Sabatier Principle For Interfacial (Heterogeneous) Enzyme Catalysis

You might also like

Download as pdf or txt
Download as pdf or txt
You are on page 1of 16

Subscriber access provided by EKU Libraries

Article
Sabatier Principle for Interfacial (Heterogeneous) Enzyme Catalysis
Jeppe Kari, Johan Pelck Olsen, Kenneth Jensen, Silke Flindt Badino,
Kristian Bertel Rømer Mørkeberg Krogh, Kim Borch, and Peter Westh
ACS Catal., Just Accepted Manuscript • DOI: 10.1021/acscatal.8b03547 • Publication Date (Web): 12 Nov 2018
Downloaded from http://pubs.acs.org on November 12, 2018

Just Accepted

“Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted
online prior to technical editing, formatting for publication and author proofing. The American Chemical
Society provides “Just Accepted” as a service to the research community to expedite the dissemination
of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in
full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully
peer reviewed, but should not be considered the official version of record. They are citable by the
Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore,
the “Just Accepted” Web site may not include all articles that will be published in the journal. After
a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web
site and published as an ASAP article. Note that technical editing may introduce minor changes
to the manuscript text and/or graphics which could affect content, and all legal disclaimers and
ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or
consequences arising from the use of information contained in these “Just Accepted” manuscripts.

is published by the American Chemical Society. 1155 Sixteenth Street N.W.,


Washington, DC 20036
Published by American Chemical Society. Copyright © American Chemical Society.
However, no copyright claim is made to original U.S. Government works, or works
produced by employees of any Commonwealth realm Crown government in the
course of their duties.
Page 1 of 15 ACS Catalysis

1
2
3
4 Sabatier Principle for Interfacial (Heterogeneous) Enzyme
5
6
Catalysis
7 Jeppe Kari1, Johan P. Olsen2, Kenneth Jensen2, Silke F. Badino1, Kristian B.R.M Krogh2, Kim Borch2 and Peter
8 Westh1*
9 1Research Unit for Functional Biomaterials, Roskilde University, 1 Universitetsvej, DK-4000, Denmark.
10 2Novozymes A/S, Krogshøjvej 36, DK-2880, Bagsværd, Denmark.
11 *corresponding author. Email pwesth@ruc.dk
12
13
14 ABSTRACT: The Sabatier Principle states that optimal catalysis occurs when interactions between
15 catalyst and substrate are of intermediary strength. Although qualitative in nature, this concept has
16 proven extremely useful within (non-biochemical) heterogeneous catalysis. In the current work, we
17 show that the principle may be applied to an interfacial enzyme reaction. Specifically, we studied the
18 breakdown of cellulose by different cellulases (wild types and variants) and found that the results
19
could be rationalized in so-called volcano plots that are emblematic of the principle. This implies that
20
21 the rate of the complex enzymatic reaction can be described by a single parameter (binding strength),
22 and we show how this may help elucidating e.g. rate-controlling steps and relationships of substrate
23 load and enzymatic efficacy. On a more general level, we propose that the Sabatier Principle may be
24 widely applicable to interfacial enzyme processes, and hence open an avenue to the application within
25 biocatalysis of some of the principles and practices originally developed for heterogeneous catalysis.
26
27
28 KEYWORDS: cellulase; cellulose; enzyme kinetics; protein engineering; heterogeneous catalysis;
29 Sabatier principle; volcano curve; Linear free energy relationship
30
31
32 Enzyme kinetics provides the experimental link between structure and function in biocatalysis. Most
33
work in the field is at least partially rooted in the seminal model of Michaelis and Menten 1, in which
34
35 the first step of the process is the association of two freely diffusible species, enzyme and substrate.
36
37 This picture, however, is not representative for a large group of reactions that involve surface
38
associated enzyme or insoluble substrate. It has been argued that most enzyme reactions in vivo
39
40 actually occur in the heterogeneous environment of an interface 2, and interfacial reactions also
41
42 dominate industrial- 3 and bioanalytical 4 applications of enzymes. In light of this, it may be useful to
43
classify enzyme reactions with respect to the state of the enzyme and substrate. Indeed, this idea
44
45 mirrors the immensely successful distinction within conventional (non-biochemical) catalysis,
46
47 between homogeneous (bulk) and heterogeneous (interfacial) processes 5. If we transfer this concept
48
49
to enzyme reactions, there appears to be three situations that are commonly encountered and
50 fundamentally different with respect to the state of enzyme and substrate. These classes of reactions
51
52 are exemplified by the cartoons and experimental data in Fig. 1. All three panels show traditional
53
54 saturation kinetics, where the reaction rate levels off towards Vmax as the substrate concentration
55 increases. The first case (Fig 1A) describes a standard (homogenous) enzyme reaction, where both
56
57 enzyme and substrate are in solution, while the two other cases describe interfacial reactions. This is
58
59 either surface-bound enzyme acting on a diffusible substrate as in Fig. 1B, or an insoluble substrate
60 modified by dissolved enzyme (Fig. 1C). It is tempting to suggest that the wide range of principles and

1
ACS Paragon Plus Environment
ACS Catalysis Page 2 of 15

1
2
3 practices developed within (non-biochemical) heterogeneous catalysis could be useful in attempts to
4
5 rationalize the kinetics of interfacial enzyme reactions such as those in Figs. 1B and 1C. This link
6
7 remains essentially unexploited perhaps because catalyst have traditionally been classified as either
8 homogenous, heterogeneous or biochemical 6-8, without much considerations of connection between
9
10 the two latter. In the current work, we exemplify this connection, and demonstrate how one of the
11
12 most fundamental concepts in conventional heterogeneous catalysis, the Sabatier Principle, can be
13 directly applied to an interfacial enzyme reaction of the type in Fig. 1C.
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34 FIG.1. Steady-state rates (v0) plotted against substrate concentration for three different types of enzyme
35
reactions. Symbols are experimental data (see details in the Supporting Information) and solid lines are best fit
36
37 to the Michaelis-Menten equation. A) Homogeneous enzyme kinetics with enzyme and substrate in aqueous
38
solution. The data reflects hydrolysis of a chromogenic substrate analog by the cellulase Cel7A from Trichoderma
39
40 reesei. B) Heterogeneous enzyme kinetics of a surface-immobilized enzyme (Cellobiose Dehydrogenase (CDH)
41
from P. chrysosporium acting on dissolved cellobiose. C) Heterogeneous enzyme kinetics of a soluble enzyme,
42
43 Cel7A, acting on an insoluble substrate (cellulose). In all cases, we see the conventional hyperbolic growth
44
45 towards Vmax, where all enzyme molecules are engaged in a complex when the substrate becomes in large
46 excess. This is illustrated in the cartoons, where the enzyme is consistently green while the substrate is black.
47
48
49 The century-old Sabatier Principle states that efficient catalysis occur when the catalyst binds its
50
51 reactant with an intermediate strength 9. Weaker interaction is unfavorable because the population
52
53 of intermediate (the Michaelis complex for an enzyme reaction) becomes very low. Stronger binding
54
is also unfavorable for the catalytic rate because a very stable intermediate will turn over and
55
56 dissociate slowly. This concept is widely applied within inorganic, heterogeneous catalysis 10-11, and
57
58 although qualitative in nature, it has proven very useful as guidance both in mechanistic analyses and
59
the selection or design of new catalysts. The advantage of the Sabatier Principle is that it simplifies
60

2
ACS Paragon Plus Environment
Page 3 of 15 ACS Catalysis

1
2
3 the problem by introducing a single parameter (the stability of the intermediate) that describes
4
5 catalytic efficacy. Experimentally, the principle is readily illustrated in a so-called volcano plot, which
6
7 has some measure of the catalytic rate on the ordinate and the stability of the intermediate on the
8 abscissa 12. The appearance of a maximum in such plots corroborates the general principle, and its
9
10 location defines the optimal binding strength for catalysis under the given conditions. The idea of an
11
12 intermediary stability of the intermediate is also deeply rooted in enzymology and extensively used
13 both to explain the basics of enzyme catalysis 13-14, and in more specialized treatments of biocatalysis
14
15 15-16.Nevertheless, the Sabatier Principle and volcano plots have not been widely used in this field.
16
17 Recently, Lin et al. 17 reported Sabatier-like kinetic behavior of designed DNA-enzyme nanostructures,
18
but it was concluded that the volcano plot relied on substrate interactions with the DNA-scaffold of
19
20 the nanostructure and not actual enzyme-substrate contacts. In the current work, we show that a
21
22 group of cellulases including 3 wild type enzymes and 12 enzyme variants with different affinity for
23
their insoluble substrate show the characteristic Sabatier behavior. The volcano plot derived from the
24
25 kinetic measurements helped us reconcile earlier controversies regarding the rate-limiting step for
26
27 cellulases, and on a more general level, we suggest that the approach could provide a strong tool for
28
the understanding and design of interfacial enzymes. Judging from the experiences within
29
30 conventional heterogeneous catalysis, the potential of this approach could be significant.
31
32
33
Results
34
35 Real-time progress curves for a range of substrate loads were measured for all 15 enzymes as
36
37 described in the Methods section, and the raw data can be found in the Supporting Information. As
38
39
often seen for cellulases 18-19, we observed a transient burst in activity followed by a near-linear
40 progress curve. We defined the initial steady-state rate, v0, as the slope of the linear part of the
41
42 progress curve and plotted vo as a function of the substrate load for all enzymes. Examples for the
43
44 three wild types (Cel6A, Cel7A and Cel12A) are shown in Fig. 2, and the analogous plots for the variants
45 can be found in the Supporting Information. We used non-linear regression to analyze these plots with
46
𝑉𝑚𝑎𝑥𝑆0
47 respect to the Michaelis Menten equation, 𝑣0 = 𝑆0 + 𝐾𝑀, and the resulting parameters are given as the
48
49 turnover number, Vmax/E0, and KM, in Tab. 1.
50
51
52
53
54
55
56
57
58
59
60

3
ACS Paragon Plus Environment
ACS Catalysis Page 4 of 15

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30 Fig.2. Michaelis Menten plots for the three wild-type enzymes, Cel6A, Cel7A and Cel12A. Symbols are
31 experimental data and lines are best fits of the Michaelis Menten equation. Dashed lines are extrapolations of
32
33 the Michaelis Menten curves. The substrate was microcrystalline cellulose (Avicel).
34
35
36 To test the applicability of the Sabatier Principle, we used the specific rate (v0/E0 in s-1) at a fixed
37
38 substrate load as a measure of catalytic efficacy, and the Michalis constant, KM, as a measure of
39
enzyme-substrate affinity. The choice of KM was based on the suggestion that this parameter provides
40
41 a reasonable measure of the dissociation constant of the enzyme-substrate complex for this type of
42
43 reaction 20. We expressed affinity as the relative standard free energy of enzyme-substrate binding,
44
45
Go as
46
K 
47 G o   RT ln  M ,i  (1)
 K 
48 M , ref

49
50
51 where KM,i is the Michaelis constant for the enzyme in question and KM,ref is the value for a reference
52
53 enzyme. We chose the Cel6A wild-type as reference, and it follows that Go is zero for this enzyme
54
55 and negative/positive for enzymes with higher/lower substrate affinity. The choice of reference only
56 serves to define zero – it does not affect the relative position of the variants.
57
58
59
60

4
ACS Paragon Plus Environment
Page 5 of 15 ACS Catalysis

1
2
3 Table 1. Kinetic parameters for the investigated enzymes; the three wild types, Cel6A, Cel7A and Cel12A from
4
5 Trichoderma reesei, and 12 variants of Cel7A. Mutations in the Cel7A variants are given by the one-letter code.
6 Cel6A and Cel7A have separate Carbohydrate Binding Modules (CBMs) while Cel12A does not have a CBM.
7
8 Variants 1-9 have the normal CBM and linker from Cel7A, but are mutated in the catalytic domain. Variants 10-
9 12 do not have a CBM and linker, and some of them are further mutated in the catalytic domain as listed.
10
11 Experimental data for the Cel6A wild type 21, Cel7A wild type and variants 1, 10 and 11 are taken from an earlier
12 publication 22. The other enzymes were characterized using the same procedure.
13
14
15
16 Enzyme Mutation Vmax/E0 (s-1) KM (g/l)
17 Cel7A wild type None 0.20 ±0.01 1.5 ±0.2
18
19 Cel7A variant 1 W38A 0.38 ±0.01 5.9 ±0.3
20
Cel7A variant 2 A100W 0.17 ±0.01 1.2 ±0.2
21
22 Cel7A variant 3 Q101A 0.23 ±0.01 2.2 ±0.3
23
24 Cel7A variant 4 I203T 0.25 ±0.01 2.6 ±0.3
25 Cel7A variant 5 Q101A, Y247F, I203T 0.26 ±0.01 2.2 ±0.3
26
27 Cel7A variant 6 Q101A, Y247F, T246C, Y371C 0.20 ±0.01 1.9 ±0.4
28
29 Cel7A variant 7 N197A, N200A 0.29 ±0.01 2.4 ±0.2
30 Cel7A variant 8 T246C, Y371C 0.21 ±0.01 1.6 ±0.4
31
32 Cel7A variant 9 Q101A, Y247F, T246C, Y371C, R251A, 0.47 ±0.03 13.5 ±2.1
33 S174A, W38A
34 Cel7A variant 10 Catalytic domain, W38A 0.53 ±0.03 24.3 ±2.9
35
36 Cel7A variant 11 Catalytic domain, Wild type 0.34 ±0.02 12.6 ±1.8
37
38
Cel7A variant 12 Catalytic domain Q101A, Y247F, I203T 0.49 ±0.03 16.4 ±2.3
39 Cel12A wild type None 0.54 ±0.02 28.0 ±2.2
40
41 Cel6A wild type None 0.40 ±0.01 5.0 ±0.5
42
43
44 Figure 3 shows specific rates plotted as a function of Go for all investigated enzymes at different
45
46 substrate loads. Specifically, the figure shows the activity of the enzymes at 1 g/l, 10 g/l, 60 g/l and at
47 saturation where the maximal turnover, Vmax/E0 is reached (designated S0 → ∞ in the figure). This
48
49 figure unveils some clear correlations between binding strength and activity, which are discussed
50
51 below.
52
53
54
55
56
57
58
59
60

5
ACS Paragon Plus Environment
ACS Catalysis Page 6 of 15

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
Figure 3. Example of volcano plots for cellulases acting on insoluble cellulose (Avicel). Specific rates, v0/E0, at
35
36 different loads of substrate were plotted as a function of the strength of enzyme-substrate interaction. The
37
38 binding strength, Go, was estimated from the Michaelis constants (Tab. 1) as shown in eq. (1). Symbols
39 represent experimental data, and solid lines are to guide the eye. The vertical transparent lines indicate the
40
41 location of the three wild types as illustrated above the figure. The label S0 in the box specifies saturation
42 values, Vmax/E0, taken from Tab. 1.
43
44
45
46
Discussion
47 The Sabatier Principle makes up an essential tool within non-biochemical, heterogeneous catalysis.
48
49 Thus, the correlation between affinity and activity as expressed in a volcano plot is conceptually
50
51
simple, easy to employ and facilitates both mechanistic analyses and identification of new catalysts 10.
52 To evaluate applicability of the Sabatier Principle to an interfacial (heterogeneous) enzyme reaction,
53
54 we studied relationships between substrate affinity and catalytic efficacy for a group of 15 cellulases.
55
56 We used the wild types Cel6A, Cel7A and Cel12A from the filamentous fungus Trichoderma reesei,
57 which are among the most thoroughly investigated cellulases, as well as 12 variants of Cel7A. Results
58
59 in Fig. 3 showed typical volcanos when the catalytic rate was plotted against substrate affinity at
60

6
ACS Paragon Plus Environment
Page 7 of 15 ACS Catalysis

1
2
3 intermediate substrate loads (10 and 60 g/l). This is a direct documentation of the Sabatier Principle
4
5 for an enzyme reaction, and in the following, we discuss corollaries of this with respect to rate
6
7 limitation of cellulolytic enzymes and interfacial enzyme catalysis in more general terms.
8 We first note that the optimal affinity for catalysis, i.e. the location of the apex in Fig. 3, Goapex ,
9
10 moved towards lower values (stronger binding) as the substrate became more dilute. At 60 g/l, for
11
12 example, Goapex was about +3 kJ/mol, but at 10 g/l it had fallen to around 0. An analogous shift
13
induced by changes in reactant concentration has also been seen for inorganic catalysts 23-24, and
14
15 probably reflects dilution-induced dissociation of the complex according to the Le Châtelier’s Principle.
16
17 To compensate for a lower complex concentration under dilute conditions, the optimal affinity for
18
catalysis shifts towards stronger binding. This explanation also accounts for the results at both very
19
20 low- and very high substrate loads (i.e. at respectively 1 g/l and saturation with maximal turnover).
21
22 Under these conditions, we did not observe maxima in Fig. 3, and we suggest that this simply reflects
23
24 that Goapex fell outside the investigated range of Go. In other words, high catalytic efficacy in
25 dilute substrate suspensions will require tighter binding (lower Go) than the range covered here,
26
27 and as a result, we only see the downslope on the weak-binding side of the volcano for a load of 1 g/l
28
29 (red line in Fig.3). Conversely, at saturation, where all enzymes are engaged in a complex, catalysis can
30 be improved by looser binding, and we only see the upslope for the curve representing Vmax/E0 (black)
31
32 in Fig. 3. One way to further assess this interpretation would be to obtain experimental data for
33
34 enzymes with higher or lower affinity than those studied here. Cel7A has much stronger substrate
35 binding 25-26 than average hydrolases 27, and hence, weaker binding might be straightforward to
36
37 engineer. Much stronger binding, on the other hand, could be difficult to achieve.
38
39 One interpretation of the apex in the volcano plots is that it marks the boundary between dissociation-
40
control and association-control of the overall enzymatic rate (see Fig 4). To illustrate this, we may
41
42 consider enzymes that are located to the left of the apex (Go < Goapex). Such enzymes form stable
43
44 substrate complexes that tend to accumulate, and the overall reaction rate is hence governed by their
45
46
dissociation. For less stable complexes to the right of the apex (Go > Goapex), the overall process
47 will be accelerated by tighter binding, and one may say that the reaction is association controlled. This
48
49 aspect of the volcano plot is interesting both as a general tool and in specific discussions of rate
50
51 limitation for Cel7A. To illustrate the latter, we note that there has been some controversy regarding
52 the rate-limiting step for Cel7A. Some work has concluded that the rate of association (i.e. the
53
54 formation of a catalytically competent complex) is slow and hence limits the overall reaction rate 28-
55 29,
56 while others have reached the opposite conclusion and suggested a dissociation-controlled
57 mechanism 30-31. The shift in the location of the maximum in Fig. 3 suggest that these controversies
58
59 may rely at least in part on the influence of the substrate load. Thus, the substrate affinity of wild type
60

7
ACS Paragon Plus Environment
ACS Catalysis Page 8 of 15

1
2
3 Cel7A corresponds to Go = -3 kJ/mol and this is on the downslope for low substrate loads (S0=1 g/l).
4
5 It follows that the reaction is association controlled under these conditions. At loads of 10 g/l or higher,
6
7 on the other hand, wild type Cel7A is on the upslope suggesting dissociation-control. We emphasize
8 that this approach to rate-control is qualitative in nature and hence quite coarse compared to rigorous
9
10 analyses of microkinetic reaction schemes. The big advantage, however, is that the approach is model
11
12 free and hence readily applicable on the basis of experimental data without detailed microkinetic
13
understanding of the reaction. This is valuable for cellulolytic reactions, which are only beginning to
14
15 be understood on the level of elementary steps 32-35. We suggest that this simplifying power of volcano
16
17 plots could be a very useful tool in attempts to assess rate control for a range of enzymes acting on
18
insoluble substrates.
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38 Figure 4. Illustration of a Sabatier analysis in interfacial (heterogenous) enzyme catalysis. The highest activity
39
40 under a given experimental condition is found when adsorption- and desorption rates is balanced. This is
41 achieved when the enzyme has an intermediate substrate affinity, such that the stability of the enzyme-
42
43 substrate complex is neither too strong or too week.
44
45
46 Many cellulases are multi-domain enzymes with one or more Carbohydrate Binding Modules (CBM).
47
48 The CBM is considered non-catalytic 36, and primarily serves the purpose of promoting adsorption 37-
49 39. This role has been directly documented in adsorption studies 38, 40, and also appeared from kinetic
50
51 experiments, where enzymes without CBM had a much higher KM regardless of whether a CBM had
52
53 been artificially added to a CBM-less wild type or removed from a wild type with CBM 41. In addition
54
to promoting affinity, CBMs have been shown to help targeting the enzyme to specific crystal planes
55
56 or regions of the substrate 42-44. Although these roles of the CBM obviously appear to promote enzyme
57
58 efficacy, over half of the (wild type) cellulases identified in a recent sequence analysis study did not
59
have a CBM 45. This limited exploitation of CBMs in cellulase evolution appears puzzling, but might be
60

8
ACS Paragon Plus Environment
Page 9 of 15 ACS Catalysis

1
2
3 related to the course of the volcano plot. To illustrate this, we consider the results in Tab.1, which
4
5 show that removal of the CBM changed Go from -3.0 kJ/mol (for wild type Cel7A) to +2.3 kJ/mol for
6
7 variant 11, which was the wild-type catalytic domain without linker and CBM. According to Fig. 3, this
8 shift of over 5 kJ/mol is associated with major change in catalytic efficacy. At a substrate load of 10
9
10 g/l, for example, it would change the reaction from dissociation-control with CBM (Fig. 4, left-side of
11
12 the curve) to association-control without CBM (Fig. 4, right-side of the curve). This implies that a CBM
13
can be advantageous or detrimental for the activity of a given cellulase depending on the dry-matter
14
15 content at which it is working and the substrate affinity of the CBM-less enzyme. As a result,
16
17 evolutionary pressure could be for or against a CBM depending on the location of the apex defined by
18
the specific conditions faced by the organism in question. This interpretation is in line with recent
19
20 experimental studies on the effect of the CBM on activity at different substrate loads and
21
22 temperatures 45-48.
23
The wild types used in this study represents distinctly different types of cellulases. Not only do Cel6A,
24
25 Cel7A and Cel12A belong to different Glycoside Hydrolase families with different overall folds, they
26
27 also differ with respect to catalytic mechanism, mode of substrate attack, degree of processivity and
28
direction of processive movement. In spite of these differences, which essentially span the whole
29
30 range of hydrolytic cellulases, their activity-affinity relationships condense into a simple volcano curve,
31
32 which they share with a group of Cel7A variants. This remarkable unifying power of the volcano plot
33
34
appears to have a significant potential within research and technology of cellulases and possibly other
35 interfacial enzymes. One particularly interesting application, which is directly inspired by work on
36
37 inorganic catalysts 24, is computer-assisted design of industrial enzymes. This could be used, for
38
39 example, in attempts to improve catalytic activity under process conditions and it would involve two
40 steps. First, an experimental volcano plot akin to Fig. 3 should be made under relevant conditions. In
41
42 the second step, variants should be tested in silico with respect to their strength of substrate binding
43
44 using protein-ligand free energy calculations 49-50. The pivot of the strategy is the simple and model
45 free connection between activity and affinity, which replaces the computationally intractable problem
46
47 of assessing catalytic speed with the much more amenable challenge of calculating ligand binding
48
49 strength.
50 In conclusion, we have found that enzymatic efficacy within a group of cellulases could be rationalized
51
52 with respect to the Sabatier Principle. Most of the cellulases had a complex structure with three
53
54 domains (catalytic-, linker- and binding domain), which all interact to different extents with the
55 substrate surface 37, 39, 51. In spite of this complex mode of interaction, the enzymes shared a common
56
57 volcano curve. In fact, even the four investigated enzymes without linker and binding domain (wild
58
59 type of Cel12A and Variants 10-12) fell on the same curve, and this further supports the notion of a
60

9
ACS Paragon Plus Environment
ACS Catalysis Page 10 of 15

1
2
3 simple yet robust relationship between affinity and activity. If this relationship extends beyond the
4
5 single group of enzymes (cellulases) tested here, it could provide a powerful framework for both
6
7 fundamental studies of heterogeneous enzyme catalysis as exemplified in Figs. 1B and 1C, and for
8 practical enzyme design. As a first attempt to assess broader applicability of the principle, we explored
9
10 the literature and found a couple of reports with comprehensive data on both affinity and activity for
11
12 interfacial enzymes other than cellulases. One example addressed the breakdown of starch granules
13 by a range of amylase variants 52, while another investigated hydrolysis of precipitated Serum Albumin
14
15 by variants of Cellulomonas bogoriensis chymotrypsin 53. Although these studies were not rationalized
16
17 along the lines of the Sabatier Principle, they both found an apex in enzyme activity that could be
18
correlated to an intermediate binding strength. These results offer some further support of a more
19
20 general use of the Sabatier Principle for interfacial enzymes, but more experimental work is needed.
21
22 If indeed the Sabatier Principle turns out to be widely applicable to interfacial enzyme reactions, it
23
may act as a bridge between heterogeneous catalysis and biocatalysis, and hence allow enzymologists
24
25 to tap into some of the sophisticated principles and practices developed for inorganic catalysis.
26
27
28
Materials and methods
29
30 Enzymes. Structures and properties of the investigated wild-types from Trichoderma reesei Cel6A,
31
32 Cel7A and Cel12A (also known as respectively CBH2, CBH1 and EG3) have been reviewed recently 54.
33
Briefly, Cel6A is an inverting cellobiohydrolase, which is composed by a catalytic domain and a
34
35 Carbohydrate Binding Module (CBM) connected by a flexible, glycosylated linker. Cel6A is an exo-lytic
36
37 enzyme that attacks the non-reducing end of the cellulose strand and moves processively towards the
38
39
reducing end while cleaving off cellobiose as its main product. Cel7A is also a processive (exo-lytic)
40 cellobiohydrolase with CBM and linker, but it attacks the reducing end of the cellulose strand and uses
41
42 the retaining hydrolytic mechanism. Finally, Cel12A is an endolytic enzyme with little or no
43
44 processivity. It also uses the retaining mechanism, and the enzyme from Trichoderma reesei (used
45 here) does not have a linker and CBM.
46
47 Mutagenesis, expression and purification. The three wild types from Trichoderma reesei described
48
49 above as well as 12 variants of Cel7A (see Tab 1 for mutations) were expressed heterologously in
50 Aspergillus oryzae and purified as described elsewhere22, 55. The purified enzymes showed a single
51
52 band in SDS NuPAGE 4-12% Bis-Tris gel (GE Healthcare) and their concentrations were determined by
53
54 absorbance at 280 nm using extinction coefficients calculated from their amino acid composition 56.
55
56 Kinetics. All measurements were made in a standard 50mM acetate buffer, 2mM CaCl2, pH 5.0 using
57
58 real time measurements with enzyme-functionalized biosensors operated in the amperometric mode.
59
60 The sensors were designed, produced and calibrated in-house as detailed elsewhere 21, 57-58.

10
ACS Paragon Plus Environment
Page 11 of 15 ACS Catalysis

1
2
3 Specifically, we used sensors functionalized with cellulose dehydrogenase (CDH) from Phanerochaete
4
5 chrysosporium 57 to study the retaining cellulases Cel7A and Cel12A (and all variants of Cel7A) and
6
7 sensors functionalized with pyranose dehydrogenase (PDH) from Agaricus meleagris to study the
8 kinetics of the inverting enzyme Cel6A 21. The substrate was Avicel PH101 (Sigma-Aldrich, St. Louis,
9
10 MO), which was suspended in the standard buffer without any further processing. To perform a kinetic
11
12 measurement, we transferred 3 ml suspension to a stirred, double-jacket beaker, which was
13 thermostated at 25.0 °C (c.f. Fig. 1). The reaction was started by the addition of enzyme from a syringe
14
15 pump (Fusion 100, Chemyx, Stafford, USA) to a final concentration of 0.10 µM, and the progress curve
16
17 was recorded continuously for approximately 300s. To produce Michaelis Menten plots, we made
18
progress curves at about ten different substrate loads for each of the 15 enzymes in Tab. 1. The specific
19
20 loads were chosen to be reasonably distributed above and below KM after this parameter had been
21
22 approximately determined in preliminary experiments. In most cases, we used about 10xKM for the
23
highest substrate load, but in some trials, we could not get higher than 5-8 times KM because the
24
25 highest load that could be practically handled in these experiments was about 150 g/l. Nevertheless,
26
27 KM and Vmax could be well resolved as indicated by the error margins in Tab. 1. Experimental data for
28
the Cel6A wild type, Cel7A wild type and variants 1, 10 and 11 are taken from an earlier publication 21-
29
30 22, which used the same experimental protocol.
31
32
Supporting Information
33
34
35 Progress curves and steady-state analysis of all investigated enzymes. Material and Method
36
concerning data shown in figure 1.
37
38
39 Acknowledgements
40
41
The research was supported by Innovation Fund Denmark (Grants 5150-00020 to PW) and Novo
42 Nordisk foundation (Grant number NNF15OC0016606 to PW).
43
44
45 Author contributions
46
47 JK, KB and PW conceived and coordinated the study. SB, KK and KJ provided technical assistance with
48 expression and purification of the enzymes. JK and JO designed, performed and analyzed the
49
50 experiments. JK and PW wrote the paper. All authors reviewed the results and approved the final
51
52 version of the manuscript
53
54 Competing interests
55
56 JPO, KJ, KBRMK and KB are employed at Novozymes, a major producer of industrial enzymes.
57
58
59
60

11
ACS Paragon Plus Environment
ACS Catalysis Page 12 of 15

1
2
3 References
4
5 1. Segel, I. H., Enzyme kinetics: behavior and analysis og rapid equilibrium and steady-state
6 enzyme systems. John Wiley & Sons Inc.: New York, 1975.
7 2. McLaren, A. D.; Packer, L., Some aspects of enzyme reactions in heterogenous systems. Adv.
8 Enzymol. Relat. Areas Mol. Biol. 1970, 33, 245-308.
9
3. Kirk, O.; Borchert, T. V.; Fuglsang, C. C., Industrial enzyme applications. Curr. Opin. Biotechnol.
10
11 2002, 13 (4), 345-351.
12 4. Gutiérrez, O. A.; Chavez, M.; Lissi, E., A Theoretical Approach to Some Analytical Properties of
13 Heterogeneous Enzymatic Assays. Anal. Chem. 2004, 76 (9), 2664-2668.
14 5. Rothenberg, G., Catalysis: Concepts and Green Applications. Wiley-VCH Verlag GmbH & Co. :
15 Weinheim, Germany., 2008.
16 6. Lam, M. K.; Lee, K. T.; Mohamed, A. R., Homogeneous, heterogeneous and enzymatic catalysis
17 for transesterification of high free fatty acid oil (waste cooking oil) to biodiesel: A review. Biotechnol.
18
Adv. 2010, 28 (4), 500-518.
19
7. Oyama, S. T.; Somorjai, G. A., Homogeneous, heterogeneous, and enzymatic catalysis. J. Chem.
20
21 Educ. 1988, 65 (9), 765.
22 8. Zecchina, A.; Groppo, E., Heterogeneous, homogeneous, and enzymatic catalysis: three
23 branches of the same scientific chapter. Introductory remarks to the “Concepts in catalysis” issue.
24 Rendiconti Lincei 2017, 28 (1), 1-4.
25 9. Sabatier, P., Hydrogénations et déshydrogénations par catalyse. Ber. Dtsch. Chem. Ges. 1911,
26 44, 1984-2001.
27 10. Bligaard, T.; Norskov, J. K.; Dahl, S.; Matthiesen, J.; Christensen, C. H.; Sehested, J., The
28
Bronsted-Evans-Polanyi relation and the volcano curve in heterogeneous catalysis. J. Catal. 2004,
29
30 224 (1), 206-217.
31 11. Nørskov, J.; Studt, F.; Abild-Pedersen, F.; Bligaard, T., Fundamental Concepts in Heterogeneous
32 Catalysis. John Wiley & Sons: Hoboken, New Jersie, 2014.
33 12. Balandin, A. A., The multiplet theory of catalysis - energy factors in catalysis. Russ. Chem. Rev.
34 1964, 33 (5), 258-275.
35 13. Fersht, A., Structure and Mechanism in Protein Science. 2nd ed.; W.H. Freeman and Company:
36 New York, 1998.
37
14. Nelson, D. L.; Cox, M. M., Lehninger Principles of Biochemistry. W.H. Freeman: New York,
38
39
2017.
40 15. Fersht, A. R., Catalysis, binding and enzyme-substrate complementarity. Proc. R. Soc. Lond. B
41 Biol. Sci. 1974, 187 (1089), 397-407.
42 16. Pettersson, G., Effect of evolution on the kinetic properties of enzymes. Eur. J. Biochem. 1989,
43 184 (3), 561-6.
44 17. Lin, J. L.; Wheeldon, I., Kinetic Enhancements in DNA-Enzyme Nanostructures Mimic the
45 Sabatier Principle. Acs Catalysis 2013, 3 (4), 560-564.
46 18. Cruys-Bagger, N.; Tatsumi, H.; Ren, G. R.; Borch, K.; Westh, P., Transient Kinetics and Rate-
47
Limiting Steps for the Processive Cellobiohydrolase Cel7A: Effects of Substrate Structure and
48
49 Carbohydrate Binding Domain. Biochemistry 2013, 52 (49), 8938-8948.
50 19. Murphy, L.; Cruys-Bagger, N.; Damgaard, H. D.; Baumann, M. J.; Olsen, S. N.; Borch, K.; Lassen,
51 S. F.; Sweeney, M.; Tatsumi, H.; Westh, P., Origin of Initial Burst in Activity for Trichoderma reesei
52 endo-Glucanases Hydrolyzing Insoluble Cellulose J. Biol. Chem. 2012, 287, 1252-1260.
53 20. Cruys-Bagger, N.; Elmerdahl, J.; Praestgaard, E.; Borch, K.; Westh, P., A steady-state theory for
54 processive cellulases. FEBS J. 2013, 280 (16), 3952-3961.
55 21. Cruys-Bagger, N.; Badino, S. F.; Tokin, R.; Gontsarik, M.; Fathalinejad, S.; Jensen, K.; Toscano,
56
M. D.; Sorensen, T. H.; Borch, K.; Tatsumi, H.; Valjamae, P.; Westh, P., A pyranose dehydrogenase-
57
58
based biosensor for kinetic analysis of enzymatic hydrolysis of cellulose by cellulases. Enzyme Microb
59 Technol 2014, 58-59, 68-74.
60

12
ACS Paragon Plus Environment
Page 13 of 15 ACS Catalysis

1
2
3 22. Kari, J.; Olsen, J.; Borch, K.; Cruys-Bagger, N.; Jensen, K.; Westh, P., Kinetics of
4
Cellobiohydrolase (Cel7A) Variants with Lowered Substrate Affinity. J. Biol. Chem. 2014, 289 (47),
5
6
32459-32468.
7 23. Jacobsen, C. J. H.; Dahl, S.; Boisen, A.; Clausen, B. S.; Topsøe, H.; Logadottir, A.; Nørskov, J. K.,
8 Optimal Catalyst Curves: Connecting Density Functional Theory Calculations with Industrial Reactor
9 Design and Catalyst Selection. J. Catal. 2002, 205 (2), 382-387.
10 24. Norskov, J. K.; Bligaard, T.; Rossmeisl, J.; Christensen, C. H., Towards the computational design
11 of solid catalysts. Nat. Chem. 2009, 1 (1), 37-46.
12 25. Colussi, F.; Sorensen, T. H.; Alasepp, K.; Kari, J.; Cruys-Bagger, N.; Windahl, M. S.; Olsen, J. P.;
13 Borch, K.; Westh, P., Probing Substrate Interactions in the Active Tunnel of a Catalytically Deficient
14
Cellobiohydrolase (Cel7). J. Biol. Chem. 2015, 290 (4), 2444-2454.
15
16 26. Beckham, G. T.; Matthews, J. F.; Peters, B.; Bomble, Y. J.; Himmel, M. E.; Crowley, M. F.,
17 Molecular-Level Origins of Biomass Recalcitrance: Decrystallization Free Energies for Four Common
18 Cellulose Polymorphs. J. Phys. Chem. B 2011, 115 (14), 4118-4127.
19 27. Sousa, S. F.; Ramos, M. J.; Lim, C.; Fernandes, P. A., Relationship between Enzyme/Substrate
20 Properties and Enzyme Efficiency in Hydrolases. ACS Catalysis 2015, 5 (10), 5877-5887.
21 28. Fox, J. M.; Levine, S. E.; Clark, D. S.; Blanch, H. W., Initial- and Processive-Cut Products Reveal
22 Cellobiohydrolase Rate Limitations and the Role of Companion Enzymes. Biochemistry 2012, 51 (1),
23
442-452.
24
25
29. Maurer, S. A.; Bedbrook, C. N.; Radke, C. J., Cellulase Adsorption and Reactivity on a Cellulose
26 Surface from Flow Ellipsometry. Ind. Eng. Chem. Res. 2012, 51 (35), 11389-11400.
27 30. Cruys-Bagger, N.; Elmerdahl, J.; Praestgaard, E.; Tatsumi, H.; Spodsberg, N.; Borch, K.; Westh,
28 P., Pre-steady state kinetics for the hydrolysis of insoluble cellulose by Trichoderma reesei Cel7A. J.
29 Biol. Chem. 2012, 287, 18451-18458.
30 31. Jalak, J.; Valjamae, P., Mechanism of Initial Rapid Rate Retardation in Cellobiohydrolase
31 Catalyzed Cellulose Hydrolysis. Biotechnol. Bioeng. 2010, 106 (6), 871-883.
32 32. Jalak, J.; Kurasin, M.; Teugjas, H.; Valjamae, P., Endo-exo Synergism in Cellulose Hydrolysis
33
Revisited. J. Biol. Chem. (In press) 2012, 287 (34), 28802-28815.
34
35 33. Knott, B. C.; Momeni, M. H.; Crowley, M. F.; Mackenzie, L. F.; Gotz, A. W.; Sandgren, M.;
36 Withers, S. G.; Stahlberg, J.; Beckham, G. T., The Mechanism of Cellulose Hydrolysis by a Two-Step,
37 Retaining Cellobiohydrolase Elucidated by Structural and Transition Path Sampling Studies. J. Am.
38 Chem. Soc. 2014, 136 (1), 321-329.
39 34. Sorensen, T. H.; Cruys-Bagger, N.; Borch, K.; Westh, P., Free Energy Diagram for the
40 Heterogeneous Enzymatic Hydrolysis of Glycosidic Bonds in Cellulose. J. Biol. Chem. 2015, 290 (36),
41 22203-22211.
42
35. Jung, J.; Sethi, A.; Gaiotto, T.; Han, J. J.; Jeoh, T.; Gnanakaran, S.; Goodwin, P. M., Binding and
43
44 movement of individual Cel7A cellobiohydrolases on crystalline cellulose surfaces revealed by single-
45 molecule fluorescence imaging. The Journal of biological chemistry 2013, 288 (33), 24164-72.
46 36. Armenta, S.; Moreno-Mendieta, S.; Sánchez-Cuapio, Z.; Sánchez, S.; Rodríguez-Sanoja, R.,
47 Advances in molecular engineering of carbohydrate-binding modules. Proteins: Struct., Funct., Bioinf.
48 2017, 85 (9), 1602-1617.
49 37. Tomme, P.; Vantilbeurgh, H.; Pettersson, G.; Vandamme, J.; Vandekerckhove, J.; Knowles, J.;
50 Teeri, T.; Claeyssens, M., Studies of the cellulolytic system of trichoderma-reesei qm-9414 - analysis
51
of domain function in 2 cellobiohydrolases by limited proteolysis. Eur. J. Biochem. 1988, 170 (3), 575-
52
53
581.
54 38. Vantilbeurgh, H.; Tomme, P.; Claeyssens, M.; Bhikhabhai, R.; Pettersson, G., Limited
55 proteolysis of the cellobiohydrolase i from trichoderma-reesei - separation of functional domains.
56 FEBS Lett. 1986, 204 (2), 223-227.
57 39. Linder, M.; Teeri, T. T., The roles and function of cellulose-binding domains. J. Biotechnol.
58 1997, 57 (1-3), 15-28.
59
60

13
ACS Paragon Plus Environment
ACS Catalysis Page 14 of 15

1
2
3 40. Stahlberg, J.; Johansson, G.; Pettersson, G., A new model for enzymatic-hydrolysis of cellulose
4
based on the 2-domain structure of cellobiohydrolase-I. Bio-Technology 1991, 9 (3), 286-290.
5
6
41. Sorensen, T. H.; Cruys-Bagger, N.; Windahl, M. S.; Badino, S. F.; Borch, K.; Westh, P.,
7 Temperature Effects on Kinetic Parameters and Substrate Affinity of Cel7A Cellobiohydrolases. J.
8 Biol. Chem. 2015, 290 (36), 22193-22202.
9 42. Boraston, A. B.; Bolam, D. N.; Gilbert, H. J.; Davies, G. J., Carbohydrate-binding modules: fine-
10 tuning polysaccharide recognition. Biochem. J. 2004, 382, 769-781.
11 43. Lehtio, J.; Sugiyama, J.; Gustavsson, M.; Fransson, L.; Linder, M.; Teeri, T. T., The binding
12 specificity and affinity determinants of family 1 and family 3 cellulose binding modules. Proc. Natl.
13 Acad. Sci. U. S. A. 2003, 100 (2), 484-489.
14
44. Fox, J. M.; Jess, P.; Jambusaria, R. B.; Moo, G. M.; Liphardt, J.; Clark, D. S.; Blanch, H. W., A
15
16 single-molecule analysis reveals morphological targets for cellulase synergy. Nat. Chem. Biol. 2013,
17 9, 356.
18 45. Varnai, A.; Siika-aho, M.; Viikari, L., Carbohydrate-binding modules (CBMs) revisited: reduced
19 amount of water counterbalances the need for CBMs. Biotechnol. Biofuels 2013, 6, 30.
20 46. Le Costaouec, T.; Pakarinen, A.; Varnai, A.; Puranen, T.; Viikari, L., The role of carbohydrate
21 binding module (CBM) at high substrate consistency: Comparison of Trichoderma reesei and
22 Thermoascus aurantiacus Cel7A (CBHI) and Cel5A (EGII). Bioresour. Technol. 2013, 143, 196-203.
23
47. Sørensen, T. H.; Cruys-Bagger, N.; Windahl, M. S.; Badino, S.; Borch, K.; Westh, P.,
24
25
Temperature effects on kinetic parameters and substrate affinity of Cel7A cellobiohydrolases. J. Biol.
26 Chem. 2015, 290 (36), 22193-22202.
27 48. Takashima, S.; Ohno, M.; Hidaka, M.; Nakamura, A.; Masaki, H., Correlation between cellulose
28 binding and activity of cellulose-binding domain mutants of Humicola grisea cellobiohydrolase 1.
29 FEBS Lett. 2007, 581 (30), 5891-5896.
30 49. Perez, A.; Morrone, J. A.; Simmerling, C.; Dill, K. A., Advances in free-energy-based simulations
31 of protein folding and ligand binding. Curr. Opin. Struct. Biol. 2016, 36, 25-31.
32 50. Wang, L.; Wu, Y.; Deng, Y.; Kim, B.; Pierce, L.; Krilov, G.; Lupyan, D.; Robinson, S.; Dahlgren, M.
33
K.; Greenwood, J.; Romero, D. L.; Masse, C.; Knight, J. L.; Steinbrecher, T.; Beuming, T.; Damm, W.;
34
35 Harder, E.; Sherman, W.; Brewer, M.; Wester, R.; Murcko, M.; Frye, L.; Farid, R.; Lin, T.; Mobley, D. L.;
36 Jorgensen, W. L.; Berne, B. J.; Friesner, R. A.; Abel, R., Accurate and Reliable Prediction of Relative
37 Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation
38 Protocol and Force Field. J. Am. Chem. Soc. 2015, 137 (7), 2695-2703.
39 51. Payne, C. M.; Resch, M. G.; Chen, L. Q.; Crowley, M. F.; Himmel, M. E.; Taylor, L. E.; Sandgren,
40 M.; Stahlberg, J.; Stals, I.; Tan, Z. P.; Beckham, G. T., Glycosylated linkers in multimodular
41 lignocellulose-degrading enzymes dynamically bind to cellulose. Proc. Natl. Acad. Sci. U. S. A. 2013,
42
110 (36), 14646-14651.
43
44 52. Hardesty, J. O. Biocatalysis at the solid-liquid interface: Subtilisin on surface-bound
45 polypeptides and amylase variants on starch granules. Stanford University, Ann Arbor, Ml, 2008.
46 53. Feller, B. E.; Kellis, J. T.; Cascão-Pereira, L. G.; Robertson, C. R.; Frank, C. W., Interfacial
47 Biocatalysis on Charged and Immobilized Substrates: The Roles of Enzyme and Substrate Surface
48 Charge. Langmuir 2011, 27 (1), 250-263.
49 54. Payne, C. M.; Knott, B. C.; Mayes, H. B.; Hansson, H.; Himmel, M. E.; Sandgren, M.; Stahlberg,
50 J.; Beckham, G. T., Fungal Cellulases. Chem. Rev. 2015, 115 (3), 1308-1448.
51
55. Borch, K.; Jensen, K.; Krogh, K.; Mcbrayer, B.; Westh, P.; Kari, J.; Olsen, J. P.; Sørensen, T. H.;
52
53
Windahl, M. S.; Xu, H. New cellobiohydrolase variant having cellobiohydrolase activity useful for
54 making transgenic plant, and for fermenting a cellulosic material for producing fermentation product
55 e.g. ethanol, n-butanol, isobutanol, acids, alcohols. PCT International Patent Appl.
56 WO/2014/138672, 2014.
57 56. Gasteiger, E.; Gattiker, A.; Hoogland, C.; Ivanyi, I.; Appel, R. D.; Bairoch, A., ExPASy: the
58 proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 2003, 31 (13),
59 3784-3788.
60

14
ACS Paragon Plus Environment
Page 15 of 15 ACS Catalysis

1
2
3 57. Cruys-Bagger, N.; Ren, G.; Tatsumi, H.; Baumann, M. J.; Spodsberg, N.; Andersen, H. D.;
4
Gorton, L.; Borch, K.; Westh, P., An amperometric enzyme biosensor for real-time measurements of
5
6
cellobiohydrolase activity on insoluble cellulose. Biotechnology and bioengineering 2012, 109 (12),
7 3199-204.
8 58. Cruys-Bagger, N.; Tatsumi, H.; Borch, K.; Westh, P., A graphene screen-printed carbon
9 electrode for real-time measurements of unoccupied active sites in a cellulase. Anal. Biochem. 2014,
10 447, 162-168.
11 59. Sorensen, T. H., Windahl, M. S., McBrayer, B., Kari, J., Olsen, J. P., Borch, K., and Westh, P.
12 Loop variants of the thermophile Rasamsonia emersonii Cel7A with improved activity against
13 cellulose. (2016) Biotechnology and bioengineering
14
15
16
17 TOC graphic
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60

15
ACS Paragon Plus Environment

You might also like