"In silico structural biology correlated with experiment"
The Department of Bioinformatics & Structural Biochemistry (DBSB) was set in 1999 aiming to consistently implement computational biology techniques - bioinformatics, modeling, simulation - and use them to guide experimental research in molecular biology and biochemistry.
Historically the main focus of DBSB was the investigation of glycoprotein (GP) folding & degradation and the relation between glycosylation and GP structure. On this line DBSB works in co-ordination with the Department of Molecular Cell Biology and colleagues from the Department of Biochemistry, University of Oxford, UK. Results have shed light onto the structure of glycans attached to the nascent protein chain and their role in the ER quality control and degradation [1,7-5,14,20,33]. The way glycosylation affects GP structure was also assessed using bioinformatics approach. To this end DBSB has developed SAGS: "Structural Assessment of Glycosylation Sites" - a comprehensive Data Base curating structural information on glycans and glycoproteins, with significant applications in modeling biological systems at molecular level [4,13,15,20-21,32].
DBSB was also involved in more general aspects of the physics of protein folding and structure. Configurations along the folding pathway and in the native state are degenerate and the experimental data has to be interpreted in the frame of statistical mechanics. In collaboration with colleagues from CEA Saclay and Heidelberg University we have investigated unfolded and native protein states using molecular simulation in combination with Small Angle and Quasielastic Neutron Scattering.
These studies have resulted in a better understanding of the folding process and the motility gradients in proteins explaining their stability and ability to interact with other molecules [2,3,8-12].
Combining bioinformatics with principles of protein folding and dynamics results in many applications in molecular life sciences such as building probabilistic models when the experimental structures are not available, or probing in silico biomolecular interactions.
Presently a significant part of our work is devoted to developing techniques in this field and applying them to a variety of problems in structural biology and molecular medicine. For example in collaboration with colleagues from IBAR and Oxford University we continue to investigate the structural aspects of processes along the secretory pathway; with colleagues from Yale, Levin Cancer Institute USA or Warsaw University Poland we are looking into protein-DNA interactions in a number of systems relevant in molecular medicine & biotechnology[29,34,36,38,42,43]; with groups from Universities of Wageningen, Haifa, Zurich, MPI-Koln, INRA-France etc we are involved in investigating the molecular basis of plant-pathogen interaction [16-17,22-24,26-27,31,39,41,45-47].
In 2012 Adina Milac (researcher ID: C-1070-2011) joined the DBSB coming from National Institute of Health, NIH Bethesda, USA where she carried out two PostDoc stages in Lawrence Tabak's and Robert Guy's lab. Adina brought in fresh molecular modeling & simulation techniques and new research topics related to structure-function relation in ion-channel systems and drug-design [19,27,28,34,38,44].
Along the years, DBSB work was financed by a large number of national and international grants among of which we mention 1 EU-IP-FP6 ("Bioexploit": 2005-2011); 1 EU-FP5 ("Nonema": 2001-2004); 2 UK - Wellcome Trust ( "Tyrosinase Folding": 1998-2001; "Glycoprotein Database": 2002-2005) or the national grant PN-II-ID-PCE 168 ("in silico": 2007-2011).
The models generated so far in this process allowed us to make predictions upon systems behavior. Subsequently predictions were successfully validated experimentally and resulted in a better understanding of the molecular bases underlying the investigated biological functions - some of them with potentially important applications in molecular medicine, biotechnology and pharmacology [16-52].
Research in the above mentioned fields continues and is currently financed within the frame of a number of grants and research collaborations such as CNSC PN2-ID-PCE-2011-3-0342 " Modeling molecular complexes and assemblies with experimental and bioinformatic constraints" (2011-2016).
A-JP is currently member of the MC of COST Action "Sustain" FA1208-11941: " Pathogen-informed strategies for sustainable broad-spectrum crop resistance" (2013-2018) and also Co-PI in the USA-NIH grant 4R37 AI032524 "Structure of RAG1-RAG2-DNA complexes" (2012-2017) carried by David Schatz. In this project a key role is played by Marius Surleac, who also is involved in a related European collaboration of DBSB funded by ERANET-HIVERA PNIII-P3-53/2016-2019: "INinRAGI".
We also have ongoing projects to developing new statistical and machine learning techniques useful in simulation and bioinformatics. Here the central stage was taken by Laurentiu Spiridon returned at the fall of 2016 from PostDoc stages at Illinois Institute of Thechnology where he has developped extremely efficient, robotic based algorithms for MC simulations. Laurentiu will be assisted by Teodor, our MSc Student and Eliza Martin who runs also her onw PhD on Statistical Techniques in Bioinformatics with a focus on Bayesian Statistics and Machine Learning techniques for structure prediction.
Another priority of DBSB, in which Cristian Munteanu plays the key role is now to coupling computational techniques with Mass Spectrometry, Surface Plasmon Resonance and data derived from the Highthroughput Drug Screening Platform of IBAR, aiming to step up the scale of biological system investigation to global proteome and interactome level [35,40, 44].
All the above computational work is supervised by our expert in Parallel Computing Marius Micluta who plays the central role in managing our High Perforance Computing Centre - the key element of all our Biocomputing / Bioinformatics programs and projects.
Genome-wide functional analyses of plant coiled-coil NLR-type pathogen receptors reveal essential roles of their N-terminal domain in oligomerization, networking, and immunity., PLoS biology, 16(12), e2005821, 2018
Wróblewski T, Spiridon L, Martin EC, Petrescu AJ, Cavanaugh K, Truco MJ, Xu H, Gozdowski D, Pawłowski K, Michelmore RW, Takken FLW
Distinct Roles of Non-Overlapping Surface Regions of the Coiled-Coil Domain in the Potato Immune Receptor Rx1., Plant physiology, 178(3), 1310-1331, 2018
Slootweg EJ, Spiridon LN, Martin EC, Tameling WIL, Townsend PD, Pomp R, Roosien J, Drawska O, Sukarta OCA, Schots A, Borst JW, Joosten MHAJ, Bakker J, Smant G, Cann MJ, Petrescu AJ, Goverse A
The Design of New HIV-IN Tethered Bifunctional Inhibitors using Multiple Microdomain Targeted Docking., Current medicinal chemistry, 2018
Ciubotaru M, Musat MG, Surleac M, Ionita E, Petrescu AJ, Abele E, Abele R
Clonal lineage of high grade serous ovarian cancer in a patient with neurofibromatosis type 1(Gynecologic Oncology Reports), 2018
Eric Norris, Wendell D. Jones, Marius D. Surleac, Andrei José Petrescu, Darla D Destephanis, Qing Zhang, Issam S. Hamadeh, Jeffrey S. Kneisl, Chad Livasy, Ram N. Ganapathi, David L. Tait, Mahrukh K. Ganapathi
Characterization and expression analysis of Galnts in developing Strongylocentrotus purpuratus embryos., PloS one, 12(4), e0176479, 2017
Famiglietti AL, Wei Z, Beres TM, Milac AL, Tran DT, Patel D, Angerer RC, Angerer LM, Tabak LA
Assessment of ganglioside age-related and topographic specificity in human brain by Orbitrap mass spectrometry., Analytical biochemistry, 521, 40-54, 2017
Sarbu M, Dehelean L, Munteanu CVA, Vukelić Ž, Zamfir AD
Heavy metal accumulation by Saccharomyces cerevisiae cells armed with metal binding hexapeptides targeted to the inner face of the plasma membrane., Applied microbiology and biotechnology, 101(14), 5749-5763, 2017
Ruta LL, Kissen R, Nicolau I, Neagoe AD, Petrescu AJ, Bones AM, Farcasanu IC
Roles of the C-terminal domains of topoisomerase IIα and topoisomerase IIβ in regulation of the decatenation checkpoint., Nucleic acids research, 45(10), 5995-6010, 2017
Kozuki T, Chikamori K, Surleac MD, Micluta MA, Petrescu AJ, Norris EJ, Elson P, Hoeltge GA, Grabowski DR, Porter ACG, Ganapathi RN, Ganapathi MK
Inhibition of N-glycan processing modulates the network of EDEM3 interactors., Biochemical and biophysical research communications, 486(4), 978-984, 2017
Butnaru CM, Chiritoiu MB, Chiritoiu GN, Petrescu SM, Petrescu AJ
Cell death triggering and effector recognition by Sw-5 SD-CNL proteins from resistant and susceptible tomato isolines to Tomato spotted wilt virus., Molecular plant pathology, 17(9), 1442-1454, 2016
De Oliveira AS, Koolhaas I, Boiteux LS, Caldararu OF, Petrescu AJ, Oliveira Resende R, Kormelink R
An LRR/Malectin Receptor-Like Kinase Mediates Resistance to Non-adapted and Adapted Powdery Mildew Fungi in Barley and Wheat(Front Plant Sci), 2016
Jeyaraman Rajaraman, Dimitar Douchkov, Götz Hensel, Francesca L. Stefanato, Anna Gordon, Nelzo Ereful, Octav F. Caldararu, Andrei-Jose Petrescu, Jochen Kumlehn, Lesley A. Boyd, Patrick Schweizer
SPRYSEC Effectors: A Versatile Protein-Binding Platform to Disrupt Plant Innate Immunity., Frontiers in plant science, 7, 1575, 2016
Diaz-Granados A, Petrescu AJ, Goverse A, Smant G
QSAR Approaches Applied to Antidepressants Induced Neurogenesis--in vivo and in silico Applications., Mini reviews in medicinal chemistry, 16(3), 230-40, 2015
Avram S, Borcan F, Borcan LC, Milac AL, Mihailescu D
Phosphoketolases from Lactococcus lactis, Leuconostoc mesenteroides and Pseudomonas aeruginosa: Dissimilar sequences, similar substrates but distinct enzymatic characteristics, Applied Microbiology and Biotechnology, 18(98), 7855-67, 2014
Petrareanu G, Balasu MC, Vacaru AM, Munteanu CVA, Ionescu AE, Matei I, Szedlacsek SE
Structure-biological function relationship extended to mitotic arrest-deficient 2-like protein Mad2 native and mutants-new opportunity for genetic disorder control., International journal of molecular sciences, 15(11), 21381-400, 2014
Avram S, Milac A, Mernea M, Mihailescu D, Putz MV, Buiu C
Decapping Scavenger (DcpS) enzyme: advances in its structure, activity and roles in the cap-dependent mRNA metabolism., Biochimica et biophysica acta, 1839(6), 452-62, 2014
Milac AL, Bojarska E, Wypijewska del Nogal A
Value of dopachrome tautomerase detection in the assessment of melanocytic tumors., Melanoma research, 24(3), 219-36, 2014
Filimon A, Zurac SA, Milac AL, Sima LE, Petrescu SM, Negroiu G
Analysis of decapping scavenger cap complex using modified cap analogs reveals molecular determinants for efficient cap binding., The FEBS journal, 280(24), 6508-27, 2013
Wypijewska del Nogal A, Surleac MD, Kowalska J, Lukaszewicz M, Jemielity J, Bisaillon M, Darzynkiewicz E, Milac AL, Bojarska E
Characterization of the anti-HBV activity of HLP1-23, a human lactoferrin-derived peptide., Journal of medical virology, 85(5), 780-8, 2013
Florian PE, Macovei A, Lazar C, Milac AL, Sokolowska I, Darie CC, Evans RW, Roseanu A, Branza-Nichita N
More effective dithiocarbamate derivatives inhibiting carbonic anhydrases, generated by QSAR and computational design., Journal of enzyme inhibition and medicinal chemistry, 28(2), 350-9, 2013
Avram S, Milac AL, Carta F, Supuran CT
3D-QSAR study indicates an enhancing effect of membrane ions on psychiatric drugs targeting serotonin receptor 5-HT1A., Molecular bioSystems, 8(5), 1418-25, 2012
Avram S, Milac AL, Mihailescu D
More effective antimicrobial mastoparan derivatives, generated by 3D-QSAR-Almond and computational mutagenesis., Molecular bioSystems, 8(2), 587-94, 2012
Avram S, Buiu C, Borcan F, Milac AL
Structural models of TREK channels and their gating mechanism., Channels (Austin, Tex.), 5(1), 23-33, 2011
Milac A, Anishkin A, Fatakia SN, Chow CC, Sukharev S, Guy HR
Analyses of gating thermodynamics and effects of deletions in the mechanosensitive channel TREK-1: comparisons with structural models., Channels (Austin, Tex.), 5(1), 34-42, 2011
Maksaev G, Milac A, Anishkin A, Guy HR, Sukharev S
Symmetry-restrained molecular dynamics simulations improve homology models of potassium channels., Proteins, 78(4), 932-49, 2010
Anishkin A, Milac AL, Guy HR
Structural and functional characterization of a novel, host penetration-related pectate lyase from the potato cyst nematode Globodera rostochiensis., Molecular plant pathology, 8(3), 293-305, 2007
Kudla U, Milac AL, Qin L, Overmars H, Roze E, Holterman M, Petrescu AJ, Goverse A, Bakker J, Helder J, Smant G
Substrate-induced conformational changes and dynamics of UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferase-2., Journal of molecular biology, 373(2), 439-51, 2007
Milac AL, Buchete NV, Fritz TA, Hummer G, Tabak LA
Evaluation of a neural networks QSAR method based on ligand representation using substituent descriptors. Application to HIV-1 protease inhibitors., Journal of molecular graphics & modelling, 25(1), 37-45, 2006
Milac AL, Avram S, Petrescu AJ
In planta secretion of a calreticulin by migratory and sedentary stages of root-knot nematode., Molecular plant-microbe interactions : MPMI, 18(12), 1277-84, 2005
Jaubert S, Milac AL, Petrescu AJ, de Almeida-Engler J, Abad P, Rosso MN
Mutations in dopachrome tautomerase (Dct) affect eumelanin/pheomelanin synthesis, but do not affect intracellular trafficking of the mutant protein., The Biochemical journal, 391(Pt 2), 249-59, 2005
Costin GE, Valencia JC, Wakamatsu K, Ito S, Solano F, Milac AL, Vieira WD, Yamaguchi Y, Rouzaud F, Petrescu AJ, Lamoreux ML, Hearing VJ
Origin, distribution and 3D-modeling of Gr-EXPB1, an expansin from the potato cyst nematode Globodera rostochiensis., FEBS letters, 579(11), 2451-7, 2005
Kudla U, Qin L, Milac A, Kielak A, Maissen C, Overmars H, Popeijus H, Roze E, Petrescu A, Smant G, Bakker J, Helder J
Statistical analysis of the protein environment of N-glycosylation sites: implications for occupancy, structure, and folding., Glycobiology, 14(2), 103-14, 2004
Petrescu AJ, Milac AL, Petrescu SM, Dwek RA, Wormald MR
Gerontomics: Multi-omics prediction system for prioritization of gerontological interventions
Project director: Robi Tacutu
Starting 02.09.2016, the Institute of Biochemistry of the Romanian Academy is implementing the project “Multi-omics prediction system for prioritization of gerontological interventions”, co-funded through European Fund for Regional Development, in accordance with the funding contract signed by the Ministry of National Education and Scientific Research. The total funding for the project is 8.524.757,50 lei, of which 8.502.557,50 lei represent non-reimbursable funding. The project’s duration is 48 months.
Structure Assisted Investigation of Critical Protein Families Involved in Plant Immunity
Project director: Andrei-José Petrescu
This project aims to address a number of structural aspects related to key elements of the plant immune system and its pathogen interactors using a combined approach intricating experimental and computational steps. To this end we intend to build on our previous results in the field and further develop experimental, bioinformatics and molecular modeling methods appropriate for solving the specific problems implied by this proposal.
Mass spectrometry based investigation of the oxidative stress as a potential key-player in the immunobiology of melanoma
02/05/2018 - 30/04/2020
Project director: Cristian Munteanu
A promising approach of the therapeutic strategy in melanoma is immunotherapy. One of the most promising melanoma antigens is tyrosinase, which was frequently found as overexpressed in melanomas. It wash shown that this protein undergoes unproductive folding in the endoplasmic reticulum (ER) leading to the selection of the incorrectly folded molecules for degradation via the ubiquitin proteasome system. The current project aims to obtain epitopes with potential increased clinical outcome.
Databases: SAGS DB - Structural Assesment of Glycosylation Site Database
Simulation Hardware: 1 HP-HPC Cluster (4 TFlop - effective power); 1 Bull-HPC Cluster
Simulation Software: Charmm, Amber, NAMD
Modeling Hardware: 1 HP-Graphic Station ProLiant WS460c; 1 Octane 2x600 SGI Workstation
Modeling Software: Accelrys Discovery Studio, BCI Raptor, Modeller etc