Bioinformatics & Structural Biochemistry

Bioinformatics & Structural Biochemistry Department

Bioinformatics & Structural Biochemistry

Main Focus

"In silico structural biology correlated with experiment"

Mission Statement

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.

Overview

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 School of Medicine USA; Levin Cancer Institute USA; 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 California - Berkeley and Davis, 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].

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].

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); PN2-ID-PCE-2011-3-0342 "Modeling molecular complexes and assemblies with experimental and bioinformatic constraints" (2011-2016); L.Spiridon - PN-III-P1-1.1.-TE-2016-1852 "Free energy prediction of biomolecular processes using high speed robotic algorithms" (2018-2020); PN-III-P4-ID-PCE-2020-2444 "Usage of high speed robotic algorithms for in-silico assisted experimental research of large biomolecular systems" (2021-2023), and many other national research consortiums.

DBBS was also member of the MC of COST Action "Sustain" FA1208-11941: "Pathogen-informed strategies for sustainable broad-spectrum crop resistance" (2013-2018) while  AJ-P was also Co-PI in the USA-NIH grant 4R37 AI032524 "Structure of RAG1-RAG2-DNA complexes" (2012-2017) and NIH 1R01 AI137079-01A1/2018 "Function and evolutionary origin of RAG1 endonuclease" carried by Professor David Schatz from the Departmentof of Immunobiology, Yale School of Medicine.

 

Our group continues to develop research strategies in computational driven experimental research by currently focussing on developing bioinformatics resources, new machine learning and statistical mechanics techniques for structural prediction and a new generation of highly effective molecular simulation methods. 

For instance Laurentiu Spiridon who returned at the fall of 2016 from PostDoc stages at Illinois Institute of Thechnology is currently developping extremely efficient, robotic based algorithms for HMC simulations.

Teodor Sulea and Floriana Bectas, PhD students are using MD simulation techniques and also tesing the new HMC algorithms in modeling structures, processes and interactions various biomolecular systems while Eliza Martin, PostDoc has developed Machine Learning techniques for fast identification of the main CC/TIR; NBS and LRR domain signatures, critical for the delineation of NOD like receptors in large sequence datasests. This work was instrumental in generating NLRscape - the Atlas of plant NOD like receptors (NLRs) - a web resource developed by DBSB for plant research community interested in NLR evolutionary dynamics and artificial evolution attempts aimed at expanding NLR diversity via bioengineering. 

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.

Andrei-José Petrescu, PhD
Andrei-José Petrescu, PhD

Head of Department

Andrei heads the Department of Bioinformatics since 1999. He developed computational assisted work relevant in many fields of molecular life sciences reflected by a large web of collaborations with groups from Oxford, Yale, Berkeley, Wageningen and many other advanced research centers. More...

Eliza Martin, Ph.D. student
Eliza Martin, Ph.D. student

Research assistant

Eliza Martin is a researcher in the Institute of Biochemistry of the Romanian Academy. Eliza is currently working in Bioinformatics & Structural Biochemistry in the Bioinformatics & Structural Biochemistry.

Floriana Bectas
Floriana Bectas

Floriana Bectas is a researcher in the Institute of Biochemistry of the Romanian Academy. Floriana is currently working in Bioinformatics & Structural Biochemistry in the Bioinformatics & Structural Biochemistry.

Laurentiu Spiridon, Dr.
Laurentiu Spiridon, Dr.

Laurentiu Spiridon is a researcher in the Institute of Biochemistry of the Romanian Academy. Laurentiu is currently working in Bioinformatics & Structural Biochemistry in the Bioinformatics & Structural Biochemistry.

Teodor Asvadur Sulea
Teodor Asvadur Sulea

Teodor Asvadur Sulea is a researcher in the Institute of Biochemistry of the Romanian Academy. Teodor Asvadur is currently working in Bioinformatics & Structural Biochemistry in the Bioinformatics & Structural Biochemistry.

Year
  1. Martin EC, Ion CF, Ifrimescu F, Spiridon L, Bakker J, Goverse A, Petrescu AJ.Martin EC et al . "NLRscape: an atlas of plant NLR proteins", Nucleic Acids Res., (2022)
    IF: 19.16AI: 5.51
  2. Har-Zahav A, Lixandru D, Cheishvili D, Matei IV, Florea IR, Aspritoiu VM, Blus-Kadosh I, Meivar-Levy I, Serban AM, Popescu I, Szyf M, Ferber S, Dima SOHar-Zahav A et al . "The role of DNA demethylation in liver to pancreas transdifferentiation", Stem cell research & therapy 13(1): 476, (2022)
    IF: 8.07
  3. Martin EC, Spiridon L, Goverse A, Petrescu AJ.Martin EC et al . "NLRexpress-A bundle of machine learning motif predictors-Reveals motif stability underlying plant Nod-like receptors diversity", Front Plant Sci. 13: 975888, (2022)
    IF: 6.63AI: 1.17
  4. van Grinsven IL, Martin EC, Petrescu AJ, Kormelink R.van Grinsven IL et al . "Tsw - A case study on structure-function puzzles in plant NLRs with unusually large LRR domains", Front Plant Sci 13: 983693, (2022)
    IF: 6.63AI: 1.17
  5. Suteanu-Simulescu A, Zamfir AD, Ica R, Sarbu M, Munteanu CVA, Gadalean F, Vlad A, Bob F, Jianu DC, Petrica LSuteanu-Simulescu A et al . "High-Resolution Tandem Mass Spectrometry Identifies a Particular Ganglioside Pattern in Early Diabetic Kidney Disease of Type 2 Diabetes Mellitus Patients", Molecules (Basel, Switzerland) 27(9), (2022)
    IF: 4.93AI: 0.67
  6. Iulia-Roxana Angelescu, Silvia-Simona Grosu-Tudor # 1, Lucia-Roxana Cojoc, Gabriel-Mihai Maria, Gabriela N Chirițoiu, Cristian V A Munteanu, Medana ZamfirIulia-Roxana Angelescu et al . "Isolation, characterization, and mode of action of a class III bacteriocin produced by Lactobacillus helveticus 34.9", World J Microbiol Biotechnol .(38): 220, (2022)
    IF: 4.25AI: 0.64
  7. Szedlacsek HS, Bajusz D, Badea RA, Pop A, Bică CC, Ravasz L, Mittli D, Mátyás D, Necula-Petrăreanu G, Munteanu CVA, Papp I, Juhász G, Hritcu L, Keserű GM, Szedlacsek SE.Szedlacsek HS et al . "Designed Peptide Inhibitors of STEP Phosphatase-GluA2 AMPA Receptor Interaction Enhance the Cognitive Performance in Rats", JOURNAL OF MEDICINAL CHEMISTRY 1520-4804(ISSN 0022-2623), (2021)
    IF: 7.45
  8. Baudin M, Martin EC, Sass C, Hassan JA, Bendix C, Sauceda R, Diplock N, Specht CD, Petrescu AJ, Lewis JDBaudin M et al . "A natural diversity screen in Arabidopsis thaliana reveals determinants for HopZ1a recognition in the ZAR1-ZED1 immune complex", Plant, cell & environment 44(2): 629-644, (2021)
    IF: 6.16AI: 1.91
  9. Munteanu CVA, Chirițoiu GN, Chirițoiu M, Ghenea S, Petrescu AJ, Petrescu ȘMMunteanu CVA et al . "Affinity proteomics and deglycoproteomics uncover novel EDEM2 endogenous substrates and an integrative ERAD network", Molecular & cellular proteomics : MCP: 100125, (2021)
    IF: 5.91AI: 2.26
  10. Patras L, Ionescu AE, Munteanu C, Hajdu R, Kosa A, Porfire A, Licarete E, Rauca VF, Sesarman A, Luput L, Bulzu P, Chiroi P, Tranca RA, Meszaros MS, Negrea G, Barbu-Tudoran L, Potara M, Szedlacsek S, Banciu MPatras L et al . "Trojan horse treatment based on PEG-coated extracellular vesicles to deliver doxorubicin to melanoma in vitro and in vivo", Cancer biology & therapy: 1-16, (2021)
    IF: 4.74
  11. Manica G, Ghenea S, Munteanu CVA, Martin EC, Butnaru C, Surleac M, Chiritoiu GN, Alexandru PR, Petrescu AJ, Petrescu SMManica G et al . "EDEM3 Domains Cooperate to Perform Its Overall Cell Functioning", Int. J. Mol. Sci. 4(22): 2172, (2021)
    IF: 4.56
  12. Manoliu LCE, Martin EC, Milac AL, Spiridon LManoliu LCE et al . "Effective Use of Empirical Data for Virtual Screening against APJR GPCR Receptor", Molecules (Basel, Switzerland) 26(16), (2021)
    IF: 4.41AI: 0.60
  13. Mernea M, Martin EC, Petrescu AJ, Avram SMernea M et al . "Deep Learning in the Quest for Compound Nomination for Fighting COVID-19", Current medicinal chemistry 28(28): 5699-5732, (2021)
    IF: 4.18AI: 0.75
  14. Iacob R, Herlea V, Savu L, R Florea I, M Ilie V, Terinte-Balcan G, Gherghiceanu M, Uta M, Popa C, Iacob S, V Matei I, Jardan C, Lixandru D, Dima S, Meivar-Levy I, Ferber S, Popescu IIacob R et al . "Phenotypic assessment of liver-derived cell cultures during in vitro expansion", Regenerative medicine, (2021)
    IF: 2.59
  15. Matei IV, Meivar-Levy I, Lixandru D, Dima S, Florea IR, Ilie VM, Albulescu R, Popescu I, Ferber SMatei IV et al . "The effect of liver donors' age, gender and metabolic state on pancreatic lineage activation", Regenerative medicine, (2021)
    IF: 2.59
  16. Chirițoiu GN, Chirițoiu M, Munteanu CVAChirițoiu GN et al . "Dataset of human EDEM2 melanoma cells proteomics, affinity proteomics and deglycoproteomics", Data in brief 39: 107471, (2021)
  17. Gheorghe RO, Deftu A, Filippi A, Grosu A, Bica-Popi M, Chiritoiu M, Chiritoiu G, Munteanu C, Silvestro L, Ristoiu VGheorghe RO et al . "Silencing the Cytoskeleton Protein Iba1 (Ionized Calcium Binding Adapter Protein 1) Interferes with BV2 Microglia Functioning", Cellular and molecular neurobiology, (2020)
    IF: 3.80
  18. Martin EC, Sukarta OCA, Spiridon L, Grigore LG, Constantinescu V, Tacutu R, Goverse A, Petrescu AJMartin EC et al . "LRRpredictor-A New LRR Motif Detection Method for Irregular Motifs of Plant NLR Proteins Using an Ensemble of Classifiers", Genes (Basel) 11(3): 286, (2020)
    IF: 3.33
  19. Ionescu AE, Mentel M, Munteanu CVA, Sima LE, Martin EC, Necula-Petrareanu G, Szedlacsek SEIonescu AE et al . "Analysis of EYA3 Phosphorylation by Src Kinase Identifies Residues Involved in Cell Proliferation", International Journal of Molecular Sciences 20(24): 6307, (2019)
    IF: 4.18
  20. Ciubotaru M, Musat MG, Surleac M, Ionita E, Petrescu AJ, Abele E, Abele RCiubotaru M et al . "The Design of New HIV-IN Tethered Bifunctional Inhibitors using Multiple Microdomain Targeted Docking", Current medicinal chemistry 26(15): 2574-2600, (2019)
    IF: 3.89
  21. Munteanu CVA, Chiritoiu GN, Petrescu AJ, Petrescu ȘMMunteanu CVA et al . "Profiling Optimal Conditions for Capturing EDEM Proteins Complexes in Melanoma Using Mass Spectrometry", Advances in experimental medicine and biology 1140: 155-167, (2019)
    IF: 2.13
  22. Sarbu M, Dehelean L, Munteanu CVA, Ica R, Petrescu AJ, Zamfir ADSarbu M et al . "Human caudate nucleus exhibits a highly complex ganglioside pattern as revealed by high-resolution multistage Orbitrap MS", Journal of Carbohydrate Chemistry 38(9), (2019)
    IF: 0.80
  23. Wróblewski T, Spiridon L, Martin EC, Petrescu AJ, Cavanaugh K, Truco MJ, Xu H, Gozdowski D, Pawłowski K, Michelmore RW, Takken FLWWróblewski T et al . "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)
    IF: 8.39
  24. 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 ASlootweg EJ et al . "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)
    IF: 6.30
  25. 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. GanapathiEric Norris et al . "Clonal lineage of high grade serous ovarian cancer in a patient with neurofibromatosis type 1", Gynecologic Oncology Reports 23: 41-44, (2018)
  26. Kozuki T, Chikamori K, Surleac MD, Micluta MA, Petrescu AJ, Norris EJ, Elson P, Hoeltge GA, Grabowski DR, Porter ACG, Ganapathi RN, Ganapathi MKKozuki T et al . "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)
    IF: 11.56
  27. Ruta LL, Kissen R, Nicolau I, Neagoe AD, Petrescu AJ, Bones AM, Farcasanu ICRuta LL et al . "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)
    IF: 3.67
  28. Famiglietti AL, Wei Z, Beres TM, Milac AL, Tran DT, Patel D, Angerer RC, Angerer LM, Tabak LAFamiglietti AL et al . "Characterization and expression analysis of Galnts in developing Strongylocentrotus purpuratus embryos", PloS one 12(4): e0176479, (2017)
    IF: 2.77
  29. Butnaru CM, Chiritoiu MB, Chiritoiu GN, Petrescu SM, Petrescu AJButnaru CM et al . "Inhibition of N-glycan processing modulates the network of EDEM3 interactors", Biochemical and biophysical research communications 486(4): 978-984, (2017)
    IF: 2.56
  30. Sarbu M, Dehelean L, Munteanu CVA, Vukelić Ž, Zamfir ADSarbu M et al . "Assessment of ganglioside age-related and topographic specificity in human brain by Orbitrap mass spectrometry", Analytical biochemistry 521: 40-54, (2017)
    IF: 2.27
  31. De Oliveira AS, Koolhaas I, Boiteux LS, Caldararu OF, Petrescu AJ, Oliveira Resende R, Kormelink RDe Oliveira AS et al . "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)
    IF: 4.70
  32. 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 SchweizerJeyaraman Rajaraman et al . "An LRR/Malectin Receptor-Like Kinase Mediates Resistance to Non-adapted and Adapted Powdery Mildew Fungi in Barley and Wheat", Front Plant Sci 7, (2016)
    IF: 4.30
  33. Diaz-Granados A, Petrescu AJ, Goverse A, Smant GDiaz-Granados A et al . "SPRYSEC Effectors: A Versatile Protein-Binding Platform to Disrupt Plant Innate Immunity", Frontiers in plant science 7: 1575, (2016)
    IF: 4.30
  34. Ciubotaru M, Surleac MD, Metskas LA, Koo P, Rhoades E, Petrescu AJ, Schatz DG.Ciubotaru M et al . "The architecture of the 12RSS in V(D)J recombination signal and synaptic complexes", Nucleic Acids Research 43(2): 917-931, (2015)
    IF: 9.20AI: 3.60
  35. Sueldo DJ, Shimels M, Spiridon LN, Caldararu O, Petrescu AJ, Joosten MH, Tameling WI. et alSueldo DJ et al . "Random Mutagenesis of the Nucleotide-Binding Domain of NRC1 (NB-LRR Required for Hypersensitive Response-Associated Cell Death-1), a Downstream Signalling Nucleotide-Binding, Leucine-Rich Repeat (NB-LRR) Protein, Identifies Gain-Of-Function Mutations in the Nucleotide-Binding Pocket", New Phytologist 208(1): 210-223, (2015)
    IF: 7.43AI: 2.50
  36. Zhang YH, Shetty K, Surleac MD, Petrescu AJ, Schatz DG.Zhang YH et al . "Mapping and Quantitation of the Interaction between the Recombination Activating Gene Proteins RAG1 and RAG2", Journal of Biological Chemistry 290(19): 11802‐11817, (2015)
    IF: 4.26AI: 1.60
  37. Sarbu M, Munteanu CV, Dehelean L, Petrescu AJ, Peter-Katalinic J, Zamfir AD.Sarbu M et al . "Identification and structural characterization of novel O- and N-glycoforms in the urine of a Schindler disease patient by Orbitrap mass spectrometry", Journal of Mass Spectrometry 50(9): 1044‐1056, (2015)
    IF: 2.54AI: 0.70
  38. GABRIELA N. CHIRIȚOIU, CRISTIAN V.A. MUNTEANU, NICULINA MITREAGABRIELA N. CHIRIȚOIU et al . "COMBINING HETEROLOGOUS BACTERIAL EXPRESSION SYSTEM WITH AFFINITY CHROMATOGRAPHY PURIFICATION TO OBTAIN NATIVE MOUSE TYROSINASE", Farmacia 2(63): 254-261, (2015)
    IF: 1.16
  39. Avram S, Borcan F, Borcan LC, Milac AL, Mihailescu DAvram S et al . "QSAR Approaches Applied to Antidepressants Induced Neurogenesis--in vivo and in silico Applications", Mini reviews in medicinal chemistry 16(3): 230-40, (2015)
  40. Sela H, Spiridon LN, Ashkenazi H, Bhullar NK, Brunner S, Petrescu AJ, Fahima T, Keller B, Jordan T.Sela H et al . "Three-dimensional Modeling and Diversity Analysis Reveals Distinct AVR Recognition Sites and Evolutionary Pathways in Wild and Domesticated Wheat Pm3 R Genes", Molecular Plant Microbe Interactions 27(8): 835-845, (2014)
    IF: 3.94AI: 1.30
  41. Petrareanu G, Balasu MC, Vacaru AM, Munteanu CVA, Ionescu AE, Matei I, Szedlacsek SEPetrareanu G et al . "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)
    IF: 3.34
  42. Avram S, Milac A, Mernea M, Mihailescu D, Putz MV, Buiu CAvram S et al . "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)
  43. Milac AL, Bojarska E, Wypijewska del Nogal AMilac AL et al . "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)
  44. Filimon A, Zurac SA, Milac AL, Sima LE, Petrescu SM, Negroiu GFilimon A et al . "Value of dopachrome tautomerase detection in the assessment of melanocytic tumors", Melanoma research 24(3): 219-36, (2014)
  45. Ciubotaru M, Trexler AJ, Spiridon LN, Surleac MD, Rhoades E, Petrescu AJ, Schatz DG.Ciubotaru M et al . "RAG and HMGB1 create a large bend in the 23RSS in the V(D)J recombination synaptic complexes", Nucleic Acids Research 41(4): 2437-2454, (2013)
    IF: 8.81AI: 3.40
  46. Slootweg EJ, Spiridon LN, Roosien J, Butterbach P, Pomp R, Westerhof L, Wilbers R, Bakker E, Bakker J, Petrescu AJ, Smant G, Goverse A.Slootweg EJ et al . "Structural determinants at the interface of the ARC2 and leucine-rich repeat domains control the activation of the plant immune receptors Rx1 and Gpa2", Plant Physiology 162(3): 1510‐1528, (2013)
    IF: 7.39AI: 2.40
  47. Wypijewska del Nogal A, Surleac MD, Kowalska J, Lukaszewicz M, Jemielity J, Bisaillon M, Darzynkiewicz E, Milac AL, Bojarska EWypijewska del Nogal A et al . "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)
    IF: 3.99
  48. Flangea C, Petrescu AJ, Seidler DG, Munteanu CV, Zamfir ADFlangea C et al . "Identification of an unusually sulfated tetrasaccharide chondroitin/dermatan motif in mouse brain by combining chip-nanoelectrospray multistage MS2 -MS4 and high resolution MS", Electrophoresis 34(11): 1581‐1592, (2013)
    IF: 3.16AI: 0.60
  49. Florian PE, Macovei A, Lazar C, Milac AL, Sokolowska I, Darie CC, Evans RW, Roseanu A, Branza-Nichita NFlorian PE et al . "Characterization of the anti-HBV activity of HLP1-23, a human lactoferrin-derived peptide", Journal of medical virology 85(5): 780-8, (2013)
    IF: 2.22AI: 0.70
  50. Avram S, Milac AL, Carta F, Supuran CTAvram S et al . "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)
  51. Sela H, Spiridon LN, Petrescu AJ, Akerman M, Mandel-Gutfreund Y, Nevo E, Loutre C, Keller B, Schulman AH, Fahima T.Sela H et al . "Ancient Diversity of Splicing Motifs and Protein Surfaces in the Wild Emmer Wheat (Triticum Dicoccoides) LR10 Coiled Coil (CC) and Leucine-Rich Repeat (LRR) Domains", Molecular Plant Pathology 13(3): 276‐287, (2012)
    IF: 4.49AI: 1.30
  52. Avram S, Milac AL, Mihailescu DAvram S et al . "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)
    IF: 3.35AI: 1.20
  53. Avram S, Buiu C, Borcan F, Milac ALAvram S et al . "More effective antimicrobial mastoparan derivatives, generated by 3D-QSAR-Almond and computational mutagenesis", Molecular bioSystems 8(2): 587-94, (2012)
  54. Maekawa T, Cheng W, Spiridon LN, Töller A, Lukasik E, Saijo Y, Liu P, Shen QH, Micluta MA, Somssich IE, Takken FLW, Petrescu AJ, Chai J, Schulze-Lefert PMaekawa T et al . "Coiled-coil domain-dependent homodimerization of intracellular barley immune receptors defines a minimal functional module for triggering cell death", Cell Host Microbe 9(3): 187‐199, (2011)
    IF: 13.50AI: 7.00
  55. Grozav AG, Willard BB, Kozuki T, Chikamori K, Micluta MA, Petrescu AJ, Kinter M, Ganapathi R, Ganapathi MK.Grozav AG et al . "Tyrosine 656 in Topoisomerase IIβ Is Important for the Catalytic Activity of the Enzyme: Identification Based on Artifactual +80-Da Modification at This Site", Proteomics 11(5): 829‐842, (2011)
    IF: 4.50AI: 1.00
  56. Milac A, Anishkin A, Fatakia SN, Chow CC, Sukharev S, Guy HRMilac A et al . "Structural models of TREK channels and their gating mechanism", Channels (Austin, Tex.) 5(1): 23-33, (2011)
  57. Maksaev G, Milac A, Anishkin A, Guy HR, Sukharev SMaksaev G et al . "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)
  58. Slootweg E, Roosien J, Spiridon LN, Petrescu AJ, Tameling W, Joosten M, Pomp R, van Schaik C, Dees R, Borst JW, Smant G, Schots A, Bakker J, Goverse A.Slootweg E et al . "Nucleocytoplasmic Distribution Is Required for Activation of Resistance by the Potato NB-LRR Receptor Rx1 and Is Balanced by Its Functional Domains", Plant Cell 22(12): 4195‐4215, (2010)
    IF: 9.40AI: 4.00
  59. Anishkin A, Milac AL, Guy HRAnishkin A et al . "Symmetry-restrained molecular dynamics simulations improve homology models of potassium channels", Proteins 78(4): 932-49, (2010)
  60. Balasu MC, Spiridon LN, Miron S, Craescu CT, Scheidig AJ, Petrescu AJ, Szedlacsek SE.Balasu MC et al . "Interface analysis of the complex between ERK2 and PTP-SL", , (2009)
  61. Rehman S, Postma W, Tytgat T, Prins P, Qin L, Overmars H, Vossen J, Spiridon LN, Petrescu AJ, Goverse A, Bakker J, Smant G.Rehman S et al . "A secreted SPRY domain-containing protein (SPRYSEC) from the plant-parasitic nematode Globodera rostochiensis interacts with a CC-NB-LRR protein from a susceptible tomato", Mol Plant Microbe Interact 22(3): 330-340, (2009)
  62. Kudla U, Milac AL, Qin L, Overmars H, Roze E, Holterman M, Petrescu AJ, Goverse A, Bakker J, Helder J, Smant GKudla U et al . "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)
  63. Milac AL, Buchete NV, Fritz TA, Hummer G, Tabak LAMilac AL et al . "Substrate-induced conformational changes and dynamics of UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferase-2", Journal of molecular biology 373(2): 439-51, (2007)
  64. Milac AL, Avram S, Petrescu AJMilac AL et al . "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)
    AI: 0.90
  65. Avram S, Milac AL, Flonta M-LAvram S et al . "Computer-Aided Drug Design for Typical and Atypical Antipsychotic Drugs", Curr.Comp.Aid.Drug.Des 4(1): 347-364, (2005)
  66. Jaubert S, Milac AL, Petrescu AJ, de Almeida-Engler J, Abad P, Rosso MNJaubert S et al . "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)
  67. Costin GE, Valencia JC, Wakamatsu K, Ito S, Solano F, Milac AL, Vieira WD, Yamaguchi Y, Rouzaud F, Petrescu AJ, Lamoreux ML, Hearing VJCostin GE et al . "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)
  68. Kudla U, Qin L, Milac A, Kielak A, Maissen C, Overmars H, Popeijus H, Roze E, Petrescu A, Smant G, Bakker J, Helder JKudla U et al . "Origin, distribution and 3D-modeling of Gr-EXPB1, an expansin from the potato cyst nematode Globodera rostochiensis", FEBS letters 579(11): 2451-7, (2005)
  69. Petrescu A-J, Milac AL, Petrescu SM, Dwek RA, Wormald MRPetrescu A-J et al . "Statistical analysis of the protein core around N-glycosylation sites. Implications on occupancy, folding and function", Glycobiology 14: 103-114, (2004)
  70. Petrescu AJ, Milac AL, Petrescu SM, Dwek RA, Wormald MRPetrescu AJ et al . "Statistical analysis of the protein environment of N-glycosylation sites: implications for occupancy, structure, and folding", Glycobiology 14(2): 103-14, (2004)
  71. Petrescu SM, Popescu CI, Petrescu A-J, Dwek RAPetrescu SM et al . "The glycosylation of tyrosinase in melanoma cells and the effect on antigen presentation", Adv. Exp. Med. Biol 535: 257-269, (2003)
  72. Hinsen K, Petrescu A-J, Dellerue S, Belissent-Funel MC, Kneller GRHinsen K et al . "Liquid-like and solid-like motions in proteins", J.Mol. Liquids 98-99: 381-398, (2002)
  73. Wormald MR, Petrescu AJ, Pao YL, Glithero A, Elliott T, Dwek RAWormald MR et al . "Conformational studies of oligosaccharides and glycopeptides: complementarity of NMR, X-ray crystallography, and molecular modelling", Chemical reviews 102(2): 371-86, (2002)
  74. Dellerue S, Petrescu AJ, Smith JC, Bellissent-Funel MCDellerue S et al . "Radially softening diffusive motions in a globular protein", Biophysical journal 81(3): 1666-76, (2001)
  75. Dellerue S, Petrescu A-J, Smith JC, Longeville S, Bellissent-Funel M-CDellerue S et al . "Collective Dynamics of a Photosyntethic Protein Probed by Neutron Spin-Echo Spectroscopy and Molecular Dynamics Simulation", Physica B. 276-278: 514-515, (2000)
  76. Hinsen K, Petrescu A-J, Delerue S, Bellissent-Funel M-C, Kueller GRHinsen K et al . "Harmonicity in slow protein dynamics", Chem.Phys.(261): 25-37, (2000)
  77. Branza-Nichita N, Petrescu AJ, Negroiu G, Dwek RA, Petrescu SMBranza-Nichita N et al . "N-glycosylation processing and glycoprotein folding-lessons from the tyrosinase-related proteins", Chemical reviews 100(12): 4697-712, (2000)
  78. Petrescu AJ, Calmettes P, Durand D, Receveur V, Smith JCPetrescu AJ et al . "Change in backbone torsion angle distribution on protein folding", Protein science : a publication of the Protein Society 9(6): 1129-36, (2000)
  79. Petrescu SM, Branza-Nichita N, Negroiu G, Petrescu AJ, Dwek RAPetrescu SM et al . "Tyrosinase and glycoprotein folding: roles of chaperones that recognize glycans", Biochemistry 39(18): 5229-37, (2000)
  80. Branza-Nichita N, Negroiu G, Petrescu AJ, Garman EF, Platt FM, Wormald MR, Dwek RA, Petrescu SMBranza-Nichita N et al . "Mutations at critical N-glycosylation sites reduce tyrosinase activity by altering folding and quality control", The Journal of biological chemistry 275(11): 8169-75, (2000)
  81. Dellerues S, Petrescu A-J, Smith JC, Longenille S, Bellisent-Funnel MCDellerues S et al . "Collective dynamics of a photosintetic protein probed by NES spectroscopy and MD simulation", Physica B 276-278: 514-515, (1999)
  82. Nichita-Branza N, Petrescu A-J, Dwek RA, Wormald M, Platt F, Petrescu S-MNichita-Branza N et al . "Tyrosinase folding and copper loading in vivo: a crucial role for calnexin and a-glucosidase II", Biochem. Biophys. Res. Commun.(261): 720-725, (1999)
  83. Negroiu G, Branza-Nichita N, Costin GE, Titu H, Petrescu AJ, Dwek RA, Petrescu SMNegroiu G et al . "Investigation of the intracellular transport of tyrosinase and tyrosinase related protein (TRP)-1. The effect of endoplasmic reticulum (ER)-glucosidases inhibition", Cellular and molecular biology (Noisy-le-Grand, France) 45(7): 1001-10, (1999)
  84. Negroiu G, Branza-Nichita N, Petrescu AJ, Dwek RA, Petrescu SMNegroiu G et al . "Protein specific N-glycosylation of tyrosinase and tyrosinase-related protein-1 in B16 mouse melanoma cells", The Biochemical journal 344 Pt 3: 659-65, (1999)
  85. Petrescu AJ, Petrescu SM, Dwek RA, Wormald MRPetrescu AJ et al . "A statistical analysis of N- and O-glycan linkage conformations from crystallographic data", Glycobiology 9(4): 343-52, (1999)
  86. Petrescu AJ, Butters TD, Reinkensmeier G, Petrescu S, Platt FM, Dwek RA, Wormald MRPetrescu AJ et al . "The solution NMR structure of glucosylated N-glycans involved in the early stages of glycoprotein biosynthesis and folding", The EMBO journal 16(14): 4302-10, (1997)
  87. Petrescu SM, Petrescu AJ, Titu HN, Dwek RA, Platt FMPetrescu SM et al . "Inhibition of N-glycan processing in B16 melanoma cells results in inactivation of tyrosinase but does not prevent its transport to the melanosome", The Journal of biological chemistry 272(25): 15796-803, (1997)
  88. Albulescu R, Petrescu AJ, Sârbu M, Grigore A, Ica R, Munteanu CVA, Albulescu A, Militaru IV, Zamfir AD, Petrescu SM, Tănase CAlbulescu R et al . "Mass Spectrometry for Cancer Biomarkers", pp 477, Proteomics Technologies and Applications, InTechOpen, (2019).
    ISBN: 978-1-78984-611-9
  89. Surleac MD, Spiridon LN, TacutuR, Milac AL, Petrescu SM, Petrescu AJSurleac MD et al . "Structural Assessment of Glycosylation Sites Database - SAGS – An Overall View on N-Glycosylation", pp 3-20, Glycosilation, InTech, (2012).
    ISBN: 978-953-51-0771-2
  90. Petrescu SM, Petrescu A-J, Platt FM, Dwek RAPetrescu SM et al . pp 41-42, Glycosylation and Glycoprotein Folding, Wellcome Trust Reviews, (2000).
    ISBN: 184129019X
Structure Assisted Investigation of Critical Protein Families Involved in Plant Immunity 2017-2019
Acronym: STRASSIST
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.

ERRIS

 

Databases:

1. SAGS DB - Structural Assesment of Glycosylation Site Database

2. NLRscape - an Atlas of plant NOD like receptors

 

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