TO P R E T S A M
Biomolecular Sciences Unraveling structure and function of (membrane) proteins
UNIVERSITY OF GRONINGEN THE NETHERLANDS Founded in 1614
Top Master program Biomolecular Sciences
In search of academic excellence, students have always been on the move. Recently the importance of student mobility has been recognized by the European Ministers of Education. Exchange of students between different countries is seen as an essential element for social and human growth of Europe. To further this goal it was agreed that all over Europe undergraduate (bachelor) and graduate (master and Ph.D.) programs would be made compatible. The Faculty of Mathematics and Natural Sciences of the University of Groningen aims for a leading position in education and research by offering four master programs that are linked to top-research groups in the Faculty. For these so-called Top Master programs the brightest and most ambitious students from all over the world will be selected. After having received their master’s degree the students are expected to enroll in the ensuing Ph.D. program. TOP MASTER PROGRAM BIOMOLECULAR SCIENCES This masters program is supervised by the Groningen Biomolecular Sciences and Biotechnology Institute (GBB), a research and graduate school of the Faculty of Mathematics and Natural Sciences that coordinates biomolecular and biotechnological research within the University of Groningen. The GBB forges together over 200 researchers and it is unique in that it unites multidisciplinary research in the areas of molecular biology, genetics, biochemistry and biophysical chemistry in order to understand the structure and function of proteins related to the functioning of a living cell in its environment. If this field of research is interesting to you, you should apply for admission to the Top Master program in biomolecular sciences at the RuG.
DESCRIPTION OF THE PROGRAM The two years multidiscipinary study program focuses on Biomolecular Sciences with a strong emphasis on performing research. The first year is mainly spent on in-depth theoretical courses with a focus on the structure and function of the biomembrane and membrane proteins, covering the essential elements from molecular biology, genetics, biophysical chemistry, and biochemistry. Roughly half of these courses consist of compulsory modules, dealing with basic topics such as: biogenesis of the bacterial cell envelope, signal transduction, genomics and proteomics of (membrane) proteins, biophysical analysis of bio-membranes and proteins, advanced protein crystallography and protein engineering. The other courses may be chosen from a list of advanced and often highly specialised topics. Practical training obtained in the second year during two research projects forms the major part of the study. The study concludes with the writing of a research proposal, which is intended to help you to continue your career in biomolecular research. All courses are provided in English, but we encourage foreign students to learn some Dutch. In some respects the program is tailor-made. Depending on your research interests or future career prospects you can design your own program and choice of topics for the preparation of a colloquium and an essay in the field of biomolecular sciences. You will have a personal mentor to guide you during your training and help you with career planning. FIELDS OF RESEARCH AT GBB GBB aims to perform multidisciplinary research of the highest standard in the field of biomolecular science, with a focus on proteins. We aim to contribute to our understanding of the structure, activity, and dynamic behavior of proteins in relation to their function in the cell, and to obtain insight in the fundamental properties of proteins that are relevant for applications in biotechnology and medicine. GBB’s main research topics are outlined below:
Structural biology and protein structure-function exploration This research focuses on the structure determination of proteins at atomic resolution using X-ray crystallographic methods. Proteins under investigation are enzymes (involved in carbohydrate metabolism and biotransformation of synthetic compounds) and membrane proteins, aiming at detailed analysis of active sites and reaction mechanisms. Larger protein complexes are studied at high resolution using single particle electron microscopy. Here, sophisticated classification programs are applied to sort out projections, while their frequencies are correlated to proteins identified by mass spectroscopic methods. Molecular dynamics aims at the development of tools (simulation software, atomic force fields, theoretical models) that can be used to understand and predict the physico-chemical interactions and dynamic processes within or between proteins, nucleic acids, and lipids. In particular, interest is on protein folding, protein-protein interactions, and enzyme-substrate interactions. Mechanisms and structures of membrane proteins Research in the field of membrane protein biochemistry is mainly focused on bacterial transporters in order to elucidate the molecular mechanisms of transmembrane protein export and solute transport. Examples are I) multi-drug resistance proteins involved in antibiotic- and cytostatic drug-resistance, II) proteins of the Sec system involved in secretion, and III) ABC-transporters and mechanosensitive channels involved in osmoregulation. Emphasis is on the energetics and mechanisms of the translocation process, the mechanisms of membrane protein insertion and assembly, and the structural analysis of the proteins involved. Proteomics tools are increasingly used to study concerted regulation and functional interactions. Genomics and proteomics In-house DNA-microarray facilities are used for transcriptome analysis as part of the functional genomics studies of Gram-positive bacteria (e.g. Bacillus, Lactococcus), especially to explore and visualize complex regulatory gene networks. This research aims at obtaining a more comprehensive understanding of the specific role of all proteins involved in complex processes
such as secretion, peptide metabolism, sporulation, and competence development. Another topic is the investigation, using high-throughput approaches, of the physiological function and bio-technological potential of gene clusters encoding putative carbohydrate-converting enzymes in bacteria and fungi. A structural genomics program aims to determine all protein structures of the Shigella host invasion vector. Microbial biotechnology and biocatalysis Research in this area focuses on three topics. One is the production and derivatization of peptide antibiotics by studying the role of microbodies in production, the transport of β-lactams across cell- and organelle membranes, the structure of key proteins in the fermentative and biocatalytic production of β-lactams, and the enzymology and engineering of biocatalysts for the production of semi-synthetic β-lactams. In another topic, the focus is on the development of starch- and sucroseacting enzymes (CGTase family) and their products using highthroughput screening to select for enzyme activities, and on the structure determination of these enzymes to obtain mechanistic insights. Furthermore, biocatalysts for converting synthetic compounds (epoxides, halogen compounds) are studied, emphasizing on haloalkane- and haloalcohol-dehalogenases and epoxide hydrolases, and their use in enantioselective production of fine chemicals. Signal transduction in complex cellular processes The mechanism of action of growth factors, cytokines and hormones are studied in relation to growth, differentiation and development in higher organisms. This research is mainly focused on the role and mechanisms of transforming growth factor-_ superfamily and interleukin-6 in relation to human diseases. In the microorganism Dictyostelium, the process of how extracellular cAMP is transduced to further signals and cellular responses is investigated. Here, emphasis is on the action of the involved enzymes guanylyl cyclase and phosphodiesterase. The regulation of programmed cell death in various developmental processes and stress responses are studied in Arabidopsis and tomato, aiming at applicable results for plant biotechnology with respect to stress tolerance, durable disease resistance, and improved crop characteristics (productivity, shelf life).
Gene- and protein networks involved in assembly and import of peroxisomal matrix and membrane proteins are studied in yeasts to understand peroxisome biogenesis and homeostasis. In all, molecular biological, in vivo fluorescence methodologies (using confocal microscopical approaches), ultrastructural analysis and functional genomics approaches are combined. DURATION OF THE PROGRAM 24 months CAREER PROSPECTS TopMaster students who graduate at GBB will have developed all-round research skills, making them well-qualified candidates to develop a scientific career by performing a Ph.D. study in biomolecular research. They have also a great potential to make careers in major life science companies over the world, including the companies which collaborate with GBB such as DSM, Akzo Nobel, Unilever, and FCDF. Job possibilities are also expanding in the region of Groningen, where new life sciences industries and SME’s with a demand for well-trained staff develop. ADMISSION REQUIREMENTS Final admission is by selection on an individual basis by the Board of Examinations of GBB, following interviews with preselected top-level candidates. A Bachelor’s degree in the area of biochemistry, biophysical chemistry, molecular biology or molecular genetics and sufficient proficiency in English (e.g. TOEFL score of 550–600) are required. DEADLINE FOR APPLICATIONS The deadline for application is 1 February. For more information about applying: Graduate School Office Faculty of Mathematics and Natural Sciences Mrs. E.T van Dijken Nijenborgh 4, 9747 AG Groningen The Netherlands Phone: +31 50 363 4615/ 4619 Fax: +31 50 363 4500 E-mail: e.t.van.dijken@rug.nl
For information about the curriculum and GBB, contact: E.G. Vrieling E-mail: e.g.vrieling@rug.nl www.rugtopmasters.nl (for application and general information) www.rug.nl/gbb