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Kikowska M, Piotrowska-Kempisty H, Kucińska M, Murias M, Budzianowski J, Budzianowska A, Kaczmarek M, Kowalczyk M, Stochmal A, Thiem B. Saponin Fractions from Eryngium planum L. Induce Apoptosis in Ovarian SKOV-3 Cancer Cells. PLANTS (BASEL, SWITZERLAND) 2023; 12:2485. [PMID: 37447047 DOI: 10.3390/plants12132485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023]
Abstract
(1) The cytotoxicity and antioxidant activity of different fractions as well as the pro-apoptotic activity of saponin fractions from Eryngium planum L. in SKOV-3 was investigated. (2) In screening studies, the cytotoxicity of six fractions on SKOV-3 was examined by LDH and SRB assays. The most active fractions-triterpenoid saponins-were selected for further investigation. To determine the mechanism of saponin fractions' cytotoxicity, their ability to induce apoptosis was examined via Annexin V assay. The effect of the saponin fractions on caspase 3 activity was measured using a Caspase 3 Assay Kit. The expression of 84 apoptosis-related genes was investigated in cancer cells exposed to saponin fractions from the roots. The radical scavenging capacity of different fractions was determined via DPPH assay. (3) The pronounced cytotoxic effects in SKOV-3 were demonstrated by saponin fractions from the leaves and roots. Those saponin fractions were chosen for further investigation. The treatment of cancer cell lines with saponins obtained from the roots provoked a significant increase in apoptotic cells. In the SKOV-3 cells, saponins caused upregulation of pro-apoptotic genes and a decrease in anti-apoptotic genes. The activation of caspase 3 was correlated with an increased DFFA expression level in the treated SKOV-3 cells. The most active fractions were phenolic acids from the shoots and roots. (4) To the best of our knowledge, the current study is the first to demonstrate that the barrigenol-type triterpenoid saponin fraction from the roots of E. planum inhibits SKOV-3 cell proliferation and induces apoptosis, which may be regulated by the expression of genes mostly specific to a mitochondria-related pathway.
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Affiliation(s)
- Małgorzata Kikowska
- Laboratory of Pharmaceutical Biology and Biotechnology, Department and Division of Practical Cosmetology and Skin Diseases Prophylaxis, Poznan University of Medical Sciences, Collegium Pharmaceuticum, 3 Rokietnicka St., 60-806 Poznan, Poland
| | | | - Małgorzata Kucińska
- Department of Toxicology, Poznan University of Medical Sciences, Dojazd 30, 60-631 Poznań, Poland
| | - Marek Murias
- Department of Toxicology, Poznan University of Medical Sciences, Dojazd 30, 60-631 Poznań, Poland
| | - Jaromir Budzianowski
- Laboratory of Pharmaceutical Biology and Biotechnology, Department and Division of Practical Cosmetology and Skin Diseases Prophylaxis, Poznan University of Medical Sciences, Collegium Pharmaceuticum, 3 Rokietnicka St., 60-806 Poznan, Poland
| | - Anna Budzianowska
- Laboratory of Pharmaceutical Biology and Biotechnology, Department and Division of Practical Cosmetology and Skin Diseases Prophylaxis, Poznan University of Medical Sciences, Collegium Pharmaceuticum, 3 Rokietnicka St., 60-806 Poznan, Poland
| | - Mariusz Kaczmarek
- Department of Clinical Immunology, Poznan University of Medical Sciences, 5 Rokietnicka, 60-806 Poznań, Poland
| | - Mariusz Kowalczyk
- Department of Biochemistry and Crop Quality, Institute of Soil Science and Plant Cultivation, State Research Institute, 10 Czartoryskich St., 24-100 Puławy, Poland
| | - Anna Stochmal
- Department of Biochemistry and Crop Quality, Institute of Soil Science and Plant Cultivation, State Research Institute, 10 Czartoryskich St., 24-100 Puławy, Poland
| | - Barbara Thiem
- Laboratory of Pharmaceutical Biology and Biotechnology, Department and Division of Practical Cosmetology and Skin Diseases Prophylaxis, Poznan University of Medical Sciences, Collegium Pharmaceuticum, 3 Rokietnicka St., 60-806 Poznan, Poland
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Roterman I, Sieradzan A, Stapor K, Fabian P, Wesołowski P, Konieczny L. On the need to introduce environmental characteristics in ab initio protein structure prediction using a coarse-grained UNRES force field. J Mol Graph Model 2022; 114:108166. [PMID: 35325843 DOI: 10.1016/j.jmgm.2022.108166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 02/09/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
Abstract
During the protein folding process in computer simulations involving the use of a United RESidue (UNRES) force field, an additional module was introduced to represent directly the presence of a polar solvent in water form. This module implements the fuzzy oil drop model (FOD) where the 3D Gauss function expresses the presence of a polar environment which directs the polypeptide chain folding process towards the generation of a centric hydrophobic core. Sample test polypeptide chains of 8 proteins with chain lengths ranging from 37 to 75 aa were simulated in silico using the UNRES (U) package with an implicit solvent model and a built-in module expressing the FOD model (UNRES-FOD-UNRES (U + F) interleaved simulation). The protein structure obtained by both *** simulation schemes, i.e., accordingly***U and U + F, for all the analyzed protein models shows the presence of a hydrophobic core including where it is absent in the native structure. The proposed FOD-M model (M-modified) explaining the source of this phenomenon reveals the need to modify the external field expressing the role of a folding environment. The modification takes into account the influence of other than polar factors present in the folding environment.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College Medyczna 7, 30-688, Kraków, Poland.
| | - Adam Sieradzan
- Faculty of Chemistry, Gdansk University, Wita Stwosza 63, 80-308, Gdańsk, Poland.
| | - Katarzyna Stapor
- Faculty of Automatic, Electronics and Computer Science, Department of Applied Informatics, Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland.
| | - Piotr Fabian
- Faculty of Automatic, Electronics and Computer Science, Department of Algorithmics and Software, Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland.
| | - Patryk Wesołowski
- Faculty of Chemistry, Gdansk University, Wita Stwosza 63, 80-308, Gdańsk, Poland; Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, ul. Abrahama 58, 80-307, Gdańsk, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry - Jagiellonian University - Medical College, Kopernika 7, 31-034, Kraków, Poland.
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Assembly of platforms for signal transduction in the new era: dimerization, helical filament assembly, and beyond. Exp Mol Med 2020; 52:356-366. [PMID: 32139779 PMCID: PMC7156525 DOI: 10.1038/s12276-020-0391-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 01/31/2020] [Indexed: 11/08/2022] Open
Abstract
Supramolecular organizing center (SMOC)-mediated signal transduction is an emerging concept in the field of signal transduction that is ushering in a new era. The formation of location-specific, higher-order SMOCs is particularly important for cell death and innate immune signaling processes. Several protein interaction domains, including the death domain (DD) superfamily and the CIDE domain, are representative mediators of SMOC assembly in cell death and innate immune signaling pathways. DD superfamily- and CIDE domain-containing proteins form SMOCs that activate various caspases and provide signaling scaffold platforms. These assemblies can lead to signal transduction and amplification during signaling events. In this review, we summarize recent findings on the molecular basis of DD superfamily- and CIDE domain-mediated SMOC formation. Improved understanding of large molecular signaling complexes that form during innate (nonspecific) immune responses could help develop treatments for multiple diseases including cancer. Correct cell signaling requires precise protein interactions and binding, which are mediated by specific sites on the surface of the protein molecules involved. Innate immune responses and cell death mechanisms rely on such protein interactions, and defects can cause signaling abnormalities and trigger disease. Hyun Ho Park and co-workers at Chung-Ang University in Seoul, South Korea, reviewed recent insights into the presence of supramolecular organizing centers (SMOCs), localized complexes of signaling proteins that form during immune responses. The researchers highlight existing understanding of SMOC assembly processes. A better understanding of SMOCs will help to explain enzyme activation, signal amplification and cell signaling control mechanisms.
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Crystal structure and mutation analysis revealed that DREP2 CIDE forms a filament-like structure with features differing from those of DREP4 CIDE. Sci Rep 2018; 8:17810. [PMID: 30546036 PMCID: PMC6292858 DOI: 10.1038/s41598-018-36253-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/16/2018] [Indexed: 11/26/2022] Open
Abstract
Cell death-inducing DFF45-like effect (CIDE) domain-containing proteins, DFF40, DFF45, CIDE-A, CIDE-B, and FSP27, play important roles in apoptotic DNA fragmentation and lipid homeostasis. The function of DFF40/45 in apoptotic DNA fragmentation is mediated by CIDE domain filament formation. Although our recent structural study of DREP4 CIDE revealed the first filament-like structure of the CIDE domain and its functional importance, the filament structure of DREP2 CIDE is unclear because this structure was not helical in the asymmetric unit. In this study, we present the crystal structure and mutagenesis analysis of the DREP2 CIDE mutant, which confirmed that DREP2 CIDE also forms a filament-like structure with features differing from those of DREP4 CIDE.
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Endometrial Polyps and Benign Endometrial Hyperplasia Have Increased Prevalence of DNA Fragmentation Factors 40 and 45 (DFF40 and DFF45) Together With the Antiapoptotic B-Cell Lymphoma (Bcl-2) Protein Compared With Normal Human Endometria. Int J Gynecol Pathol 2018; 37:431-440. [DOI: 10.1097/pgp.0000000000000442] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Banas T, Pitynski K, Okon K, Winiarska A. Non-endometrioid and high-grade endometrioid endometrial cancers show DNA fragmentation factor 40 (DFF40) and B-cell lymphoma 2 protein (BCL2) underexpression, which predicts disease-free and overall survival, but not DNA fragmentation factor 45 (DFF45) underexpression. BMC Cancer 2018; 18:418. [PMID: 29653556 PMCID: PMC5899339 DOI: 10.1186/s12885-018-4333-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 04/04/2018] [Indexed: 12/23/2022] Open
Abstract
Background The expression of DNA fragmentation factor 45 (DFF45) and B-cell lymphoma 2 (BCL2) in glands of the normal human endometrium is related to phases of the menstrual cycle and decreases after menopause, whereas the expression of DNA fragmentation factor 40 (DFF40) is stable. Moreover, DF45, BCL2 and DFF40 underexpression has been reported in numerous malignancies, including uterine leiomyosarcomas. In this study, we aimed to investigate DFF45, BCL2 and DFF40 expression in endometrioid and non-endometrioid types of endometrial cancers (ECs). We also evaluated the correlations between DFF45, BCL2 and DFF40 expression levels and clinicopathological parameters and determined the value of these three proteins as prognostic markers of disease-free survival (DFS) and overall survival (OS). Methods Immunohistochemistry was performed to evaluate DFF45, BCL2 and DFF40 expression in 342 cases of ECs. Student’s t-test, the Mann-Whitney U-test, and the chi-squared test were used for the statistical analyses as appropriate. The Cox-Mantel test, Cox’s proportional hazard model, and relative risk analyses were used to evaluate associations between DFF40, DFF45, and BCL2 expression and clinicopathological characteristics. Results DFF40 and BCL2, but not DFF45, were significantly underexpressed in non-endometrioid and high-grade endometrioid ECs compared with low- and moderate-grade endometrioid ECs. Women with DFF40- and BCL2-negative tumors had higher risks of disease recurrence, lymph node involvement, lympho-vascular space infiltration, and deep myometrial invasion compared with women with DFF40- and BCL2-positive tumors. Additionally, women with DFF40- and BCL2-negative tumors had significantly lower OS and DFS than women with DFF40- and BCL2-positive tumors. A multivariable analysis of the model, including the clinicopathological characteristics and immunohistochemical results, showed that negative BCL2 expression, lymph node involvement, and high-stage and high-grade disease were independent predictors of OS, whereas negative BCL2 expression, lymph node involvement, and high-stage disease were independent predictors of DFS. Conclusions Compared with low- and moderate-grade endometrioid ECs, non-endometrioid and high-grade endometrioid ECs showed significant DFF40 and BCL2 underexpression. The absence of DFF40 and BCL2 expression negatively affects DFS and OS. Further prospective studies are warranted to assess the potential utility of DFF40 and BCL2 as targets in the diagnosis or treatment of ECs.
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Affiliation(s)
- Tomasz Banas
- Department of Gynecology and Oncology, Jagiellonian University, 21 Kopernika Street, 30-501, Krakow, Poland.
| | - Kazimierz Pitynski
- Department of Gynecology and Oncology, Jagiellonian University, 21 Kopernika Street, 30-501, Krakow, Poland
| | - Krzysztof Okon
- Department of Pathomorphology, Jagiellonian University Medical College, Krakow, Poland
| | - Aleksandra Winiarska
- Department of Pathomorphology, Jagiellonian University Medical College, Krakow, Poland
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Kikuchi J, Ito K, Date Y. Environmental metabolomics with data science for investigating ecosystem homeostasis. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 104:56-88. [PMID: 29405981 DOI: 10.1016/j.pnmrs.2017.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/19/2017] [Accepted: 11/19/2017] [Indexed: 05/08/2023]
Abstract
A natural ecosystem can be viewed as the interconnections between complex metabolic reactions and environments. Humans, a part of these ecosystems, and their activities strongly affect the environments. To account for human effects within ecosystems, understanding what benefits humans receive by facilitating the maintenance of environmental homeostasis is important. This review describes recent applications of several NMR approaches to the evaluation of environmental homeostasis by metabolic profiling and data science. The basic NMR strategy used to evaluate homeostasis using big data collection is similar to that used in human health studies. Sophisticated metabolomic approaches (metabolic profiling) are widely reported in the literature. Further challenges include the analysis of complex macromolecular structures, and of the compositions and interactions of plant biomass, soil humic substances, and aqueous particulate organic matter. To support the study of these topics, we also discuss sample preparation techniques and solid-state NMR approaches. Because NMR approaches can produce a number of data with high reproducibility and inter-institution compatibility, further analysis of such data using machine learning approaches is often worthwhile. We also describe methods for data pretreatment in solid-state NMR and for environmental feature extraction from heterogeneously-measured spectroscopic data by machine learning approaches.
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Affiliation(s)
- Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan.
| | - Kengo Ito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yasuhiro Date
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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Kim CM, Jeon SH, Choi JH, Lee JH, Park HH. Interaction mode of CIDE family proteins in fly: DREP1 and DREP3 acidic surfaces interact with DREP2 and DREP4 basic surfaces. PLoS One 2017; 12:e0189819. [PMID: 29240809 PMCID: PMC5730196 DOI: 10.1371/journal.pone.0189819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 12/01/2017] [Indexed: 11/19/2022] Open
Abstract
Cell death-inducing DNA fragmentation factor 45 (DFF45)-like effector (CIDE) domains were initially identified as protein interaction modules in apoptotic nucleases and are now known to form a highly conserved family with diverse functions that range from cell death to lipid homeostasis. In the fly, four CIDE domain-containing proteins (DFF-related protein [DREP]-1–4) and their functions, including interaction relationships, have been identified. In this study, we introduced and investigated acidic side-disrupted mutants of DREP1, DREP2, and DREP3. We discovered that the acidic surface patches of DREP1 and DREP3 are critical for the homo-dimerization. In addition, we found that the acidic surface sides of DREP1 and DREP3 interact with the basic surface sides of DREP2 and DREP4. Our current study provides clear evidence demonstrating the mechanism of the interactions between four DREP proteins in the fly.
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Affiliation(s)
- Chang Min Kim
- School of Natural Science, Department of Chemistry and Biochemistry and Graduate School of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea
| | - Sun Hee Jeon
- School of Natural Science, Department of Chemistry and Biochemistry and Graduate School of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea
| | - Jun-Hyuk Choi
- Department of Metrology for Quality of Life, Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Inchon, Republic of Korea
| | - Hyun Ho Park
- School of Natural Science, Department of Chemistry and Biochemistry and Graduate School of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea
- * E-mail:
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Karczyńska AS, Mozolewska MA, Krupa P, Giełdoń A, Liwo A, Czaplewski C. Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information. Proteins 2017; 86 Suppl 1:228-239. [PMID: 29134679 DOI: 10.1002/prot.25421] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/09/2017] [Accepted: 11/10/2017] [Indexed: 11/09/2022]
Abstract
A new approach to assisted protein-structure prediction has been proposed, which is based on running multiplexed replica exchange molecular dynamics simulations with the coarse-grained UNRES force field with restraints derived from knowledge-based models and distance distribution from small angle X-ray scattering (SAXS) measurements. The latter restraints are incorporated into the target function as a maximum-likelihood term that guides the shape of the simulated structures towards that defined by SAXS. The approach was first verified with the 1KOY protein, for which the distance distribution was calculated from the experimental structure, and subsequently used to predict the structures of 11 data-assisted targets in the CASP12 experiment. Major improvement of the GDT_TS was obtained for 2 targets, minor improvement for other 2 while, for 6 target GDT_TS deteriorated compared with that calculated for predictions without the SAXS data, partly because of assuming a wrong multimeric state (for Ts866) or because the crystal conformation was more compact than the solution conformation (for Ts942). Particularly good results were obtained for Ts909, in which use of SAXS data resulted in the selection of a correctly packed trimer and, subsequently, increased the GDT_TS of monomer prediction. It was found that running simulations with correct oligomeric state is essential for the success in SAXS-data-assisted prediction.
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Affiliation(s)
| | - Magdalena A Mozolewska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland.,Institute of Computer Science, Polish Academy of Sciences, ul. Jana Kazimierza 5, Warsaw, 01-248, Poland
| | - Paweł Krupa
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland.,Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, Warsaw, PL-02668, Poland
| | - Artur Giełdoń
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland.,School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul, 130-722, Republic of Korea
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland
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Banas T, Pitynski K, Okon K, Czerw A. DNA fragmentation factors 40 and 45 (DFF40/DFF45) and B-cell lymphoma 2 (Bcl-2) protein are underexpressed in uterine leiomyosarcomas and may predict survival. Onco Targets Ther 2017; 10:4579-4589. [PMID: 29075126 PMCID: PMC5609795 DOI: 10.2147/ott.s142979] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES DNA fragmentation factors 40 and 45 (DFF40 and DFF45) are responsible for final DNA-laddering during apoptosis, whereas Bcl-2 (B-cell lymphoma 2) is an apoptosis inhibitor. Our aim was to investigate the expression of DFF40, DFF45, and Bcl-2 in uterine leiomyosarcomas (uLMS), leiomyomas (uLM), and the normal myometrium. Furthermore, the correlation between DFF40, DFF45, and Bcl-2 expression and clinicopathological parameters in leiomyosarcomas was assessed. Their prognostic value in disease-free survival (DFS) and overall survival (OS) was also calculated. MATERIALS AND METHODS This study included 53 cases of uLMS from patients matched for age and menopausal status with 53 cases of uLM and 53 controls of normal myometrium (uM). Case samples of uterine myometrium from leiomyosarcomas (uLMS-M) and leiomyomas (uLM-M) were also studied. Immunohistochemical scoring was undertaken for DFF40, DFF45, and Bcl-2. RESULTS DFF40, DFF45, and Bcl-2 were significantly underexpressed in uLMS compared with uLMS-M and uM. In uLMS samples, no correlation between the analyzed proteins was observed. Negative DFF40 and Bcl-2, but not DFF45, staining was a predictor of poorer DFS and OS in women with uLMS. uLM showed DFF40 and Bcl-2 overexpression compared with uM and uLM-M, with a significant positive correlation between DFF40 and DFF45. No differences in DFF40, DFF45, and Bcl-2 expression were observed between the uLMS-M, uLM-M, and uM samples, with a significant positive correlation between DFF40 and DFF45 expression. CONCLUSION DFF40, DFF45, and Bcl-2 are significantly underexpressed in uLMS, but only a lack of DFF40 and Bcl-2 negatively influences DFS and OS. Disruption of DFF40 and DFF45 expression was observed in uLMS, but not in uLM or control and case myometrium; this may play a role in tumor pathogenesis.
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Affiliation(s)
| | | | - Krzysztof Okon
- Department of Pathomorphology, Jagiellonian University Medical College, Krakow
| | - Aleksandra Czerw
- Department of Public Health, Faculty of Health Science, Medical University of Warsaw.,Department of Health Promotion and Postgraduate Education, National Institute of Public Health - National Institute of Hygiene, Warsaw, Poland
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Kit OI, Vodolazhsky DI, Dimitriadi SN, Kutilin DS, Timoshkina NN, Gudueva EN, Frantsiyants EM. The activity of proapoptotic genes increases after renal ischemia/reperfusion. Mol Biol 2017. [DOI: 10.1134/s0026893317030098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Harrison RL, Rowley DL, Mowery J, Bauchan GR, Theilmann DA, Rohrmann GF, Erlandson MA. The Complete Genome Sequence of a Second Distinct Betabaculovirus from the True Armyworm, Mythimna unipuncta. PLoS One 2017; 12:e0170510. [PMID: 28103323 PMCID: PMC5245865 DOI: 10.1371/journal.pone.0170510] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/05/2017] [Indexed: 11/19/2022] Open
Abstract
The betabaculovirus originally called Pseudaletia (Mythimna) sp. granulovirus #8 (MyspGV#8) was examined by electron microscopy, host barcoding PCR, and determination of the nucleotide sequence of its genome. Scanning and transmission electron microscopy revealed that the occlusion bodies of MyspGV#8 possessed the characteristic size range and morphology of betabaculovirus granules. Barcoding PCR using cytochrome oxidase I primers with DNA from the MyspGV#8 collection sample confirmed that it had been isolated from the true armyworm, Mythimna unipuncta (Lepidoptera: Noctuidae) and therefore was renamed MyunGV#8. The MyunGV#8 genome was found to be 144,673 bp in size with a nucleotide distribution of 49.9% G+C, which was significantly smaller and more GC-rich than the genome of Pseudaletia unipuncta granulovirus H (PsunGV-H), another M. unipuncta betabaculovirus. A phylogeny based on concatenated baculovirus core gene amino acid sequence alignments placed MyunGV#8 in clade a of genus Betabaculovirus. Kimura-2-parameter nucleotide distances suggested that MyunGV#8 represents a virus species different and distinct from other species of Betabaculovirus. Among the 153 ORFs annotated in the MyunGV#8 genome, four ORFs appeared to have been obtained from or donated to the alphabaculovirus lineage represented by Leucania separata nucleopolyhedrovirus AH1 (LeseNPV-AH1) during co-infection of Mythimna sp. larvae. A set of 33 ORFs was identified that appears only in other clade a betabaculovirus isolates. This clade a-specific set includes an ORF that encodes a polypeptide sequence containing a CIDE_N domain, which is found in caspase-activated DNAse/DNA fragmentation factor (CAD/DFF) proteins. CAD/DFF proteins are involved in digesting DNA during apoptosis.
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Affiliation(s)
- Robert L. Harrison
- Invasive Insect Biocontrol and Behavior Laboratory, Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, Maryland, United States of America
- * E-mail:
| | - Daniel L. Rowley
- Invasive Insect Biocontrol and Behavior Laboratory, Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Joseph Mowery
- Electron and Confocal Microscopy Unit, Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Gary R. Bauchan
- Electron and Confocal Microscopy Unit, Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, Maryland, United States of America
| | - David A. Theilmann
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, British Columbia, Canada
| | - George F. Rohrmann
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | - Martin A. Erlandson
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
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Ito K, Tsutsumi Y, Date Y, Kikuchi J. Fragment Assembly Approach Based on Graph/Network Theory with Quantum Chemistry Verifications for Assigning Multidimensional NMR Signals in Metabolite Mixtures. ACS Chem Biol 2016; 11:1030-8. [PMID: 26789380 DOI: 10.1021/acschembio.5b00894] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The abundant observation of chemical fragment information for molecular complexities is a major advantage of biological NMR analysis. Thus, the development of a novel technique for NMR signal assignment and metabolite identification may offer new possibilities for exploring molecular complexities. We propose a new signal assignment approach for metabolite mixtures by assembling H-H, H-C, C-C, and Q-C fragmental information obtained by multidimensional NMR, followed by the application of graph and network theory. High-speed experiments and complete automatic signal assignments were achieved for 12 combined mixtures of (13)C-labeled standards. Application to a (13)C-labeled seaweed extract showed 66 H-C, 60 H-H, 326 C-C, and 28 Q-C correlations, which were successfully assembled to 18 metabolites by the automatic assignment. The validity of automatic assignment was supported by quantum chemical calculations. This new approach can predict entire metabolite structures from peak networks of biological extracts.
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Affiliation(s)
- Kengo Ito
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 235-0045, Japan
| | - Yu Tsutsumi
- Bruker BioSpin K.K., 3-9 Moriya-cho, Kanagawa-ku, Yokohama 221-0022, Japan
| | - Yasuhiro Date
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 235-0045, Japan
| | - Jun Kikuchi
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 235-0045, Japan
- Graduate
School of Bioagricultural Sciences and School of Agricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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14
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Profiles of teleost DNA fragmentation factor alpha and beta from rock bream (Oplegnathus fasciatus): molecular characterization and genomic structure and gene expression in immune stress. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0359-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Sieradzan AK, Krupa P, Scheraga HA, Liwo A, Czaplewski C. Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations. J Chem Theory Comput 2015; 11:817-31. [PMID: 25691834 PMCID: PMC4327884 DOI: 10.1021/ct500736a] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The UNited RESidue (UNRES) model of polypeptide chains is a coarse-grained model in which each amino-acid residue is reduced to two interaction sites, namely, a united peptide group (p) located halfway between the two neighboring α-carbon atoms (Cαs), which serve only as geometrical points, and a united side chain (SC) attached to the respective Cα. Owing to this simplification, millisecond molecular dynamics simulations of large systems can be performed. While UNRES predicts overall folds well, it reproduces the details of local chain conformation with lower accuracy. Recently, we implemented new knowledge-based torsional potentials (Krupa et al. J. Chem. Theory Comput. 2013, 9, 4620–4632) that depend on the virtual-bond dihedral angles involving side chains: Cα···Cα···Cα···SC (τ(1)), SC···Cα···Cα···Cα (τ(2)), and SC···Cα···Cα···SC (τ(3)) in the UNRES force field. These potentials resulted in significant improvement of the simulated structures, especially in the loop regions. In this work, we introduce the physics-based counterparts of these potentials, which we derived from the all-atom energy surfaces of terminally blocked amino-acid residues by Boltzmann integration over the angles λ(1) and λ(2) for rotation about the Cα···Cα virtual-bond angles and over the side-chain angles χ. The energy surfaces were, in turn, calculated by using the semiempirical AM1 method of molecular quantum mechanics. Entropy contribution was evaluated with use of the harmonic approximation from Hessian matrices. One-dimensional Fourier series in the respective virtual-bond-dihedral angles were fitted to the calculated potentials, and these expressions have been implemented in the UNRES force field. Basic calibration of the UNRES force field with the new potentials was carried out with eight training proteins, by selecting the optimal weight of the new energy terms and reducing the weight of the regular torsional terms. The force field was subsequently benchmarked with a set of 22 proteins not used in the calibration. The new potentials result in a decrease of the root-mean-square deviation of the average conformation from the respective experimental structure by 0.86 Å on average; however, improvement of up to 5 Å was observed for some proteins.
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Affiliation(s)
- Adam K. Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-180 Gdańsk, Poland
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, N.Y., 14853-1301, U.S.A
| | - Paweł Krupa
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-180 Gdańsk, Poland
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, N.Y., 14853-1301, U.S.A
| | - Harold A. Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, N.Y., 14853-1301, U.S.A
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-180 Gdańsk, Poland
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-180 Gdańsk, Poland
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16
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Elahi M, Islam MM, Noguchi K, Yohda M, Toh H, Kuroda Y. Computational prediction and experimental characterization of a "size switch type repacking" during the evolution of dengue envelope protein domain III (ED3). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:585-92. [PMID: 24373879 DOI: 10.1016/j.bbapap.2013.12.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/17/2013] [Accepted: 12/19/2013] [Indexed: 11/16/2022]
Abstract
Dengue viruses (DEN) are classified into four serotypes (DEN1-DEN4) exhibiting high sequence and structural similarities, and infections by multiple serotypes can lead to the deadly dengue hemorrhagic fever. Here, we aim at characterizing the thermodynamic stability of DEN envelope protein domain III (ED3) during its evolution, and we report a structural analysis of DEN4wt ED3 combined with a systematic mutational analysis of residues 310 and 387. Molecular modeling based on our DEN3 and DEN4 ED3 structures indicated that the side-chains of residues 310/387, which are Val(310)/Ile(387) and Met(310)/Leu(387) in DEN3wt and DEN4wt, respectively, could be structurally compensated, and that a "size switch type repacking" might have occurred at these sites during the evolution of DEN into its four serotypes. This was experimentally confirmed by a 10°C and 5°C decrease in the thermal stability of, respectively, DEN3 ED3 variants with Met(310)/Ile(387) and Val(310)/Leu(387), whereas the variant with Met(310)/Leu(387), which contains a double mutation, had the same stability as the wild type DEN3. Namely, the Met310Val mutation should have preceded the Leu387Ile mutation in order to maintain the tight internal packing of ED3 and thus its thermodynamic stability. This view was confirmed by a phylogenetic reconstruction indicating that a common DEN ancestor would have Met(310)/Leu(387), and the intermediate node protein, Val(310)/Leu(387), which then mutated to the Val(310)/Ile(387) pair found in the present DEN3. The hypothesis was further confirmed by the observation that all of the present DEN viruses exhibit only stabilizing amino acid pairs at the 310/387 sites.
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Affiliation(s)
- Montasir Elahi
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture & Technology, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
| | - Monirul M Islam
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture & Technology, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
| | - Keiichi Noguchi
- Instrumentation Analysis Center, Tokyo University of Agriculture & Technology, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture & Technology, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
| | - Hiroyuki Toh
- Computational Biology Research Center, AIST Tokyo Waterfront Bio-IT Research Building, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture & Technology, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan.
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17
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Krupa P, Sieradzan AK, Rackovsky S, Baranowski M, Ołldziej S, Scheraga HA, Liwo A, Czaplewski C. Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states. J Chem Theory Comput 2013; 9. [PMID: 24273465 DOI: 10.1021/ct4004977] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The UNited RESidue (UNRES) coarse-grained model of polypeptide chains, developed in our laboratory, enables us to carry out millisecond-scale molecular-dynamics simulations of large proteins effectively. It performs well in ab initio predictions of protein structure, as demonstrated in the last Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP10). However, the resolution of the simulated structure is too coarse, especially in loop regions, which results from insufficient specificity of the model of local interactions. To improve the representation of local interactions, in this work we introduced new side-chain-backbone correlation potentials, derived from a statistical analysis of loop regions of 4585 proteins. To obtain sufficient statistics, we reduced the set of amino-acid-residue types to five groups, derived in our earlier work on structurally optimized reduced alphabets, based on a statistical analysis of the properties of amino-acid structures. The new correlation potentials are expressed as one-dimensional Fourier series in the virtual-bond-dihedral angles involving side-chain centroids. The weight of these new terms was determined by a trial-and-error method, in which Multiplexed Replica Exchange Molecular Dynamics (MREMD) simulations were run on selected test proteins. The best average root-mean-square deviations (RMSDs) of the calculated structures from the experimental structures below the folding-transition temperatures were obtained with the weight of the new side-chain-backbone correlation potentials equal to 0.57. The resulting conformational ensembles were analyzed in detail by using the Weighted Histogram Analysis Method (WHAM) and Ward's minimum-variance clustering. This analysis showed that the RMSDs from the experimental structures dropped by 0.5 Å on average, compared to simulations without the new terms, and the deviation of individual residues in the loop region of the computed structures from their counterparts in the experimental structures (after optimum superposition of the calculated and experimental structure) decreased by up to 8 Å. Consequently, the new terms improve the representation of local structure.
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Affiliation(s)
- Paweł Krupa
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-952 Gdańsk, Poland.,Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, N.Y., 14853-1301, U.S.A
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-952 Gdańsk, Poland
| | - S Rackovsky
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, N.Y., 14853-1301, U.S.A.,Dept. of Pharmacology and Systems Therapeutics, The Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, U.S.A
| | - Maciej Baranowski
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Kładki 24, 80-922 Gdańsk, Poland
| | - Stanisław Ołldziej
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Kładki 24, 80-922 Gdańsk, Poland
| | - Harold A Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, N.Y., 14853-1301, U.S.A
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-952 Gdańsk, Poland
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-952 Gdańsk, Poland
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18
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Lee SM, Jang TH, Park HH. Molecular basis for homo-dimerization of the CIDE domain revealed by the crystal structure of the CIDE-N domain of FSP27. Biochem Biophys Res Commun 2013; 439:564-9. [PMID: 24025675 DOI: 10.1016/j.bbrc.2013.09.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 09/03/2013] [Indexed: 12/12/2022]
Abstract
FSP27 (CIDE-3 in humans) plays critical roles in lipid metabolism and apoptosis and is known to be involved in regulation of lipid droplet (LD) size and lipid storage and apoptotic DNA fragmentation. Given that CIDE-containing proteins including FSP27 are associated with many human diseases including cancer, aging, diabetes, and obesity, studies of FSP27 and other CIDE-containing proteins are of great biological importance. As a first step toward elucidating the molecular mechanisms of FSP27-mediated lipid droplet growth and apoptosis, we report the crystal structure of the CIDE-N domain of FSP27 at a resolution of 2.0 Å. The structure revealed a possible biologically important homo-dimeric interface similar to that formed by the hetero-dimeric complex, CAD/ICAD. Comparison with other structural homologues revealed that the PB1 domain of BEM1P, ubiquitin-like domain of BAG6 and ubiquitin are structurally similar proteins. Our homo-dimeric structure of the CIDE-N domain of FSP27 will provide important information that will enable better understanding of the function of FSP27.
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Affiliation(s)
- Seung Mi Lee
- School of Biotechnology and Graduate School of Biochemistry at Yeungnam University, Gyeongsan, South Korea
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19
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Towse CL, Daggett V. When a domain is not a domain, and why it is important to properly filter proteins in databases: conflicting definitions and fold classification systems for structural domains make filtering of such databases imperative. Bioessays 2012; 34:1060-9. [PMID: 23108912 DOI: 10.1002/bies.201200116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Membership in a protein domain database does not a domain make; a feature we realized when generating a consensus view of protein fold space with our consensus domain dictionary (CDD). This dictionary was used to select representative structures for characterization of the protein dynameome: the Dynameomics initiative. Through this endeavor we rejected a surprising 40% of the 1,695 folds in the CDD as being non-autonomous folding units. Although some of this was due to the challenges of grouping similar fold topologies, the dissonance between the cataloguing and structural qualification of protein domains remains surprising. Another potential factor is previously overlooked intrinsic disorder; predictions suggest that 40% of proteins have either local or global disorder. One thing is clear, filtering a structural database and ensuring a consistent definition for protein domains is crucial, and caution is prescribed when generalizations of globular domains are drawn from unfiltered protein domain datasets.
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Affiliation(s)
- Clare-Louise Towse
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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20
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Dual apoptotic DNA fragmentation system in the fly: Drep2 is a novel nuclease of which activity is inhibited by Drep3. FEBS Lett 2012; 586:3085-9. [PMID: 22850116 DOI: 10.1016/j.febslet.2012.07.056] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 06/24/2012] [Accepted: 07/13/2012] [Indexed: 12/11/2022]
Abstract
DNA fragmentation is the hallmark of apoptotic cells and mainly mediated by the DNA fragmentation factor DFF40(CAD)/DFF45(ICAD). DFF40 is a novel nuclease, whereas DFF45 is an inhibitor that can suppress the nuclease activity. Apoptotic DNA fragmentation in the fly is controlled by four DFF-related proteins, known as Drep1, 2, 3 and 4. However, the functions of Drep2 and Drep3 are totally unknown. Here, we found that Drep2 is a novel nuclease whose activity is inhibited by Drep3 through a tight interaction with the CIDE domain. Our results suggest that the fly has dual apoptotic DNA fragmentation systems: Drep1: Drep4 and Drep2: Drep3 complexes.
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21
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Kutscher D, Pingoud A, Jeltsch A, Meiss G. Identification of ICAD-derived peptides capable of inhibiting caspase-activated DNase. FEBS J 2012; 279:2917-28. [DOI: 10.1111/j.1742-4658.2012.08673.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Banas T, Basta P, Knafel A, Skotniczny K, Jach R, Hajdyla-Banas I, Grabowska O. DFF45 expression in human endometrium is associated with menstrual cycle phases and decreases after menopause. Gynecol Obstet Invest 2012; 73:177-82. [PMID: 22378161 DOI: 10.1159/000331647] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 07/13/2011] [Indexed: 12/13/2022]
Abstract
BACKGROUND Human endometrium undergoes cyclic structural and functional modifications, and if no conception occurs menstruation is observed as the result of endometrial cell apoptosis via DFF40/DFF45 complex activation. In postmenopausal endometrium, the proliferative potential of endometrial cells is decreased, while their susceptibility to apoptosis increases. METHODS The study group comprised 104 nonpregnant adult women (78 of reproductive age and 36 after menopause) with no neoplasm or hormonal treatment during the past 6 months. Immunohistochemistry and Western blot methods were used for DFF45 identification and semiquantitative assessment of its amount. RESULTS Significantly more DFF45-positive cells were detected in the endometrial glands compared to stroma, and this pattern was constant throughout the whole menstrual cycle and also present in postmenopausal endometrial species. The lowest mean relative amount of DFF45 was detected in postmenopausal endometrial samples. In women of reproductive age, the highest mean relative amount of DFF45 was identified in an early secretory phase of the menstrual cycle, the lowest median value of the relative amount of DFF45 was observed in the late proliferative phase, and the difference was significant. CONCLUSION The DFF45 level in human endometrium corresponds to the respective phase of the menstrual cycle and decreases significantly after menopause.
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Affiliation(s)
- Tomasz Banas
- Department of Gynecology and Oncology, Jagiellonian University, 23 Kopernika Street, Krakow, Poland.
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23
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Park HH. Fifty C-terminal amino acid residues are necessary for the chaperone activity of DFF45 but not for the inhibition of DFF40. BMB Rep 2009; 42:713-8. [DOI: 10.5483/bmbrep.2009.42.11.713] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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24
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Shen H, Liwo A, Scheraga HA. An improved functional form for the temperature scaling factors of the components of the mesoscopic UNRES force field for simulations of protein structure and dynamics. J Phys Chem B 2009; 113:8738-44. [PMID: 19480420 PMCID: PMC2766665 DOI: 10.1021/jp901788q] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coarse-grained or mesoscopic models of proteins and the corresponding force fields are of great importance because they enable us to reduce the folding simulation time by several orders of magnitude compared to the all-atom approach and, consequently, reach the millisecond time scale of simulations. In the coarse-grained UNRES model for simulations of protein structure and dynamics, developed by our group, each amino acid residue is represented by a united side chain and a united peptide group located in the middle between the two neighboring alpha-carbon atoms, which assist only in the definition of the geometry. The prototype of the UNRES force field has been defined as a potential of mean force or restricted free-energy function corresponding to averaging out the degrees of freedom not present in the coarse-grained representation, which has further been approximated by a truncated Kubo cumulant series to enable us to derive analytical expressions for the corresponding terms. This force field should depend on temperature, and in its simplest form, a term corresponding to the cumulant of order n should be multiplied by f(n) = 1/T(n-1). The temperature dependence has been introduced in recent work ( J. Phys. Chem. B , 2007 , 111 , 260 - 285 ), and in order to prevent too steep a variation with temperature, the factors at the nth order cumulant terms were assumed to have a form f(n) = ln[exp(1) + exp(-1)]/ln{exp[(T/T(0))(n-1)] + exp[-(T/T(0))(n-1)]}, where T(0) = 300 K is the reference temperature. In this work, we have introduced a modified scaling factor f(n) = ln[exp(c) + exp(-c)]/ln{exp[c(T/T(0))(n-1)] + exp[-c(T/T(0))(n-1)]}, where c is an adjustable parameter, and determined c by fitting the analytical approximation of the temperature dependence of the virtual bond torsional term corresponding to rotation about the C(alpha)...C(alpha) virtual bond in terminally blocked dialanine to the respective potential of mean force calculated from the MP2/6-31G(d, p) ab initio energy surfaces of terminally blocked alanine (Ac-Ala-NHMe) and, independently, by optimizing it to obtain a sharp heat capacity curve and the lowest ensemble-averaged root-mean-square deviation over the C(alpha) atoms of 1GAB used as a training protein. Both approaches gave consistent results, and c = 1.4 has been selected as the optimal value of this parameter. The force field with the new temperature scaling factors has been optimized using 1GAB as the training protein. The new force field has been tested on a series of medium size alpha-helical proteins and found to perform better than that with the original temperature scaling factors.
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Affiliation(s)
- Hujun Shen
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca NY, USA 14853
| | - Adam Liwo
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca NY, USA 14853
| | - Harold A. Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca NY, USA 14853
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25
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Eckhart L, Fischer H, Tschachler E. Phylogenomics of caspase-activated DNA fragmentation factor. Biochem Biophys Res Commun 2007; 356:293-9. [PMID: 17343828 DOI: 10.1016/j.bbrc.2007.02.122] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Accepted: 02/23/2007] [Indexed: 11/20/2022]
Abstract
The degradation of nuclear DNA by DNA fragmentation factor (DFF) is a key step in apoptosis of mammalian cells. Using comparative genomics, we have here determined the evolutionary history of the genes encoding the two DFF subunits, DFFA (also known as ICAD) and DFFB (CAD). Orthologs of DFFA and DFFB were identified in Nematostella vectensis, a representative of the primitive metazoan clade cnidarians, and in various vertebrates and insects, but not in representatives of urochordates, echinoderms, and nematodes. The domains mediating the interaction of DFFA and DFFB, a caspase cleavage site in DFFA, and the amino acid residues critical for endonuclease activity of DFFB were conserved in Nematostella. These findings suggest that DFF has been a part of the primordial apoptosis system of the eumetazoan common ancestor and that the ancient cell death machinery has degenerated in several evolutionary lineages, including the one leading to the prototypical apoptosis model, Caenorhabditis elegans.
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Affiliation(s)
- Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, A-1090 Vienna, Austria.
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26
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Kikuchi J, Hirayama T. Practical Aspects of Uniform Stable Isotope Labeling of Higher Plants for Heteronuclear NMR-Based Metabolomics. Metabolomics 2007; 358:273-86. [PMID: 17035691 DOI: 10.1007/978-1-59745-244-1_15] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Analytical methods for probing plant metabolism are taking on new significance in the era of functional genomics, metabolomics, and systems biology. Nuclear magnetic resonance (NMR) is becoming a key technology in plant metabolomics. Stable isotope labeling of cultured cells and higher organisms has been especially promising in that it allows the use of advanced heteronuclear NMR methodologies through a combination of in vivo and in vitro measurements. This new approach provides much better resolution of the metabolite mixture signals in the multidimensional NMR spectra than does the conventional one-dimensional 1H-NMR previously used in plant metabolomics. In this chapter, we describe the practical aspects of two key NMR technologies: uniform stable labeling of plants and in vitro heteronuclear NMR.
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Affiliation(s)
- Jun Kikuchi
- Advanced NMR Metabolomics Research Unit, RIKEN Plant Science Center, Yokohama, Japan
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27
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Hondoh T, Kato A, Yokoyama S, Kuroda Y. Computer-aided NMR assay for detecting natively folded structural domains. Protein Sci 2006; 15:871-83. [PMID: 16522794 PMCID: PMC2242495 DOI: 10.1110/ps.051880406] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Structural genomics projects require strategies for rapidly recognizing protein sequences appropriate for routine structure determination. For large proteins, this strategy includes the dissection of proteins into structural domains that form stable native structures. However, protein dissection essentially remains an empirical and often a tedious process. Here, we describe a simple strategy for rapidly identifying structural domains and assessing their structures. This approach combines the computational prediction of sequence regions corresponding to putative domains with an experimental assessment of their structures and stabilities by NMR and biochemical methods. We tested this approach with nine putative domains predicted from a set of 108 Thermus thermophilus HB8 sequences using PASS, a domain prediction program we previously reported. To facilitate the experimental assessment of the domain structures, we developed a generic 6-hour His-tag-based purification protocol, which enables the sample quality evaluation of a putative structural domain in a single day. As a result, we observed that half of the predicted structural domains were indeed natively folded, as judged by their HSQC spectra. Furthermore, two of the natively folded domains were novel, without related sequences classified in the Pfam and SMART databases, which is a significant result with regard to the ability of structural genomics projects to uniformly cover the protein fold space.
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Affiliation(s)
- Takayuki Hondoh
- Protein Research Group, RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230-0045, Japan
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28
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Nhan TQ, Liles WC, Schwartz SM. Role of caspases in death and survival of the plaque macrophage. Arterioscler Thromb Vasc Biol 2005; 25:895-903. [PMID: 15718496 DOI: 10.1161/01.atv.0000159519.07181.33] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This review considers the role of macrophage cell death in formation of the necrotic core and in plaque progression, and lists many of the possible mediators of macrophage cell death. Among these, perhaps the most cited toxic agent is oxidized low-density lipoprotein (oxLDL). Whereas oxLDL can kill macrophage, and whereas the form of death is morphologically apoptotic, caspase inhibitors appear to be ineffective in preventing death. This finding is consistent with recent literature showing how the canonical caspase pathways are used for physiological cellular functions other than cell death. Plaque macrophages appear to be among the cells with this nonapoptotic signaling function for activated caspases. In many of the other cell types, caspase activation appears to play a critical role in cell differentiation. We discuss possible functions of plaque macrophage using the nondeath caspase pathway. Recent literature shows that physiological and developmental functions of many cell types require active caspases without progressing to cell death. We discuss the role of macrophage cell death in plaque progression, possible mediators of macrophage cell death, and the possible functions of plaque macrophage using the nondeath caspase pathway.
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Affiliation(s)
- Thomas Q Nhan
- Department of Pathology, University of Washington, Seattle, Wash 98195-4717, USA
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29
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Fuentes-Prior P, Salvesen G. The protein structures that shape caspase activity, specificity, activation and inhibition. Biochem J 2004; 384:201-32. [PMID: 15450003 PMCID: PMC1134104 DOI: 10.1042/bj20041142] [Citation(s) in RCA: 609] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2004] [Revised: 08/31/2004] [Accepted: 09/27/2004] [Indexed: 02/07/2023]
Abstract
The death morphology commonly known as apoptosis results from a post-translational pathway driven largely by specific limited proteolysis. In the last decade the structural basis for apoptosis regulation has moved from nothing to 'quite good', and we now know the fundamental structures of examples from the initiator phase, the pre-mitochondrial regulator phase, the executioner phase, inhibitors and their antagonists, and even the structures of some substrates. The field is as well advanced as the best known of proteolytic pathways, the coagulation cascade. Fundamentally new mechanisms in protease regulation have been disclosed. Structural evidence suggests that caspases have an unusual catalytic mechanism, and that they are activated by apparently unrelated events, depending on which position in the apoptotic pathway they occupy. Some naturally occurring caspase inhibitors have adopted classic inhibition strategies, but other have revealed completely novel mechanisms. All of the structural and mechanistic information can, and is, being applied to drive therapeutic strategies to combat overactivation of apoptosis in degenerative disease, and underactivation in neoplasia. We present a comprehensive review of the caspases, their regulators and inhibitors from a structural and mechanistic point of view, and with an aim to consolidate the many threads that define the rapid growth of this field.
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Key Words
- apoptosis
- caspase
- inhibitor
- inhibitor of apoptosis protein (iap)
- protease
- zymogen
- alps, autoimmune lymphoproliferative syndrome
- apaf-1, apoptotic protease activating factor-1
- asc/pycard, apoptosis-associated speck-like protein containing a card/pyd- and card-containing molecule
- bir, baculoviral iap repeat
- cad, caspase-activated dnase
- card, caspase-recruitment domain
- carp, caspase-associated ring protein
- ced, cell death-defective
- clarp, caspase-like apoptosis-regulatory protein
- cradd/raidd, caspase-2 and ripk1 domain-containing adaptor with death domain/rip-associated protein with a death domain
- crma, cytokine response modifier a
- dd, death domain
- ded, death effector domain
- dff, dna fragmentation factor
- diablo, direct iap-binding protein with low pi
- diap1, drosophila inhibitor of apoptosis 1
- disc, death-inducing signalling complex
- dronc, drosophila nedd2-like caspase
- fadd, fas (tnfrsf6)-associated via death domain
- flice, fadd-like ice
- flip, flice inhibitory protein
- iap, inhibitor of apoptosis protein
- ibm, iap binding motif
- icad, inhibitor of cad
- ice, interleukin-1β-converting enzyme
- ipaf/clan, ice-protease-activating factor/card, lrr and nacht-containing protein
- lrr, leucine-rich repeat
- nacht, ntpase-domain named after naip, ciita, het-e and tp1
- nalp1, nacht, lrr and pyrin domain containing 1
- nbd, nucleotide-binding domain
- nf-κb, nuclear factor-κb
- nod, nucleotide-binding and oligomerization domain-containing protein
- parp, poly(adp-ribose) polymerase
- pidd, p53-induced protein with a death domain
- rick/cardiak, rip-like interacting clarp kinase/card-containing ice-associated kinase
- ring, really interesting new gene
- rip, receptor-interacting protein
- serpin, serine protease inhibitor
- smac, second mitochondrial activator of caspases
- tfpi, tissue factor pathway inhibitor
- tlr, toll-like receptor
- tnf, tumour necrosis factor
- tradd, tnfrsf1a-associated via death domain
- traf, tnf receptor-associated factor
- trail, tnf-related apoptosis-inducing ligand
- xiap/birc4, x-linked iap/baculoviral iap repeat-containing 4
- p1, p2, …pn and p1′, p2′, …pm′ designate the side chains in substrates and inhibitors in the n- and c-terminal direction respectively from the p1–p1′ scissile peptide bond
- s1, s2, …sn and s1′, s2′, …sm′ refer to the cognate pockets on the protease that accept these side chains [1]
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Affiliation(s)
- Pablo Fuentes-Prior
- *Abteilung Strukturforschung, Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, D82152, Planegg-Martinsried, Germany and Cardiovascular Research Center, Sant Antoni Ma. Claret 167, 08025 Barcelona, Spain
| | - Guy S. Salvesen
- †The Program in Apoptosis and Cell Death Research, Burnham Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, U.S.A
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Ołdziej S, Liwo A, Czaplewski C, Pillardy J, Scheraga HA. Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 2. Off-Lattice Tests of the Method with Single Proteins. J Phys Chem B 2004. [DOI: 10.1021/jp0403285] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stanisław Ołdziej
- Baker Laboratory of Chemistry and Chemical Biology and Cornell Theory Center, Cornell University, Ithaca, New York 14853-1301, and Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
| | - Adam Liwo
- Baker Laboratory of Chemistry and Chemical Biology and Cornell Theory Center, Cornell University, Ithaca, New York 14853-1301, and Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
| | - Cezary Czaplewski
- Baker Laboratory of Chemistry and Chemical Biology and Cornell Theory Center, Cornell University, Ithaca, New York 14853-1301, and Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
| | - Jarosław Pillardy
- Baker Laboratory of Chemistry and Chemical Biology and Cornell Theory Center, Cornell University, Ithaca, New York 14853-1301, and Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
| | - Harold A. Scheraga
- Baker Laboratory of Chemistry and Chemical Biology and Cornell Theory Center, Cornell University, Ithaca, New York 14853-1301, and Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
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Kikuchi J, Shinozaki K, Hirayama T. Stable isotope labeling of Arabidopsis thaliana for an NMR-based metabolomics approach. PLANT & CELL PHYSIOLOGY 2004; 45:1099-104. [PMID: 15356336 DOI: 10.1093/pcp/pch117] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Nuclear magnetic resonance (NMR) will become a key technology in plant metabolomics with the use of stable isotope labeling and advanced hetero-nuclear NMR methodologies. To demonstrate the power of this approach, we performed multi-dimensional hetero-nuclear NMR analysis of metabolic movement of carbon and nitrogen nuclei in Arabidopsis thaliana. First, distinct ethanol-stress response was investigated using (13)C-labeled wild type and an ethanol-hypersensitive mutant plants. Furthermore, we followed nitrogen fluxes in (15)N-labeled seeds during the initiation of germination in vivo. The future role of stable isotope-labeling combined with advanced hetero-nuclear NMR in plant metabolomics is discussed.
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Affiliation(s)
- Jun Kikuchi
- Protein Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045 Japan
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Woo EJ, Kim YG, Kim MS, Han WD, Shin S, Robinson H, Park SY, Oh BH. Structural Mechanism for Inactivation and Activation of CAD/DFF40 in the Apoptotic Pathway. Mol Cell 2004; 14:531-9. [PMID: 15149602 DOI: 10.1016/s1097-2765(04)00258-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2003] [Revised: 03/01/2004] [Accepted: 03/24/2004] [Indexed: 01/30/2023]
Abstract
CAD/DFF40 is responsible for the degradation of chromosomal DNA into nucleosomal fragments and subsequent chromatin condensation during apoptosis. It exists as an inactive complex with its inhibitor ICAD/DFF45 in proliferating cells but becomes activated upon cleavage of ICAD/DFF45 into three domains by caspases in dying cells. The molecular mechanism underlying the control and activation of CAD/DFF40 was unknown. Here, the crystal structure of activated CAD/DFF40 reveals that it is a pair of molecular scissors with a deep active-site crevice that appears ideal for distinguishing internucleosomal DNA from nucleosomal DNA. Ensuing studies show that ICAD/DFF45 sequesters the nonfunctional CAD/DFF40 monomer and is also able to disassemble the functional CAD/DFF40 dimer. This capacity requires the involvement of the middle domain of ICAD/DFF45, which by itself cannot remain bound to CAD/DFF40 due to low binding affinity for the enzyme. Thus, the consequence of the caspase-cleavage of ICAD/DFF45 is a self-assembly of CAD/DFF40 into the active dimer.
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Affiliation(s)
- Eui-Jeon Woo
- Division of Molecular and Life Sciences, Department of Life Sciences and Center for Biomolecular Recognition, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, South Korea
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Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R. Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins 2004; 53 Suppl 6:491-6. [PMID: 14579338 DOI: 10.1002/prot.10540] [Citation(s) in RCA: 219] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This article presents an overview of the SAM-T02 method for protein fold recognition and the UNDERTAKER program for ab initio predictions. The SAM-T02 server is an automatic method that uses two-track hidden Markov models (HMMS) to find and align template proteins from PDB to the target protein. The two-track HMMs use an amino acid alphabet and one of several different local structure alphabets. The UNDERTAKER program is a new fragment-packing program that can use short or long fragments and alignments to create protein conformations. The HMMs and fold-recognition alignments from the SAM-T02 method were used to generate the fragment and alignment libraries used by UNDERTAKER. We present results on a few selected targets for which this combined method worked particularly well: T0129, T0181, T0135, T0130, and T0139.
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Affiliation(s)
- Kevin Karplus
- Computer Engineering Department, University of California, Santa Cruz 95064, USA.
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Aloy P, Stark A, Hadley C, Russell RB. Predictions without templates: New folds, secondary structure, and contacts in CASP5. Proteins 2003; 53 Suppl 6:436-56. [PMID: 14579333 DOI: 10.1002/prot.10546] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We present the assessment of CASP5 predictions in the new fold category. For coordinate predictions, we considered five targets with new folds and eight lying on the fold recognition borderline. We performed detailed visual and numerical comparisons between predicted and experimental structures to assess prediction accuracy. The two procedures largely agreed, but the visual inspection identified instances where metrics, such as GDT_TS, ranked what we considered incorrect predictions highly. We found the quality of the best predictions to be very good: for nearly every target at least one group predicted a structure close to the correct one. However, selection of the best of five models is still problematic. The group of David Baker once again proved to be best overall, with many individual highlights. However, high quality and consistency were also seen from others, suggesting that the community is moving toward general procedures to predict accurate structures for proteins showing no resemblance to anything seen before. Predictions for secondary structure showed at best limited progress since CASP4. The number of targets is probably too small to spot differences in performance between methods, suggesting that such predictions might be better evaluated with schemes involving more proteins. For contact predictions, accuracies are still low, although there were several instances of accurate and useful contacts predicted de novo, and new approaches hint at future progress.
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