Reuter group

Molecular Modeling of Proteins

To investigate the dynamical properties of proteins, we use a range of different molecular modeling tools such as molecular dynamics and normal modes analysis. Structure prediction methods and hybrid QM/MM methods and are also important tools in our research.

Currently, we are mostly interested in two projects:

• Proteinase 3: a serine proteases of the neutrophils with original properties
• Slow dynamics of transmembrane proteins

Serine proteases of the neutrophils

Inflammation is the first response of the immune system to infection or irritation and is characterized by pain, warmth, redness, swelling. Neutrophils are the most abundant type of leukocytes, and are an integral part of the immune system. During the acute phase of inflammation, they leave the vasculature and migrate toward the site of inflammation. Proteinase 3 (PR3), human neutrophil elastase (HNE) and cathepsin G are highly homologous serine proteases of the polymorphonuclear neutrophils (PMN). They are deleterious mediators involved in proteolytic degradation of connective tissues and are associated with several inflammatory diseases such as emphysema, cystic fibrosis, rheumatoid arthritis and vasculitis.
Although these proteases have been for a long time thought to have similar localization, ligand specificity and function they might have very different physiologic roles. Specifically, PR3 behaves as a peripheral membrane protein 4 and its membrane expression is a risk factor in chronic inflammatory diseases. In addition, PR3 has intracellular specific protein substrates resulting in the involvement of PR3 in regulation of intracellular functions such as proliferation or apoptosis. These activities were not observed for HNE. PR3 is thus a potential drug target in inflammatory diseases and leukemia.
We have, together with our collaborators, identified the cleavage site of P21waf1 by PR3. We subsequently described the network of interaction stabilizing complexes between PR3 and several peptidic ligand, this led us to design a consensus peptide specific for PR3 and inactive with HNE. With the goal of understanding the influence of a polymorphism on the function and catalytic activity of PR3, we have investigated the structure of intermediates along the catalytic reaction pathway. We thus have gained important new insight into the reaction mechanism, and have prepared the grounds for the rational design of drugs specific of PR3. Several points, however, remain to be investigated.

Slow dynamics of proteins

Large amplitude deformations of proteins are often decisive to function. In recent years, normal mode analysis (NMA) has become the method of choice to investigate the slowest motions in macromolecular systems. NMA is especially useful for large biomolecular assemblies, such as transmembrane channels or virus capsids.

Alpha-helical transmembrane (TM) proteins represent approximately 20-30% of all open reading-frames in the genome of complex organisms. They are involved in many biological processes such as sight, smell, muscle contraction, photosynthesis, etc. Their signalling function is most often achieved by movements of the helices constituting the transmembrane bundle; the movements can be of different nature, involving the whole bundle like in the case of the mechanosensitive channel or individual helices displacements such as those accomplished by the Ca-ATPase to transport calcium ions through the sarcoplasmic reticulum membrane.

Our group is developing web-based normal modes analysis (NMA) tools:

• webnma
  The server is meant to provide users with simple and automated computation and analysis of low-frequency normal modes for proteins: normalized squared atomic displacements, vector field representation, animation of the vibration associated to the first modes, deformation and domain analysis, dynamical domains, overlap between normal modes and a structure difference vector, animation of transconformations
• tmma
  TMM@ performs normal modes calculations on alpha-helical TM protein, and identifies the most mobile helices in terms of rotation, translation, and slide of the helices. It also investigates the tendency of the TM alpha helical bundle to undergo a twist motion around its own axis.

Selected publications:

• L. Skjaerven, S.M. Hollup, N. Reuter. (2008) Normal mode analysis for proteins. Theochem: Journal of Molecular Structure , in press
• E. Hajjar, M. Mihajlovic, V. Witko-Sarsat, T. Lazaridis, and N. Reuter (2008) Computational prediction of the binding of Proteinase3 to lipid bilayers. Proteins: Structure, Function and Bioinformatics 71(4): 1655-69
• E. Hajjar, B. Korkmaz and N. Reuter (2007) Differences in the substrate binding sites of murine and human Proteinase3 and Neutrophil Elastase FEBS Letters 581(29): 5685-5690
• L. Skjaerven, I. Jonassen and N. Reuter (2007) TMM@: a web application for the analysis of transmembrane helix mobility. BMC Bioinformatics 8:232
• Hajjar E, Korkmaz B, Gauthier F, Brandsdal BO, Witko-Sarsat V, Reuter N (2006) Inspection of the binding sites of proteinase3 for the design of a highly specific substrate. J. Med. Chem. 49(4):1248-1260
• Hollup S, Saelensminde G, Reuter N (2005) WEBnm@: a web application for normal mode analyses of proteins. BMC Bioinformatics, 6, art.52
• Dublet B, Ruello A, Pederzoli M, Hajjar E, Courbebaisse M, Canteloup S, Reuter N, Witko-Sarsat V (2005) Cleavage of p21/WAF1/CIP1 by proteinase 3 modulates differentiation of a monocytic cell line. J. Biol. Chem. 280 (34): 30242-30253
• Reuter N, Hinsen K, Lacapère JJ (2003) Transconformations of the SERCA1 CaATPase: A Normal Mode Study. Biophys. J. 85:2186-2197
• Reuter N, Lin H and Thiel W (2002) Green Fluorescent Proteins: Empirical force field for the neutral and deprotonated forms of the chromophore. Molecular dynamic simulations of the wild-type and S65T mutant. J. Phys. Chem. B. 106: 6310-6321
• Reuter N, Dejaegere A, Maigret B, Karplus M, (2000) Frontier bonds in QM/MM methods : A comparison of different approaches. J. Phys. Chem. A. 104:1720-1735