A quality metric for homology modeling: the H-factor

di Luccio, Eric,Koehl, Patrice BioMed Central 2011 BMC bioinformatics Vol.12 No.-

<P><B>Background</B></P><P>The analysis of protein structures provides fundamental insight into most biochemical functions and consequently into the cause and possible treatment of diseases. As the structures of most known proteins cannot be solved experimentally for technical or sometimes simply for time constraints, <I>in silico </I>protein structure prediction is expected to step in and generate a more complete picture of the protein structure universe. Molecular modeling of protein structures is a fast growing field and tremendous works have been done since the publication of the very first model. The growth of modeling techniques and more specifically of those that rely on the existing experimental knowledge of protein structures is intimately linked to the developments of high resolution, experimental techniques such as NMR, X-ray crystallography and electron microscopy. This strong connection between experimental and <I>in silico </I>methods is however not devoid of criticisms and concerns among modelers as well as among experimentalists.</P><P><B>Results</B></P><P>In this paper, we focus on homology-modeling and more specifically, we review how it is perceived by the structural biology community and what can be done to impress on the experimentalists that it can be a valuable resource to them. We review the common practices and provide a set of guidelines for building better models. For that purpose, we introduce the H-factor, a new indicator for assessing the quality of homology models, mimicking the R-factor in X-ray crystallography. The methods for computing the H-factor is fully described and validated on a series of test cases.</P><P><B>Conclusions</B></P><P>We have developed a web service for computing the H-factor for models of a protein structure. This service is freely accessible at http://koehllab.genomecenter.ucdavis.edu/toolkit/h-factor.</P>

Nrf2-mediated induction of phase 2 detoxifying enzymes by glyceollins derived from soybean exposed to Aspergillus sojae

Kim, Hyo Jung,di Luccio, Eric,Kong, Ah-Ng Tony,Kim, Jong-Sang Wiley (John WileySons) 2011 BIOTECHNOLOGY JOURNAL Vol.6 No.5

<P>Numerous antioxidants have been reported to cause transcriptional activation of several antioxidant enzymes through binding antioxidant-response element on their promoter region. We, therefore, attempted to examine whether glyceollins, which share common structural features with many phase 2 enzyme inducers and antioxidant activity, could induce detoxifying/antioxidant enzymes. Glyceollins induced NAD(P)H:quinone oxidoreductase activity in a dose-dependent manner in both mouse hepatoma Hepa1c1c7 and its mutant BPRc1 cells. The compounds also increased the expression of some representative antioxidant enzymes, such as heme oxygenase 1,gamma-glutamylcysteine synthase, and glutathione reductase, by promoting nuclear translocation of the NF-E2-related factor-2 (Nrf2). Furthermore, phosphorylation of Akt and antioxidant response element-mediated reporter gene expression were enhanced by glyceollins but suppressed by LY294002, an inhibitor of phosphoinositide 3-kinases (PI3K). This suggests that glyceollins may cause Nrf2-mediated phase 2 enzyme induction through activation of the PI3K signaling pathway as well as interaction with Keap1. Our molecular docking simulations also suggest that the glyceollin isomers tightly bind into the binding pocket around Cys151, preventing Nrf2 from docking to Keap1. In conclusion, the current data suggest that glyceollins induced phase 2 detoxifying enzymes likely through promoting nuclear translocation of Nrf2, which is known to be regulated by phosphorylation of Nrf2 and/or disrupting Keap1-Nrf2 complex formation.</P>

The structural basis of substrate promiscuity in UDP-hexose 4-epimerase from the hyperthermophilic Eubacterium <i>Thermotoga maritima</i>

Shin, Sun-Mi,Choi, Jin Myung,di Luccio, Eric,Lee, Yong-Jik,Lee, Sang-Jae,Lee, Sang Jun,Lee, Sung Haeng,Lee, Dong-Woo Elsevier 2015 Archives of biochemistry and biophysics Vol.585 No.-

<P><B>Abstract</B></P> <P>UDP-galactose 4-epimerase (GalE) catalyzes the interconversion of UDP-glucose (UDP-Glc) and UDP-galactose (UDP-Gal), which is a pivotal step in the Leloir pathway for <SMALL>D</SMALL>-galactose metabolism. Although GalE is widely distributed in prokaryotes and eukaryotes, little information is available regarding hyperthermophilic GalE. We overexpressed the TM0509 gene, encoding a putative GalE from <I>Thermotoga maritima</I> (TMGalE), in <I>Escherichia coli</I> and characterized the encoded protein. To further investigate the molecular basis of this enzyme's catalytic function, we determined the crystal structures of TMGalE and TMGalE bound to UDP-Glc at resolutions of 1.9 Å and 2.0 Å, respectively. The enzyme was determined to be a homodimer with a molecular mass of 70 kDa. The enzyme could reversibly catalyze the epimerization of UDP-GalNAc/UDP-GlcNAc as well as UDP-Gal/UDP-Glc at elevated temperatures, with an apparent optimal temperature and pH of 80 °C and 7.0, respectively. Our data showed that TM0509 is a UDP-galactosugar 4-epimerase involved in <SMALL>D</SMALL>-galactose metabolism; consequently, this study provides the first detailed characterization of a hyperthermophilic GalE. Moreover, the promiscuous substrate specificity of TMGalE, which is more similar to human GalE than <I>E. coli</I> GalE, supports the notion that TMGalE might exhibit the earliest form of sugar-epimerizing enzymes in the evolution of galactose metabolism.</P> <P><B>Highlights</B></P> <P> <UL> <LI> TMGalE is an enzyme that catalyzes the epimerization of UDP-hexose. </LI> <LI> We determined the crystal structures of TMGalE in complex with NAD<SUP>+</SUP> and UDP-glucose. </LI> <LI> This study provides molecular basis for the substrate promiscuity of TMGalE. </LI> <LI> The crystal structure may provide structural guide-lines for protein evolution. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>

Recombinant Protein Expression and Purification of the Human HMTase MMSET/NSD2

Morishita, Masayo,Mevius, Damiaan,Shen, Yunpeng,Di Luccio, Eric Institute of Agricultural Science and Technology 2013 慶北大農學誌 Vol.31 No.3

Chromatin remodelers that include histone methyl transferases (HMTases) are becoming a focal point in cancer drug development. The NSD family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L are bona fide oncogenes found aberrantly expressed in several cancers, suggesting their potential role for novel therapeutic strategies. Several histone modifiers including HMTase have clear roles in human carcinogenesis but the extent of their functions and regulations are not well understood, especially in pathological conditions. The extents of the NSDs biological roles in normal and pathological conditions remain unclear. In particular, the substrate specificity of the NSDs remains unsettled and discrepant data has been reported. NSD2/MMSET is a focal point for therapeutic interventions against multiple myeloma and especially for t(4;14) myeloma, which is associated with a significantly worse prognosis than other biological subgroups. Multiple myeloma is the second most common hematological malignancy in the United States, after non-Hodgkin lymphoma. Herein, as a first step before entering a pipeline for protein x-ray crystallography, we cloned, recombinantly expressed and purified the catalytic SET domain of NSD2. Next, we demonstrated the catalytic activities, in vitro, of the recombinantly expressed NSD2-SET on H3K36 and H4K20, its biological targets at the chromatin.

BIX-01294 inhibits oncoproteins NSD1, NSD2 and NSD3

Morishita, M.,Mevius, D. E.,Shen, Y.,Zhao, S.,di Luccio, E. Springer Science + Business Media 2017 MEDICINAL CHEMISTRY RESEARCH Vol.26 No.9

Recombinant Protein Expression and Purification of the Human HMTase MMSET/NSD2

Masayo Morishita,Damiaan Mevius,Yunpeng Shen,Eric di Luccio 경북대학교 농업생명과학대학 2013 Current Research on Agriculture and Life Sciences Vol.31 No.3

Chromatin remodelers that include histone methyl transferases (HMTases) are becoming a focal point in cancer drug development. The NSD family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L are bona fide oncogenes found aberrantly expressed in several cancers, suggesting their potential role for novel therapeutic strategies. Several histone modifiers including HMTase have clear roles in human carcinogenesis but the extent of their functions and regulations are not well understood, especially in pathological conditions. The extents of the NSDs biological roles in normal and pathological conditions remain unclear. In particular, the substrate specificity of the NSDs remains unsettled and discrepant data has been reported. NSD2/MMSET is a focal point for therapeutic interventions against multiple myeloma and especially for t(4;14) myeloma, which is associated with a significantly worse prognosis than other biological subgroups. Multiple myeloma is the second most common hematological malignancy in the United States, after non-Hodgkin lymphoma. Herein, as a first step before entering a pipeline for protein x-ray crystallography, we cloned, recombinantly expressed and purified the catalytic SET domain of NSD2. Next, we demonstrated the catalytic activities, in vitro, of the recombinantly expressed NSD2-SET on H3K36 and H4K20, its biological targets at the chromatin.

Biosynthesis of (R)-(-)-1-Octen-3-ol in Recombinant Saccharomyces cerevisiae with Lipoxygenase-1 and Hydroperoxide Lyase Genes from Tricholoma matsutake

이난영,최두호,김미경,정민지,권해준,김동현,김영국,Eric di Luccio,Manabu Arioka,윤혁준,김종국 한국미생물·생명공학회 2020 Journal of microbiology and biotechnology Vol.30 No.2

Tricholoma matsutake is an ectomycorrhizal fungus, related with the host of Pinus densiflora. Most of studies on T. matsutake have focused on mycelial growth, genes and genomics, phylogenetics, symbiosis, and immune activity of this strain. T. matsutake is known for its unique fragrance in Eastern Asia. The most major component of its scent is (R)-(-)-1-octen-3-ol and is biosynthesized from the substrate linoleic acid by the sequential reaction of lipoxygenase and peroxide lyase. Here, we report for the first time the biosynthesis of (R)-(-)- 1-octen-3-ol of T. matsutake using the yeast Saccharomyces cerevisiae as a host. In this study, cDNA genes correlated with these reactions were cloned from T. matsutake, and expression studies of theses genes were carried out in the yeast Saccharomyces cerevisiae. The product of these genes expression study was carried out with Western blotting. The biosynthesis of (R)-(-)- 1-octen-3-ol of T. matsutake in recombinant Saccharomyces cerevisiae was subsequently identified with GC-MS chromatography analysis. The biosynthesis of (R)-(-)-1-octen-3-ol with S. cerevisiae represents a significant step forward.

Cloning of the Setd1b gene of Mus musculus, a novel histone methyl transferase target in the epigenetic therapy of cancers

Morishita, Masayo,Cho, Minju,Ryu, Juhee,Mevius, Damiaan E.H.F.,Di Luccio, Eric 경북대학교 농업과학기술연구소 2010 慶北大農學誌 Vol.28 No.-

The epigenetic therapy of cancers is emerging as an effective and valuable approach to both chemotherapy and the chemoprevention of cancer. The utilization of epigenetic targets that include histone methyltransferase (HMTase), Histone deacetylatase, and DNA methyltransferase, are emerging as key therapeutic targets. SET containing proteins such as the HMTase Setd1b has been found significantly amplified in cancerous cells. In order to shed some light on the histone methyl transferase family, we cloned the Setd1b gene from Mus musculus and build a collection of vectors for recombinant protein expression in E.coli that will pave the way for further structural biology studies. We prospect the role of the Setd1b pathway in cancer therapy and detail its unique value for designing novel anti-cancer epigenetic-drugs.

[P8-09] Nrf2-mediated Induction of Detoxifying Enzymes by Glyceollins Derived from Soybean Exposed to Aspergillus sojae

Hyo Jung Kim,Chae Lim Jung,Dae Hwan Nam,Eric di Luccio,Jia Park,Ji Sun Lim,Min Young Han,Ye-Seul Hong,Jong-Sang Kim 한국식품영양과학회 2010 한국식품영양과학회 학술대회발표집 Vol.2010 No.10

Identification of LEM-14 inhibitor of the oncoprotein NSD2

Shen, Yunpeng,Morishita, Masayo,Lee, Doohyun,Kim, Shinae,Lee, Taeho,Mevius, Damiaan E.H.F.,Roh, Yeonjeong,di Luccio, Eric Elsevier 2019 Biochemical and biophysical research communication Vol.508 No.1

<P><B>Abstract</B></P> <P>The NSD family (NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1) are histone lysine methyltransferases (HMTases) essential for chromatin regulation. The NSDs are oncoproteins, drivers of a number of tumors and are considered important drug-targets but the lack of potent and selective inhibitors hampers further therapeutic development and limits exploration of their biology. In particular, MMSET/NSD2 selective inhibition is being pursued for therapeutic interventions against multiple myeloma (MM) cases, especially in multiple myeloma t(4;14)(p16.3;q32) translocation that is associated with a significantly worse prognosis than other MM subgroups. Multiple myeloma is the second most common hematological malignancy, after non-Hodgkin lymphoma and remains an incurable malignancy.</P> <P>Here we report the discovery of LEM-14, an NSD2 specific inhibitor with an <I>in vitro</I> IC<SUB>50</SUB> of 132 μM and that is inactive against the closely related NSD1 and NSD3. LEM-14-1189, a LEM-14 derivative, differentially inhibits the NSDs with <I>in vitro</I> IC<SUB>50</SUB> of 418 μM (NSD1), IC<SUB>50</SUB> of 111 μM (NSD2) and IC<SUB>50</SUB> of 60 μM (NSD3). We propose LEM-14 and derivative LEM-14-1189 as tools for studying the biology of the NSDs and constitute meaningful steps toward potent NSDs therapeutic inhibitors.</P> <P><B>Highlights</B></P> <P> <UL> <LI> NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1 are histone methyltransferases and oncoproteins. </LI> <LI> Inhibition of NSD2 in multiple myeloma t(4;14)(p16.3;q32) is urgently needed. </LI> <LI> We report the discovery of a NSD2 specific inhibitor and derivatives that differentially inhibits the NSDs. </LI> <LI> We investigate the molecular mechanism for NSD2 specific inhibition. </LI> <LI> We propose our inhibitors LEM-14 and LEM-14-1189 as tools for studying the biology of the NSDs and for drug-design. </LI> </UL> </P>