Substrate channelling as an approach to cascade reactions.

Millions of years of evolution have produced biological systems capable of efficient one-pot multi-step catalysis. The underlying mechanisms that facilitate these reaction processes are increasingly providing inspiration in synthetic chemistry. Substrate channelling, where intermediates between enzymatic steps are not in equilibrium with the bulk solution, enables increased efficiencies and yields in reaction and diffusion processes. Here, we review different mechanisms of substrate channelling found in nature and provide an overview of the analytical methods used to quantify these effects. The incorporation of substrate channelling into synthetic cascades is a rapidly developing concept, and recent examples of the fabrication of cascades with controlled diffusion and flux of intermediates are presented.

[1]  William C. Deloache,et al.  Spatial organization of enzymes for metabolic engineering. , 2012, Metabolic engineering.

[2]  David A. Matthews,et al.  Structure of and kinetic channelling in bifunctional dihydrofolate reductase–thymidylate synthase , 1994, Nature Structural Biology.

[3]  Jun Hyoung Lee,et al.  Improved Production of l-Threonine in Escherichia coli by Use of a DNA Scaffold System , 2012, Applied and Environmental Microbiology.

[4]  Hao Yan,et al.  Interenzyme substrate diffusion for an enzyme cascade organized on spatially addressable DNA nanostructures. , 2012, Journal of the American Chemical Society.

[5]  F. Raushel,et al.  Enzymes with molecular tunnels. , 2003, Accounts of chemical research.

[6]  N. Ban,et al.  The multienzyme architecture of eukaryotic fatty acid synthases. , 2008, Current opinion in structural biology.

[7]  Jackie Y. Ying,et al.  Nanostructured catalysts for organic transformations. , 2013, Accounts of chemical research.

[8]  R. Turner,et al.  A self-organizing chemical assembly line. , 2013, Journal of the American Chemical Society.

[9]  Y.‐H.P. Zhang,et al.  Substrate channeling and enzyme complexes for biotechnological applications. , 2011, Biotechnology advances.

[10]  I. Schlichting,et al.  Loop closure and intersubunit communication in tryptophan synthase. , 1998, Biochemistry.

[11]  Zhiyong Tang,et al.  Core-shell palladium nanoparticle@metal-organic frameworks as multifunctional catalysts for cascade reactions. , 2014, Journal of the American Chemical Society.

[12]  K. Mosbach,et al.  Construction of an artificial bifunctional enzyme, beta-galactosidase/galactose dehydrogenase, exhibiting efficient galactose channeling. , 1989, Biochemistry.

[13]  C. Niemeyer,et al.  DNA-directed assembly of artificial multienzyme complexes. , 2008, Biochemical and biophysical research communications.

[14]  S. Mann,et al.  Membrane-mediated cascade reactions by enzyme-polymer proteinosomes. , 2014, Chemical communications.

[15]  J. Lindsay,et al.  Molecular architecture of the pyruvate dehydrogenase complex: bridging the gap. , 2006, Biochemical Society transactions.

[16]  Tae Seok Moon,et al.  Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli. , 2010, Metabolic engineering.

[17]  F. Jordan,et al.  Structure and Function of the Catalytic Domain of the Dihydrolipoyl Acetyltransferase Component in Escherichia coli Pyruvate Dehydrogenase Complex* , 2014, The Journal of Biological Chemistry.

[18]  P. Srere,et al.  Complexes of sequential metabolic enzymes. , 1987, Annual review of biochemistry.

[19]  Vincent T. Metzger,et al.  A model study of sequential enzyme reactions and electrostatic channeling. , 2014, The Journal of chemical physics.

[20]  T. Gedeon,et al.  Encapsulation of an enzyme cascade within the bacteriophage P22 virus-like particle. , 2014, ACS chemical biology.

[21]  R. Veech,et al.  Equilibrium constants of the malate dehydrogenase, citrate synthase, citrate lyase, and acetyl coenzyme A hydrolysis reactions under physiological conditions. , 1973, The Journal of biological chemistry.

[22]  Pamela A Silver,et al.  Natural strategies for the spatial optimization of metabolism in synthetic biology. , 2012, Nature chemical biology.

[23]  I. Rayment,et al.  The structure of carbamoyl phosphate synthetase determined to 2 . 1 AÊ resolution , 1998 .

[24]  I. Willner,et al.  Control of biocatalytic transformations by programmed DNA assemblies. , 2010, Chemistry.

[25]  P. Braun,et al.  Autonomic molecular transport by polymer films containing programmed chemical potential gradients. , 2015, Journal of the American Chemical Society.

[26]  Jie Chao,et al.  Single-step rapid assembly of DNA origami nanostructures for addressable nanoscale bioreactors. , 2013, Journal of the American Chemical Society.

[27]  Mojca Benčina,et al.  DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency , 2011, Nucleic acids research.

[28]  D. Knighton,et al.  Electrostatic channeling in the bifunctional enzyme dihydrofolate reductase-thymidylate synthase. , 1996, Journal of molecular biology.

[29]  M. Roy,et al.  The tryptophan synthase bienzyme complex transfers indole between the alpha- and beta-sites via a 25-30 A long tunnel. , 1990, Biochemistry.

[30]  Abdul Waheed,et al.  Metabolon catalyzed pyruvate/air biofuel cell. , 2010, Journal of the American Chemical Society.

[31]  Xiaobo Li,et al.  A yolk-shell nanoreactor with a basic core and an acidic shell for cascade reactions. , 2012, Angewandte Chemie.

[32]  Teruyuki Nagamune,et al.  Fine Tuning of Spatial Arrangement of Enzymes in a PCNA-Mediated Multienzyme Complex Using a Rigid Poly-L-Proline Linker , 2013, PloS one.

[33]  F. Tostevin,et al.  Clustering and optimal arrangement of enzymes in reaction-diffusion systems. , 2013, Physical review letters.

[34]  Ken Motokura,et al.  An acidic layered clay is combined with a basic layered clay for one-pot sequential reactions. , 2005, Journal of the American Chemical Society.

[35]  Daisuke Tsuchiya,et al.  Structural basis for channelling mechanism of a fatty acid β‐oxidation multienzyme complex , 2004, The EMBO journal.

[36]  James K. Stoops,et al.  The remarkable structural and functional organization of the eukaryotic pyruvate dehydrogenase complexes , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[37]  S. Minteer,et al.  Improved Bioelectrocatalytic Oxidation of Sucrose in a Biofuel Cell with an Enzyme Cascade Assembled on a DNA Scaffold , 2014 .

[38]  Fei Wu,et al.  Krebs cycle metabolon: structural evidence of substrate channeling revealed by cross-linking and mass spectrometry. , 2015, Angewandte Chemie.

[39]  P. Ouyang,et al.  Spatial co-localization of multi-enzymes by inorganic nanocrystal-protein complexes. , 2014, Chemical communications.

[40]  Sarit S. Agasti,et al.  Modulation of the catalytic behavior of alpha-chymotrypsin at monolayer-protected nanoparticle surfaces. , 2006, Journal of the American Chemical Society.

[41]  Zhongyi Jiang,et al.  Bioinspired Approach to Multienzyme Cascade System Construction for Efficient Carbon Dioxide Reduction , 2014 .

[42]  E. Padlan,et al.  Three-dimensional structure of the tryptophan synthase alpha 2 beta 2 multienzyme complex from Salmonella typhimurium. , 1988, The Journal of biological chemistry.

[43]  J Ovádi,et al.  Substrate channeling. , 1999, Methods.

[44]  E. Bayer,et al.  The cellulosome--a treasure-trove for biotechnology. , 1994, Trends in biotechnology.

[45]  C. You,et al.  Annexation of a high-activity enzyme in a synthetic three-enzyme complex greatly decreases the degree of substrate channeling. , 2014, ACS synthetic biology.

[46]  Hidehiko Hirakawa,et al.  Molecular Assembly of P450 with Ferredoxin and Ferredoxin Reductase by Fusion to PCNA , 2010, Chembiochem : a European journal of chemical biology.

[47]  C. You,et al.  Self-assembly of synthetic metabolons through synthetic protein scaffolds: one-step purification, co-immobilization, and substrate channeling. , 2013, ACS synthetic biology.

[48]  B Mattiasson,et al.  An immobilized three-enzyme system: a model for microenvironmental compartmentation in mitochondria. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[49]  J Ovádi,et al.  Physiological significance of metabolic channelling. , 1991, Journal of theoretical biology.

[50]  Ned S Wingreen,et al.  Enzyme clustering accelerates processing of intermediates through metabolic channeling , 2014, Nature Biotechnology.

[51]  Maïté Marguet,et al.  Cascade reactions in multicompartmentalized polymersomes. , 2014, Angewandte Chemie.

[52]  Wilfred Chen,et al.  Positional Assembly of Enzymes on Bacterial Outer Membrane Vesicles for Cascade Reactions , 2014, PloS one.

[53]  H. Hess,et al.  Origins of activity enhancement in enzyme cascades on scaffolds. , 2013, ACS nano.

[54]  Donald Hilvert,et al.  Directed Evolution of a Protein Container , 2011, Science.

[55]  C. Roberts,et al.  Modeling of enhanced catalysis in multienzyme nanostructures: effect of molecular scaffolds, spatial organization, and concentration. , 2015, Journal of chemical theory and computation.

[56]  Danielle Tullman-Ercek,et al.  Engineering nanoscale protein compartments for synthetic organelles. , 2013, Current opinion in biotechnology.

[57]  Jeffrey D Varner,et al.  Engineering the spatial organization of metabolic enzymes: mimicking nature's synergy. , 2008, Current opinion in biotechnology.

[58]  Gabriel C. Wu,et al.  Synthetic protein scaffolds provide modular control over metabolic flux , 2009, Nature Biotechnology.

[59]  I. Wheeldon,et al.  Kinetic Enhancements in DNA–Enzyme Nanostructures Mimic the Sabatier Principle , 2013 .

[60]  Changyan Cao,et al.  Core-shell structured mesoporous silica as acid-base bifunctional catalyst with designated diffusion path for cascade reaction sequences. , 2012, Chemical communications.

[61]  Yusuke Yamada,et al.  Nanocrystal bilayer for tandem catalysis. , 2011, Nature chemistry.

[62]  Dmitri A. Brevnov,et al.  Growth of Patterned Nanopore Arrays of Anodic Aluminum Oxide , 2003 .

[63]  K. Anderson,et al.  Serine modulates substrate channeling in tryptophan synthase. A novel intersubunit triggering mechanism. , 1991, The Journal of biological chemistry.

[64]  Marco Filice,et al.  Cascade Reactions Catalyzed by Bionanostructures , 2014 .

[65]  C. You,et al.  Facilitated substrate channeling in a self-assembled trifunctional enzyme complex. , 2012, Angewandte Chemie.

[66]  Jie Zhu,et al.  Tuning Enzyme Kinetics through Designed Intermolecular Interactions Far from the Active Site , 2015 .

[67]  Evidence for enzyme complexes in the phenylpropanoid and flavonoid pathways , 1999 .

[68]  J. Mccammon,et al.  Channeling by Proximity: The Catalytic Advantages of Active Site Colocalization Using Brownian Dynamics , 2010, The journal of physical chemistry letters.

[69]  Kirsten Jørgensen,et al.  Metabolon formation and metabolic channeling in the biosynthesis of plant natural products. , 2005, Current opinion in plant biology.

[70]  J. Carere,et al.  Characterization of an aldolase-dehydrogenase complex from the cholesterol degradation pathway of Mycobacterium tuberculosis. , 2013, Biochemistry.

[71]  R. Perham,et al.  Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. , 2000, Annual review of biochemistry.

[72]  G. Baillie Compartmentalized signalling: spatial regulation of cAMP by the action of compartmentalized phosphodiesterases , 2009, The FEBS journal.

[73]  Madhavan Nallani,et al.  A three-enzyme cascade reaction through positional assembly of enzymes in a polymersome nanoreactor. , 2009, Chemistry.

[74]  Jan C M van Hest,et al.  Positional assembly of enzymes in polymersome nanoreactors for cascade reactions. , 2007, Angewandte Chemie.

[75]  F. Raushel,et al.  Channeling of substrates and intermediates in enzyme-catalyzed reactions. , 2001, Annual review of biochemistry.

[76]  J. V. van Hest,et al.  Chemical approaches for the construction of multi-enzyme reaction systems. , 2013, Current opinion in structural biology.

[77]  J. Kirsch,et al.  A novel, definitive test for substrate channeling illustrated with the aspartate aminotransferase/malate dehydrogenase system. , 1999, Biochemistry.

[78]  G. Baillie,et al.  Compartmentalisation of second messenger signalling pathways. , 2014, Current opinion in genetics & development.

[79]  Christopher M. Jakobson,et al.  Influence of Electrostatics on Small Molecule Flux through a Protein Nanoreactor. , 2015, ACS synthetic biology.

[80]  U. Bornscheuer,et al.  Cascade catalysis--strategies and challenges en route to preparative synthetic biology. , 2015, Chemical communications.

[81]  Ian Wheeldon,et al.  Design and Analysis of Enhanced Catalysis in Scaffolded Multienzyme Cascade Reactions , 2014 .

[82]  Pamela A. Silver,et al.  In vivo co-localization of enzymes on RNA scaffolds increases metabolic production in a geometrically dependent manner , 2014, Nucleic acids research.

[83]  Nuo Wang,et al.  Substrate channeling between the human dihydrofolate reductase and thymidylate synthase , 2016, Protein science : a publication of the Protein Society.

[84]  F. Raushel,et al.  Restricted Passage of Reaction Intermediates through the Ammonia Tunnel of Carbamoyl Phosphate Synthetase* , 2000, The Journal of Biological Chemistry.

[85]  Itamar Willner,et al.  Enzyme cascades activated on topologically programmed DNA scaffolds. , 2009, Nature nanotechnology.

[86]  Fang Zhang,et al.  Amine-Functionalized GO as an Active and Reusable Acid–Base Bifunctional Catalyst for One-Pot Cascade Reactions , 2014 .

[87]  A. Elcock,et al.  Electrostatic channeling of substrates between enzyme active sites: comparison of simulation and experiment. , 1997, Biochemistry.

[88]  Steven J. Broadwater,et al.  One-pot multi-step synthesis: a challenge spawning innovation. , 2005, Organic & biomolecular chemistry.

[89]  Dongsheng Liu,et al.  Regulation of an enzyme cascade reaction by a DNA machine. , 2013, Small.

[90]  K. Anderson,et al.  First three-dimensional structure of Toxoplasma gondii thymidylate synthase-dihydrofolate reductase: insights for catalysis, interdomain interactions, and substrate channeling. , 2013, Biochemistry.

[91]  I. Willner,et al.  Self-assembly of enzymes on DNA scaffolds: en route to biocatalytic cascades and the synthesis of metallic nanowires. , 2009, Nano letters.

[92]  B. Winkel,et al.  Metabolic channeling in plants. , 2004, Annual review of plant biology.

[93]  K. Mosbach,et al.  Preparation and kinetic characterization of a fusion protein of yeast mitochondrial citrate synthase and malate dehydrogenase. , 1994, Biochemistry.

[94]  Faisal A. Aldaye,et al.  Organization of Intracellular Reactions with Rationally Designed RNA Assemblies , 2011, Science.

[95]  Chun You,et al.  Enzymatic transformation of nonfood biomass to starch , 2013, Proceedings of the National Academy of Sciences.

[96]  M. Oh,et al.  Butyrate production in engineered Escherichia coli with synthetic scaffolds. , 2013, Biotechnology and bioengineering.

[97]  G. Samjeské,et al.  The co-catalytic effect of Sn, Ru and Mo decorating steps of Pt(111) vicinal electrode surfaces on the oxidation of CO , 2001 .

[98]  R. Koepsel,et al.  Rational tailoring of substrate and inhibitor affinity via ATRP polymer-based protein engineering. , 2014, Biomacromolecules.

[99]  Aiman Alam-Nazki,et al.  Spatial Control of Biochemical Modification Cascades and Pathways. , 2015, Biophysical journal.

[100]  Wilfred Chen,et al.  Functional assembly of a multi-enzyme methanol oxidation cascade on a surface-displayed trifunctional scaffold for enhanced NADH production. , 2013, Chemical communications.

[101]  D. Roos,et al.  Heterologous expression and characterization of the bifunctional dihydrofolate reductase-thymidylate synthase enzyme of Toxoplasma gondii. , 1996, Biochemistry.

[102]  H. Kung,et al.  Inspiration from Nature for Heterogeneous Catalysis , 2014, Catalysis Letters.

[103]  Alisdair R Fernie,et al.  The spatial organization of metabolism within the plant cell. , 2013, Annual review of plant biology.

[104]  E. W. Miles,et al.  The Molecular Basis of Substrate Channeling* , 1999, The Journal of Biological Chemistry.

[105]  Hao Yan,et al.  Multi-enzyme complexes on DNA scaffolds capable of substrate channelling with an artificial swinging arm. , 2014, Nature nanotechnology.

[106]  Oliver Yu,et al.  Synthetic scaffolds increased resveratrol biosynthesis in engineered yeast cells. , 2012, Journal of biotechnology.

[107]  J. L. Smith,et al.  Coupled formation of an amidotransferase interdomain ammonia channel and a phosphoribosyltransferase active site. , 1997, Biochemistry.

[108]  O. Byron,et al.  A New Level of Architectural Complexity in the Human Pyruvate Dehydrogenase Complex* , 2006, Journal of Biological Chemistry.

[109]  K. Mosbach,et al.  Metabolic compartmentation: symbiotic, organellar, multienzymic, and microenvironmental. , 1974, Annual review of microbiology.