Theoretical esterases: Difference between revisions

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''De Novo'' protein design and synthesis has been a goal of biochemistry for decades and has wide sweeping implications in many fields. The advent of computers has given rise to computer programs such as RosettaMatch which are capable of identifying sequences compatible with given protein skeletons. In August of 2012, the Richter Lab and collaborators published an attempted to design an esterase from a theoretically functional protein backbone. This article is a summary of their contribution to the field of ''de Novo'' esterase design.

As described in Richter et al, esterases use serines and cysteines as nucleophilic donors in the first step of ester hydrolysis. Either the oxygen in the backbone or residues such as asparagine or glutamine deprotonate the nucleophile. Hydrogen bond donors such as the NH backbone or residues in the active site create an “oxyanion hole” to stabilize any oxyanion formed during catalysis.

As described in Richter et al, esterases use serines and cysteines as nucleophilic donors in the first step of ester hydrolysis. Either the oxygen in the backbone or residues such as asparagine or glutamine deprotonate the nucleophile. Hydrogen bond donors such as the NH backbone or residues in the active site create an “oxyanion hole” to stabilize any oxyanion formed during catalysis <ref name="computational">PMID:22871159</ref>.

== Relevance ==

The general term esterases are used to categorize enzymes that split esters during hydrolysis into an acid and an alcohol. Esterases are a wide range of enzymes- from differences in substrate specificity, structure, to its biological function in downstream effects. They play an extremely important role in diseases such as cancer and diabetes and for this reason they are widely studied for their possibility in mimicking for drug development. Richter et al computationally studied the mechanism of esterases.

Theoretical protein design, while still a relatively unused field, has been used with success before. The video game FoldIt allows players to compete by altering existing protein structures and proposing new structures with points assigned for lowering the energy of folding associated with the molecule. Khatib et. Al were able to use the crowdsourcing capabilities of FoldIt to solve the structure of M-PMV retroviral protease. Much like the goal of Richter et. Al, Eiben et. Al were able to use FoldIt to increase the activity of a Diels-Alderase.

== Design ==

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== Implications ==

None of the proposed de novo structures were able to create a functional, efficient esterase as designed. While it is worth being appreciative of the fact that the Richter lab and collaborators were able to get as close as they were, both the technology of protein structure predication and our own knowledge of protein folding mechanisms must increase before we can reliably design proteins from the bottom up.

None of the proposed de novo structures were able to create a functional, efficient esterase as designed. While it is worth being appreciative of the fact that the Richter lab and collaborators were able to get as close as they were, both the technology of protein structure predication and our own knowledge of protein folding mechanisms must increase before we can reliably design proteins from the bottom up <ref name="fold it">PMID:22267011</ref><ref name="crystal solve foldit">PMID:21926992</ref>.

== Structural highlights ==

A conserved element in esterases and ester hydrolysis are catalytic dyads and triads. Richter et al studied a class of esterases with a catalytic Cys-His in the active site, deemed a “catalytic dyad.” Figure 1 shows crystal structures of the four active designs.

A conserved element in esterases and ester hydrolysis are catalytic dyads and triads. Richter et al studied a class of esterases with a catalytic Cys-His in the active site, deemed a “catalytic dyad.” Figure 6 in [http://www.ncbi.nlm.nih.gov/pubmed/22871159 Richter ''et al''] shows crystal structures (green) compared to the design model (purple) of the four active designs in (a) ECH 13, (b) ECH 19, (c) ECH 14, (d) FR 29.

In (a), the crystal structure, His100 interacts with C45. In the design model, His100 makes a hydrogen bond with Asp10. While the RMSD between the crystal structure and design model in (b) decreases, the catalytic His226 in the dyad does not interact with Cys161, but it does interact with Tyr250 and the oxygen in F221. In (c) the dyad was not formed. Cys132 loop with residues 127-140 moves up and away fom active site and His104 reorients and therefore rendering this design model inactive. In (d), resides 106-132 (containing the catalytis His125) moves outward towards Cys9 and creats a large shift in the backbond of His125 and Cys9, the catalytic dyad.

~~</StructureSection>~~

== References ==

1. Richter, F.; Blomberg, R.; Khare, S. D.; Kiss, G.; Kuzin, A. P.; Smith, A. J. T.; Gallaher, J.; Pianowski, Z.; Helgeson, R. C.; Grjasnow, A.; Xiao, R.; Seetharaman, J.; Su, M.; Vorobiev, S.; Lew, S.; Forouhar, F.; Kornhaber, G. J.; Hunt, J. F.; Montelione, G. T.; Tong, L.; Houk, K. N.; Hilvert, D.; Baker, D. Computational Design of Catalytic Dyads and Oxyanion Holes for Ester Hydrolysis. J. Am. Chem. Soc. 2012, 134, 16197-16206.

Theoretical esterases: Difference between revisions

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@@ Line 3: / Line 3: @@
 ''De Novo'' protein design and synthesis has been a goal of biochemistry for decades and has wide sweeping implications in many fields. The advent of computers has given rise to computer programs such as RosettaMatch which are capable of identifying sequences compatible with given protein skeletons.  In August of 2012, the Richter Lab and collaborators published an attempted to design an esterase from a theoretically functional protein backbone.  This article is a summary of their contribution to the field of ''de Novo'' esterase design.
-As described in Richter et al, esterases use serines and cysteines as nucleophilic donors in the first step of ester hydrolysis. Either the oxygen in the backbone or residues such as asparagine or glutamine deprotonate the nucleophile. Hydrogen bond donors such as the NH backbone or residues in the active site create an “oxyanion hole” to stabilize any oxyanion formed during catalysis.
+As described in Richter et al, esterases use serines and cysteines as nucleophilic donors in the first step of ester hydrolysis. Either the oxygen in the backbone or residues such as asparagine or glutamine deprotonate the nucleophile. Hydrogen bond donors such as the NH backbone or residues in the active site create an “oxyanion hole” to stabilize any oxyanion formed during catalysis <ref name="computational">PMID:22871159</ref>.
 == Relevance ==
 The general term esterases are used to categorize enzymes that split esters during hydrolysis into an acid and an alcohol. Esterases are a wide range of enzymes- from differences in substrate specificity, structure, to its biological function in downstream effects. They play an extremely important role in diseases such as cancer and diabetes and for this reason they are widely studied for their possibility in mimicking for drug development. Richter et al computationally studied the mechanism of esterases.
+Theoretical protein design, while still a relatively unused field, has been used with success before.  The video game FoldIt allows players to compete by altering existing protein structures and proposing new structures with points assigned for lowering the energy of folding associated with the molecule.  Khatib et. Al were able to use the crowdsourcing capabilities of FoldIt to solve the structure of M-PMV retroviral protease.  Much like the goal of Richter et. Al, Eiben et. Al were able to use FoldIt to increase the activity of a Diels-Alderase.
 == Design ==
@@ Line 16: / Line 18: @@
 == Implications ==
-None of the proposed de novo structures were able to create a functional, efficient esterase as designed. While it is worth being appreciative of the fact that the Richter lab and collaborators were able to get as close as they were, both the technology of protein structure predication and our own knowledge of protein folding mechanisms must increase before we can reliably design proteins from the bottom up.
+None of the proposed de novo structures were able to create a functional, efficient esterase as designed. While it is worth being appreciative of the fact that the Richter lab and collaborators were able to get as close as they were, both the technology of protein structure predication and our own knowledge of protein folding mechanisms must increase before we can reliably design proteins from the bottom up <ref name="fold it">PMID:22267011</ref><ref name="crystal solve foldit">PMID:21926992</ref>.
 == Structural highlights ==
-A conserved element in esterases and ester hydrolysis are catalytic dyads and triads. Richter et al studied a class of esterases with a catalytic Cys-His in the active site, deemed a “catalytic dyad.” Figure 1 shows crystal structures of the four active designs.
+A conserved element in esterases and ester hydrolysis are catalytic dyads and triads. Richter et al studied a class of esterases with a catalytic Cys-His in the active site, deemed a “catalytic dyad.” Figure 6 in [http://www.ncbi.nlm.nih.gov/pubmed/22871159 Richter ''et al''] shows crystal structures (green) compared to the design model (purple) of the four active designs in (a) ECH 13, (b) ECH 19, (c) ECH 14, (d) FR 29.
+In (a), the crystal structure, His100 interacts with C45. In the design model, His100 makes a hydrogen bond with Asp10. While the RMSD between the crystal structure and design model in (b) decreases, the catalytic His226 in the dyad does not interact with Cys161, but it does interact with Tyr250 and the oxygen in F221. In (c) the dyad was not formed. Cys132 loop with residues 127-140 moves up and away fom active site and His104 reorients and therefore rendering this design model inactive. In (d), resides 106-132 (containing the catalytis His125) moves outward towards Cys9 and creats a large shift in the backbond of His125 and Cys9, the catalytic dyad.
-</StructureSection>
 == References ==
 <references/>
-. Richter, F.; Blomberg, R.; Khare, S. D.; Kiss, G.; Kuzin, A. P.; Smith, A. J. T.; Gallaher, J.; Pianowski, Z.; Helgeson, R. C.; Grjasnow, A.; Xiao, R.; Seetharaman, J.; Su, M.; Vorobiev, S.; Lew, S.; Forouhar, F.; Kornhaber, G. J.; Hunt, J. F.; Montelione, G. T.; Tong, L.; Houk, K. N.; Hilvert, D.; Baker, D. Computational Design of Catalytic Dyads and Oxyanion Holes for Ester Hydrolysis. J. Am. Chem. Soc. 2012, 134, 16197-16206.