Elodie Laine July 3 rd 2012, JOBIM, Rennes BiMoDyM, Molecular - PowerPoint PPT Presentation

Elodie Laine July 3 rd 2012, JOBIM, Rennes BiMoDyM, Molecular Oncology and Pharmacology Team, Labex LERMIT LBPA, CNRS-ENS de Cachan

Biological context 518 protein kinases -2% of the proteome highly conserved through evolution highly oncogenic PKA ( 1ATP) most studied pharmaceutical targets : • ~ 10 approved inhibitors • > 50 in clinical trials Receptor Tyrosine Kinases (RTKs) 20 subfamilies Elodie Laine JOBIM – 03/07/2012 2/22

Biological context Receptor Tyrosine Kinases (RTKs) KIT receptor AMLs (10%) , Mastocytoses (44%) , GISTs (10%) GISTs (68%) Mastocytoses (>90%) , Germinal tumors (26%) ,  Biological processes: AMLs (9%) Proliferation, differenciation, survival …  Pathologies : Cancer, arthritis, Alzheimer’s disease Elodie Laine JOBIM – 03/07/2012 3/22

KIT inactive and active structures Juxta-membrane region (JMR) In (1T45) Ac (1PKG) Activation (A-) loop Mutation D816V : mastocytoses + resistance to Imatinib Elodie Laine JOBIM – 03/07/2012 4/22

Role of KIT D816V mutation 50-ns molecular dynamics simulations JMR WT A-loop MU D816V JMR A-loop local destabilisation (A-loop) + long-range re-organization (JMR) Elodie Laine JOBIM – 03/07/2012 5/22

Role of KIT D816V mutation X-ray structures In Ac facilitated JMR departure from PTK Leverage of JMR auto- inhibitory action is likely to Release of an trigger kinase activation access to catalytic and substrate binding sites Laine et al. 2011 PLOS Comput. Biol. Elodie Laine JOBIM – 03/07/2012 6/22

Short- and Long-range D816V effects ? How does the mutation of D816 into V induce a structural reorganization of a remote site distant by more than 15 Å ? Elodie Laine JOBIM – 03/07/2012 7/22

Interaction network & Atomic fluctuations 100 WT MU D816V Prevalence (%) Hydrogen Bonds 80 C-helix 60 40 JM-S 20 • JMR-PTK interaction network is altered Hydrophobic Contacts • A-loop and JMR C-helix P/A-loops atomic fluctuations are modified JM-S Elodie Laine JOBIM – 03/07/2012 8/22

Outline Biological Questions  Information transmission How do the mutation effects propagate between two distant sites of the protein ?  From characterizing to designing Can the dynamics of the protein, hence its function, be rationally modulated ? Allosteric coupling Global conformational change Local atomic fluctuations modification propagated through a pathway of well- propagated through multiple micro- defined interactions dynamic pathways Monod et al. 1965, J. Mol. Biol. Tsai et al. 2008, J. Mol. Biol. Koshland et al. 1966, Biochem. Schrank et al. 2009 , PNAS Elodie Laine JOBIM – 03/07/2012 9/22

Outline Biological Questions  Information transmission How do the mutation effects propagate between two distant sites of the protein ?  From characterizing to designing Can the dynamics of the protein, hence its function, be rationally modulated ? hemoglobin purR Allosteric coupling Global conformational change Local atomic fluctuations modification propagated through a pathway of well- propagated through multiple micro- defined interactions dynamic pathways Monod et al. 1965, J. Mol. Biol. Tsai et al. 2008, J. Mol. Biol. Koshland et al. 1966, Biochem. Schrank et al. 2009 , PNAS Elodie Laine JOBIM – 03/07/2012 9/22

Principle of the method MONETA Conformational Ensemble All-atom molecular dynamics simulations Modular Network Representation residues clusters {M} linked by chains of residues {c} M1 c 1 hub c 4 Dynamical c 2 c 5 Correlations c 3 c 6 c 7 + M2 Topology M3 c 8 Elodie Laine JOBIM – 03/07/2012 10/22

Communication pathways Communication pathways represent chains of residues that mechanically transmit information Communication pathways generation • Start from a chosen residue x i • Create as many paths as x i ’s neighbors What is a neighbor ? • Grow path if the new neighbors - not adjacent in the sequence communicate fast with all the members of range (i-1 ; i+1) forbidden the current path - connected by interaction(s) Occupancy factor > 50% - fast communication CP < mean val [i-4 ; i+4] Commute times T Δr ij > CP(i,j) ~ < Δr ij Chennubhotla & Bahar 2007 Elodie Laine JOBIM – 03/07/2012 11/22

Structural mapping of communication profile Per residue communication efficiency The structural fragments of KIT that present communication hubs were previously reported as playing crucial functional roles in the activation/deactivation mechanisms of other receptor tyrosine kinases or cytoplasmic kinases. Elodie Laine JOBIM – 03/07/2012 12/22

Modulation of KIT communication profile Communcation effciciency is enhanced ( ) or reduced ( ) upon D816V mutation Elodie Laine JOBIM – 03/07/2012 13/22

Independent dynamic segments Independent dynamic segments display the most striking features of the protein local dynamics Principal Component Analysis (PCA) A-loop Information by mode (global) 100 Prévalence (%) Essential dynamics space 80 (19-20 modes ~ 80 % fluct.) 60 40 Local Feature Analysis (LFA) 20 JMR Information by atom (local) Most striking dynamic features (19-20 segments) Zhang & Wriggers, 2006 Elodie Laine JOBIM – 03/07/2012 14/22

Independent dynamic segments LFA correlation patterns WT IDS-3 IDS-2 IDS-8 IDS-2 IDS-3 IDS-8 MU IDS-3 IDS-2 IDS-8 Elodie Laine JOBIM – 03/07/2012 15/22

Relationship between IDS & CP IDS are essentially isolated residues, hence IDS and CP are complementary Elodie Laine JOBIM – 03/07/2012 16/22

Communication between A-loop and JMR WT MU Communication routes are established in WT between the two regulatory segments, whereas in MU a decoupling is observed Elodie Laine JOBIM – 03/07/2012 17/22

Design of a double mutant 50-ns molecular dynamics simulations of D816V/D792E 26ns 38ns 50ns 14ns JMR dbMU A-loop A-loop Atomic fluctuations WT MU dbMU ß-sheets 823-828 helix/turn 816-819 Elodie Laine JOBIM – 03/07/2012 18/22

Design of a double mutant Secondary structure assignments Elodie Laine JOBIM – 03/07/2012 19/22

Communication between A-loop and JMR WT MU dbMU Elodie Laine JOBIM – 03/07/2012 20/22

Communication between A-loop and JMR WT MU dbMU The additional D792E mutation efficiently restored the communication as observed in the wild type protein Elodie Laine JOBIM – 03/07/2012 20/22

Conclusion & Perspectives MOdular NETwork Analysis of protein structures • Two-component modeling framework based on dynamical correlations and topology of the protein that accounts for the duality of allosteric coupling • Enables to localize and visualize information transmission throughout protein structures and to rationally understand the determinants of signal propagation • Applicability to KIT receptor :  communication breakage put in evidence in D816V-mutated KIT  design of a double mutant in which D816V long-range effect is neutralized  in vitro measurements of wt, mu and dbmu mutant activation rates…?  in vitro measurements of wt, mu and dbmu mutant activation rates…?  improvements of the method:  improvements of the method:  other dynamical correlations measures  more sophisticated algorithm for path generation  other dynamical correlations measures  more sophisticated algorithm for path generation  application to drug design…?  application to drug design …? Elodie Laine JOBIM – 03/07/2012 21/22

Acknowledgements ByMoDyM, LBPA, ENS de Cachan, LabEx LERMIT (France) Luba Tchertanov Funding: Elodie Laine OSEO-ISI Manuela Leal da Silva ENS Cachan, France Poster n ° 65 Isaure Chauvot de Beauchêne Priscila da S. Figueiredo Celestino Florent Langenfeld Rohit Arora Samuel Demarest Loic Etheve Former members : S. Abdel Azeim J. André Collaboration : E. Solary (IGR) P. Dubreuil (CRCM) F. Piazza (U. d’Orléans) A. Blondel (Institut Pasteur) B. Roux (U. of Chicago) 24 P. BISCH (U. Federal do Rio de Janeiro)