Institut de Biologie StructuraleGrenoble / France


Deciphering the Dynamic Interaction Profile of an Intrinsically Disordered Protein by NMR Exchange Spectroscopy

Intrinsically Disordered Proteins (IPDs) are functionally active despite lacking a well-defined three-dimensional structure. Their great flexibility allows them to easily adapt to the surface of their partners and they are able to fold during interaction. In some cases, they may even form a so-called fuzzy complex, in which the IPD does not adopt a single conformation defined on the partner’s surface, but continues to sample multiple conformations in a highly dynamic complex.
The FDP group of the IBS, in collaboration with researchers from IAB Grenoble and the ENS Paris, succeeded in obtaining an atomic resolution description of the dynamics of an IDP in complex with its partner using nuclear magnetic resonance spectroscopy. Researchers applied this approach to the dynamic signaling complex formed between the mitogen-activated protein kinase (MAPK) p38α and the intrinsically disordered regulatory domain of the MAPK kinase MKK4.. The study shows that MKK4 uses a combination of interaction modes to link to p38α, leading to a complex displaying significantly different dynamics between linked regions. The results show how IPDs can engage in very specific interactions without having a strong binding affinity.

Deciphering the Dynamic Interaction Profile of an Intrinsically Disordered Protein by NMR Exchange Spectroscopy. Delaforge E, Kragelj J, Tengo L, Palencia A, Milles S, Bouvignies G, Salvi N, Blackledge M, Jensen MR. Journal of the American Chemical Society;140(3):1148-1158

Capture of a «phantom » state of green fluorescent proteins

Green fluorescent proteins (GFPs) are genetically encoded markers allowing the localization of down to individual proteins by optical microscopy. Their fluorophore is formed from three amino acids and is located at the center of a beta barrel that protects it from the environment. GFPs have high absorption coefficient and fluorescence yield, but only moderate photostability. They can reversibly form temporary nonfluorescent “dark” states before definitely losing fluorescence after about 100000 excitation/emission cycles.
At the IBS, the Pixel team has previously solved the structures of some of such dark states. All of them showed considerable chemical modifications which raised the question as to their irreversibility. Therefore, it was suspected that a reversible gateway state should exist the knowledge of which would allow to improve the GFP’s behavior. But little was known on this putative « phantom » state: its chemical character (triplet, radical, biradical ?), its yield (percents, permills ?), its lifetime (nano-, micro-, millisecondes ?), its reactivity (oxidative, reductive, both ?), its absorption spectrum (UV, VIS, IR ?).
Thanks to a collaboration with the team of Klaus BRETTEL at I2BC (CEA Saclay), the Pixel team of the DYNAMOP group at the IBS exposed the paradigmatic fluorescent protein EGFP to a study by transient absorption spectroscopy. This technique has previously been applied to fluorescent proteins very little. Pushing it to its resolution limits allowed the detection of the spectral signature of the « phantom » dark state and its characterization by answering all of the above questions. These findings open the way for a better understanding of the photophysical functioning of fluorescent proteins and fuel the hope for finding keys to their further optimization.

A Long-Lived Triplet State Is the Entrance Gateway to Oxidative Photochemistry in Green Fluorescent Proteins. Byrdin M, Duan C, Bourgeois D, Brettel K. Journal of the American Chemical Society;. doi: 10.1021/jacs.7b12755

How bacteria converse in floating biofilms

Biofilms are bacterial communities with high antibiotic resistance. Within biofilms, bacteria exchange information chemically - a mechanism called quorum-sensing. Researchers at the Institute de Biologie Structurale in Grenoble, the University of the Mediterranean in Marseille and the Jacobs University in Bremen have shown that the gram-negative pathogen Providencia stuartii forms floating communities within which adjacent cells are in apparent contact,before depositing as canonical surface-attached biofilms. Because porins are the most abundant proteins in the outer membrane of gram-negative bacteria, they hypothesized that they could be involved in cell-to-cell contact and undertook a structure-function relationship study on the two porins of P. stuartii, Omp-Pst1 and Omp-Pst2. The crystal structures reveal that these porins can selfassociate through their extracellular loops, forming dimers of trimers (DOTs) that could enable cell-to-cell contact within floating communities. Support for this hypothesis was obtained by studying the porin-dependent aggregation of liposomes and model cells. The observation that facing channels are open in the two porin structures suggests that DOTs could not only promote cell-to-cell contact but also contribute to intercellular communication. Proteins involved in this interaction could be new targets in the fight against biofilms.

Porin self-association enables cell-to-cell contact in Providencia stuartii floating communities. El-Khatib M, Nasrallah C, Lopes J, Tran QT, Tetreau G, Basbous H, Fenel D, Gallet B, Lethier M, Bolla JM, Pagès JM, Vivaudou M, Weik M, Winterhalter M, Colletier JP. Proceedings of the National Academy of Sciences of the United States of America. 2018 Feb 23. pii: 201714582. doi: 10.1073/pnas.1714582115.