Biophysical characterization of proteinprotein

Transcription

1 Biophysical characterization of proteinprotein interactions Rob Meijers EMBL Hamburg EMBO Global Exchange Lecture Course Hyderabad 2012

2 Bottom up look at protein-protein interactions Role of hydrogen bonds Role of hydrophobic interactions Techniques to measure kinetics: Surface plasmon resonance Isothermal titration calorimetry Thermophoresis Cross-linking Native mass spectrometry

3 A hydrogen-bonds only interface: Dscam

4 A simple mechanosensory neuron Each bristle is innervated by a single neuron Each mechanosensory axon pathfinds into the CNS

5 Reducing Dscam diversity impairs precise axon targeting Chen et al 2006 Cell 125,607 R265: Exon deleted Exon R87/R87 R265/R265 R265/R265 R265/R265 R265/R265 50μm

6 Exclusive homophilic adhesion From: Woj et al. Cell (2007)

7 A horse shoe shape D1-D2 fold onto D3-D4 Confirmed by EM Meijers et al, Nature 449 (2007) 487

8 Dimerization mode for two isoforms

9 Homophilic interactions D3-D3 D2-D2 & D3-D3 Most variable parts Anti-parallel Little overlap between D2 and D3 D2-D2

10 Antiparallel, symmetric interactions D2-D2 D3-D3

11 Epitope swap

12 Binding swap

13 Hydrogen bonds contribution Highly specific 1-2 kcal/mol per hydrogen bond Not very strong

14 Quaternary complex T cell TCR CD4 pmhc Antigen Presenting Cell Wang, Meijers et al (2001) PNAS 98, 10799

15 TCR recognition unit crystallized Murine MHC+Human CD4 Mouse model produced 10 years later Yin et al. (2012) PNAS 108, 15960

16 Immunodeficiency on a molecular level T cell T cell TCR CD4 CD4 pmhc gp120 Antigen Presenting Cell HIV Kwong et al 1998 Nature 393, 648

17 CD4 structure 4 immunoglobulin domains N-terminal domain: Phenylalanine sticks out into the solvent Wu et al 1997 Nature 387, 527

18 A buried hydrophobic residue Cd4/MHC class II structure: Phenylalanine 49 is buried Surrounded by hydrogen bonds

19 Hotspot theory Hydrophobic residues lie at the center of the binding interface Contribute most free energy Water displacement = entropy gain Clackson & Wells, Science (1995) 267, 383

20 Alanine scanning on TCR/pMHC binding Wu et al. Nature (2002) 418, 552

21 Resulting model; used SPR

22 Surface plasmon resonance Allows you to measure: Specificity Affinity Kinetics One interacting partner ( ligand ) is attached to the surface of a chip The second interaction partner ( analyte ) is flown over the surface of the chip. Binding of molecules to the sensor surface generates a response that is proportional to the bound mass.

23 Applications Specificity (yes/no binding response) Search for binding partners Screen for inhibitors Look for activity after protein purification Test cell culture lines for expression of a given protein Kinetics (rates of reactions) Complex formation Complex dissociation Affinity (strength of binding) Ligand Fishing Recover analyte from a complex mixture with mass spec

24 The chip: 200 euros per

25 ph scouting

26 Immobilization

27 Basic steps during an SPR experiment 1) Decide on chip to use 2) Decide on which molecule will be the ligand and which will be the analyte 3) Prepare the ligand and analyte 4) Choose immobilization strategy 5) Pre-concentrate ligand on chip prior to activation ( ph scouting ) 6) Immobilize ligand onto sensor chip 7) Inject analyte and record response 8) Regenerate surface 9) Analyze data

28 The sensogram

29 Overall structure and SDS/PAGE Song G et al. PNAS 2005;102: by National Academy of Sciences

30 Binding of the L I domains to ICAM-3 measured with SPR I ICAM ICAM ICAM I Song G et al. PNAS 2005;102: by National Academy of Sciences

31 Surface acoustic wave resonance Sound wave instead of light Better penetration, higher sensitivity Can be used to immobilize cells and check ligand binding

32 Thermodynamics of protein-protein interactions G = H-T S = -RTlnK a In a single ITC experiment you get Affinity (K D ): strength of binding Heat of binding ( H) and entropy ( S): mechanism Stoichiometry (n): number of binding sites Enzyme kinetics

33 ITC experimental principle X + M XM Syringe Reference Sample

34 Fit to model (1) One Set of Sites Symmetrical S-shaped curve One or more binding sites with the same affinity The number of sites is determined by the stoichiometry N Same result by loading the ligand in the syringe or in the cell Two Sets of Sites Non symmetrical curve Two set of Indipendent binding sites with different affinity The number of sites is determined by the stoichiometry N 1 and N 2. Different result by loading the ligand in the syringe or in the cell. Sequential Binding Sites Non symmetrical curve Non-indepoendent binding sites The number of binding sites is defined by the user Different result by loading the ligand in the syringe or in the cell

35 Binding stoichiometry: common problems N < 1 N > 1 N = 1 the protein concentration is lower than you think the protein is impure the protein (polypeptide) is pure but not all correctly folded the ligand concentration is higher than you think the simple single site binding model is inappropriate your protein has multiple binding sites the ligand concentration is lower than you think the simple single site binding model is inappropriate, You re lucky

36 SPR vs ITC Advantages: You can work with dirty sample to fish out specific interactions You need less material (~20 ug of immobilized ligand) -You can compare different ligands at the same time Disadvantages: ITC gives you thermodynamic data (dg) ITC kinetics is more accurate Topology of binding is limited in SPR Small molecules <100 Da don t work But now, there is.

37 Thermophoresis Heat sample by 2K Molecules dissipate When fluorescently labeled Equilibrate depending on size of hydration shell, charge distribution Duhr and Braun (2006) PNAS 103, pp19678

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40 Current technology Jerabek-Willemsen et al. 2011

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47 Mass spectrometry MS/MS + Ion mobility : Native mass spec Detailed folding state Protein-protein interactions Synapt G2-S HDMS Waters, UK

48 Instrumentation Synapt G2-S HDMS Waters, UK S.D. Pringle et al., Int J Mass Spectrom 2007

49 Ion mobility derived particle size Ruotolo et al Nature Protocols (2008) 3, 1139 in combination with SAXS 49 12/12/12

50 Collision cell gives activation energy Oligomers and/or complexes fly Can be perturbed by increased gas pressure Gives indication of complex integrity Barrera & Robinson, Ann Rev Biochem (2011) 80, 247