As a Principal investigator (01/2010 – present )
Structural biology: Epigenetics at the atomic details.
Our lab uses structural biology tools to study the structure, functions and regulatory pathways of transcription coregulators for designing drugs suitable for epigenetic therapies. Our goal is to understand the link between histone-code and diseases, especially cancers.
My laboratory studies the functions, structures, and mechanisms of transcription factors for developing new drugs against cancers, neurodegenerative diseases, and stroke. Work in my research group is multi-disciplinary and it incorporates many processes of the early-stage drug development. My research is at the interface between biochemistry, pharmacology, neuroscience, structural biology, and computational biology. Methods development concerns news tools in bioinformatics and molecular modeling of proteins for our research needs.
Prior joining the Kyungpook National University, I was a postdoctoral researcher at the University of California at Davis consecutively in David K. Wilson’s lab (Molecular and Cellular biology dept.) and in Patrice Koehl’s lab (Genome center).
For more informations, visit the diluccio lab website at KNU: http://webbuild.knu.ac.kr/~diluccio/
As a Postdoctoral researcher (11/ 2003 to 12/2009)
di Luccio E & Koehl P. BMC Bioinformatics 2011 Feb 4;12:48
di Luccio E et al. Journal of Molecular Biology – Manuscript in preparation
di Luccio E. & Wilson D.K. Biochemistry 2008 Apr 1;47(13):4039-50
di Luccio et al. J. Mol. Biol. 2007 Jan 19;365(3):783-98 – JMB Cover
di Luccio et al. Biochem. J. 2006 Nov 15;400(1):105-14
in Pr. Patrice Koehl’s laboratory at UC Davis
I was researching to the molecular modeling of proteins including membrane proteins. The number of protein sequence in databases approaches 6 millions but the number of experimentally determined structure in the protein data bank (PDB) is slowly rising to 53,000 with only ~ 4300 unique structures. Moreover, membrane proteins constitute around 20-30% of most proteomes but only 3% of them populate the PDB. It is clear that structural genomic efforts could not keep-up. Many proteins structures continue to evade experimental methodsbecause of technical difficulties (cloning, protein expression, purification, solubility, stability, crystallization issues). Among them are some high profile drug targets. Protein structure prediction, especially homology modelling is a viable, fast and accurate method to generate a 3D structure. It exploits the 3D similarity between a known and the unknown structure, to build a model of the unknown. The main drawback of this technique concerns the accuracy of models generated and the lack of direct cross-validation methods, which keeps on fuelling many debates and critics.
Using my background in both homology modeling and X-ray crystallography, I developed a modeling etiquette with precise quality control checkpoints to improve the quality of models.I also designed and validated a new comprehensive validation algorithm (R-factor like) to cross-validate models. I am also developing novel strategies to include biological restraints into homology modeling procedures in order to improve its accuracy especially for low sequence identity template. My research also applied to membrane proteins as well.
in Pr. David K. Wilson laboratory at UC Davis
I used X-Ray crystallography to focus on the xylose prokaryotic and eucaryotic assimilation pathways. As the world faces a critical shortage of oil in a near future, the fermentation of xylose contained in agricultural byproducts to produce ethanol represent a viable alternative. Tremendous efforts are being made in protein engineering to optimize yeast enzymes to efficiently produce ethanol out of bio-waste. Xylose is metabolized through three bottleneck enzyme: xylose reductase (XR), xylitol dehydrogenase (XDH) and xylulose kinase (XK) producing the xylose-5-phosphate (X5P). X5P furthers enter the non-oxidative branch of the pentose phosphate pathway. The xylose reductase belong the aldo-keto reductase (AKRs) superfamilly and rely on NADPH to reversibly reduce carbonyl-containing compounds to the corresponding alcohols. Xylitol dehydrogenase catalyzes the oxidation of xylitol to xylulose using NAD+ andxylulose kinasephosphorylates D-xylulose into X5P. In eukaryotes capable of assimilating xylose, X5P is produced through the action of xylose reductase, xylitol dehydrogenase and D-xylulose kinase. The first two enzymes are replaced in prokaryotes with xylose isomerase that interconvert xylose and xylulose directly. Also forefficientxyloseutilizationathighfluxrates,cosubstratesshouldberecycledbetweenthe NAD-specificxylitol dehydrogenaseandtheNADPH-preferringxylose reductase step. A small number of AKRs have been found with dual NADPH/NADH specificity, usually preferring NADPH, but none are exclusive for NADH. NADH is preferable over NADPH because of its stability and is 10 fold cheaper. A key finding in our previous studies was a specific glutamate (Glu225) only found in the active site of the dual specificity NADPH/NADH enzyme AKR2B5, that is able to change conformations to accommodate both the 2′-phosphate of NADP+ and NADH.
Exploiting this observation, I successfully isolated, cloned and characterized four new AKRs able to use NADH as co-substrate. Homology modeling provided structural information to support the kinetic analysis. My findings allowed the identification of a “NADH binding sequence signature” among the wide AKRs superfamilly and will help the metabolic engineering of optimized strain of yeast for efficiently ferment xylose to ethanol. Among the xylose reductase (XR), the xylitol dehydrogenase (XDH) and the xylulose kinase (XK) enzymes, XK has been less well studied and little was known about its structure and kinetic mechanism. To address this question, I solved the apo and D-xylulose-bound crystal structures of E. coli XK. The dimeric state was observed directly by a cryo-EM reconstruction at 36-Å resolution in collaboration with specialist Pr. henning Stahlberg at UC Davis. I determined the catalytic mechanism supported by relevant site-directed mutants and kinetics analysis.
In parallel, I studied the tryptophan catabolism pathway via kynurenine at a structural level. This pathway is a six-step enzyme machinery leading to thede novo biosynthesis of nicotinate mononucleotide (NaMN), a precursor of nicotinamide adenine dinucleotide (NAD+) and is important in regulating tryptophan cellular concentrations. Numbers of medical conditions arise from improper tryptophan concentration.Low tryptophan levels are associated with inhibited T-cell responses, proliferation of viruses, protozoan parasites, and other pathogens in eukaryotic cells and also with decreased proliferation of tumor cells. In pregnant women, high tryptophan concentrations can lead to fetal immunotolerance problems. Among the six enzymes steps, the Quinolinic Acid Phosphoribosyl Transferase (QAPRTase) is of major interest. QAPRTase is involved in both the trypotophan regulation and in clearing quinolinate off the brain. Improper regulation of quinolinate concentrations is linked to the eosinophilia-myalgia syndrome and quinolinate itself is a major neurotoxin.QPRTase is encoded by the BNA6 gene in yeast and catalyzes the formation of nicotinate mononucleotide from quinolinate and 5-phosphoribosyl-1-pyrophosphate (PRPP). I solved the crystal structures of the apo, singly bound forms with the substrates quinolinate and PRPP and the structure of the Michaelis complex was approximated by PRPP and the quinolinate analogue phthalate bound to the active site. Exploiting the collection of structures, I determined the catalytic mechanism of the Saccharomyces cerevisiae QAPRTase.
Separately to the other projects, I studied the Odorant binding proteins (OBPs) in collaboration with specialist Pr. Walter Leal at UC Davis. OBPs are a small class of protein (15 KDa) highly soluble found at a high concentration level in antennae of insects or nasal mucosa of vertebrates. OBP functions as odorant and pheromone molecule carriers and therefore are key in the olfaction chain of events. Insect olfaction drives behaviors suchashost-seeking,oviposition,andmating. A thorough understanding of the insect olfaction is crucial, since it’s an efficient way to fight against highly invasive agricultural pests.In that matter, the Navel Orange Worm (NOW), Amyelois transitella (Walker) is a serious insect pest of numerous crops (walnut, Figs) and causes heavy damage to almond and pistachios fields. To address this problem I solved the 1.1Å high resolution structure of AtraOBP from NOW compexed with either (12Z,14Z)-heptadeca-12,14-dienal (major pheromone) or (11Z,13Z)-hexadeca-11,13-dien-1-ol (secondary antagonist). The structure analysis provided significant informations regarding the binding of both molecule and gave valuable insight to further design efficient antagonists.
As a graduate student (2000-2003)
di Luccio et al. Peptides 2005 Jul;26(7):1095-108
di Luccio et al. Biochem. J. 2002 Jan 15;361:409-16
di Luccio et al. Biochem. J. 2001 Sep 15;358:681-92
CNRS UMR 6560 laboratory in Marseille France
During my Ph.D. in Neuroscience I worked on potassium channels and short scorpion toxins structures. Potassium channels are ubiquitously found in eukaryotic and prokaryotic cells, and are involved in the control of electrical and non-electrical cellular functions. They modulate a number of cellular events such as muscle contraction, neuroendocrine secretion, frequency and duration of action potentials, electrolyte homeostasis, and resting membrane potential. Potassium channels are also found to be key in a wide range of pathological cascade events ranging from neurological diseases to HIV infections, making them major drug targets. Short scorpion toxins are small peptide of 30-40 amino acids with 3 to 4 disulfide bonds that selectively inhibit potassium channels with a very high affinity (nM to pM). This class of peptidic inhibitor with high affinity and high selectivity toward ionic channel are therefore premium research tools to study ionic channels. For my research, I focused on the engineering of scorpion toxin to develop a new class of potassium channels inhibitors with enhanced selectivity and activity. I first study the in vitro oxidation/folding of synthetic scorpion toxin, which is an important step for getting active peptides. Using an integrative approach mixing MALDI-TOF mass spectrometry, circular dichroism and electrophysiology, I validated the hypothesis of a correlation between the apparition of the secondary structures, the formation of disulfides bonds and the apparition of the pharmacological activity. I thus developed new methods to more efficiently produce such relevant synthetic peptides.
I built 3D-models of human voltage-gated K+ channels and human small-conductance Ca2+-sensitive K+ (SKCa) channels by comparative modeling. Using docking software to compute the interaction channel-toxin, I accurately correlated experimental Kd values with docking energy for various toxins. This gave valuable insight on both the binding surfaces and the keys residues involved but also allowed to predict the affinity of virtually any peptide toward a specific potassium channel.
