3453-33-6Relevant academic research and scientific papers
Multiple catalytic aldolase antibodies suitable for chemical programming
Goswami, Rajib Kumar,Huang, Zheng-Zheng,Forsyth, Jane S.,Felding-Habermann, Brunhilde,Sinha, Subhash C.
, p. 3821 - 3824 (2009)
Chemical programming of nine murine antibodies with catalytic aldolase activity was examined using compounds, equipped with diketone or pro-vinyl ketone linkers that inhibit integrin adhesion receptor functions. The results showed that most Abs were progr
Aldolase Cascade Facilitated by Self-Assembled Nanotubes from Short Peptide Amphiphiles
Afrose, Syed Pavel,Das, Dibyendu,Reja, Antara
, p. 4329 - 4334 (2020)
Early evolution benefited from a complex network of reactions involving multiple C?C bond forming and breaking events that were critical for primitive metabolism. Nature gradually chose highly evolved and complex enzymes such as lyases to efficiently facilitate C?C bond formation and cleavage with remarkable substrate selectivity. Reported here is a lipidated short peptide which accesses a homogenous nanotubular morphology to efficiently catalyze C?C bond cleavage and formation. This system shows morphology-dependent catalytic rates, suggesting the formation of a binding pocket and registered enhancements in the presence of the hydrogen-bond donor tyrosine, which is exploited by extant aldolases. These assemblies showed excellent substrate selectivity and templated the formation of a specific adduct from a pool of possible adducts. The ability to catalyze metabolically relevant cascade transformations suggests the importance of such systems in early evolution.
A modular assembly strategy for improving the substrate specificity of small catalytic peptides
Tanaka, Fujie,Barbas III, Carlos F.
, p. 3510 - 3511 (2002)
In contrast to large proteins, small peptide catalysts typically display limited specificity for small molecule substrates. This is presumably a result of the limited opportunities small peptides have to fold in a manner that provides for the formation of an isolated reaction vessel that effectively binds and sequesters substrates from bulk solvent while at the same time catalyzing their transformation. For the preparation of small peptide catalysts that possess improved substrate specificity, we have developed a modular assembly strategy that involves appending phage display-derived substrate binding-domain modules to catalytically active peptide domains. We demonstrate the potential of this strategy with the construction of a small 35-amino acid residue aldolase peptide with improved substrate specificity. The advantages of this approach are that it reduces the demand on the functionalization of the catalytic site and it is modular, therefore making its adaptation to a variety of specificities rapid. The modular assembly strategy studied here may present advantages over exhaustive searches of large random-sequence peptide libraries for peptides with singular function. Copyright
Active site plasticity of a computationally designed retro-aldolase enzyme
Obexer, Richard,Studer, Sabine,Giger, Lars,Pinkas, Daniel M.,Gruetter, Markus G.,Baker, David,Hilvert, Donald
, p. 1043 - 1050 (2014)
RA110 is a computationally designed retro-aldolase enzyme that utilizes amine catalysis to convert 4-hydroxy-4-(6-methoxy-2-naphthyl)-2-butanone to 6-methoxy-2-naphthaldehyde and acetone. The original design accelerated substrate cleavage by a factor of 12 000 over background, and its activity was subsequently increased more than a thousand-fold by directed evolution. The X-ray structure of the evolved catalyst covalently modified with a 1,3-diketone inhibitor deviates substantially from the design model, however, with the ligand adopting a completely different orientation than predicted. Moreover, significant activity was maintained even after relocation of the reactive lysine within the apolar binding pocket. These results suggest that the success of the original design is not ascribable to atomically accurate molecular recognition, but rather to successful placement of a reactive lysine adjacent to an apolar binding pocket. Nevertheless, the stabilizing interactions observed at the active site of the evolved variant suggest that improvements in the precision of design calculations will afford enzymes with higher catalytic activities. What's that in your pocket? A computationally designed and experimentally optimized retro-aldolase enzyme utilizes amine catalysis for substrate cleavage. However, substantial differences between the original design model and experimental structure highlight the need for improved computational protocols. Generating catalysts with true enzyme-like activities will require more than simply placing a reactive lysine adjacent to a hydrophobic pocket.
Origins of catalysis by computationally designed retroaldolase enzymes
Lassila, Jonathan K.,Baker, David,Herschlag, Daniel
, p. 4937 - 4942 (2010)
We have investigated recently reported computationally designed retroaldolase enzymes with the goal of understanding the extent and the origins of their catalytic power. Direct comparison of the designed enzymes to primary amine catalysts in solution revealed a rate acceleration of 105-fold for the most active of the designed retroaldolases. Through pH-rate studies of the designed retroaldolases and evaluation of a Bronsted correlation for a series of amine catalysts, we found that lysine pKa values are shifted by 3-4 units in the enzymes but that the catalytic contributions fromthe shifted pKa values are estimated to be modest, about 10-fold. For the most active of the reported enzymes, we evaluated the catalytic contribution of two other design components: a motif intended to stabilize a bound water molecule and hydrophobic substrate binding interactions. Mutational analysis suggested that the bound water motif does not contribute to the rate acceleration. Comparison of the rate acceleration of the designed substrate relative to a minimal substrate suggested that hydrophobic substrate binding interactions contribute around 103-fold to the enzymatic rate acceleration. Altogether, these results suggest that substrate binding interactions and shifting the pKa of the catalytic lysine can account for much of the enzyme's rate acceleration. Additional observations suggest that these interactions are limited in the specificity of placement of substrate and active site catalytic groups. Thus, future design efforts may benefit from a focus on achieving precision in binding interactions and placement of catalytic groups.
De Novo-designed enzymes as small-molecule-regulated fluorescence imaging tags and fluorescent reporters
Liu, Yu,Zhang, Xin,Tan, Yun Lei,Bhabha, Gira,Ekiert, Damian C.,Kipnis, Yakov,Bjelic, Sinisa,Baker, David,Kelly, Jeffery W.
, p. 13102 - 13105 (2014)
Enzyme-based tags attached to a protein-of-interest (POI) that react with a small molecule, rendering the conjugate fluorescent, are very useful for studying the POI in living cells. These tags are typically based on endogenous enzymes, so protein engineering is required to ensure that the small-molecule probe does not react with the endogenous enzyme in the cell of interest. Here we demonstrate that de novo-designed enzymes can be used as tags to attach to POIs. The inherent bioorthogonality of the de novo-designed enzyme - small-molecule probe reaction circumvents the need for protein engineering, since these enzyme activities are not present in living organisms. Herein, we transform a family of de novo-designed retroaldolases into variable-molecular-weight tags exhibiting fluorescence imaging, reporter, and electrophoresis applications that are regulated by tailored, reactive small-molecule fluorophores.
Quantitative Packaging of Active Enzymes into a Protein Cage
Azuma, Yusuke,Zschoche, Reinhard,Tinzl, Matthias,Hilvert, Donald
, p. 1531 - 1534 (2016)
Genetic fusion of cargo proteins to a positively supercharged variant of green fluorescent protein enables their quantitative encapsulation by engineered lumazine synthase capsids possessing a negatively charged lumenal surface. This simple tagging system provides a robust and versatile means of creating hierarchically ordered protein assemblies for use as nanoreactors. The generality of the encapsulation strategy and its effect on enzyme function were investigated with eight structurally and mechanistically distinct catalysts.
The influence of protein dynamics on the success of computational enzyme design
Ruscio, Jory Z.,Kohn, Jonathan E.,Ball, K. Aurelia,Head-Gordon, Teresa
, p. 14111 - 14115 (2009)
We characterize the molecular dynamics of a previously described computational de novo designed enzyme optimized to perform a multistep retrol-aldol reaction when engineered into a TIM barrel protein scaffold. The molecular dynamics simulations show that
Preparation method of 6-methoxy-2-naphthaldehyde
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Paragraph 0016-0035, (2021/11/19)
The invention discloses a preparation method of 6-methoxy-2-naphthaldehyde. The preparation method comprises the following step: carrying out a chemical reaction on 6-methoxy-2-acetonaphthone and a catalyst in an organic solvent, wherein gas is introduced when the reaction is started, a molar ratio of the 6-methoxy-2-acetonaphthone to the catalyst is 1: (0.01-10), a reaction temperature is 20-180 DEG C, and reaction time is 0.1-72 hours. According to the preparation method disclosed by the invention, no harsh reaction conditions such as high temperature and high pressure exist in a process route, the process route is simple, reaction conditions are mild, the raw materials are cheap and easy to obtain, operation is simple and convenient, and the preparation method is suitable for environment-friendly industrial production of the 6-methoxy-2-naphthaldehyde.
Engineered Artificial Carboligases Facilitate Regioselective Preparation of Enantioenriched Aldol Adducts
MacDonald, Duncan S.,Garrabou, Xavier,Klaus, Cindy,Verez, Rebecca,Mori, Takahiro,Hilvert, Donald
supporting information, p. 10250 - 10254 (2020/09/21)
Controlling regio- A nd stereoselectivity of aldol additions is generally challenging. Here we show that an artificial aldolase with high specificity for acetone as the aldol donor can be reengineered via single active site mutations to accept linear and cyclic aliphatic ketones with notable efficiency, regioselectivity, and stereocontrol. Biochemical and crystallographic data show how the mutated residues modulate the binding and activation of specific aldol donors, as well as their subsequent reaction with diverse aldehyde acceptors. Broadening the substrate scope of this evolutionarily na?ve catalyst proved much easier than previous attempts to redesign natural aldolases, suggesting that such proteins may be excellent starting points for the development of customized biocatalysts for diverse practical applications.
