Supplementary methods
Construction of GST-CDK11 peptides
For the construction of GST-peptides, complementary oligonucleotides encoding 11 amino acids of
CDK11p110 were annealed and cloned into pGEX-4T-1 (GE Healthcare) using Bam HI and Sma I
restriction enzyme sites and confirmed by DNA sequencing. Oligonucleotides are as follows:
GST-CDK11 peptide (amino acids 67-77),
gatccTCCCCGTATAGAAGAGAAGACTCTATGGAAGAC (Sense),
GTCTTCCATAGAGTCTTCTCTTCTATACGGGGAc (antisense);
GST-CDK11 peptide (amino acids 154-164),
gatccAGGGAAGTGGCAAGGGAGCATTCCAGGAGAGAA (sense),
TTCTCTCCTGGAATGCTCCCTTGCCATTTCCCTc;
GST-CDK11 peptide (amino acids
205-215),
gatccCGGGAGGCCCGCAGGGAAGTGTCTGCACATCAC (Sense),
GTGATGTGCAGACACTTCCCTGCGGGCGTCCCGc (antisense);
GST-CDK11 peptide (amino acids 270-280),
gatccAGCGACAGCGAGAGGAAGACCAGCTCGGCCGAG (sense),
CTCGGCCGAGCTGGTCTTCCTCTCGCTGTCGCTc (antisense);
GST-CDK11 peptide (amino acids 693-703),
gatccTACTTCCCCGGGAGGAGGATCAGCGCTGAGGAC (Sense),
GTCCTCAGCGCTGATCCTCCTCCCGGGGAAGTAc (antisense);
GST-CDK11 peptide (amino acids 732-742),
gatccCAGCGTGTGAGCGGGGCACAGCCCGAGGCCC (Sense),
GGGCCTCGGGCTGGTGCCCCGCTTCACACGCTGc (antisense).
Enzymatic in-gel digestion
In-gel digestion was carried out with 12.5 ng/µl sequencing grade modified trypsin
(Promega, Madison, WI) in 50mM NH4HCO3 buffer (pH 7.8) at 37℃ for overnight.
Produced tryptic peptides were extracted with 5% formic acid in 50% ACN solution at room
temperature for 20min. The supernatants were collected and dried with SpeedVac.
Resuspended samples in 0.1% formic acid were purified and concentrated using C18
ZipTips (Millipore, MA) before MS analysis.
Analysis by nano-LC-ESI-MS/MS
The tryptic peptides were loaded onto a fused silica microcapillary column (12 cm x 75
µm) packed with C18 reversed phase resin (5 µm, 200 Å). Peptide separation was conducted
with a series of step gradients composed of initial isobaric flow for 5min with 3% solvent B
(0.1% formic acid in acetonitrile), then linear gradient from 3% to 40% for 40min. At the end
of each running, 90% of solvent B was eluted for 10min with the flow rate 250nL/min.
The % gradient of solvent B was against solvent A (0.1% formic acid in H2O). The column
was directly connected to LTQ linear ion-trap mass spectrometer (Finnigan, CA) equipped
with a nano-electrospray ion source. The electrospray voltage was set at 1.95 kV, and the
threshold for switching from MS to MS/MS was 500. The normalized collision energy for
MS/MS was 35% of main radio frequency amplitude (RF) and the duration of activation was
30 ms. All spectra were acquired in data-dependent scan mode. Each full MS scan was
followed by five MS/MS scan corresponding from the most intense to the fifth intense peaks
of full MS scan.
Data analysis
The acquired LC-ESI-MS/MS fragment spectra was searched in the BioWorksBrowserTM
(version Rev. 3.3.1 SP1, Thermo Fisher Scientific Inc., CA) with the SEQUEST search
engines
against
National
Center
for
Biotechnology
Information
(http://www.ncbi.nlm.nih.gov/) non-redundant human database. The searching conditions
were trypsin enzyme specificity, a permissible level for two missed cleavages, peptide
tolerance; ±2 amu, a mass error of ±1 amu on fragment ions and fixed modifications of
carbamidomethylation of cysteine (+57 Da) and oxidation of methionine (+16 Da) residues.