Chem Soc Rev - GBernardes Lab
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This journal is © The Royal Society of Chemistry 2018 Chem. Soc. Rev., 2018, 47, 8977--8979 | 8977 Cite this: Chem. Soc. Rev., 2018, 47, 8977 Protein engineering through chemical, genetic and computational manipulation Itaru Hamachi* ab and Gonçalo J. L. Bernardes * cd Biocomplexity—the study of complex structures and behaviours that take place in biological systems—goes beyond direct protein production from genes to higher orders of complexity that can be added after a gene has been translated into a protein. These processes can significantly expand the functionality of a protein by adding specific chemical groups to specific sites. The ability to use chemical and enzymatic methods to introduce specific groups into folded proteins is now a powerful strategy to add functional capacity to a protein. This strategy can help to elucidate the role of such post- translational groups on a protein and promises protein therapeutics and glyco- conjugate vaccines with optimal proper- ties. Furthermore, a number of methods have been developed towards the total synthesis of proteins. These methods enable the synthesis of complex proteins that have oligosaccharides at pre-defined positions, which cannot be achieved by other means. The sequence of proteins can also be evolved by directed evolution, in order to catalyse the formation of even non-natural bonds, or computationally to design a sequence that has high affinity and specificity for a complementary sequence present on an antigen of inter- est. This themed issue highlights different approaches by which a protein’s structure and functional capacity can be explored, either by adding functional groups or by evolving the native sequence. These approaches may be used to elucidate the role of naturally occurring post-translational a Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Kyoto, Japan. E-mail: [email protected] b Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan c Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Portugal d Department of Chemistry, University of Cambridge, Cambridge, UK. E-mail: [email protected] Itaru Hamachi Itaru Hamachi obtained his PhD at the Department of Synthetic Chemistry of Kyoto University in 1988 under the supervision of Prof. I. Tabushi. He started his academic career as an assistant professor in Prof. T. Kunitake’s group at Kyushu University in 1988, and then moved to S. Shinkai’s lab in the same depart- ment as an associate professor. In 2001, he became a full professor there and returned back to Kyoto University (Department of Syn- thetic Chemistry and Biological Chemistry) in 2005. He is also now a research director of the ERATO project supported by JST. His interest has recently been in chemical biology, organic chemistry in multimolecular crowding biosystems, and supramolecular multicomponent systems. Gonçalo J. L. Bernardes Gonçalo Bernardes, after completing his DPhil degree in 2008 at the University of Oxford, UK, under- took postdoctoral work at the Max-Planck Institute of Colloids and Interfaces, Germany, and ETH Zu ¨rich, Switzerland, and worked as a Group Leader at Alfama Lda in Portugal. He started his inde- pendent research career in 2013 at the University of Cambridge as a Royal Society University Research Fellow, and in 2018 he was appointed as University Lecturer. He is also the Director of the Chemical Biology unit at iMM Lisboa. In 2016, Gonçalo’s research was recognised with the award of the Chem. Soc. Rev. Emerging Investigator Lectureship. His research group inter- ests focus on the use of chemistry principles to tackle challenging biological problems for understanding and fighting cancer. DOI: 10.1039/c8cs90125b rsc.li/chem-soc-rev Chem Soc Rev EDITORIAL
Transcript of Chem Soc Rev - GBernardes Lab
This journal is©The Royal Society of Chemistry 2018 Chem. Soc. Rev., 2018, 47, 8977--8979 | 8977
Cite this: Chem. Soc. Rev., 2018,
47, 8977
Protein engineering through chemical, geneticand computational manipulation
Itaru Hamachi*ab and Gonçalo J. L. Bernardes *cd
Biocomplexity—the study of complexstructures and behaviours that take placein biological systems—goes beyond directprotein production from genes to higherorders of complexity that can be addedafter a gene has been translated into a
protein. These processes can significantlyexpand the functionality of a protein byadding specific chemical groups tospecific sites. The ability to use chemicaland enzymatic methods to introducespecific groups into folded proteins isnow a powerful strategy to add functionalcapacity to a protein. This strategy canhelp to elucidate the role of such post-translational groups on a protein andpromises protein therapeutics and glyco-conjugate vaccines with optimal proper-ties. Furthermore, a number of methodshave been developed towards the totalsynthesis of proteins. These methodsenable the synthesis of complex proteins
that have oligosaccharides at pre-definedpositions, which cannot be achieved byother means. The sequence of proteinscan also be evolved by directed evolution,in order to catalyse the formation of evennon-natural bonds, or computationally todesign a sequence that has high affinityand specificity for a complementarysequence present on an antigen of inter-est. This themed issue highlights differentapproaches by which a protein’s structureand functional capacity can be explored,either by adding functional groups orby evolving the native sequence. Theseapproaches may be used to elucidate therole of naturally occurring post-translational
a Department of Synthetic Chemistry and Biological
Chemistry, Kyoto University, Kyoto, Japan.
E-mail: [email protected] Core Research for Evolutional Science and
Technology (CREST), Japan Science and Technology
Agency (JST), Tokyo, Japanc Instituto de Medicina Molecular, Faculdade de
Medicina da Universidade de Lisboa, Portugald Department of Chemistry, University of Cambridge,
Cambridge, UK. E-mail: [email protected]
Itaru Hamachi
Itaru Hamachi obtained his PhDat the Department of SyntheticChemistry of Kyoto University in1988 under the supervision ofProf. I. Tabushi. He started hisacademic career as an assistantprofessor in Prof. T. Kunitake’sgroup at Kyushu University in1988, and then moved to S.Shinkai’s lab in the same depart-ment as an associate professor. In2001, he became a full professorthere and returned back to KyotoUniversity (Department of Syn-
thetic Chemistry and Biological Chemistry) in 2005. He is alsonow a research director of the ERATO project supported by JST. Hisinterest has recently been in chemical biology, organic chemistryin multimolecular crowding biosystems, and supramolecularmulticomponent systems.
Gonçalo J. L. Bernardes
Gonçalo Bernardes, after completinghis DPhil degree in 2008 at theUniversity of Oxford, UK, under-took postdoctoral work at theMax-Planck Institute of Colloidsand Interfaces, Germany, and ETHZurich, Switzerland, and workedas a Group Leader at Alfama Ldain Portugal. He started his inde-pendent research career in 2013 atthe University of Cambridge as aRoyal Society University ResearchFellow, and in 2018 he wasappointed as University Lecturer.
He is also the Director of the Chemical Biology unit at iMM Lisboa. In2016, Gonçalo’s research was recognised with the award of the Chem.Soc. Rev. Emerging Investigator Lectureship. His research group inter-ests focus on the use of chemistry principles to tackle challengingbiological problems for understanding and fighting cancer.
DOI: 10.1039/c8cs90125b
rsc.li/chem-soc-rev
Chem Soc Rev
EDITORIAL
8978 | Chem. Soc. Rev., 2018, 47, 8977--8979 This journal is©The Royal Society of Chemistry 2018
modifications, or to create protein con-jugates as therapeutics or vaccines. Thisissue also includes reviews on syntheticantibodies by computational design andthe use of proteins as building blocks tocreate nanostructures.
Directed evolution of enzymes uses ourcapacity to take enzymes found in natureand by applying design principles ofchemical reactivity their DNA blueprintmay be tweaked to improve their catalyticcapacity or—even more excitingly—tocatalyse the creation of a new bond. Forher work on directed evolution of enzymes,Frances Arnold has been awarded theNobel Prize in Chemistry 2018. In herreview, together with co-workers, she des-cribes how enzyme engineering strategiescan be applied to amino acid synthases toproduce artificial synthases capable of pro-ducing amino acids beyond the twentycanonical ones. The generation of thesesynthases enables the efficient andenvironmentally friendly production of awide variety of non-canonical amino acidsthat have non-natural side-chains with dif-ferent chemical properties and reactivities(DOI: 10.1039/C8CS00665B). Combinedwith genetic encoding methods, theseside-chains may add new structural orfunctional features into designer proteins.
The introduction of specific groups,such as fluorophores or cytotoxic drugs,at pre-determined sites on a protein ofinterest offers ways to track and followtheir uptake and intracellular traffickingand to precisely deliver a potent anti-cancer drug into a tumour while sparinghealthy tissues. The use of enzymes toachieve site-specific labelling of proteinsoffers advantages, such as specificity andconjugation efficiency. Distefano and co-workers start by reviewing key methodsdeveloped in the last five years to chemi-cally install modifications on proteinseither in the test tube or bioorthogonallyin cells and even organisms. The authorsthen detail advances in enzymatic proteinlabelling in four sections that describemethods based on peptidases, transferases,ligases, and oxidoreductases. Methodsbased on enzymes typically achieve highspecificity for the intended site and reac-tion conversion efficiencies (DOI: 10.1039/C8CS00537K). Equally, the chemicalcovalent attachment of polymers, such
as polyethylene glycol, to therapeutic pro-teins is a successful strategy to modulatea protein’s pharmacokinetic properties(i.e., extension of half-life in circulation)and reduce potential immunogenicity.Maynard and Ko report on advances inthe synthetic design of polymers for pro-tein modulation and strategies to achievesite-specific modification. The site andpolymer-to-protein ratio have been shownto dramatically influence the protein’sactivity and properties, thus methods thatallow attachment of the polymer at definedsites are increasingly important (DOI:10.1039/C8CS00606G).
Successful vaccine design often requiresthe covalent linkage of oligosaccharideantigens, which are poorly immunogenic,into protein carriers that are highlyimmunogenic. Adamo and Berti describehow antimicrobial glycoconjugate vaccinedesign has evolved from more classicalapproaches that used heterogeneous mix-tures into new designs that place a focuson synthetic purity of the oligosaccharideas well as the final glycoprotein vaccineconstruct. This focus on chemical precisionand purity is enabling further insights atthe molecular level on the mode of actionof glycoconjugate vaccines and hopefullywill lead to more efficient vaccines in thefuture (DOI: 10.1039/C8CS00495A).
As an alternative to post-translationalchemical modification of proteins, chem-ists have and continue to advance efforts toapply synthetic logic into the assembly ofproteins. In this context, native and expres-sed chemical ligation enables the chemo-and regio-selective formation of a nativeamide bond between unprotected poly-peptides from synthetic and recombinantorigins. The application of this strategy nowallows construction of proteins of moderatesize that have, for example, definedpost-translational modifications installedthrough synthesis at pre-defined sites. Thistechnique is extremely powerful and recentadvances in the field of chemical ligationare discussed by Payne, Becker and co-workers in their review that includesexamples in which such approaches havegenerated post-translationally modifiedproteins that cannot be obtained by geneticmeans (DOI: 10.1039/C8CS00573G).
Instead of conjugating synthetic groupsat a site of the sequence of a protein to
increase functional capacity, Weil and co-workers describe the use of proteins asbuilding blocks in combination with site-selective chemical reactions to buildprecise protein-based nanostructures. Parti-cular emphasis is placed on the design ofprotein building blocks, recognition unitsand linkers, and their subsequent assemblyinto structurally defined, functional proteinnanostructures for applications in catalysis,materials and biomedical sciences (DOI:10.1039/C8CS00590G).
Computational methods play anincreasingly important role in the de novodesign of proteins as well as in precisesequence alterations to modulate theirproperties and stability. The in silicorational design of antibodies specific toa disease-relevant antigen is referredto as the third-generation method byVendruscolo and co-workers in theirreview. This third-generation approachis the next logical step in antibody dis-covery after in vivo (first generation) andin vitro (second generation) approaches(DOI: 10.1039/C8CS00523K). This reviewprovides an in-depth discussion of currentapproaches for de novo protein design andincludes examples of when their use hasdramatically accelerated discoveries in thebiomedical field. In a second example ofthe power of computational methods forprotein engineering, Kazlauskas describesthe development of web-based tools thatenable the identification of amino acidreplacements or additions to a protein’soriginal sequence to fine-tune theirstability and, thus, functional state. Forexample, destabilization of the unfoldedform of a protein by addition of a dis-ulfide linkage or through introduction ofprolines may lead to stabilization of thefolded form. Other sources of potentialprotein destabilization, such as oxida-tion, proteolytic cleavage or aggregationof partially unfolded states are also dis-cussed along with ways on how to pre-vent these (DOI: 10.1039/C8CS00014J).
In conclusion, this themed issueshows that methods for engineering pro-teins, the workhorses of biology, providemany opportunities to develop interdis-ciplinary approaches that range fromcomputational to synthetic to biochem-ical. Given the great progress in proteinengineering, we are being equipped with
Editorial Chem Soc Rev
This journal is©The Royal Society of Chemistry 2018 Chem. Soc. Rev., 2018, 47, 8977--8979 | 8979
valuable methods for modifying and manipu-lating molecularly complicated proteinsand are now ready to go further towardnew directions. Systems design of an artifi-cial protein/enzyme network by using aset of well-controlled engineered proteinswould create novel intelligent soft-matterand sophisticated biomaterials in synthetic
biology, which would also give some insightfor a design principle of proto-cells. Elabo-rately invading or controlling a natural pro-tein/gene network with engineered proteinsshould afford new discoveries in a variety offields of biology/medicine, that could havesubstantial impact on chemical biology andlead to new biopharmaceutical applications
beyond the conventional vaccine and pro-tein therapeutics. This themed issue clearlysuggests that development of non-canonicalmolecules and strategies are keenly desir-able in order to evoke new functions ofproteins beyond natural systems. It is nowthe era for challenging the higher level ofbiocomplexity using integrated chemistry.
Chem Soc Rev Editorial
