NMR Dynamics based on chemical exchange and Hydrogen Exchange

Transcription

1 NMR Dynamics based on chemical exchange and Hydrogen Exchange NMR dynamic methods Applications for monitoring calcium signaling Detecting intermediates and excited states EXSY, CPMG, RDC/PRE Amide exchange and application to proteins and protein folding Developing MRI contrast agent

2 Ca2+ Homeostasis and Signaling ([Ca2+]e 10 3 M) Ca2+ channels GPCR E NCX STIM1 RTK IP3R RyR SERCA SERCA ([Ca2+]i M) MCU/MiCa Letm1 Ca2+ IP3R Uniporter RyR CaM NCX/HCX Genes transcription (NFAT, CREB, DREAM) [Ca2+]I activated Buffers Buffers Effectors Ca2+ Ca2+iOscillation frequency 10-6 μs 10-3 ms 1 s 103 min 106 h

3 The Connexin Family Tree Söhl et al., Nat. Rev. Neurosci. 6: ,

4 Identifying CaM Binding Region in Gap Junction Connexins Score Cx50_m Cx46_h Cx44_s Cx43_h CaMKI_h CaMKII_h NH 2 COOH TKKFRLEGTLLRTYVCHI RGRVRMAGALLRTYVFNI RGKVRIAGALLRTYVFNI HGKVKMRGGLLRTYIISI FAKSKWKQAFNATAVVRH NARRKLKGAILTTMLATR 310 xxbxb#xxx#xxxx#xxx Y. Zhou. JJ Yang JBC. 2007; Zhou Y, Yang JJ. Biophys J ; Y. Chen,.. JJ Yang Biochem J. 2011

5 ppm-h [Cx43]/[CaM] 0:1 0.4:1 0.8:1 1.2:1 Monitoring Cx Peptide and Calmodulin [Cx44]/[CaM] 0: T29 T A : : : K94 D64 G33 G61 G25 K148 A57 1.2: [Cx43]/[CaM] 2.0:1 Y. Zhou. JJ Yang JBC T29 T H (ppm) A H (ppm)

6 Strong Binding Indication by Slow Exchange CaM : Cx50p 1 : Free G CaM + Cx43p 1 : : : bound Y. Chen,.. JJ Yang Biochem J. 2011

7 HSQC Spectra of Holo-CaM with Cx50 Peptide Y. Chen,.. JJ Yang Biochem J Holo-CaM Holo-CaM + Cx50p G33 G134 T29 T117 T70 F19 A128 L116 K21 I100 I27 N137 V136 D64 I130 A57 K148 K94 A147 7

8 Integration of Calcium Signaling Via CaSR LB1 LB2 Site 2 Site 1 Site 3 Site 4 site5 Identification of Ca 2+ binding sites in ECD of CaSR How can CaSR sense the change of Ca 2+ o, Phe within a narrow range? (multiple sites? cooperativity?) Identification of CaM binding region in c-tail of CaSR Y. Huang, JJ Yang, J Biol Chem. 2007; Yun Huang.. JJ Yang Biochemistry 2009; Y Hang, JJ Yang, JBC 2010, Zhang, C, 2014

9 NMR Dynamic Experiments Initial NMR dynamics experiments in 1970s. Rapid advancements due to ability to label specific positions in bio-molecules and methodologies development Magnetization exchange spectroscopy (EXSY)-slow exchange 0.5 s -1 to over 50 s -1 CPMG relaxation dispersion: chemical shifts100~2000s -1, R1rho can extend to more rapid exchange (dot) Residual dipolar coupling (RDC) and PRE Spin relaxation for ns-ps CPMG and PRE are sensitive to low-lying excited states with populations > 0.5% H/D exchange can detect high energy excited states with much lower population A.Mittermaier, L. Kay (2009) Trends Biochem. Sci. 34, 601. A. Mittermaier, L. Kay (2006) Science. 312, 224 K. Wuthrich, G Wagner,(1978) Trends Biochem. Sci. 3, 227

10 Exchange Spectroscopy (EXSY) Mittermaier et al (2009) Trends Biochem. Sci. 34, 601.

11 Slow conformational exchange in the protease ClpP ClpP, an oligomeric protease comprising 14 subunits with a total molecular mass of 300 kda. (a) Surface representation of ClpP with two monomers shown as yellow and blue ribbons. Locations of dynamic isoleucine residues are identified by green and red circles. Substrate entry pores are indicated with blue arrows. (b) The 1 H/ 13 C methyl TROSY correlation spectrum collected for a uniformly [ 15 N, 2 H], Ile δ1 [ 13 C, 1 H] labeled ClpP sample. I149 and I151 are each associated with two δ1 methyl peaks, designated F and S, reflecting slow exchange between two distinct, functionally important, conformations. (5 0 C, rotational correlational time >0.4 us) R.Sprangers, PNAS, et al.2005 Wang JM, Cell, 1997

12 Carr Purcell Meiboom Gill (CPMG) Relaxation Dispersion 100 s s -1 Exchange between ground state and excited state is in the millisecond time scale A k AB k BA B k ex = k AB + k BA k BA > k AB Shape of the dispersion depend on: populations of the two states chemical shift difference the rate of exchange In a typical series of experiments, variable numbers of refocusing pulses are applied to magnetization as it evolves under the influence of a chemical shift that varies stochastically due to the exchange process Baldwin et al (2009) Nature Chem Biol 5, 808.

13 Minisec Dynamics Relaxation Dispersion of DHFR Boehr et al (2006) Science 313, 1638.

14 Relaxation Dispersion (Continue) Differences in chemical shifts between ground and excited states ( ) correlate with differences in peak positions between intermediates ( ), suggesting the excited states are similar to the conformation of the intermediates in the preceding or following step in the catalytic cycle. Boehr et al (2006) Science 313, 1638.

15 Residual Dipolar Coupling (RDC) Mittermaier et al (2009) Trends Biochem. Sci. 34, 601.

16 Spin Relaxation and Paramagnetic Relaxation Enhancement Mittermaier et al (2009) Trends Biochem. Sci. 34, 601.

17 PRE Study of Maltose Binding Protein PRE of holo form agree with X- ray structure PRE of apo form is larger than X-ray structure The apo form is in a transient close form (5%) Grey: N-terminal domain Blue: C-terminal domain, apo Red: C-terminal domain, holo Mittermaier et al (2009) Trends Biochem. Sci. 34, 601.

18 Hydrogen Exchange Method Hydrogen exchange (HX) techniques is described for measuring the approximate exchange rates of the more labile amide protons in a macromolecule. The exchangeable amides in proteins are:

19 Exchangeable Nucleotides

20 Hydrogen-Exchange Chemistry A minimum ~ ph 3.5 > 1hr at ph 3 Hx rate is catalyzed by OH - and H + k intrinsic k ex = k oh [OH - ] + k H [H + ] + k w All exchange rates are referenced to random coil polyala at 0 C. HX rates are sensitive to ph,local chemical environment, solvent, sidechain type, neighboring amino acids and temperature k intrinsic for each amino acid is different < 1ms at ph 10 pd = ph* Bai. And Englander. (1993) Proteins, 17, 75; Koide S.. and Wright PE J Biomol NMR Nov;6(3):

21 Simulated Exchange Rates for Labile Protons of Polypeptides In H 2 O solution at 25 C. Im stands for imidazole ring NH, Gua for guanidinium NH, bb for backbone. The amide protons have a large range of possible exchange rates under physiological ph (ph ). Wuthrich &Wagner JMB 1979

22 HX vs. Protein Structure In proteins, HX rates can be altered: H-bonding Shielding in the center of protein Shielding by binding another molecules ph and temperature Extremely slow exchange can be months,yrs Protection factor p = k intrinsic /k obs p > for slow exchange Amide exchange rate contains information about secondary structural elements

23 Hx Mechanism (Ex1/EX2) k o Close Open Exchanged p k cl k intrinc -Hvidt & Nielsen, 1966 Solvent penetrates protein secondary structure A protected amide hydrogen is closed to exchange and becomes accessible to exchange through an open state at the exchange rate for an unstructured peptide. Ex1: k intrinc >> k cl k obs = k op independent of ph Ex2: k intrinc << k cl k obs = k op k intrinc ph dependent Ex2 is typically encounted in proteins under conditions where folded state is stable and intrinsic exchange is relative slow

24 HX is an excellent way to look at the stability of proteins The rates of amide proton exchange for individual protons can be related to equilibrium constants for opening of individual hydrogen bonds. Knowing the equilibrium constants, one can calculate the free energy for the conformational transition which allows exchange to occur. When certain protons are only exposed in the completely unfolded form then the equilibrium constants and Gs correspond to the global unfolding reaction. These protons are usually the slowest exchanging protons in the molecule. G HX = -RT ln(k obs / k intrinc ) For mutation, the change of stability: G HX = ( G HX ) wt - ( G HX ) mut =-RT ln (kex wt /kex mut )

25 Amide Exchange Rates Adding D 2 O to our H 2 O solution and take spectra at different times, signals from different amide protons will decrease in size at different rates. We look at the NH to Ha fingerprint at different times in DQF-COSY or HSQC. t = 0 - No D 2 O 4.0 Add D 2 O t = t (Has) 4.0 t = t (NHs) 7.0

26

27 Amide Exchange Rates in ACP Kima Y, et al, BBRC, 2006 Residues at the center of helices and hydrophobic core have slow exchange rates The overall protection factors (< ) are smaller than other proteins suggesting that ACP has high mobility Helix II exchanges faster than helix I and helix III suggesting that Helix II is highly dynamic.

28 Unfolding/Folding and Misfolding

29 Competition Hydrogen Exchange 25x dilution Drop ph 3.8 Concentrating 6M GuHCl H 2 O ph 7.5 D 2 O Phosphate buffer ph7.5 1min NMR The refolding experiment involved dilution of droplets of protein denatured in 6 M GuHCl in H 2 O solution into a denaturant free solution of D 2 O to initiate refolding and hydrogen exchange simultaneously. After folding completed, HX is quenched by lowing the ph. Comparing 2D NMR spectrum of the refolded protein with that was not denatured. Residues protected early in refolding can be detected using NMR.

30 Competition HX of lysozyme Using 65 slowly exchanging amide hydrogen as probes. The majority of residues in b- domain have exchange >30%. The majority of residues in a- domain have exchange <30% suggesting that two structural domains of lysozyme are folding domains that differ significantly in the extent to which protected structure accumulates early in the folding process. Miranker et al., Nature, 1991

31 Pulsed-Label Hydrogen Exchange After an adjustable refolding time, t f, the protein is subjected to a short high ph pulse, where exchange of the unprotected NHs is very fast. NHs protected by structure within the folding time does not exchange during the short pulse After a pulse time t p. The D to H exchange is quenched by rapidly lowering the ph. After folding completed, the pattern of NH and ND labels in the refolded protein is analyzed by 2D NMR. Increasing t f time, proton occupancies measured in the NMR spectrum decreases. Plotting proton occupancy vs. folding time t f.

32 Identifying Folding Pathway by HX Pulse-Labeling (a) pure 2-state All probes achieve 100% protection at the same rate in a single kinetic step. (b) U -> I -> N sequential, I has A&B H-bonds with the same HX constant (c) U1 -> N(30%) U2 -> N(70%) two heterogeneous parallel paths (d) U1-> N U2->I->N contribution of intermediate and heterogeneous folding

33 Parallel Folding Pathway of Lysozyme All probes (50% of 126 amides) have one fast phase and one slow phase Fast phase rates for both a- and b domains are 10 ms Slow phase rates for a is 65 ms and b is 350 ms, respectively. a domains folds before b domain and different populations of molecules folded by kinetically distinct pathways

34 Additional Methods for Amide-Water Exchange Hwang TL, Mori S. Shaka, AJ, and van Zijl PC, Application of Phase-Modulated CLEAN Chemical EX-change Spectroscopy (CLEANEX-PM) to detect water-protein proton exchange and intermolecular NOEs. JACS, 1997, 119, Hwang TL, van Zijl PC, Mori S. Accurate quantitation of water-amide proton exchange rates using the phase-modulated CLEAN chemical EXchange (CLEANEX-PM) approach with a Fast- HSQC (FHSQC) detection scheme.j Biomol NMR Feb;11(2): Clean SEA-HSQC: a method to map solvent exposed amides in large non-deuterated proteins with gradient-enhanced HSQC J Biomol NMR 2002 Aug;23(4): Mori S, Abeygunawardana C, Johnson MO, van Zijl PC. Improved sensitivity of HSQC spectra of exchanging protons at short interscan delays using a new fast HSQC (FHSQC) detection scheme that avoids water saturation. J Magn Reson B 1995 Jul;108(1):94-8 Erratum in: J Magn Reson B 1996 Mar;110(3):321 Bougault C, Feng L, Glushka J, Kupce E, Prestegard JH. Quantitation of rapid proton-deuteron amide exchange using hadamard spectroscopy. J Biomol NMR Apr;28(4): Miranker A., Robinson CVm Radford, SE, Aplin RT, Dobson CM. Detection of transient protein folding populations by mass spectrometry. Science Nov 5;262(5135): Carulla N, Caddy GL, Hall DR, Zurdo J, Gairi M, Feliz M, Giralt E, Robinson CV, Dobson CM. Molecular recycling within amyloid fibrils.nature Jul 28;436(7050): Feng L, Orlando R, Prestegard JH. Mass spectrometry assisted assignment of NMR resonances in 15N labeled proteins.j Am Chem Soc Nov 10;126(44): Macnaughtan MA, Kane AM, Prestegard JH. Mass spectrometry assisted assignment of NMR resonances in reductively 13C-methylated proteins. J Am Chem Soc Dec 21;127(50):

35 CLEANEX-PM spin-locking sequence: 135 (x) 120 (-x) 110 (x) 110 (-x) 120 (x) 135 (-x) CLEANX-PM has the ability to specifically monitor water-proton exchange without 1) exchange relayed NOE/ROE from rapidly exchanging protons (hydroxyl or amide groups) in the macromolecules, 2) intra-molecular NOE/ROE peaks from protein CaH protons which has chemical shifts coincident with water, or TOCSY-type interactions.

36 FHSQC CLEANEX-PM The FHSQC indicates proton signal that remain at the amide resonance through out the pulse sequence. The CLEANEX-PM indicates 1 H signals that initiate in the 1 H 2 O resonance and then transfer to 1 H amide resonance during the mixing period of the pulse sequence. Staphylococcal nuclease Hwang et al., 1998

37

38 Conventional [1H,15N]-HSQC spectrum of human ubiquitin. A 0.5 mm15n-labeled sample was prepared in 50 mmpotassium phosphate buffer in H2O/D2O 5/95, ph= MHz with cryoprobe. it required approximately 21 min using 128 t1 time increments and 4 scans per increment.

39 Reconstructed Hadamard [1H,15N]- HSQC Spectra for Ubiquitin (A) Data in 1 H 2 O collected with 128 t1 increments in 20 min. The sample was then lyophilized overnight and brought back to its initial volume with 99.9% 2 H 2 O and immediately returned to the spectrometer for rapid collection of a series of Hadamard spectra. (B) First point after 1 min in 2 H 2 O collected with 4 scans in 42 s.

40 Cross-peak intensities as a function of time Lines are best fits to I(t) =I o (exp(-kt)+const). The precision of the data is quite high with the estimated errors for rates in the range of min- 1 being on the order of 5%. Rates derived also show reasonable agreement with previously published rates.

41 Intermediates Determined by H/D Exchange Englander (2005) PNAS 102, 4741.

42 Limitations of Clinically approved Contrast agents Low relaxivity and requires high dose injection ( M) Paramagnetic nanoparticles Low sensitivity, and low accuracy/specificity Low S/N, Conc> 0.10 mm No capability for biomarkers at um~ nm for molecular imaging Low resolution Detection size > 1-2 cm Non-ideal PK/PD with limited MRI window required for high quality imaging Gd Toxicity/Blackbox warning There is a strong need to develop MRI contrast agents with high relaxivity, optimized in vivo retention time, organ preference, and targeting capability. Lauffer et al, 1987, Xue et al., 2013, 2014

43 Yang, JJ, JACS, 2010, Wei et al., 2009, Qiao et al., 2011 i Contrast Agents vs. relaxation ii Gd K ex Gd K ex Rs Rf Rf Gd K ex Rf 1 T 1 T 1M cq M 1 c 1 T 1e 1 m 1 R Current CAs A major barrier to the application of MRI technique is its low sensitivity and contrast limited by the fast rotational correlation time of the molecule (ps). Macromolecule generated by either covalent binding or the non-covalent nature of the binding between the monomeric agent and the macromolecules has the improvement in proton relaxivity is much less than the expected increase based on the molecular-weight increase due to high internal mobility of the paramagnetic moiety and limited water exchange rate. ProCAs developed by protein design with increased relaxivity by controlling relaxation and the capability of targeting specific molecular entities such as cancer biomarkers.

44 Increase Both R1 and R2 by Protein Design Relaxivity (mm -1 s -1 ) r2, r 2, ProCA32 r1, r 1, ProCA32 r2, r 2, Gd-DTPA Clinical r1, r 1, Gd-DTPA Clinical 1.4 T 3 T 7 T 30 1 T T 1 T 1M 1 2nd 2nd 1 T1m 1 T 2nd 1m 2 15 cq cq 2nd M 2nd m 1 c 2 g 2 2 I B S( S 1)( 0 ) ( r 2nd ) 6 4 GdH 1 T 2 [ 1e 1 m 7 2nd c2 (1 2nd s c2 2 ) 1 R 3 2nd c1 (1 2nd I c1 At 20 MHz with rgdh2nd=5 Å and q=6, the second sphere relaxivity could potentially ] 2 ) Larmar frequency (MHz) Protein-based Contrast Agents (ProCAs)

45 ProCA1 as a MRI contrast agent A H 2 O PEG H 2 O K 45 PEG D 62 D 58 D 56 K 47 PEG Gd E 15 D 64 K ns 9.20 ns q = 1. 8 q=2.0 Sample Gd 3+ Zn 2+ Ca 2+ Mg 2+ Log (K Gd /K Zn ) Log (K Gd /K Ca ) DTPA DTPA- BMA na * na * 45 Log (K Gd /K Mg ) CA1.CD <2.22 < >9.84 >10.06

46 Enhancement % HER2targeted ProCA Detects Breast and Ovarian Cancers depending on HER2 Expression Levels Pre 30 min 24 hr MDA-MB-231 SKOV-3 24 hr 24 hr Intensity Enhancement Blood Vessel Blood Vessel SKOV-3 MDA-MB-231 Positive tumor stained with ProCA1-affi-m 4 hr 4 hr Positive tumor stained with HER2 antibody Positive tumor stained with ProCA1-affi-m Positive tumor stained with HER2 antibody 0 5 min 30 min 3 hr 24 hr 52 hr Time points Excellent Tumor Penetration And Distribution, Superior Than

47 Protein-based Contrast Agents (ProCAs) Xue, 2013, 2014, Qiao, 2014, L. Wei et al., 2010, Fan Pu unpublished A H 2 O PEG H 2 O D 62 E 15 D 58 Gd K 66 D 56 D 64 K 45 K 47 PEG PEG GRPR, GPCR First computational design of Gd 3+ -binding site in proteins as novel protein MRI reagents with strong metal stability and selectivity fold in vitro increases in R1 and R2, high R1 at 7T 100 fold increase in in vivo detection resolution. Extend to earlier and accurate detection of liver lesion size from > 2 cm to <0.25 mm micrometstasis by dual ratiometric imaging ProCAs increase specificity by enabling molecular imaging of breast and prostate cancer biomarkers Her2/EGFR and GRPR with enhanced sensitivity, optimized retention time, and proper tissue/tumor penetration fold low dose injection, biocompatible, no acute toxicty