Docking and Molecular Dynamics Studies on the Stereoselectivity in the Enzymatic Synthesis

Docking and Molecular Dynamics Studies on the Stereoselectivity in the Enzymatic Synthesis of Carbohydrates

Natércia F. Brás, Pedro A. Fernandes, Maria J. Ramos*

REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do

Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal

* Corresponding author, E-mail address:

Supporting Information

Table SI-1: Summary of the distances involved in the main interactions established between the carbohydrates and the neighbour aminoacids of the active siteof Exo-1,3-ß-Glycosidase from Candida albicans. These average values were obtained after equilibration of MD simulations. (D= Donor, A=Acceptor)

Residue / Exo-(1,3)-Glucosidase from Candida albicans
Solution 1 / d(Å) / Solution 2 / d(Å) / Solution 3 / d(Å)
Glu27 / COO-↔ HO-C3 (D) / 1.74 / COO- ↔ HO-C3 (D) / 2.56 / COO- ↔ HO-C3 (D) / 1.79
COO- ↔ HO-C4 (D) / 1.66 / COO- ↔ HO-C4 (D) / 1.81 / COO- ↔ HO-C4 (D) / 1.67
Phe144 / Apolar ring ↔ Sugar ring (A) / Apolar ring ↔ Sugar ring (A)
Asp145 / COO- ↔ HO-C6 (D) / 1.92
Asn146 / CO ↔ HO-C3 (D) / 1.99 / NH2 ↔ HO-C3 (D) / 2.87 / NH2 ↔ HO-C3 (D) / 3.08
Glu192 / COO- ↔ HO-C3 (A) / 4.49 / COO- ↔ HO-C3 (A) / 1.71 / COO- ↔ HO-C3 (A) / 2.76
COO- ↔ HO-C4 (A) / 1.66 / COO- ↔ HO-C4 (A) / 2.28
Tyr255 / OH ↔ -OOC (Glu286) / 2.04 / OH ↔ -OOC (Glu286) / 1.96 / OH ↔ -OOC (Glu286) / 1.92
Trp363 / Apolar ring ↔ Sugar ring (D) / Apolar ring ↔ Sugar ring (D) / Apolar ring ↔ Sugar ring (D)
Water / OH ↔ HO-C6 (A) / 2.00 / OH ↔ HO-C6 (D) / 1.56 / OH ↔ HO-C1 (A) / 2.07

Table SI-2: Summary of the distances involved in the main interactions established between the carbohydrates and the neighbour aminoacids of the active siteof ß-Glucanase from Humicola insolens. These average values were obtained after equilibration of MD simulations. (D= Donor, A=Acceptor)

Residue / β-Glucanase from Humicola insolens
Solution 1 / d(Å) / Solution 2 / d(Å) / Solution 3 / d(Å)
Arg108 / NH2 ↔ OH-C4 (D) / 2.55
Asp173 / COO- ↔ HO-C3 (D) / 1.77 / COO- ↔ O ring (A) / 3.18
Glu197 / COO- ↔ HO-C2 (D) / 2.07 / COO- ↔ HO-C2 (D) / 1.69 / COO- ↔ HO-C2 (D) / 1.84
Asp199 / COO- ↔ HO-C4 (D) / 1.61 / COO- ↔ HO-C6 (D) / 3.51 / COO- ↔ HO-C6 (D) / 2.04
COO- ↔ HO-C6 (D) / 2.33
Glu202 / COO- ↔ HO-C3 (A) / 2.32 / COO- ↔ HO-C6 (A) / 1.64 / COO- ↔ HO-C4 (A) / 2.15
COO- ↔ HO-C4 (A) / 1.60 / COO- ↔ HO (Water) / 2.23 / COO- ↔ HO (Water) / 1.89
Hie209 / NH ↔ OH-C4 (A) / 2.56 / NH ↔ OH-C4 (D) / 3.15
Asn237 / NH2 ↔ HO-C1 (A) / 2.77
Trp356 / Apolar ring ↔ Sugar ring (A) / Apolar ring ↔ Sugar ring (A)
Water / OH ↔ HO-C1 (A) / 1.65 / OH ↔ HO-C1 (A) / 1.48 / OH ↔ HO-C4 (D) / 2.03
Water / OH ↔ HO-C6 (D) / 2.20 / OH ↔ HO-C6 (A) / 2.35

Table SI-3: Summary of the distances involved in the main interactions established between the carbohydrates and the neighbour aminoacids of the active siteof ß(1-3)-Glycosidase from Thermus thermophilus. These average values were obtained after equilibration of MD simulations. (D= Donor, A=Acceptor)

Residue / β(1-3)-Glycosidase from Thermus thermophilus
Solution 1 / d(Å) / Solution 2 / d(Å)
Gln18 / NH2 ↔ HO-C4 (D) / 2.00 / NH2 ↔ HO-C4 (D) / 1.92
Glu164 / COO- ↔ HO-C3 (A) / 1.82
Tyr284 / OH ↔ -OOC (Glu335) / 1.86 / OH ↔ -OOC (Glu335) / 1.89
Glu338 / COO- ↔ HO-C2 (D) / 1.54 / COO- ↔ HO-C2 (D) / 1.56
Trp385 / Apolar ring ↔ Sugar ring (D) / Apolar ring ↔ Sugar ring (D)
Glu392 / COO- ↔ HO-C4 (A) / 1.70 / COO- ↔ HO-C4 (D) / 2.01
COO- ↔ HO-C6 (A) / 2.59

Table SI-4: Summary of the distances involved in the main interactions established between the carbohydrates and the neighbour aminoacids of the active siteofß-Galactosidase from Escherichia coli. These average values were obtained after equilibration of MD simulations. (D= Donor, A=Acceptor)

Residue / β-Galactosidase from Escherichia coli
Solution 1 / d(Å) / Solution 2 / d(Å) / Solution 3 / d(Å)
Asn102 / NH2 ↔ HO-C4 (D) / 2.04 / NH2 ↔ HO-C4 (D) / 3.78 / NH2 ↔ HO-C4 (D) / 3.77
Asp201 / COO- ↔ HO-C4 (D) / 2.34
Asn460 / NH2 ↔ HO-C2 (D) / 1.95 / NH2 ↔ HO-C2 (D) / 1.91 / NH2 ↔ HO-C2 (D) / 1.90
Glu461 / COO- ↔ HO-C3 (A) / 1.68
COO- ↔ HO-C4 (A) / 1.70
Tyr503 / OH ↔ -OOC (Glu525) / 1.84 / OH ↔ COO- (Glu525) / 1.90 / OH ↔ -OOC (Glu525) / 1.84
Lys517 / NH2 ↔ HO-C6 (A) / 1.85
Glu537 / COO- ↔ HO-C2 (D) / 1.62 / COO- ↔ HO-C2 (D) / 1.59 / COO- ↔ HO-C2 (D) / 1.59
Trp568 / Apolar ring ↔ Sugar ring (D) / Apolar ring ↔ Sugar ring (D) / Apolar ring ↔ Sugar ring (D)
Trp999 / Apolar ring ↔ Sugar ring (D)
Water / OH ↔ HO-C3 (D) / 1.80 / OH ↔ HO-C3 (A) / 1.83

Table SI-5: Summary of the distances involved in the main interactions established between the carbohydrates and the neighbour aminoacids of the active siteofß-Galactosidase from Penicillium sp. These average values were obtained after equilibration of MD simulations. (D= Donor, A=Acceptor)

Residue / β-Galactosidase from Penicillium sp.
Solution 1 / d(Å) / Solution 2 / d(Å) / Solution 3 / d(Å)
Asn140 / NH2 ↔ HO-C4 (D) / 4.11 / NH2 ↔ HO-C4 (A) / 3.89 / NH2 ↔ HO-C4 (D) / 2.72
Glu142 / COO- ↔ HO-C4 (D) / 1.83 / COO- ↔ HO-C6 (D) / 1.70 / COO- ↔ HO-C4 (D) / 1.70
COO- ↔ HO-C6 (D) / 1.71 / COO- ↔ HO-C3 (A) / 2.00 / COO- ↔ HO-C4 (A) / 2.28
Asn199 / NH2 ↔ HO-C2 (D) / 1.93 / NH2 ↔ HO-C2 (D) / 2.94 / NH2 ↔ HO-C2 (D) / 2.73
Tyr261 / OH ↔ -OOC (Glu299) / 1.84 / OH ↔ -OOC (Glu299) / 1.79 / OH ↔ -OOC (Glu299) / 1.94
Glu299 / OH ↔ HO-C2 (D) / 1.64 / OH ↔ HO-C2 (D) / 1.69 / OH ↔ HO-C2 (D) / 1.75
Tyr343 / Apolar ring ↔ Sugar ring (D) / Apolar ring ↔ Sugar ring (D) / Apolar ring ↔ Sugar ring (D)
Glu807 / COO- ↔ HO-C3 (A) / 1.54
Trp809 / Apolar ring ↔ Sugar ring (A)

Table SI-6: Summary of the distances involved in the main interactions established between the carbohydrates and the neighbour aminoacids of the active siteofß-Glycosidase from Sulfolobus sulfaticuris.These average values were obtained after equilibration of MD simulations. (D= Donor, A=Acceptor)

Residue / β-Glycosidase from Sulfolobus sulfaticuris
Solution 1 / d(Å) / Solution 2 / d(Å) / Solution 3 / d(Å)
Gln20 / CO ↔ HO-C3 (D) / 2.19 / CO ↔ HO-C3 (D) / 1.76
Ans205 / NH2 ↔ HO-C2 (D) / 2.09 / NH2 ↔ HO-C2 (D) / 1.95 / NH2 ↔ HO-C2 (D) / 1.87
Glu206 / COO- ↔ HO-C2 (A) / 1.82 / COO- ↔ HO-C3 (A) / 1.86 / COO- ↔ HO-C6 (A) / 1.59
COO- ↔ HO-C2 (A) / 1.71 / COO- ↔ HO-C4 (A) / 1.76
Tyr320 / OH ↔ -OOC (Glu382) / 1.93 / OH ↔ -OOC (Glu382) / 1.93 / OH ↔ -OOC (Glu382) / 1.88
Glu385 / OH ↔ HO-C2 (D) / 1.55 / OH ↔ HO-C2 (D) / 1.55 / OH ↔ HO-C2 (D) / 1.53
Tyr423 / Apolar ring ↔ Sugar ring (D) / Apolar ring ↔ Sugar ring (D) / Apolar ring ↔ Sugar ring (D)
Glu430 / COO- ↔ HO-C4 (D) / 1.84

Graphic SI-1: RMSD average values (Å) obtained for the backbone of Exo-1,3-ß-Glycosidase from Candida albicans(black) and for the acceptor sugar (grey).

A) Solution 1, B) Solution 2 and C) Solution 3.

Graphic SI-2: RMSD average values (Å) obtained for the backbone of ß-Glucanase from Humicola insolens(black) and for the acceptor sugar (grey).

A) Solution 1, B) Solution 2 and C) Solution 3.

Graphic SI-3: RMSD average values (Å) obtained for the backbone of ß(1-3)-Glycosidase from Thermus thermophilus(black) and for the acceptor sugar (grey).

A) Solution 1 and B) Solution 2.

Graphic SI-4: RMSD average values (Å) obtained for the backbone of ß-Galactosidase from Escherichia coli(black) and for the acceptor sugar (grey).

A) Solution 1, B) Solution 2 and C) Solution 3.

Graphic SI-5: RMSD average values (Å) obtained for the backbone of ß-Galactosidase from Penicillium sp.(black) and for the acceptor sugar (grey).

A) Solution 1, B) Solution 2 and C) Solution 3.

Graphic SI-6: RMSD average values (Å) obtained for the backbone of ß-Glycosidase from Sulfolobus sulfaticuris(black) and for the acceptor sugar (grey).

A) Solution 1, B) Solution 2 and C) Solution 3.

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