Beta version (currently under testing). If you would like to visit the old website, click here.

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, 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.

Andrei-José Petrescu, Dr.
Andrei-José Petrescu, Dr.

Head of Department

Andrei-José Petrescu is a researcher in the Institute of Biochemistry of the Romanian Academy. Andrei-José is currently working in Bioinformatics & Structural Biochemistry in the Bioinformatics & Structural Biochemistry.

Adina-Luminita Milac, Ph.D habil
Adina-Luminita Milac, Ph.D habil

Researcher III

Adina-Luminita Milac is a researcher in the Institute of Biochemistry of the Romanian Academy. Adina-Luminita is currently working in Bioinformatics & Structural Biochemistry in the Bioinformatics & Structural Biochemistry.

Cristian Munteanu, Dr.
Cristian Munteanu, Dr.

Research Scientist

ACADEMIC CAREER 2016 – present: Research Scientist (CS) at the Institute of Biochemistry of the Romanian Academy (IBRA) 2014 – 2016: Research Assistant at IBRA EDUCATION AND TRAINING 2011 – 2016: Ph.D. in Biology at 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.

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.

Petruta Alexandru, Dr.
Petruta Alexandru, Dr.

Research Scientist

Petruta Alexandru is a researcher in the Institute of Biochemistry of the Romanian Academy. Petruta is currently working in Molecular Cell Biology in the Molecular Cell Biology.

Year
Gerontomics: Multi-omics prediction system for prioritization of gerontological interventions 2016-2021
Acronym: Gerontomics
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 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.

Mass spectrometry based investigation of the oxidative stress as a potential key-player in the immunobiology of melanoma 02/05/2018 - 30/04/2020
Acronym: IMUNOPEP
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.

ERRIS

 

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