miR-125b, that is known to regulate the activation of pro-inflammatory M1 macrophages. We show that the parasite fhe-miR-125b loads onto the mammalian Argonaut protein (Ago-2) within macrophages during infection and, therefore, propose that it mimics host miR-125b to negatively regulate the production of inflammatory cytokines. The hijacking of the miRNA machinery controlling innate cell function could be a fundamental mechanism by which worm parasites disarm the early immune responses of their host to ensure successful infection.
- Published
- 2021
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42. Insights into the evolution of allosteric properties. The NADH binding site of hexameric type II citrate synthases
- Author
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Philip G. Hultin, Gary D. Brayer, Robert Maurus, David John Stokell, Nham T. Nguyen, Ayeda Ayed, and Harry W. Duckworth
- Subjects
Models, Molecular ,NADH binding ,Stereochemistry ,Protein Conformation ,Dimer ,Protein subunit ,Allosteric regulation ,Molecular Sequence Data ,Citrate (si)-Synthase ,Biology ,Crystallography, X-Ray ,Biochemistry ,Evolution, Molecular ,chemistry.chemical_compound ,Protein structure ,Allosteric Regulation ,Escherichia coli ,Transferase ,Amino Acid Sequence ,Protein Structure, Quaternary ,Peptide sequence ,chemistry.chemical_classification ,Sequence Homology, Amino Acid ,Genetic Variation ,NAD ,Enzyme ,chemistry ,Dimerization ,Allosteric Site - Abstract
Study of the hexameric and allosterically regulated citrate synthases (type II CS) provides a rare opportunity to gain not only an understanding of a novel allosteric mechanism but also insight into how such properties can evolve from an unregulated structural platform (the dimeric type I CS). To address both of these issues, we have determined the structure of the complex of NADH (a negative allosteric effector) with the F383A variant of type II Escherichia coli CS. This variant was chosen because its kinetics indicate it is primarily in the T or inactive allosteric conformation, the state that strongly binds to NADH. Our structural analyses show that the six NADH binding sites in the hexameric CS complex are located at the interfaces between dimer units such that most of each site is formed by one subunit, but a number of key residues are drawn from the adjacent dimer. This arrangement of interactions serves to explain why NADH allosteric regulation is a feature only of hexameric type II CS. Surprisingly, in both the wild-type enzyme and the NADH complex, the two subunits of each dimer within the hexameric conformation are similar but not identical in structure, and therefore, while the general characteristics of NADH binding interactions are similar in each subunit, the details of these are somewhat different between subunits. Detailed examination of the observed NADH binding sites indicates that both direct charged interactions and the overall cationic nature of the sites are likely responsible for the ability of these sites to discriminate between NADH and NAD(+). A particularly novel characteristic of the complex is the horseshoe conformation assumed by NADH, which is strikingly different from the extended conformation found in its complexes with most proteins. Sequence homology studies suggest that this approach to binding NADH may arise out of the evolutionary need to add an allosteric regulatory function to the base CS structure. Comparisons of the amino acid sequences of known type II CS enzymes, from different Gram-negative bacteria taxonomic groups, show that the NADH-binding residues identified in our structure are strongly conserved, while hexameric CS molecules that are insensitive to NADH have undergone key changes in the sequence of this part of the protein.
- Published
- 2003
43. The characterization of extracellular vesicles-derived microRNAs in Thai malaria patients
- Author
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Nutpakal Ketprasit, Iris Simone Cheng, Fiona Deutsch, Nham Tran, Mallika Imwong, Valery Combes, and Duangdao Palasuwan
- Subjects
Malaria ,Patients ,Plasmodium falciparum ,Plasmodium vivax ,Extracellular vesicles ,microRNAs ,Arctic medicine. Tropical medicine ,RC955-962 ,Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background Extracellular vesicles (EVs) have been broadly studied in malaria for nearly a decade. These vesicles carry various functional biomolecules including RNA families such as microRNAs (miRNA). These EVs-derived microRNAs have numerous roles in host-parasite interactions and are considered promising biomarkers for disease severity. However, this field lacks clinical studies of malaria-infected samples. In this study, EV specific miRNAs were isolated from the plasma of patients from Thailand infected with Plasmodium vivax and Plasmodium falciparum. In addition, it is postulated that these miRNAs were differentially expressed in these groups of patients and had a role in disease onset through the regulation of specific target genes. Methods EVs were purified from the plasma of Thai P. vivax-infected patients (n = 19), P. falciparum-infected patients (n = 18) and uninfected individuals (n = 20). EV-derived miRNAs were then prepared and abundance of hsa-miR-15b-5p, hsa-miR-16-5p, hsa-let-7a-5p and hsa-miR-150-5p was assessed in these samples. Quantitative polymerase chain reaction was performed, and relative expression of each miRNA was calculated using hsa-miR-451a as endogenous control. Then, the targets of up-regulated miRNAs and relevant pathways were predicted by using bioinformatics. Receiver Operating Characteristic with Area under the Curve (AUC) was then calculated to assess their diagnostic potential. Results The relative expression of hsa-miR-150-5p and hsa-miR-15b-5p was higher in P. vivax-infected patients compared to uninfected individuals, but hsa-let-7a-5p was up-regulated in both P. vivax-infected patients and P. falciparum-infected patients. Bioinformatic analysis revealed that these miRNAs might regulate genes involved in the malaria pathway including the adherens junction and the transforming growth factor-β pathways. All up-regulated miRNAs could potentially be used as disease biomarkers as determined by AUC; however, the sensitivity and specificity require further investigation. Conclusion An upregulation of hsa-miR-150-5p and hsa-miR-15b-5p was observed in P. vivax-infected patients while hsa-let-7a-5p was up-regulated in both P. vivax-infected and P. falciparum-infected patients. These findings will require further validation in larger cohort groups of malaria patients to fully understand the contribution of these EVs miRNAs to malaria detection and biology.
- Published
- 2020
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44. Knowledge sharing and innovation capability at both individual and organizational levels: An empirical study from Vietnam’s telecommunication companies
- Author
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Nham Tuan Phong, Nguyen Tuyet-Mai, Tran Nam Hoai, and Nguyen Hao Anh
- Subjects
knowledge sharing ,knowledge donating ,knowledge collecting ,firm innovation capability ,individual innovation capability ,Business ,HF5001-6182 - Abstract
This paper aims at investigating the relationship between knowledge sharing activities and innovation capability at both individual and organizational levels. By reviewing extensive literature, a conceptual framework is built with integrating three factors: knowledge sharing, individual innovation capability and firm innovation capability. This study applies structural equation modeling (SEM) to analyze the data collected from 392 employees working at major Vietnam’s telecommunication companies. Empirical results show that knowledge sharing including knowledge donating, knowledge collecting play an important role in improving individual innovation capability. There is no direct link between knowledge collecting and organizational innovation capability, while knowledge donating has direct positive impact on product and managerial innovation. Furthermore, the individual innovation capability acts as a mediating variable between knowledge sharing practices and firm innovation capability. Implications for academics and practitioners are provided in this study.
- Published
- 2020
- Full Text
- View/download PDF
45. Mycobacterial Trehalose Synthase as a potential drug target for tuberculosis
- Author
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Yuan Pan, Ran Zhang, Adeleke Aguda, Stephen G. Withers, Sami Caner, Nham T. Nguyen, and Gary D. Brayer
- Subjects
Inorganic Chemistry ,Tuberculosis ,Structural Biology ,Chemistry ,Drug target ,medicine ,General Materials Science ,Physical and Theoretical Chemistry ,Condensed Matter Physics ,Trehalose synthase ,medicine.disease ,Biochemistry ,Microbiology - Abstract
Trehalose synthase (TreS) catalyzes the reversible conversion of maltose to trehalose in mycobacteria as one of three biosynthetic pathways to this non-reducing disaccharide. Given the importance of trehalose to survival of mycobacteria there has been considerable interest in understanding the enzymes involved in its production; indeed the structures of the key enzymes in the other two pathways have already been determined. Herein we present the first structure of TreS from Mycobacterium smegmatis, thereby providing insights into the catalytic machinery involved in this intriguing intramolecular reaction. This structure, which is of interest both mechanistically and as a potential pharmaceutical target, reveals a narrow and enclosed active site cleft within which the intramolecular rearrangement can occur with minimal hydrolysis. We also present the structure of a complex of TreS with acarbose, revealing a hitherto unsuspected oligosaccharide binding site within the C-terminal domain. This may well provide an anchor point for the association of TreS with glycogen, thereby enhancing its role in glycogen biosynthesis and degradation.
- Published
- 2014
46. Studies of Heat shock protein 27 Interactions
- Author
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Adeleke Aguda, Sami Caner, Nham T. Nguyen, Gary D. Brayer, Amina Zoubeidi, Martin E. Gleave, Barbara Lelj-Garolla, and Susan C. Moore
- Subjects
endocrine system ,animal structures ,Chemistry ,macromolecular substances ,Condensed Matter Physics ,Biochemistry ,Inorganic Chemistry ,Heat shock factor ,Structural Biology ,Heat shock protein ,embryonic structures ,Biophysics ,General Materials Science ,Physical and Theoretical Chemistry ,Heat shock - Abstract
Human heat shock protein 27 (Hsp27) is an oligomeric and cell survival protein that has been associated with several cancers including prostrate and breast cancer. It's a known anti-apoptotic protein that functions as a molecular chaperone for several proteins. Hsp27 characteristically binds and stabilizes numerous partially unfolded proteins preventing their degradation, and has been shown to prevent actin polymerization in vitro. Several actin-binding residues involved in this interaction have been identified at the N-terminal loop and highly conserved alpha crystallin domains of Hsp27. Multiple assays have demonstrated that this hydrophobic actin-binding site is also involved in other protein binding. We therefore propose a common substrate-binding region on Hsp27 and present a model of Hsp27 binding to actin.
- Published
- 2014
47. Subsite mapping of the human pancreatic alpha-amylase active site through structural, kinetic, and mutagenesis techniques
- Author
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Yili Wang, Stephen G. Withers, Gary D. Brayer, Christopher M. Overall, Curtis Braun, Robert Maurus, Gary Sidhu, Edwin H. Rydberg, and Nham T. Nguyen
- Subjects
Models, Molecular ,Glycosylation ,Stereochemistry ,Protein Conformation ,Swine ,Molecular Sequence Data ,Oligosaccharides ,Cleavage (embryo) ,Crystallography, X-Ray ,Biochemistry ,Catalysis ,chemistry.chemical_compound ,Fluorides ,Structure-Activity Relationship ,Nucleophile ,Hydrolase ,Animals ,Humans ,Maltose ,Pancreas ,chemistry.chemical_classification ,Binding Sites ,biology ,Chemistry ,Hydrolysis ,Leaving group ,Active site ,Kinetics ,Enzyme ,Aglycone ,Amino Acid Substitution ,Carbohydrate Sequence ,Models, Chemical ,Mutagenesis ,biology.protein ,Thermodynamics ,Acarbose ,alpha-Amylases ,Alpha-amylase - Abstract
We report a multifaceted study of the active site region of human pancreatic alpha-amylase. Through a series of novel kinetic analyses using malto-oligosaccharides and malto-oligosaccharyl fluorides, an overall cleavage action pattern for this enzyme has been developed. The preferred binding/cleavage mode occurs when a maltose residue serves as the leaving group (aglycone sites +1 and +2) and there are three sugars in the glycon (-1, -2, -3) sites. Overall it appears that five binding subsites span the active site, although an additional glycon subsite appears to be a significant factor in the binding of longer substrates. Kinetic parameters for the cleavage of substrates modified at the 2 and 4' ' positions also highlight the importance of these hydroxyl groups for catalysis and identify the rate-determining step. Further kinetic and structural studies pinpoint Asp197 as being the likely nucleophile in catalysis, with substitution of this residue leading to an approximately 10(6)-fold drop in catalytic activity. Structural studies show that the original pseudo-tetrasaccharide structure of acarbose is modified upon binding, presumably through a series of hydrolysis and transglycosylation reactions. The end result is a pseudo-pentasaccharide moiety that spans the active site region with its N-linked "glycosidic" bond positioned at the normal site of cleavage. Interestingly, the side chains of Glu233 and Asp300, along with a water molecule, are aligned about the inhibitor N-linked glycosidic bond in a manner suggesting that these might act individually or collectively in the role of acid/base catalyst in the reaction mechanism. Indeed, kinetic analyses show that substitution of the side chains of either Glu233 or Asp300 leads to as much as a approximately 10(3)-fold decrease in catalytic activity. Structural analyses of the Asp300Asn variant of human pancreatic alpha-amylase and its complex with acarbose clearly demonstrate the importance of Asp300 to the mode of inhibitor binding.
- Published
- 2000
48. Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase
- Author
-
Nham T. Nguyen, Gary D. Brayer, Lawrence P. McIntosh, Gary Sidhu, Lothar Ziser, and Stephen G. Withers
- Subjects
Models, Molecular ,Stereochemistry ,Protein Conformation ,Phenylalanine ,Oxocarbenium ,Bacillus ,Xylose ,Gram-Positive Asporogenous Rods ,Crystallography, X-Ray ,Disaccharides ,Biochemistry ,Catalysis ,Substrate Specificity ,chemistry.chemical_compound ,Residue (chemistry) ,Hydrolase ,Glycosyl ,Endo-1,4-beta Xylanases ,biology ,Chemistry ,Hydrogen bond ,Active site ,Xylosidases ,Amino Acid Substitution ,Bacillus circulans ,biology.protein ,Tyrosine - Abstract
The 1.8 A resolution structure of the glycosyl-enzyme intermediate formed on the retaining beta-1,4-xylanase from Bacillus circulans has been determined using X-ray crystallographic techniques. The 2-fluoro-xylose residue bound in the -1 subsite adopts a 2,5B (boat) conformation, allowing atoms C5, O5, C1, and C2 of the sugar to achieve coplanarity as required at the oxocarbenium ion-like transition states of the double-displacement catalytic mechanism. Comparison of this structure to that of a mutant of this same enzyme noncovalently complexed with xylotetraose [Wakarchuk et al. (1994) Protein Sci. 3, 467-475] reveals a number of differences beyond the distortion of the sugar moiety. Most notably, a bifurcated hydrogen bond interaction is formed in the glycosyl-enzyme intermediate involving Heta of Tyr69, the endocyclic oxygen (O5) of the xylose residue in the -1 subsite, and Oepsilon2 of the catalytic nucleophile, Glu78. To gain additional understanding of the role of Tyr69 at the active site of this enzyme, we also determined the 1.5 A resolution structure of the catalytically inactive Tyr69Phe mutant. Interestingly, no significant structural perturbation due to the loss of the phenolic group is observed. These results suggest that the interactions involving the phenolic group of Tyr69, O5 of the proximal saccharide, and Glu78 Oepsilon2 are important for the catalytic mechanism of this enzyme, and it is proposed that, through charge redistribution, these interactions serve to stabilize the oxocarbenium-like ion of the transition state. Studies of the covalent glycosyl-enzyme intermediate of this xylanase also provide insight into specificity, as contacts with C5 of the xylose moiety exclude sugars with hydroxymethyl substituents, and the mechanism of catalysis, including aspects of stereoelectronic theory as applied to glycoside hydrolysis.
- Published
- 1999
49. Polymer-induced phase separation in Escherichia coli suspensions
- Author
-
Schwarz-Linek, Jana, Winkler, Alexander, Wilson, Laurence G., Pham, Nham T., Schilling, Tanja, Poon, Wilson C. K., Schwarz-Linek, Jana, Winkler, Alexander, Wilson, Laurence G., Pham, Nham T., Schilling, Tanja, and Poon, Wilson C. K.
- Published
- 2010
50. Allostery and functional refolding in the Gram-negative hexameric Type II citrate synthases
- Author
-
Nham T. Nguyen, L.J. Donald, Gary D. Brayer, H.W. Duckworth, and R. Maurus
- Subjects
Biochemistry ,Structural Biology ,Chemistry ,Allosteric regulation ,Gram - Published
- 2008
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