NODES - MEMBERS

AUSTRALIA

Bostjan Kobe

School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia

INPEC node since 2012

The group’s research theme is protein structure and function, with the emphasis on understanding the structural basis of intra- and intermolecular interactions formed by these macromolecules and inferring function from structure. The biological focus is on proteins involved in infection and immunity. The goal of the research is to use structural and molecular information to understand the molecular and cellular functions of proteins, validate proteins as therapeutic targets or biotechnological products, and to design new therapeutics and biotechnological applications. The primary techniques used in the laboratory are X-ray crystallography and electron microscopy, combined with a plethora of other molecular biology, biophysical, structural and computational techniques.

Keywords: epigenetics, chromatin, nucleosome, X-ray crystallography, histone modifying enzymes

Colin Jackson

AUSTRIA

Andreas Kungl

Karl-Franzens-University Graz, Institute of Pharmaceutical Sciences, Graz, Austria

INPEC node since 2002

Our research group is mainly interested in studying the interaction of complex (proteo)glycans with proteins such as chemokines, and to turn resulting insights into novel therapies. Our current indication area is immune-oncology with a focus on metastatic lung cancer.

Keywords: protein engineering, proteomics, biophysics, glycobiology, fluorescence spectroscopy, extracellular matrix, drug development

BELGIUM

Peter Tompa

BRAZIL

Richard Charles Garrat

CANADA

Jean-Francois Couture

Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada

INPEC node since 2014

Keywords: epigenetics, chromatin, nucleosome, X-ray crystallography, histone modifying enzymes

Martin Schmeing

Department of Biochemistry, McGill University, Montreal, QC, Canada

INPEC node since 2010

The general goal of the lab is to understand how some of the large enzymes in the cell act to perform their important functions.  To do this, we combine X-ray crystallography, electron microscopy, biochemical techniques and chemical biology. The main current focus of the lab is the study of nonribosomal peptide synthetases (NRPSs), large macromolecular machines that, like the ribosome, catalyze peptide bond formation. Instead of making proteins, these enzymes produce a large variety of small molecules with important and diverse biological activity. For example, NRPSs synthesize anti-fungals, anti-bacterials, anti-virals, anti-tumourigenics, siderophores, and immunosuppressants, including classic therapeutics such as penicillin and cyclosporin, and modern billion-dollar antibiotics like daptomycin.

Keywords: megaenzyme, NRPS, natural products, X-ray crystallography, electron microscopy, ribosome

DENMARK

Allan Svendsen

Protein Engineering, Novozymes A/S, Bagsvaerd, Denmark

 

INPEC node since 1991

 

Detailed understanding enzyme function and its relation to use application of daily life. Focuses on Lipase protein engineering and functional understanding as well as other application useful enzymes. Also high focus on protease protein engineering with special interest in S8 and S1 members. High focus also on Carbohydrate degrading enzymes from various GH families and especial a lot of work on GH13 amylase protein engineering. Including focus on multidomain enzymes engineering.  Protein engineering strategies and methods. Focus on assays for analysis of mutant enzymes. Biophysical characterization of mutant enzymes, stability, aggregation, surface interactions. Simulation and analysis of substrate and enzyme interactions. Interest in the biophysical implications on enzyme surroundings and effect on catalysis and binding.

Keywords: protein engineering enzymes, enzyme structure and function, atomic and coarse grain simulation. enzyme substrate structure. enzyme on surfaces. protein engineering methods. screening assays

Frans Mulder

University of Aarhus, Department of Chemistry and interdisciplinary nanoscience center iNANO, Aarhus, Denmark

 

INPEC node since 2005

 

Our lab focuses on quantitatively understanding biochemical and biological systems and processes, using the solid fundament of physical chemistry. Our main focus is proteins. We actively contribute new methodologies, such as novel NMR experiments to study protein dynamics, stability and electrostatics. We develop bioinformatics tools for protein disorder prediction as well as experimental and computational approaches for the study of intrisically disordered proteins.

Keywords: structural biology, NMR spectroscopy, protein dynamics, thermodynamics, protein biophysics, protein electrostatics, protein engineering, intrinsically disordered proteins, protein aggregation and disease, bioinformatics, metabolomics, in cell and in vivo NMR spectroscopy

Daniel Otzen

FINLAND

Adrian Goldman

University of Helsinki, Faculty of Biological and Environmental Sciences, Helskini, Finland

INPEC node since 2002

Our research focuses on understanding events at various membrane surfaces for two reasons. First, this is the most unexplored area in structural biology: less than 1% of all high-resolution protein structures are of membrane proteins. Second, despite this fact, more than 50% of all drugs interact with membrane proteins, meaning that understanding their mechanism and function is of critical importance in drug development.  In our of current research projects, we are exploring the mechanism and function of integral membrane pyrophosphatases, which occur in bacteria, archae, plants, protozoan parasites – but not in multicellular animals.  This makes them viable drug targets.  We have shown that the mechanism is “binding change”, with pumping preceding pyrophosphate hydrolysis, and have begun to develop novel pyrophosphatase inhibitors.

 

Keywords: structural biology, membrane proteins, pyrosphatases, protein engineering, protein design, receptor tyrosine kinases

Rik Wierenga

FBMM, University of Oulu, Oulu, Finland

INPEC node since 2003

Enzymes have the unique property of converting a bound molecule, the reactant, into another molecule, the product. The (very) high energy barrier between reactant and product somehow (almost) disappears once the reactant is bound in the active site pocket of the enzyme. Understanding of this phenomenon, known as biocatalysis, is one of the main aims of much current enzyme research, pointing to the importance of the electrostatic properties as well as the dynamics of the active site. We study in particular CoA-dependent, thioester dependent lipid metabolising enzymes as well as collagen prolyl 4-hydroxylases. Our protein crystallographic studies provide the three dimensional structure of the active sites of these enzymes, how the atoms are arranged, how the ligands are bound, as well as, to some extent, the dynamic properties of the active site residues. Detailed analysis of these structures, including bioinformatics and biocomputing approaches, is an essential component of our structural studies. In addition we complement our structural studies with biophysical characterization, enzyme kinetic experiments and organic chemistry.

Keywords: structural enzymology, protein crystallography, enzyme engineering, transition state analogues, thioester chemistry

Lari Lehtiö

FBMM, University of Oulu, Oulu, Finland

INPEC node since 2017

Our focus is structural biology of ADP-ribosylation and our research expands from structure and function studies of the enzymes involved to development of small molecule inhibitors to be used as drugs and as chemical tools in research. ADP-ribosylation is a post-translational protein modification controlling various enzyme activities and protein-protein as well as protein-nucleic acid interactions. Humans have a range enzymes carrying out this modification belonging to PARP/ARTD and to ecto-ART/ARTC families, but also some Sirtuins are able to catalyze ADP-ribosylation. We study how the ADP-ribosyltransferases enzymes function at the molecular level and how the modification is recognized by protein domains and removed through enzymatic hydrolysis. Our main methods are activity assays, biophysical characterization and binding studies, and structural studies where our main tool is protein crystallography. 

Keywords: ADP-ribosylation, protein crystallography, drug discovery

FRANCE

Thomas Haertle

GERMANY

Reinhard Sterner

University of Regensburg, Institute of Biophysics and physical Biochemistry, D-93040 Regensburg, Germany

 

INPEC node since 2004

 

In the focus of our research are the evolution and the design of enzymes, which are elaborate proteins that catalyze cellular reactions with high specificity and efficiency.  We are using rational design and directed evolution to engineer the stability and catalytic activity of enzymes, experimentally reconstruct the natural evolution of enzymes, assign functions to uncharacterized enzymes, and analyze allosteric interactions within multi-enzyme complexes. To this end, we apply a broad range of experimental and computational methods.

Keywords: enzyme evolution, enzyme design, functional annotation, multi-enzyme complex, allostery, ancestral sequence reconstruction, protein stability, rational design, directed evolution

GREECE

Michael Kokkinidis

INDIA

Pinak Chakrabarti

Bose Institute, Department of Biochemistry, Kolkata, India

INPEC node since 2007

Understanding the structure and folding of proteins and their interactions with other molecules, large and small, and nanoparticles using biophysical techniques (especially, X-ray crystallography), modelling and database analysis. Some specific topics are:

  • Identification of stabilizing interactions (like CH-p, CH-O, electrophile-nucleophile, aromatic-aromatic etc.) and their implications in protein structures and function

  • Analysis of protein conformation and identification of structural motifs

  • Protein folding, threading and prediction of structures

  • Molecular modelling and dynamics to understand protein function

  • Molecular recognition, protein-protein/DNA complexation and ion-binding by proteins

  • Biophysical studies on proteins from phage lambda and Vibrio cholerae

  • Design of peptides with specific structure

  • Structural bioinformatics and development of algorithms

  • Vibrio cholerae proteomics

  • Interaction of nanoparticles with proteins and their antibacterial effect.

 

Keywords: structural bioinformatics, Vibrio cholerae proteomics, X-ray crystallography, weak interactions in proteins, identification of structural motifs, protein-protein interaction, protein-nanoparticle interaction, molecular dynamics, ligand binding

P Karthe

S Krishnaswamy

ISRAEL

Gideon Schreiber

Department of Biomolecular Sciences, Weizmann Institute, Rehovot, Israel

INPEC node since 2002

Specific protein-protein interactions form a major part of the basic organization of living cells. The structure of a protein complex holds information about the relative mutual organization of two proteins in a frozen state, but not about the kinetic or thermodynamic parameters that are central to their function. For many years I have been interested in understanding the relationships between the structures of transient protein-protein interactions and their binding activity. To address this, I adopted a multidisciplinary approach including: wet biophysical bench work, protein-design and engineering and bioinformatics and applied the gained knowledge and techniques to address biological questions.

Keywords: protein-protein interaction, Interferon, Signaling, proteins, protein-engineering, structure/function

Joel Sussman

ITALY

Doriano Lamba

Consiglio Nazionale delle Ricerche – Istituto di Cristallografia, Bari, Italy

INPEC node since 2009

Our laboratory is interested in: i) the development of innovative and effective multi-target directed drugs for Alzheimer’s Disease; ii) understanding the structural basis of neuropathic chronic pain. Our specific goals are: i) Structure-activity relationships studies of acetylcholinesterase-inhibitors complexes; ii) Structural and functional studies of neutralizing antibodies (TrkA-receptor and Nerve Growth Factor); iii) Structural and functional studies of pro-neurotrophins/neurothrophins; iv) Development of painless Nerve Growth Factor mutants. Our methodological approach is based on ligand binding biophysical techniques and receptor-ligand binding assays to understand function, in combination with structural methods such as X-ray crystallography and solution Small Angle X-ray Scattering to understand structure. 

Keywords: structural and mechanistic neurobiology, structural and functional determinants of neurotrophin and pro-neurotrophin action, drug discovery for chronic pain

JAPAN

Ichio Shimada

Division of Physical Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan

INPEC node since 2008

The followings are our research interest:

1. Elucidation of the functional dynamics of membrane proteins

2. Analyses of protein-protein interactions involving intracellular signaling

3. Development of new NMR methods for analyzing the structure and dynamics of high molecular weight proteins

4. Real-time observation of the intracellular biological events using the in-cell NMR method

Keywords: structural biology, NMR, membrane protein, GPCR, ion channel, interaction, dynamics

KOREA

Hak-Sung Kim

Korea Advanced Institute of Science and Technology (KAIST), Biological Sciences, Seoul, Korea

INPEC node since 2006

Our lab is interested in creating a protein binder with high specificity and affinity for a target for therapeutic and biotechnological applications. We recently developed a new protein scaffold termed “repebody” which is composed of LRR (Leucine-rich repeat) modules, and are currently designing target-specific repebodies for various purposes. In addition, we are focusing on engineering the enzymes for practical applications by combining directed evolution, rational design and computational methods. With the idea that a number of drug targets exist inside the cells, we are developing a cytosolic protein delivery system based on bacterial toxins and zinc-finger proteins.

 

Keywords: therapeutic protein, protein and enzyme engineering, rational design, computational design, protein delivery

Seung-Goo Lee

NETHERLANDS

Dick Janssen

NORWAY

Vincent Eijsink

RUSSIA

Vladimir I. Tishkov

Vytas Svedas

SINGAPORE

Song Jianxing

SPAIN

Alberto Marina

Javier Sancho

Institute of Biocomputation and Physics of Complex Sustems, University of Zaragoza, Zaragoza, Spain

INPEC node since 2017

We study protein stability using all kind of wet and computational approaches. We try to understand the physics involved and to develop quantitative tools for the rational design of protein stability. We practise target-oriented drug discovery combining high through put screening of chemical libraries, structural determination of ligand-target complexes, medicinal chemistry and computational tools to increase complex affinity. We are working of the prediction of phenotypes for proteins carrying single-nucleotide variations. 

 

Keywords:protein stability and stabilization, target-based drug discovery, structural biology, biocomputation, genetic interpretation

SWEDEN

Bengt Mannervik

Per-Olof Syren

SWITZERLAND

Andreas Plückthun

Department of Biochemistry, University of Zurich, Zurich, Switzerland

INPEC node since 1996

We study the creation of new proteins and protein variants. The purpose of this work is to use such engineered proteins to enable research and applications which have been very difficult or even impossible so far. Examples of our endeavors are the creation of new engineered binding proteins to inhibit other proteins or to kill tumor cells, or the stabilization of proteins so that they can be studied structurally and biophysically. Our main areas of interest are novel scaffolds for selective binding (e.g. the DARPin technology we have developed), synthetic antibodies and G-protein-coupled receptors evolved to high stability and expression levels. Because of the complexity of these tasks, this research requires a highly interdisciplinary approach, combining detailed biophysical studies, computer modeling and advanced molecular biology, especially directed evolution. Many projects have close collaboration with crystallography, NMR or computational biology. Some projects also bridge protein engineering with applications, in cell biology or, in the case of tumor targeting testing in animal models.

 

Keywords: antibody engineering, scaffold engineering, repeat proteins, directed evolution and display technologies, GPCRs, structural biology, protein design

TAIWAN

Shang-Te Danny Hsu

Academia Sinica, Institute of Biological Chemistry, Taipei, Taiwan

INPEC node since 2017

Our research interests are primarily focused on the investigation of the structures and properties of biological molecules, especially proteins and quadruplex-forming G-rich oligonucleotides, in the context of folding dynamics and their relationship to biological evolution and disease. We are working on the folding and misfolding of knotted proteins, in particular, human ubiquitin C-terminal hydrolases (UCHs), which have one of the most complex protein knots identified to date. A variety of biophysical, biochemical and computational approaches are employed to help understand how disease-associated mutations and post-translational modifications of various proteins affect their folding properties, thereby causing disorders.

 

Keywords: structural biology, protein folding, NMR spectroscopy, hydrogen-deuterium exchange, ubiquitin C-terminal hydrolase, topologically knotted proteins

Andrew Wang

UNITED KINGDOM

Dafydd Jones

Molecular Bioscience Division, School of Biosciences, Cardiff University, Cardiff, UK

INPEC node since 2015

The Jones group focus on understanding the molecular basis of protein plasticity in terms of structure, function and folding, and its application to the construction of new protein components and systems. The ultimate aim is to address one of the fundamental questions in biology: how amino acid sequence encodes the information for a protein to fold to its functional 3D structure. Our group collaborates chemists, structural biologists, computer modellers and physicists. Constructing new protein components means our work is closely aligned with the areas of synthetic biology and nanoscience/nanotechnology. Much of the group's work has a basis in synthetic biology whereby we construct new protein components or modify existing proteins for new applications, including single molecule electron and charge transfer, new routes to protein post-translationals modification and interfacing with non-biological materials. Both rational protein engineering and directed evolution are used to create new proteins and structural biology, single molecule analysis, molecular dynamics, biophysics and biochemistry are used to investigate the properties of these novel proteins. 

 

Keywords: Protein engineering, protein design, structural biology, synthetic biology, expanded genetic code, directed evolution, nanoscience

ALUMNI
 

Australia: Nick Hoogenraaad, Peter Hudson

Canada: Mirek Cygler, Tony Warren

Denmark: Prof. Flemming M. Poulsen

France: Andre Menez

Germany:  Dietmar Schomburg

Italy: Alberto Di Donato

Japan: Kosuke Morikawa

The Netherlands:  Bauke W. Dijkstra

Portugal: Belarmino A Salvado Barata

Russia: Vadim V. Mesyanzhinov

Spain: Carlos Gomez-Moreno

Sweden: Tuula T. Teeri

United Kingdom: Alan Fersht, Greg Winter

USA: Phil Bryan, Edward Eisenstein