1
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Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024; 124:8740-8786. [PMID: 38959423 PMCID: PMC11273360 DOI: 10.1021/acs.chemrev.4c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
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Affiliation(s)
| | | | | | | | - Anthony P. Green
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
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2
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Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024; 124:8130-8232. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.
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Affiliation(s)
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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3
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Chernykh AV, Aloshyn D, Kuchkovska YO, Daniliuc CG, Tolmachova NA, Kondratov IS, Zozulya S, Grygorenko OO, Haufe G. Impact of β-perfluoroalkyl substitution of proline on the proteolytic stability of its peptide derivatives. Org Biomol Chem 2022; 20:9337-9350. [PMID: 36107003 DOI: 10.1039/d2ob01430k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A series of all stereoisomers of β-CF3 or β-C2F5 substituted prolines and their dipeptide derivatives were synthesized. Mouse plasma stability assay was carried out to study the impact of fluoroalkyl substituents on the proteolytic stability of proline-derived peptides. The effect of the (R)-/(S)-configuration at the C-2 atom in combination with electronic and steric effects imposed by fluoroalkyl groups was addressed to rationalize the difference in the half-life stability of diastereomeric β-CF3-Pro-Gly and β-C2F5-Pro-Gly derivatives and compared to those of parent (S)-Pro-Gly and (R)-Pro-Gly dipeptides. The steric effect was predominant when the β-CF3 or β-C2F5 group was placed properly to create a spatial interference within the pockets of proteases, thereby protecting the substances from degradation (e.g., for cis-isomeric derivatives). Otherwise, a smaller electronic effect accelerating proteolysis was in charge (i.e., for the (2S,3S) isomers).
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Affiliation(s)
- Anton V Chernykh
- Enamine Ltd., Chervonotkatska Street 78, Kyïv 02094, Ukraine. .,Taras Shevchenko National University of Kyïv, Volodymyrska Street 60, Kyïv 01601, Ukraine.
| | - Danylo Aloshyn
- Bienta/Enamine Ltd., Chervonotkatska Street 78, Kyïv 02094, Ukraine
| | | | - Constantin G Daniliuc
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster, Germany
| | | | - Ivan S Kondratov
- Enamine Ltd., Chervonotkatska Street 78, Kyïv 02094, Ukraine. .,V.P. Kukhar Institute of Bioorganic Chemistry & Petrochemistry, National Academy of Sciences of, Ukraine, Murmanska Street 1, Kyïv 02660, Ukraine
| | - Sergey Zozulya
- Bienta/Enamine Ltd., Chervonotkatska Street 78, Kyïv 02094, Ukraine
| | - Oleksandr O Grygorenko
- Enamine Ltd., Chervonotkatska Street 78, Kyïv 02094, Ukraine. .,Taras Shevchenko National University of Kyïv, Volodymyrska Street 60, Kyïv 01601, Ukraine.
| | - Günter Haufe
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster, Germany.,Cells-in-Motion Cluster of Excellence, Universität Münster, Waldeyerstraße 15, 48149 Münster, Germany
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4
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Schnitzer T, Rackl JW, Wennemers H. Stereoselective Peptide Catalysis in Complex Environments – From River Water to Cell Lysates. Chem Sci 2022; 13:8963-8967. [PMID: 36091207 PMCID: PMC9365096 DOI: 10.1039/d2sc02044k] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/27/2022] [Indexed: 11/21/2022] Open
Abstract
Many stereoselective peptide catalysts have been established. They consist, like nature's catalysts, of amino acids but have significantly lower molecular weights than enzymes. Whereas enzymes operate with exquisite chemoselectivity in complex biological environments, peptide catalysts are used in pure organic solvents and at higher concentrations. Can a peptide catalyst exhibit chemoselectivity reminiscent of enzymes? Here, we investigated the properties of tripeptide catalysts in complex mixtures in hydrophobic and aqueous solvents. We challenged the catalysts with biomolecules bearing functional groups that could interfere by coordination or reaction with the peptide, the substrates, or intermediates. H-dPro-αMePro-Glu-NHC12H15 emerged through tailoring of the trans/cis ratio of the tertiary amide as a conformationally well-defined tripeptide that catalyzes C–C bond formations with high reactivity and stereoselectivity – regardless of the solvent and compound composition. The chemoselectivity of the tripeptide is so high that it even catalyzes reactions in cell lysates. The findings provoke the question of the potential role of peptide catalysis in nature and during the evolution of enzymes. The reactivity, stereo-, and chemoselectivity of a tripeptide are so high that it catalyzes conjugate addition reactions with high stereoselectivity in complex compound mixtures—even in cell lysates.![]()
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Affiliation(s)
- Tobias Schnitzer
- Laboratory of Organic Chemistry, ETH Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Jonas W Rackl
- Laboratory of Organic Chemistry, ETH Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, ETH Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
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5
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O' Loughlin J, Napolitano S, Rubini M. Protein Design with Fluoroprolines: 4,4-Difluoroproline Does Not Eliminate the Rate-Limiting Step of Thioredoxin Folding. Chembiochem 2021; 22:3326-3332. [PMID: 34545985 PMCID: PMC9292674 DOI: 10.1002/cbic.202100418] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/20/2021] [Indexed: 01/08/2023]
Abstract
C4‐substituted fluoroprolines (4R)‐fluoroproline ((4R)‐Flp) and (4S)‐fluoroproline ((4S)‐Flp) have been used in protein engineering to enhance the thermodynamic stability of peptides and proteins. The electron‐withdrawing effect of fluorine can bias the pucker of the pyrrolidine ring, influence the conformational preference of the preceding peptide bond, and can accelerate the cis/trans prolyl peptide bond isomerisation by diminishing its double bond character. The role of 4,4‐difluoroproline (Dfp) in the acceleration of the refolding rate of globular proteins bearing a proline (Pro) residue in the cis conformation in the native state remains elusive. Moreover, the impact of Dfp on the thermodynamic stability and bioactivity of globular proteins has been seldom described. In this study, we show that the incorporation of Dfp caused a redox state dependent and position dependent destabilisation of the thioredoxin (Trx) fold, while the catalytic activities of the modified proteins remained unchanged. The Pro to Dfp substitution at the conserved cisPro76 in the thioredoxin variant Trx1P did not elicited acceleration of the rate‐limiting trans‐to‐cis isomerization of the Ile75‐Pro76 peptide bond. Our results show that pucker preferences in the context of a tertiary structure could play a major role in protein folding, thus overtaking the rules determined for cis/trans isomerisation barriers determined in model peptides.
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Affiliation(s)
- Jennie O' Loughlin
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Silvia Napolitano
- Department of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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6
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Adhikari A, Bhattarai BR, Aryal A, Thapa N, Kc P, Adhikari A, Maharjan S, Chanda PB, Regmi BP, Parajuli N. Reprogramming natural proteins using unnatural amino acids. RSC Adv 2021; 11:38126-38145. [PMID: 35498070 PMCID: PMC9044140 DOI: 10.1039/d1ra07028b] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022] Open
Abstract
Unnatural amino acids have gained significant attention in protein engineering and drug discovery as they allow the evolution of proteins with enhanced stability and activity. The incorporation of unnatural amino acids into proteins offers a rational approach to engineer enzymes for designing efficient biocatalysts that exhibit versatile physicochemical properties and biological functions. This review highlights the biological and synthetic routes of unnatural amino acids to yield a modified protein with altered functionality and their incorporation methods. Unnatural amino acids offer a wide array of applications such as antibody-drug conjugates, probes for change in protein conformation and structure-activity relationships, peptide-based imaging, antimicrobial activities, etc. Besides their emerging applications in fundamental and applied science, systemic research is necessary to explore unnatural amino acids with novel side chains that can address the limitations of natural amino acids.
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Affiliation(s)
- Anup Adhikari
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
| | - Bibek Raj Bhattarai
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
| | - Ashika Aryal
- Department of Chemistry, Birendra Multiple Campus, Tribhuvan University Bharatpur Chitwan Nepal
| | - Niru Thapa
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
| | - Puja Kc
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
| | - Ashma Adhikari
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
| | - Sushila Maharjan
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
| | - Prem B Chanda
- Department of Chemistry and Physics, Southeastern Louisiana University Hammond Louisiana 70402 USA
| | - Bishnu P Regmi
- Department of Chemistry, Florida Agricultural and Mechanical University Tallahassee Florida 32307 USA
| | - Niranjan Parajuli
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
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7
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Breunig SL, Tirrell DA. Incorporation of proline analogs into recombinant proteins expressed in Escherichia coli. Methods Enzymol 2021; 656:545-571. [PMID: 34325798 DOI: 10.1016/bs.mie.2021.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Proline residues are unique in the extent to which they constrain the conformational space available to the protein backbone. Because the conformational preferences of proline cannot be recapitulated by any of the other proteinogenic amino acids, standard mutagenesis approaches that seek to introduce new chemical functionality at proline positions unavoidably perturb backbone flexibility. Here, we detail the incorporation of proline analogs into recombinant proteins in Escherichia coli via a residue-specific mutagenesis strategy. This approach results in global replacement of proline residues with high yields of the recombinant protein of interest, minimal genetic manipulation, and maintenance of backbone conformational constraints.
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Affiliation(s)
- Stephanie L Breunig
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, United States
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, United States.
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8
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Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H. Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet. Chem Rev 2021; 121:6173-6245. [PMID: 33886302 DOI: 10.1021/acs.chemrev.0c01201] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.
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Affiliation(s)
- Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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9
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Kubyshkin V, Davis R, Budisa N. Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement. Beilstein J Org Chem 2021; 17:439-460. [PMID: 33727970 PMCID: PMC7934785 DOI: 10.3762/bjoc.17.40] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Due to the heterocyclic structure and distinct conformational profile, proline is unique in the repertoire of the 20 amino acids coded into proteins. Here, we summarize the biochemical work on the replacement of proline with (4R)- and (4S)-fluoroproline as well as 4,4-difluoroproline in proteins done mainly in the last two decades. We first recapitulate the complex position and biochemical fate of proline in the biochemistry of a cell, discuss the physicochemical properties of fluoroprolines, and overview the attempts to use these amino acids as proline replacements in studies of protein production and folding. Fluorinated proline replacements are able to elevate the protein expression speed and yields and improve the thermodynamic and kinetic folding profiles of individual proteins. In this context, fluoroprolines can be viewed as useful tools in the biotechnological toolbox. As a prospect, we envision that proteome-wide proline-to-fluoroproline substitutions could be possible. We suggest a hypothetical scenario for the use of laboratory evolutionary methods with fluoroprolines as a suitable vehicle to introduce fluorine into living cells. This approach may enable creation of synthetic cells endowed with artificial biodiversity, containing fluorine as a bioelement.
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Affiliation(s)
- Vladimir Kubyshkin
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, R3T 2N2, Canada
| | - Rebecca Davis
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, R3T 2N2, Canada
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, R3T 2N2, Canada
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, 10623 Berlin, Germany
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10
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Hayashi A, Haruna KI, Sato H, Ito K, Makino C, Ito T, Sakamoto K. Incorporation of Halogenated Amino Acids into Antibody Fragments at Multiple Specific Sites Enhances Antigen Binding. Chembiochem 2020; 22:120-123. [PMID: 32815262 DOI: 10.1002/cbic.202000429] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/08/2020] [Indexed: 01/20/2023]
Abstract
Expansion of the amino-acid repertoire with synthetic derivatives introduces novel structures and functionalities into proteins. In this study, we improved the antigen binding of antibodies by incorporating halogenated tyrosines at multiple selective sites. Tyrosines in the Fab fragment of an anti-EGF-receptor antibody 059-152 were systematically replaced with 3-bromo- and 3-chlorotyrosines, and simultaneous replacements at four specific sites were found to cause a tenfold increase in the affinity toward the antigen. Structure modeling suggested that this effect was due to enhanced shape complementarity between the antigen and antibody molecules. On the other hand, we showed that chlorination in the constant domain, far from the binding interface, of Rituximab Fab also increased the affinity significantly (up to 17-fold). Our results showed that antigen binding is tunable with the halogenation in and out of the binding motifs.
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Affiliation(s)
- Akiko Hayashi
- Laboratory for Nonnatural Amino Acid Technology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Ken-Ichi Haruna
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-Cho, Kawasaki-Ku, Kawasaki, 210-8681, Japan
| | - Haruna Sato
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-Cho, Kawasaki-Ku, Kawasaki, 210-8681, Japan
| | - Kenichiro Ito
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-Cho, Kawasaki-Ku, Kawasaki, 210-8681, Japan
| | - Chisato Makino
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-Cho, Kawasaki-Ku, Kawasaki, 210-8681, Japan
| | - Takuhiro Ito
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Kensaku Sakamoto
- Laboratory for Nonnatural Amino Acid Technology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
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11
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Elbatrawi YM, Pedretty KP, Giddings N, Woodcock HL, Del Valle JR. δ-Azaproline and Its Oxidized Variants. J Org Chem 2020; 85:4207-4219. [DOI: 10.1021/acs.joc.9b03384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yassin M. Elbatrawi
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Kyle P. Pedretty
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Nicole Giddings
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Juan R. Del Valle
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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12
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Ganguly HK, Basu G. Conformational landscape of substituted prolines. Biophys Rev 2020; 12:25-39. [PMID: 31953795 PMCID: PMC7040156 DOI: 10.1007/s12551-020-00621-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/09/2020] [Indexed: 12/16/2022] Open
Abstract
The cyclic side chain of the amino acid proline confers unique conformational restraints on its backbone and side chain dihedral angles. This affects two equilibria-one at the backbone (cis/trans) and the other at the side chain (endo/exo). Substitutions on the proline ring impose additional steric and stereoelectronic effects that can further modulate both these equilibria, which in turn can also affect the backbone dihedral angle (ϕ, ψ) preferences. In this review, we have explored the conformational landscape of several termini capped mono-(2-, 3-, 4-, and 5-) substituted proline derivatives in the Cambridge Structural Database, correlating observed conformations with the nature of substituents and deciphering the underlying interactions for the observed structural biases. The impact of incorporating these derivatives within model peptides and proteins are also discussed for selected cases. Several of these substituents have been used to introduce bioorthogonal functionality and modulate structure-specific ligand recognition or used as spectroscopic probes. The incorporation of these diversely applicable functional groups, coupled with their ability to define an amino acid conformation via stereoelectronic effects, have a broad appeal among chemical biologists, molecular biophysicists, and medicinal chemists.
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Affiliation(s)
- Himal Kanti Ganguly
- Department of Biophysics, Bose Institute, P-1/12 CIT scheme VII M, Kolkata, 700054, India.
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT scheme VII M, Kolkata, 700054, India.
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13
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Costantini NV, Ganguly HK, Martin MI, Wenzell NA, Yap GPA, Zondlo NJ. The Distinct Conformational Landscapes of 4S-Substituted Prolines That Promote an endo Ring Pucker. Chemistry 2019; 25:11356-11364. [PMID: 31237705 PMCID: PMC6710147 DOI: 10.1002/chem.201902382] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/20/2019] [Indexed: 12/28/2022]
Abstract
4-Substitution on proline directly impacts protein main chain conformational preferences. The structural effects of N-acyl substitution and of 4-substitution were examined by NMR spectroscopy and X-ray crystallography on minimal molecules with a proline 4S-nitrobenzoate. The effects of N-acyl substitution on conformation were attenuated in the 4S-nitrobenzoate context, due to the minimal role of the n→π* interaction in stabilizing extended conformations. By X-ray crystallography, an extended conformation was observed for most molecules. The formyl derivative adopted a δ conformation that is observed at the i+2 position of β-turns. Computational analysis indicated that the structures observed crystallographically represent the inherent conformational preferences of 4S-substituted prolines with electron-withdrawing 4-position substituents. The divergent conformational preferences of 4R- and 4S-substituted prolines suggest their wider structure-specific application in molecular design. In particular, the proline endo ring pucker favored by 4S-substituted prolines uniquely promotes the δ conformation [(ϕ, ψ) ≈(-80°, 0°)] found in β-turns. In contrast to other acyl capping groups, the pivaloyl group strongly promoted trans amide bond and polyproline II helix conformation, with a close n→π* interaction in the crystalline state, despite the endo ring pucker, suggesting its special capabilities in promoting compact conformations in ϕ due to its strongly electron-donating character.
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Affiliation(s)
- Nicholas V. Costantini
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Himal K. Ganguly
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Maxwell I. Martin
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Nicole A. Wenzell
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Glenn P. A. Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
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14
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Kubyshkin V, Pridma S, Budisa N. Comparative effects of trifluoromethyl- and methyl-group substitutions in proline. NEW J CHEM 2018. [DOI: 10.1039/c8nj02631a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
What is the outcome of trifluoromethyl-/methyl-substitution in each position of the proline ring? Look inside to find out.
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Affiliation(s)
- Vladimir Kubyshkin
- Biocatalysis Group
- Institute of Chemistry
- Technical University of Berlin
- Berlin 10623
- Germany
| | | | - Nediljko Budisa
- Biocatalysis Group
- Institute of Chemistry
- Technical University of Berlin
- Berlin 10623
- Germany
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15
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Evaluating the role of puckering and fluorine atom in stability and folding of fluoroproline containing proteins. BIOTECHNOL BIOPROC E 2017. [DOI: 10.1007/s12257-017-0257-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Schnitzer T, Wennemers H. Influence of the Trans/Cis Conformer Ratio on the Stereoselectivity of Peptidic Catalysts. J Am Chem Soc 2017; 139:15356-15362. [DOI: 10.1021/jacs.7b06194] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Tobias Schnitzer
- Eidgenossische Technische Hochschule Zurich, Laboratory of Organic Chemistry, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
| | - Helma Wennemers
- Eidgenossische Technische Hochschule Zurich, Laboratory of Organic Chemistry, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
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17
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Newberry RW, Raines RT. 4-Fluoroprolines: Conformational Analysis and Effects on the Stability and Folding of Peptides and Proteins. TOPICS IN HETEROCYCLIC CHEMISTRY 2016; 48:1-25. [PMID: 28690684 PMCID: PMC5501414 DOI: 10.1007/7081_2015_196] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Proline is unique among proteinogenic amino acids because a pyrrolidine ring links its amino group to its side chain. This heterocycle constrains the conformations of the main chain and thus templates particular secondary structures. Proline residues undergo post-translational modification at the 4-position to yield 4-hydroxyproline, which is especially prevalent in collagen. Interest in characterizing the effects of this modification led to the use of 4-fluoroprolines to enhance inductive properties relative to the hydroxyl group of 4-hydroxyproline and to eliminate contributions from hydrogen bonding. The strong inductive effect of the fluoro group has three main consequences: enforcing a particular pucker upon the pyrrolidine ring, biasing the conformation of the preceding peptide bond, and accelerating cis/trans prolyl peptide bond isomerization. These subtle, yet reliable modulations make 4-fluoroproline-incorporation a complement to traditional genetic approaches for exploring structure-function relationships in peptides and proteins, as well as for endowing peptides and proteins with conformational stability.
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Affiliation(s)
- Robert W Newberry
- Departments of Chemistry and Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Ronald T Raines
- Departments of Chemistry and Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
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18
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19
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Siebler C, Maryasin B, Kuemin M, Erdmann RS, Rigling C, Grünenfelder C, Ochsenfeld C, Wennemers H. Importance of dipole moments and ambient polarity for the conformation of Xaa-Pro moieties - a combined experimental and theoretical study. Chem Sci 2015; 6:6725-6730. [PMID: 30154996 PMCID: PMC6090429 DOI: 10.1039/c5sc02211h] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 07/27/2015] [Indexed: 12/04/2022] Open
Abstract
NMR spectroscopic studies with a series of proline derivatives revealed that the polarity of the environment has a significant effect on the trans : cis isomer ratio of Xaa-Pro bonds. Computational studies showed that this effect is due to differences in the overall dipole moments of trans and cis conformers. Comparisons between the conformational properties of amide and ester derivatives revealed an intricate balance between polarity effects and n → π* interactions of adjacent carbonyl groups. The findings have important implications for protein folding and signaling as well as the performance of proline-based stereoselective catalysts.
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Affiliation(s)
- Christiane Siebler
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Boris Maryasin
- Chair of Theoretical Chemistry , Department of Chemistry , University of Munich (LMU) , Butenandtstr. 7 , D-81377 Munich , Germany
- Center of Integrated Protein Science (CIPSM) at the Department of Chemistry , University of Munich (LMU) , Butenandtstr. 5-13 , D-81377 Munich , Germany
| | - Michael Kuemin
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Roman S Erdmann
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Carla Rigling
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Claudio Grünenfelder
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry , Department of Chemistry , University of Munich (LMU) , Butenandtstr. 7 , D-81377 Munich , Germany
- Center of Integrated Protein Science (CIPSM) at the Department of Chemistry , University of Munich (LMU) , Butenandtstr. 5-13 , D-81377 Munich , Germany
| | - Helma Wennemers
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
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20
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Ravikumar Y, Nadarajan SP, Hyeon Yoo T, Lee CS, Yun H. Incorporating unnatural amino acids to engineer biocatalysts for industrial bioprocess applications. Biotechnol J 2015; 10:1862-76. [DOI: 10.1002/biot.201500153] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/13/2015] [Accepted: 09/02/2015] [Indexed: 12/22/2022]
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21
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Ravikumar Y, Nadarajan SP, Yoo TH, Lee CS, Yun H. Unnatural amino acid mutagenesis-based enzyme engineering. Trends Biotechnol 2015; 33:462-70. [PMID: 26088007 DOI: 10.1016/j.tibtech.2015.05.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/07/2015] [Accepted: 05/13/2015] [Indexed: 02/09/2023]
Abstract
Traditional enzyme engineering relies on substituting one amino acid by one of the other 19 natural amino acids to change the functional properties of an enzyme. However, incorporation of unnatural amino acids (UAAs) has been harnessed to engineer efficient enzymes for biocatalysis. Residue-specific and site-specific in vivo incorporation methods are becoming the preferred approach for producing enzymes with altered or improved functions. We describe the contribution of in vivo UAA incorporation methodologies to enzyme engineering as well as the future prospects for the field, including the integration of UAAs with other new advances in enzyme engineering.
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Affiliation(s)
- Yuvaraj Ravikumar
- School of Biotechnology, Department of Biochemistry, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea
| | | | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea
| | - Chong-soon Lee
- School of Biotechnology, Department of Biochemistry, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea
| | - Hyungdon Yun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Korea.
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22
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Ohtake K, Yamaguchi A, Mukai T, Kashimura H, Hirano N, Haruki M, Kohashi S, Yamagishi K, Murayama K, Tomabechi Y, Itagaki T, Akasaka R, Kawazoe M, Takemoto C, Shirouzu M, Yokoyama S, Sakamoto K. Protein stabilization utilizing a redefined codon. Sci Rep 2015; 5:9762. [PMID: 25985257 PMCID: PMC4434908 DOI: 10.1038/srep09762] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/18/2015] [Indexed: 12/30/2022] Open
Abstract
Recent advances have fundamentally changed the ways in which synthetic amino acids are incorporated into proteins, enabling their efficient and multiple-site incorporation, in addition to the 20 canonical amino acids. This development provides opportunities for fresh approaches toward addressing fundamental problems in bioengineering. In the present study, we showed that the structural stability of proteins can be enhanced by integrating bulky halogenated amino acids at multiple selected sites. Glutathione S-transferase was thus stabilized significantly (by 5.2 and 5.6 kcal/mol) with 3-chloro- and 3-bromo-l-tyrosines, respectively, incorporated at seven selected sites. X-ray crystallographic analyses revealed that the bulky halogen moieties filled internal spaces within the molecules, and formed non-canonical stabilizing interactions with the neighboring residues. This new mechanism for protein stabilization is quite simple and applicable to a wide range of proteins, as demonstrated by the rapid stabilization of the industrially relevant azoreductase.
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Affiliation(s)
- Kazumasa Ohtake
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Atsushi Yamaguchi
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Takahito Mukai
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Hiroki Kashimura
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
| | - Nobutaka Hirano
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
| | - Mitsuru Haruki
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
| | - Sosuke Kohashi
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
| | - Kenji Yamagishi
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
| | - Kazutaka Murayama
- Biomedical Engineering Research Organization, Tohoku University, Aoba-ku, Sendai 980-8575, Japan
| | - Yuri Tomabechi
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Takashi Itagaki
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Ryogo Akasaka
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Masahito Kawazoe
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Chie Takemoto
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Mikako Shirouzu
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Kensaku Sakamoto
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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23
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Temperature sensing using red fluorescent protein. BIOTECHNOL BIOPROC E 2015; 20:67-72. [PMID: 32218680 PMCID: PMC7090752 DOI: 10.1007/s12257-014-0456-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/18/2014] [Accepted: 09/26/2014] [Indexed: 01/17/2023]
Abstract
Genetically encoded fluorescent proteins are extensively utilized for labeling and imaging proteins, organelles, cell tissues, and whole organisms. In this study, we explored the feasibility of mRFP1 and its variants for measuring intracellular temperature. A linear relationship was observed between the temperature and fluorescence intensity of mRFP1 and its variants. Temperature sensitivities of E. coli expressing mRFP1, mRFP-P63A and mRFP-P63A[(4R)-FP] were -1.27%, -1.26% and -0.77%/°C, respectively. Finally, we demonstrated the potentiality of mRFP1 and its variants as an in vivo temperature sensor.
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24
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Odar C, Winkler M, Wiltschi B. Fluoro amino acids: A rarity in nature, yet a prospect for protein engineering. Biotechnol J 2015; 10:427-46. [DOI: 10.1002/biot.201400587] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/08/2014] [Accepted: 01/09/2015] [Indexed: 01/01/2023]
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25
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Dietz D, Kubyshkin V, Budisa N. Applying γ-Substituted Prolines in theFoldonPeptide: Polarity Contradicts Preorganization. Chembiochem 2014; 16:403-6. [DOI: 10.1002/cbic.201402654] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Indexed: 11/05/2022]
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26
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Deepankumar K, Nadarajan SP, Mathew S, Lee SG, Yoo TH, Hong EY, Kim BG, Yun H. Engineering Transaminase for Stability Enhancement and Site-Specific Immobilization through Multiple Noncanonical Amino Acids Incorporation. ChemCatChem 2014. [DOI: 10.1002/cctc.201402882] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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27
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Siebler C, Erdmann RS, Wennemers H. Switchable Proline Derivatives: Tuning the Conformational Stability of the Collagen Triple Helix by pH Changes. Angew Chem Int Ed Engl 2014; 53:10340-4. [DOI: 10.1002/anie.201404935] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 06/17/2014] [Indexed: 12/14/2022]
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28
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Switchable Proline Derivatives: Tuning the Conformational Stability of the Collagen Triple Helix by pH Changes. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404935] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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29
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Yang CY, Renfrew PD, Olsen AJ, Zhang M, Yuvienco C, Bonneau R, Montclare JK. Improved stability and half-life of fluorinated phosphotriesterase using Rosetta. Chembiochem 2014; 15:1761-4. [PMID: 25066940 DOI: 10.1002/cbic.201402062] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Indexed: 12/17/2022]
Abstract
Recently we demonstrated that incorporating p-fluorophenylalanine (pFF) into phosphotriesterase dramatically improved folding, thereby leading to enhanced stability and function at elevated temperatures. To further improve the stability of the fluorinated enzyme, Rosetta was used to identify multiple potential stabilizing mutations. One such variant, pFF-F104A, exhibited enhanced activity at elevated temperature and maintained activity over many days in solution at room temperature.
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Affiliation(s)
- Ching-Yao Yang
- Department of Chemical and Biomolecular Engineering, New York University Polytechnic School of Engineering, 6 Metrotech, Brooklyn, NY 11201 (USA)
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30
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Pandey AK, Yap GPA, Zondlo NJ. (2S,4R)-4-hydroxyproline(4-nitrobenzoate): strong induction of stereoelectronic effects via a readily synthesized proline derivative. Crystallographic observation of a correlation between torsion angle and bond length in a hyperconjugative interaction. J Org Chem 2014; 79:4174-9. [PMID: 24720652 PMCID: PMC4017608 DOI: 10.1021/jo500367d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Indexed: 12/14/2022]
Abstract
(2S,4R)-4-Hydroxyproline(4-nitrobenzoate) was synthesized. The crystal structure revealed an exo ring pucker, with the nitrobenzoate pseudoaxial on the pyrrolidine envelope and antiperiplanar to C(β) and C(δ) C-H bonds. The unit cell exhibited variation in C(δ)-H/C(γ)-O and C(β)-H/C(γ)-O torsion angles, with a 15° increase in torsion angle (148° to 163°) observed to result in a 0.018 Å decrease in C(δ)-H/C(γ)-O bond length, consistent with favorable σC-H → σ*C-O hyperconjugative interactions increasing with greater orbital overlap.
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Affiliation(s)
- Anil K. Pandey
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Glenn P. A. Yap
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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31
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Biava H, Budisa N. Evolution of fluorinated enzymes: An emerging trend for biocatalyst stabilization. Eng Life Sci 2014. [DOI: 10.1002/elsc.201300049] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Hernan Biava
- Department of Biocatalysis, Institute of Chemistry Berlin Institute of Technology/TU Berlin Berlin Germany
| | - Nediljko Budisa
- Department of Biocatalysis, Institute of Chemistry Berlin Institute of Technology/TU Berlin Berlin Germany
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32
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Deepankumar K, Nadarajan SP, Ayyadurai N, Yun H. Enhancing the biophysical properties of mRFP1 through incorporation of fluoroproline. Biochem Biophys Res Commun 2013; 440:509-14. [PMID: 24080380 DOI: 10.1016/j.bbrc.2013.09.062] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 09/11/2013] [Indexed: 12/17/2022]
Abstract
Here we enhanced the stability and biophysical properties of mRFP1 through a combination of canonical and non-canonical amino acid mutagenesis. The global replacement of proline residue with (2S, 4R)-4-fluoroproline [(4R)-FP] into mRFP1 led to soluble protein but lost its fluorescence, whereas (2S, 4S)-4-fluoroproline [(4S)-FP] incorporation resulted in insoluble protein. The bioinformatics analysis revealed that (4R)-FP incorporation at Pro63 caused fluorescence loss due to the steric hindrance of fluorine atom of (4R)-FP with the chromophore. Therefore, Pro63 residue was mutated with the smallest amino acid Ala to maintain non coplanar conformation of the chromophore and helps to retain its fluorescence with (4R)-FP incorporation. The incorporation of (4R)-FP into mRFP1-P63A showed about 2-3-fold enhancement in thermal and chemical stability. The rate of maturation is also greatly accelerated over the presence of (4R)-FP into mRFP1-P63A. Our study showed that a successful enhancement in the biophysical property of mRFP1-P63A[(4R)-FP] using non-canonical amino acid mutagenesis after mutating non-permissive site Pro63 into Ala.
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33
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Rubini M, Schärer MA, Capitani G, Glockshuber R. (4R)- and (4S)-fluoroproline in the conserved cis-prolyl peptide bond of the thioredoxin fold: tertiary structure context dictates ring puckering. Chembiochem 2013; 14:1053-7. [PMID: 23712956 DOI: 10.1002/cbic.201300178] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Indexed: 12/17/2022]
Abstract
Fine-tuning protein stability: The non-natural amino acids (2S,4R)- and (2S,4S)-fluoroproline modulate protein stability by biasing the proline ring pucker and the cis/trans equilibrium of prolyl peptide bonds. We incorporated both fluoroproline stereoisomers at the invariant cis-proline residue of the thioredoxin fold. The results show that tertiary structure context overrules the conformational preferences of fluoroprolines.
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Affiliation(s)
- Marina Rubini
- Department of Organic Chemistry/Cellular Chemistry, University of Konstanz, Universitätsstrasse 10, 78464 Konstanz, Germany.
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34
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Pandey AK, Naduthambi D, Thomas KM, Zondlo NJ. Proline editing: a general and practical approach to the synthesis of functionally and structurally diverse peptides. Analysis of steric versus stereoelectronic effects of 4-substituted prolines on conformation within peptides. J Am Chem Soc 2013; 135:4333-63. [PMID: 23402492 PMCID: PMC4209921 DOI: 10.1021/ja3109664] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Functionalized proline residues have diverse applications. Herein we describe a practical approach, proline editing, for the synthesis of peptides with stereospecifically modified proline residues. Peptides are synthesized by standard solid-phase peptide synthesis to incorporate Fmoc-hydroxyproline (4R-Hyp). In an automated manner, the Hyp hydroxyl is protected and the remainder of the peptide synthesized. After peptide synthesis, the Hyp protecting group is orthogonally removed and Hyp selectively modified to generate substituted proline amino acids, with the peptide main chain functioning to "protect" the proline amino and carboxyl groups. In a model tetrapeptide (Ac-TYPN-NH2), 4R-Hyp was stereospecifically converted to 122 different 4-substituted prolyl amino acids, with 4R or 4S stereochemistry, via Mitsunobu, oxidation, reduction, acylation, and substitution reactions. 4-Substituted prolines synthesized via proline editing include incorporated structured amino acid mimetics (Cys, Asp/Glu, Phe, Lys, Arg, pSer/pThr), recognition motifs (biotin, RGD), electron-withdrawing groups to induce stereoelectronic effects (fluoro, nitrobenzoate), handles for heteronuclear NMR ((19)F:fluoro; pentafluorophenyl or perfluoro-tert-butyl ether; 4,4-difluoro; (77)SePh) and other spectroscopies (fluorescence, IR: cyanophenyl ether), leaving groups (sulfonate, halide, NHS, bromoacetate), and other reactive handles (amine, thiol, thioester, ketone, hydroxylamine, maleimide, acrylate, azide, alkene, alkyne, aryl halide, tetrazine, 1,2-aminothiol). Proline editing provides access to these proline derivatives with no solution-phase synthesis. All peptides were analyzed by NMR to identify stereoelectronic and steric effects on conformation. Proline derivatives were synthesized to permit bioorthogonal conjugation reactions, including azide-alkyne, tetrazine-trans-cyclooctene, oxime, reductive amination, native chemical ligation, Suzuki, Sonogashira, cross-metathesis, and Diels-Alder reactions. These proline derivatives allowed three parallel bioorthogonal reactions to be conducted in one solution.
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Affiliation(s)
- Anil K. Pandey
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
| | - Devan Naduthambi
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
| | - Krista M. Thomas
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
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35
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Larregola M, Moore S, Budisa N. Congeneric bio-adhesive mussel foot proteins designed by modified prolines revealed a chiral bias in unnatural translation. Biochem Biophys Res Commun 2012; 421:646-50. [PMID: 22542516 DOI: 10.1016/j.bbrc.2012.04.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 04/05/2012] [Indexed: 12/14/2022]
Abstract
Chiral bias in the unnatural translation and 'sticky' mussel proteins. The residue-specific in vivo incorporation of hydroxylated amino acids as well as other synthetic analogs, such as fluoroprolines, emerges as the method of choice for recombinant synthesis of Pro-rich mussel adhesive protein congeners. Chemical diversifications introduced in this way provide a general route towards bio-adhesive congeners endowed with properties not developed by natural evolution. Most importantly, we have found that the co-translational incorporation of (4R)-, and (4S)-hyroxylated and fluorinated analogs into mussel proteins presented a chiral bias: the expressed protein was only detectable in samples incubated with analogs with (4R)-substituents. Possible relationship of these stereochemical preferences for (4R)-stereoisomers in the translation to intracellular tRNA concentrations, ribosomal editing and proofreading or structural effects such as preorganization remains to be addressed in future studies. These studies will generally provide a mechanistic framework for the flexibility of the translational machinery and establish the boundaries of the unnatural translation.
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Affiliation(s)
- Maud Larregola
- Department of Chemistry, Biocatalysis Group, Berlin Institute of Technology/TU Berlin, Franklinstraße 29, D-10587 Berlin, Germany
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36
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Merkel L, Budisa N. Organic fluorine as a polypeptide building element: in vivo expression of fluorinated peptides, proteins and proteomes. Org Biomol Chem 2012; 10:7241-61. [DOI: 10.1039/c2ob06922a] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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37
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Holzberger B, Obeid S, Welte W, Diederichs K, Marx A. Structural insights into the potential of 4-fluoroproline to modulate biophysical properties of proteins. Chem Sci 2012. [DOI: 10.1039/c2sc20545a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Salwiczek M, Nyakatura EK, Gerling UIM, Ye S, Koksch B. Fluorinated amino acids: compatibility with native protein structures and effects on protein-protein interactions. Chem Soc Rev 2011; 41:2135-71. [PMID: 22130572 DOI: 10.1039/c1cs15241f] [Citation(s) in RCA: 327] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fluorinated analogues of the canonical α-L-amino acids have gained widespread attention as building blocks that may endow peptides and proteins with advantageous biophysical, chemical and biological properties. This critical review covers the literature dealing with investigations of peptides and proteins containing fluorinated analogues of the canonical amino acids published over the course of the past decade including the late nineties. It focuses on side-chain fluorinated amino acids, the carbon backbone of which is identical to their natural analogues. Each class of amino acids--aliphatic, aromatic, charged and polar as well as proline--is presented in a separate section. General effects of fluorine on essential properties such as hydrophobicity, acidity/basicity and conformation of the specific side chains and the impact of these altered properties on stability, folding kinetics and activity of peptides and proteins are discussed (245 references).
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Affiliation(s)
- Mario Salwiczek
- Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany.
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Zheng S, Kwon I. Manipulation of enzyme properties by noncanonical amino acid incorporation. Biotechnol J 2011; 7:47-60. [PMID: 22121038 DOI: 10.1002/biot.201100267] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 08/22/2011] [Accepted: 09/22/2011] [Indexed: 11/07/2022]
Abstract
Since wild-type enzymes do not always have the properties needed for various applications, enzymes are often engineered to obtain desirable properties through protein engineering techniques. In the past decade, complementary to the widely used rational protein design and directed evolution techniques, noncanonical amino acid incorporation (NCAAI) has become a new and effective protein engineering technique. Recently, NCAAI has been used to improve intrinsic functions of proteins, such as enzymes and fluorescent proteins, beyond the capacities obtained with natural amino acids. Herein, recent progress on improving enzyme properties through NCAAI in vivo is reviewed and the challenges of current approaches and future directions are also discussed. To date, both NCAAI methods-residue- and site-specific incorporation-have been primarily used to improve the catalytic turnover number and substrate binding affinity of enzymes. Numerous strategies used to minimize structural perturbation and stability loss of a target enzyme upon NCAAI are also explored. Considering the generality of NCAAI incorporation, we expect its application could be expanded to improve other enzyme properties, such as substrate specificity and solvent resistance in the near future.
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Affiliation(s)
- Shun Zheng
- Department of Chemical Engineering University of Virginia, Charlottesville, VA 22904, USA
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Baker PJ, Montclare JK. Enhanced Refoldability and Thermoactivity of Fluorinated Phosphotriesterase. Chembiochem 2011; 12:1845-8. [DOI: 10.1002/cbic.201100221] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Indexed: 12/13/2022]
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Mehta KR, Yang CY, Montclare JK. Modulating substrate specificity of histone acetyltransferase with unnatural amino acids. MOLECULAR BIOSYSTEMS 2011; 7:3050-5. [DOI: 10.1039/c1mb05148b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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