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https://doi.org/10.1007/s12104-017-9792-1 ARTICLE
Chemical shift assignments of the partially deuterated Fyn SH2–SH3 domain
Fabien Kieken1,2,3 · Karine Loth4,5 · Nico van Nuland1,2 · Peter Tompa1,2 · Tom Lenaerts3,6,7
Received: 3 July 2017 / Accepted: 28 November 2017
© Springer Science+Business Media B.V., part of Springer Nature 2017
Abstract
Src Homology 2 and 3 (SH2 and SH3) are two key protein interaction modules involved in regulating the activity of many proteins such as tyrosine kinases and phosphatases by respective recognition of phosphotyrosine and proline-rich regions. In the Src family kinases, the inactive state of the protein is the direct result of the interaction of the SH2 and the SH3 domain with intra-molecular regions, leading to a closed structure incompetent with substrate modification. Here, we report the 1H,
15N and 13C backbone- and side-chain chemical shift assignments of the partially deuterated Fyn SH3–SH2 domain and structural differences between tandem and single domains. The BMRB accession number is 27165.
Keywords SH3–SH2 · Tandem domains · NMR · Fyn kinase · Src family
Biological context
The Src family consists of 11 non-receptor tyrosine kinases involved in a plethora of fundamental biological processes including cell growth, differentiation, cellular adhesion, cell migration (Manning et al. 2002). The structural organization of each family member is equivalent: They are composed of
four different domains—SH1 to SH4—with a C-terminal negative regulatory tail. The SH4 domain located in the N-terminus anchors the proteins to the plasma membrane and is attributed with the varying physiological functions of the family members (Sato et al. 2009). SH3 and SH2 domains are involved in regulating kinase activity and medi- ate the interaction of the kinase with its protein partners, and SH1 is the kinase domain (Boggon and Eck 2004; Sicheri and Kuriyan 1997). Src family kinases (SFK) catalytic activ- ity is determined by intermolecular interactions and equilib- rium of phosphorylation-dephosphorylation states. Activa- tion of the kinase is triggered by the dephosphorylation of the phospho-tyrosine in the C-terminus, which in turn results in the initiation of signaling cascades that drive basic cel- lular function (Huculeci et al. 2016; Xu et al. 1999). Given their important role in fundamental physiological and patho- logical processes, members of the SFK have been widely investigated in various biological contexts.
Fyn, one of the SFK members, regulates numerous cel- lular processes including motility, growth, differentiation and signal transduction in various cell types (Saito et al.
2010). The Fyn gene has three splice variants, one of which is deemed inactive. FynT is highly expressed in cells of hematopoietic lineage and regulates immune cell functions and inflammatory responses. The other active form FynB is ubiquitous, with the highest expression in the synaptic architecture of the central nervous system, playing impor- tant roles in glutamate receptor trafficking and synaptic
* Tom Lenaerts
Tom.Lenaerts@ulb.ac.be
1 Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
2 Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussel, Belgium
3 AI-lab, Vakgroep Computerwetenschappen, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
4 Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique (CNRS) UPR 4301, Université d’Orléans, rue Charles Sadron, 45071 Orléans Cedex 2, France
5 Collegium Sciences et Techniques, Université d’Orléans, rue de Chartres, 45100 Orléans, France
6 MLG, Départment d’Informatique, Université Libre de Bruxelles, Boulevard du Triomphe, CP 212, 1050 Brussels, Belgium
7 Interuniversity Institute of Bioinformatics Brussels (IB2), ULB-VUB, La Plaine Campus, Boulevard du Triomphe, CP 1
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plasticity (Grant et al. 1992; Kojima et al. 1998; Nakazawa et al. 2001; Prybylowski et al. 2005; Suzuki and Okumura- Noji 1995). Beyond it’s basic physiological functions, Fyn has been widely investigated as a therapeutic target due to its implication in the pathophysiology of various cancers, neurodegenerative and psychiatric diseases (Nygaard et al.
2014; Ohnuma et al. 2003; Panicker et al. 2015). Fyn has been found significantly upregulated in cancer tissues, with its level correlating with aggressive disease progression and metastasis [review (Elias and Ditzel 2015)], which results from promoting cancer cell proliferation and inhibition of cell death (Elias et al. 2015; Li et al. 2003). Inhibition of Fyn function is thought to have therapeutic potential in cancer and neurodegenerative conditions. Various inhibitors of Fyn kinase domain are available; however these carry various safety liabilities and long term toxicity due to lack of speci- ficity in inhibiting kinase functions (Grant 2009).
Fyn’s SH1 activity is regulated by the intramolecular interactions with two of its domains, SH3 and SH2. SH3 domains interact primarily with sequences rich in proline, such as PxxP motifs, although they can also bind other sequences that deviate from the canonical one [review (Sak- sela and Permi 2012)], whereas SH2 domains recognize and bind phosphotyrosine residues (Pawson 1995). Fyn SH2 is responsible for the state of activation of the kinase. Phos- phorylated Tyr527 allows a direct interaction between Fyn SH2 with the C-terminus, resulting in an inactive kinase state. The kinase self-activation occurs during the dephos- phorylation of Tyr527 and/or the binding of protein partners, allowing the dissociation between SH3, SH2, and the kinase domain [review in (Roskoski 2015)].
The mechanism of propagation of the information or cross-communication between the two domains is not well investigated and has led to controversial reports. While the SH3 domain enhances Fyn SH2-mediated ligand binding (Panchamoorthy et al. 1994) and the replacement of the SH3–SH2 linker residues with glycines activates c-Src (Young et al. 2001), the analysis of the dynamics of Fyn SH3–SH2 by nuclear magnetic resonance (NMR) T1/T2/ NOE, domain alignment by residual dipolar couplings and crystallographic structure showed very little structural modifications (Ulmer et al. 2002). Nonetheless, recent work showed that sidechain dynamics plays a role in the activation process (Huculeci et al. 2016).
As no solution structure by NMR of human wild type Fyn SH3–SH2 is available, we report here on the full backbone and side-chain 1H, 15N and 13C assignment of partially deu- terated 13C, 15N-labeled Fyn SH3–SH2 in its free form using high-resolution NMR techniques. The anticipated structural resolution of the tandem domains by NMR will provide additional information on changes of structure and dynam- ics between domains, hopefully providing an explanation
for the mechanism of information propagation throughout the structure.
Methods and experiments
Protein expression and purificationThe human Fyn SH3–SH2 domain (residues 82–248), SH3 domain (82–147) and SH2 domain (148–248) were sub- cloned into a pet15b (Novagen) vector containing a throm- bin-cleavable N-terminal hexa-His tag by standard cloning methods.
Transformed BL21(DE3)star cells (Invitrogen) were grown at 37 °C in 1 L of minimal medium implemented with 0.75 g 15NH4Cl and 2 g 13C-glucose (Cambridge Isotope Laboratories). The bacteria were induced at a cell density of 0.6 by addition of 0.5 mM IPTG and were then incubated at 22 °C overnight. The cells were pelleted by centrifugation at 7000×g and the pellet kept and stored at − 80 °C for further processing. The expression of the partially deuterated and uniformly 13C/15N-labeled protein was achieved by making the minimal medium 60% in D2O (Cortecnet) complemented with 0.75 g 15NH4Cl and 2 g 13C-glucose.
The pellets were thawn and resuspended in lysis buffer (20 mM Hepes pH 7.6, 100 mM Na2SO4, 20 mM imidazole, 10 mM β-mercaptoethanol (BME), 10% glycerol containing 0.2 mM 4-(2-aminoethyl) benzenesulfonyl fluoride hydrochlo- ride (AEBSF), 5 μg/mL leupeptin and 4 units/mL of DNAse I). The cells were lysed by sonication using a Sonics Vibra- CellTM CV18 model ultrasonic processor (70% amplitude, 3 s pulse on/off for 10 min) and the lysates were centrifuged at 20,000×g for 1 h at room temperature. The supernatant was then loaded into a prepacked HisTrap column (GE Health- care). The resin was washed with 10 column volume of lysis buffer without protease inhibitor and DNAse. The proteins were eluted with 20 mM Hepes pH 7.6, 100 mM Na2SO4, 500 mM imidazole, 10 mM BME and 10% glycerol. The eluted proteins were loaded into a gel filtration Econo-Pac 10DG column (Biorad) equilibrated with 20 mM Hepes buffer pH 7.6, 100 mM Na2SO4, 10 mM BME, 10% glycerol.
The protein were eluted using the same buffer and were con- centrated by using 20 mL spinning Vivaspin 20 filters with a 10 kDa cut-off (Sartorius AG) to a concentration of 10 mg/mL.
The proteins were either snap frozen and stored at − 80 °C or incubated with 1 unit of thrombin (Calbiochem) per mg of protein overnight at room temperature to remove the His-tag.
The cleaved Fyn SH3–SH2 was separated from the tag by gel-filtration using a Superdex75 16/90 column (GE Health- care) in 50 mM sodium phosphate buffer pH 6.5, 100 mM Na2SO4, 2 mM BME. The fractions containing the protein were concentrated using a Vivaspin 20 filter with a 10 kDa
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cut-off (Sartorius AG). SDS-PAGE was used to determine the purity of the sample.
NMR spectroscopy
The concentration of partially deuterated 15N/13C sample of Fyn SH3–SH2 used for assignment was 0.7 mM in 50 mM sodium phosphate buffer pH 6.5, 100 mM Na2SO4, 2 mM BME, 10% D2O. NMR data were acquired at 25 °C on a Varian Direct-Drive System 600 MHz and an Avance III HD Bruker 700 MHz spectrometers, both equipped with a cryoprobe. Sequential assignments of the protein were car- ried out using 15N-HSQC, 13C-HSQC, HNCO, HNCA, HNCACB, following classical procedures Side-chains assignments were carried out using trosy-HBHANH, trosy- HBHA(CO)NH, HCCH-TOCSY, [1H,15N]-HSQC NOESY and [1H,13C]-HSQC NOESY. Backbone assignments were obtained using 2D 15N-HSQC, 13C-HSQC, 3D 15N and 13C NOESY-HSQC (mixing time: 100 ms) and triple-resonance experiments CBCACONH, HNCACB, HCCH-TOCSY, HBHANH, HBHACONH. 1D 1H-detected 15N-edited relaxa- tion experiments were used to calculate the average 15N T1 and T2 relaxation by fitting the integrated signal in the backbone amide 1H region of the spectrum (10.5–8.5 ppm) as a function of delay time to an exponential decay. 15N T1 and T2 spec- tra were acquired with a recycle delay of 8.0 s. T1 relaxation delays of 100, 200, 300, 400, 600, 800, 1000, 1500, 2000, 3000 and 5000 ms and T2 relaxation delays of 10, 30, 50, 70, 90, 110, 130, 150, 170 ms were used for data collection. At high magnetic field (above 500 MHz), the correlation time of a molecule (τC) can be estimated for a rigid protein with τC > > 0.5 ns as a function of the ratio of the longitudinal (T1) and transverse (T2) 15N relaxation times. By considering J(0) and J(ωN) spectral density terms and neglecting higher fre- quency terms, the correlation time of a molecule can be esti- mated using the following equation:
where νN is the 15N resonance frequency (in Hz) (Kay et al.
1989).
All 3D experiments were acquired using non-uniform sampling. All NMR spectra were processed using NMRPipe (Delaglio et al. 1995) or Bruker’s Topspin 3.2™ and analysed by NMRVIEW and CCPNMR (Johnson and Blevins 1994;
Vranken et al. 2005).
τC≈ 1 4πνN
√ 6T1
T2
−7,
Assignment and data deposition
Analysis of Fyn SH3–SH2 domain 1D 1H-detected
15N-edited relaxation experiments in solution showed a direct relation between the protein correlation time (τC) with its concentration, suggesting that the protein under the conditions of the NMR experiments is a mono- mer–dimer mixture (Fig. 1a) (Rossi et al. 2010). The cor- relation time of a monomeric protein in solution in nano- seconds is approximately 0.6 times its molecular weight in kDa. For Fyn SH3–SH2, τC is estimated to be 11.8 ns. At classical sample concentration for NMR structure deter- mination (> 0.6 mM), the τc for Fyn SH3–SH2 is above 16.5 ns. The quality of HSQC spectra decreases with incremental concentrations (Fig. 1b) and as a consequence, use of uniformly-labeled 15N/13C sample yielded no signal in all 3D experiments (Fig. 1c).
Nietlispach et al. showed that 50–60% random frac- tional deuteration increases the sensitivity of the NMR experiments due to the reduction of R2 of the molecule, allowing structure determination by NMR using 15N and
13C NOESY-HSQC (Nietlispach et al. 1996). Using this methodology on the Fyn SH3–SH2 domain, we observed a significant improvement on the quality of the NMR spectra (Fig. 1d). Using this approach with a 50% deuterated uni- formly-labeled 15N and 13C Fyn SH3–SH2 resulted in 97%
of the backbone and 94% of all 1H side chains assignment.
Due to the random nature of the deuteration processes, the chemical shifts were not corrected for 2H isotopes shifts.
The 15N-HSQC spectrum and assignment are displayed in Fig. 2a. The 1H, 13C and 15N chemical shifts were depos- ited into the BioMagResBank database (http://www.brmb.
wisc.edu/) accession number 27165.
To determine the percentage of monomer/dimer com- plexes, we performed an analysis of 1D 15N T1/T2 at 50–2000 μM concentrations (Fig. 1a). The estimated KD was calculated at 500 and 600 mM, suggesting that more than 60% of Fyn SH2–SH3 exists as a dimer at 0.7 mM. For maintenance of dominant monomeric FYN—
SH3–SH2 in solution, lower concentrations (0.1–0.2 mM) are necessary; however, such experimental prerequisites hinder spectral assignment and structure determination due to lack of signal.
Increasing sample concentrations above 1 mM also resulted in loss of NMR signal (broadened peaks; Fig. 1b).
Dimer formation favoured by higher sample concentra- tions exhibited as broadened peaks with the exception of one peak (R96), which slightly shifted without creating ambiguity for its assignment. Analysis of this chemical shift perturbation enabled KD determination in the range of 500–700 mM. Thus a concentration of 0.7 mM was subsequently selected for all the experiments in this study.
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The chemical shift index (CSI) function and DANGLE (Cheung et al. 2010) modules in CCPNMR were used to predict the secondary structure of Fyn SH3–SH2 from backbone chemical shifts (Fig. 2b). The predicted second- ary structure is an arrangement of 6 β-strands for the SH3 domain and 5 β-strands and 2 α-helices for SH2 domain, with a short α-helix in the linker between the two domains.
These data further corroborate previous reports on the structure of SH2 and SH3, as a β-sandwich consisting of six strands flanked by 2 α-helices and connected by three loops and a β-sandwich consisting of five strands flanked by three loops and a short 310 helix, respectively (Xu et al. 1999).
The structure of Fyn SH2 free in solution and in com- plex with the phosphorylated tail of the protein has been solved recently (Huculeci et al. 2016). We compared the
15N HSQC spectrum of the SH3–SH2 domain with the single SH2 domain under identical conditions to investi- gate if there is an effect of the SH3 domain on the struc- ture of SH2 domain. We observed the expected changes in the N-terminal region, but also throughout the sequence (Fig. 1e) suggesting a change in the structure of the SH2 domain when linked to the SH3 domain. A similar experiment using the free SH3 domain resulted in similar changes in the SH2 domain, with some still present, espe- cially in the loop area between b1 et b2 (Fig. 1f). These data underline the importance of studying these domains within the context of the tandem SH2–SH3 domain or even the full-length protein, as these differences may have an impact on the potential sidechain-induced communication between different parts of a protein.
a b
e f
9.5 9.0 8.5 8.0 7.5 7.0 6.5
δ(1H) [ppm]
20 40 60 80 δ(13C) [ppm]
20 40 60
80 9.5 9.0 8.5 8.0 7.5 7.0 6.5
δ(13C) [ppm]
δ(1H) [ppm]
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K248 C246
L187 L154
F151 K153 E179
W149ε
W149
R96
T97 E98
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δ(1H) [ppm]
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δ(15N) [ppm]
c d
0 500 1000 1500 2000
0 10 20 30 40 50
Concentration (µM) CorrelationTimec(ns)
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δ(1H) [ppm]
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δ(15N) [ppm]
8.0
R96
Fig. 1 Effect of protein concentration and deuteration on the NMR experiment and structural differences between Fyn SH3–SH2 and Fyn single domains SH2 and SH3. Plot of Fyn SH2–SH3 correla- tion time (τC) in function of protein concentration (a). Overlay of
15N-HSQCs of the Fyn SH3–SH2 domain collected at different pro- tein concentrations (b) (black: 50 μM; gray: 100 μM; light blue:
200 μM; dark blue: 400 μM; red: 600 μM; green: 900 μ; purple:
1.5 mM and dark green: 2 mM). 2D 1H/13C projection of the 3D HNCACB for a deuteration level of 0% (c) and 50% (d). 15N-HSQC overlay spectra of Fyn SH3–SH2 domain (black) in the presence of the His tagged Fyn SH2 (e) and SH3 (f) domains (red). Residues affected by the presence of the tandem domains have been labeled
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Acknowledgements This research is funded by the Flemish Scientific Fund (F.W.O.) via the grant G025915N. The VIB and the Jean Jeener NMR Center provided further support for our work.
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a
K248 H247
C246
V244
V243
L242 R241
C240 C239
L238 G237
A236
A235
R234
E233 T223
L224 F221
E148
Q220
A219 R218 T216 T217
I215
Y214 Y213
G212
G211
N210
D209
L208 K207
R206 I205
K204 Y203
K201 H202
V200 H199
D198
G197
K196
M195 D194
D193 W192
D191 R190 I189 S188
L187 S186
Y185
A184 G183
K182
T172T181 G171
F173 L174
I175
R176 E177
S178
R170
N168 G167
L164
A159 D158
R161
S165
F166
W149
E222
A146E147 Q145
I144, R156
S143
Y93,D142 V141 A139
V138
Y137 N136
S135 I133
Y132 G131
T130
E129 G128 T127
T126
L125 S124 R123
A122
E121 W120
W119 N118
G117
E116
S115
S114
N113
L112 I111
Q110 F109
K108
E107 6
0 1 G
10 K 5
4 0 1 3H 0 1 F
2 0 1 S
1 0 1 L D100
9 9 D 8
9 E
7 9 T
6 9 R
5 9 A
4 9 E 8
8 V
9 8 A 0 9 L
Y91
2 9 D
F 78
8 L 6 5 8 T
6 2 2 Q , 4 8 V 3 8 G
2 8 T
k n il M 5
5 1 G
L154 5
1 K 3
2 5 1 G
1 5 1 F
5 1 Y 0 7
5 1 K
L227 V228
9 2 2 Q
H230 S232Y231
Q225
E179
T180
3 6 1 L
Q162 E160
W149ε W192ε
W119ε W120ε
0 . 8 0
. 9 0
. 0 1 0
. 1
1 7.0 6.0
δ(1H) [ppm]
130.0 125.0 120.0 115.0 110.0 105.0
δ(15N) [ppm]
N210 N113
Q110 N136 Q162
Q220 Q229 Q226
Q145 Q225
SH M T G V T L 10 F V A L Y D Y E A R
20 T E D D L S F H K G
30 E K F Q I L N S S E
40 G DWWE A R S L T
50 T G E T G Y I P S N
60 Y V A P V D S I Q A
70 E E WY F G K L G R
80 K D A E R Q L L S F
90 G N P R G T F L I R
100 E S E T T K G A Y S
110 L S I R DWD D M K
120 G D H V K H Y K I R
130 K L D N G G Y Y I T
140 T R A Q F E T L QQ
150 L V Q H Y S E R A A
160 G L C C R L V V P C
170 H K
δ(13Cα) δ(13Cβ) δ(13C’)
G
b
Fig. 2 Assigned 15N-HSQC spectrum and secondary structure pre- diction of the Fyn SH3–SH2 domain. a 15N-HSQC spectrum of Fyn SH3–SH2 domain in 50 mM sodium phosphate buffer pH 6.5, 100 mM Na2SO4, 2 mM BME, 10% D2O. The assignments of back- bone side chain amides and tryptophan indole groups are labeled.
b Threshold deviation from random coil 13CO, 13Cα and 13Cβ were plotted as a function of residue number using the chemical shift index (CSI) module in CCPNMR. The cartoon represents the secondary structure of Fyn SH3–SH2 predicted by the CSI and DANGLE mod- ules in CCPNMR
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