Figure 3.13. Purified chitinases and CBP21 derived from
show a protein marker (left lane), the protein contents in the periplasmic extract from witch ChiB (mw: 55.5 kDa), ChiC (ChiC1 mw: 52 kDa, ChiC2: 36 kDa) and CBP21 (mw: 18.8 kDa finally the purified proteins. All proteins were completely purified
(section 2.15.4). Note that purified ChiC results in two protein, one full variant (ChiC2) lacking the substrate binding modules, CBM12 and
3.4 Determination of protein identity
Since EndoH treatment of AtCBM33A
gel (Figure 3.12) protein identification was carried out by gel with analyzed purified AtCBM33A
was cut out and trypsin digested according to section analyzed using MALDI-TOF MS (
against the NCBI-database for AtCBM33A with protein sequence coverage of 30 % and a score of 124 (see Appendix E for output from Mascot;
analysis).
by affinity chromatography with chitin beads according to section step purifications are shown in Appendix D, Figure
PAGE gels illustrating the purity of the purified proteins. The data show the three chitinases and CBP21 were completely purified. Note that part of the purified domain and lack the two extra binding domains, CBM12 and is truncated version of the protein is referred to as ChiC2, while the full
chitinases and CBP21 derived from S. marcescens. The coomassie-stained SDS
show a protein marker (left lane), the protein contents in the periplasmic extract from witch ChiA (mw: 61 kDa), ChiB (mw: 55.5 kDa), ChiC (ChiC1 mw: 52 kDa, ChiC2: 36 kDa) and CBP21 (mw: 18.8 kDa) was
ied proteins. All proteins were completely purified by affinity chromatography using
Note that purified ChiC results in two protein, one full-length protein (ChiC1) and one truncated nding modules, CBM12 and fibronectin III-domain.
Determination of protein identity
CBM33AHis did not result in a clear protein bond on the ) protein identification was carried out by MS-analysis. From the SDS
CBM33AHis a piece of the protein-smear (at approximately was cut out and trypsin digested according to section 2.19.1. The trypsin digested
TOF MS (see section 2.19.2) and gave a positive match
CBM33A with protein sequence coverage of 30 % and a score for output from Mascot; the protein is named ATEG_07286 length protein (ChiC1) and one truncated
the SDS-PAGE From the SDS-PAGE smear (at approximately 55 kDa) trypsin digested protein was match in search CBM33A with protein sequence coverage of 30 % and a score named ATEG_07286 in this
3.5 Binding assays
3.5.1 Substrate binding of
Binding properties of the non
periplasmic extracts of the production strains, were chitinA, xylan and filter paper; see table 2.1 for at pH 7.5 (Figure 3.).
Figure 3.14. Binding of non-purified extracts to α-chitinA, β- chitinA, xylan and amount of substrate) were analysed on SDS 1200 rpm. Note that the lanes with (pelleted by centrifugation), whereas the
after pelleting xylan). A protein marker (left lane in both gels) was used for size marker proteins in between 20 and 40 kDa are labelled.
concentrations were observed between the periplasmic extract an Neither of the proteins bound to cellulose
The binding properties of 0.7 µM purified further examined at varying pH, ranging from 3 temperature with shaking (1200 rpm).
substrate-free sample (÷) were visualized by SDS
Substrate binding of CfCBM33B-N visualized by SDS-page
the non-purified CfCBM33A-N and CfCBM33B-N, as periplasmic extracts of the production strains, were tested with different substrates (
; see table 2.1 for details on the substrate) according to section
purified CfCBM33A-N (left) and CfCBM33B-N (right) as present in
, xylan and celluloseC at pH 7.5. Samples (100 µ l periplasmic extract and an equal re analysed on SDS-PAGE after incubation for 3 hours at room temperature with shaking at with α-chitinA, β-chitinA and celluloseC show proteins bound to the substrates whereas the xylan lanes show the unbound proteins (proteins left in the supernatant A protein marker (left lane in both gels) was used for size-determination of the proteins. All marker proteins in between 20 and 40 kDa are labelled. Periplasmic extract containing the expressed protein is
representing the respective proteins (~21 kDa) is marked with an arrow.
was observed for both CfCBM33A-N and CfCBM33B did not show detectable binding to β-chitinA, while CfCBM33B-N showed strong
substrate. Data for xylan are not conclusive, because, the bound fract could not be analyzed for technical reasons. Analysis of the unbound material (Fig. 3.13) did indicate that binding to xylan is weak or absent for both proteins (no differences in protein concentrations were observed between the periplasmic extract and the unbound protein sample
celluloseC.
0.7 µM purified CfCBM33B-N towards 50 mg/ml
varying pH, ranging from 3 to 9, when incubated for 3 hours at room temperature with shaking (1200 rpm). Protein bound to the substrate (+) and protein in the
visualized by SDS-page (Figure 3.15Figure 3.12).
99 Samples (100 µl periplasmic extract and an equal PAGE after incubation for 3 hours at room temperature with shaking at show proteins bound to the substrates w the unbound proteins (proteins left in the supernatant determination of the proteins. All ntaining the expressed protein is the respective proteins (~21 kDa) is marked with an arrow.
N and CfCBM33B-N.
N showed strong are not conclusive, because, the bound fraction could not be analyzed for technical reasons. Analysis of the unbound material (Fig. 3.13) did
100
Figure 3.12. Binding of CfCBM33B-N to β added to samples containing 50 % buffer and 50 %
concentration 50 mg/ml) or with 100 % buffer (indicated by ÷) and incubated at 37°C with shaking 3 hours. The gels show protein bound to the substrate
were tested to check for pH-induced effects on the soluble protein.
The results indicate that binding is clearly pH
the pH range below 5 and above 9, while optimal binding i At pH 5, which is close to the proteins
shown by the absence of protein in the pellet upon centrifugation (not shown).
3.5.2 Binding of AtCBM33A titration calorimetry
Isothermal titration calorimetry (ITC) experiments
by Maher Abou Hachem and colleagues at the department of syste protein chemistry, Denmark Technical University
not known). ITC is a technique that measures the released or absorbed heat from a biomolecular binding event. From the measured data, dis
(average number of binding sites per mole of protein, N), enthalpy ( calculated. AtCBM33AHis was titrated with
of seven glucose units, and the results are shown in
0.5 and the calculated dissociation constant 36 µM, indicating a moderate binding affinity towards β-cyclodextrin.
N to β-chitinA vary according to pH. 0.7 µ M purified CfCBM33B added to samples containing 50 % buffer and 50 % suspension of pre-washed β-chitinA(indicated by
with 100 % buffer (indicated by ÷) and incubated at 37°C with shaking
bound to the substrate (+) and the reference solutions (÷). The reference solutions induced effects on the soluble protein.
is clearly pH-dependent. Low substrate binding is observed in the pH range below 5 and above 9, while optimal binding is seen at pH values between 6 and 8.
the proteins calculated isoelctric point, CfCBM33B-N precipitated, as of protein in the reference sample (Figure 3.15) and by the occurrence of a
on (not shown).
CBM33A
Histo β-cyclodextrin measured by isothermal
Isothermal titration calorimetry (ITC) experiments with purified AtCBM33AHis were conducted by Maher Abou Hachem and colleagues at the department of systems biology, enzyme and protein chemistry, Denmark Technical University (specifications regarding the experiment are ITC is a technique that measures the released or absorbed heat from a biomolecular binding event. From the measured data, dissociation constants (Kd), reaction stoichiometry (average number of binding sites per mole of protein, N), enthalpy (∆H) and entropy (
was titrated with β-cyclodextrin, a cyclic starch analogue consisting units, and the results are shown in Figure 3.. The measured stoichiometry is 0.5 and the calculated dissociation constant 36 µM, indicating a moderate binding affinity CBM33B-N was (indicated by +; Final chitin with 100 % buffer (indicated by ÷) and incubated at 37°C with shaking at 1200 rpm for ns (÷). The reference solutions
substrate binding is observed in between 6 and 8.
N precipitated, as ) and by the occurrence of a
cyclodextrin measured by isothermal
were conducted ms biology, enzyme and (specifications regarding the experiment are ITC is a technique that measures the released or absorbed heat from a biomolecular sociation constants (Kd), reaction stoichiometry H) and entropy (∆S) can be a cyclic starch analogue consisting . The measured stoichiometry is 0.5 and the calculated dissociation constant 36 µM, indicating a moderate binding affinity
101
0 .0 0 .5 1 .0 1 .5 2 .0
-1 2 .0 -1 0 .0 -8 .0 -6 .0 -4 .0 -2 .0 0 .0
D a ta : e g2 2 0 5 2 0 1 2 _ N D H M o d e l: O ne S ite s C hi^2 /D o F = 1 .6 9 7 E 4 N 0 .5 4 5 ±0 .0 1 2 6 S ite s K 2 .7 4 E 4 ±1 .8 8 E 3 M- 1
∆H -1 .5 0 7 E 4 ±4 7 5 .8 ca l/m o l
∆S -3 0 .2 c a l/m o l/d e g
e g 2 2 0 5 2 0 1 2 _ N D H e g 2 2 0 5 2 0 1 2 _ F it
M o la r R a tio kcal mol-1 of injectant
Figure 3.16. ITC experiment of AtCBM33His titrated with β-cyclodextrin. The Figure shows the raw data (black), the fitted line (red) and thermodynamic data derived from the experiment. See Appendix F for raw data.
102