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Calles B, Pitarch B, de Lorenzo V. The Structural Permissiveness of Triosephosphate Isomerase (TpiA) of Escherichia coli. Chembiochem 2025; 26:e202400863. [PMID: 39591528 DOI: 10.1002/cbic.202400863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2024] [Revised: 11/24/2024] [Accepted: 11/26/2024] [Indexed: 11/28/2024]
Abstract
Triosephosphate isomerase (TpiA) is widely regarded as an example of an optimally evolved enzyme due to its essential role in biological systems, its structural conservation, and its near-perfect kinetic parameters. In this study, we investigated the structural robustness of the archetypal TpiA variant from Escherichia coli using an in vitro 5-amino acid linker scanning method. The resulting library was introduced into a tpiA mutant strain for functional complementation. From this library, 16 TpiA variants that were phenotypically indistinguishable from the wild-type enzyme were selected for further analysis. Although all variants retained enzymatic activities within the wild-type range, several insertions were found in highly structured protein domains where the linker was expected to cause significant structural perturbations. Despite these potentially disruptive additions, the enzymes maintained their activity even when expressed in a dnaK mutant, suggesting that chaperones did not compensate for structural abnormalities in vivo. Additionally, when these mutant TpiA variants were produced using an in vitro transcription/translation system, they exhibited enzymatic activity comparable to, and in some cases exceeding, that of the non-mutated enzyme. AlphaFold2 exposed that insertions reconstructed the local architecture of the nearby amino acid sequences. The evolutionary implications of this remarkable structural resilience are discussed.
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Affiliation(s)
- Belén Calles
- Systems Biology Department, National Center of Biotechnology CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
| | - Borja Pitarch
- Systems Biology Department, National Center of Biotechnology CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
| | - Víctor de Lorenzo
- Systems Biology Department, National Center of Biotechnology CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
- Correspondence to National Center of Biotechnology CSIC, Calle Darwin 3, Madrid, 28049, Spain
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 258] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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Goyal B, Patel K, Srivastava KR, Durani S. De novo design of stereochemically-bent sixteen-residue β-hairpin as a hydrolase mimic. RSC Adv 2015. [DOI: 10.1039/c5ra19015k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Stepwise design of sixteen-residue β-hairpin as a hydrolase mimic involving fold design by stereochemical mutation followed by inverse-design of sequence.
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Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai–400076
- India
| | - Kirti Patel
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai–400076
- India
| | | | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai–400076
- India
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Srivastava KR, Durani S. Design of a zinc-finger hydrolase with a synthetic αββ protein. PLoS One 2014; 9:e96234. [PMID: 24816915 PMCID: PMC4015931 DOI: 10.1371/journal.pone.0096234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 04/05/2014] [Indexed: 11/18/2022] Open
Abstract
Recent advances in protein design have opened avenues for the creation of artificial enzymes needed for biotechnological and pharmaceutical applications. However, designing efficient enzymes remains an unrealized ambition, as the design must incorporate a catalytic apparatus specific for the desired reaction. Here we present a de novo design approach to evolve a minimal carbonic anhydrase mimic. We followed a step-by-step design of first folding the main chain followed by sequence variation for substrate binding and catalysis. To optimize the fold, we designed an αββ protein based on a Zn-finger. We then inverse-designed the sequences to provide stability to the fold along with flexibility of linker regions to optimize Zn binding and substrate hydrolysis. The resultant peptides were synthesized and assessed for Zn and substrate binding affinity by fluorescence and ITC followed by evaluation of catalytic efficiency with UV-based enzyme kinetic assays. We were successful in mimicking carbonic anhydrase activity in a peptide of twenty two residues, using p-nitrophenyl acetate as a CO2 surrogate. Although our design had modest activity, being a simple structure is an advantage for further improvement in efficiency. Our approach opens a way forward to evolving an efficient biocatalyst for any industrial reaction of interest.
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Affiliation(s)
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
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6
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Campbell ZT, Baldwin TO. Two lysine residues in the bacterial luciferase mobile loop stabilize reaction intermediates. J Biol Chem 2009; 284:32827-34. [PMID: 19710008 DOI: 10.1074/jbc.m109.031716] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial luciferase catalyzes the reaction of FMNH(2), O(2), and a long chain aliphatic aldehyde, yielding FMN, carboxylic acid, and blue-green light. The most conserved contiguous region of the primary sequence corresponds to a crystallographically disordered loop adjacent to the active center (Fisher, A. J., Raushel, F. M., Baldwin, T. O., and Rayment, I. (1995) Biochemistry 34, 6581-6586; Fisher, A. J., Thompson, T. B., Thoden, J. B., Baldwin, T. O., and Rayment, I. (1996) J. Biol. Chem. 271, 21956-21968). Deletion of the mobile loop does not alter the chemistry of the reaction but decreases the total quantum yield of bioluminescence by 2 orders of magnitude (Sparks, J. M., and Baldwin, T. O. (2001) Biochemistry 40, 15436-15443). In this study, we attempt to localize the loss of activity observed in the loop deletion mutant to individual residues in the mobile loop. Using alanine mutagenesis, the effects of substitution at 15 of the 29 mobile loop residues were examined. Nine of the point mutants had reduced activity in vivo. Two mutations, K283A and K286A, resulted in a loss in quantum yield comparable with that of the loop deletion mutant. The bioluminescence emission spectrum of both mutants was normal, and both yielded the carboxylic acid chemical product at the same efficiency as the wild-type enzyme. Substitution of Lys(283) with alanine resulted in destabilization of intermediate II, whereas mutation of Lys(286) had an increase in exposure of reaction intermediates to a dynamic quencher. Based on a model of the enzyme-reduced flavin complex, the two critical lysine residues are adjacent to the quininoidal edge of the isoalloxazine.
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Affiliation(s)
- Zachary T Campbell
- Department of Biochemistry and Molecular Biophysics, University of Arizona, Biological Sciences West, Tucson, Arizona 85721-0088, USA
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Balamurugan D, Yang W, Beratan DN. Exploring chemical space with discrete, gradient, and hybrid optimization methods. J Chem Phys 2009; 129:174105. [PMID: 19045331 DOI: 10.1063/1.2987711] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Discrete, gradient, and hybrid optimization methods are applied to the challenge of discovering molecules with optimized properties. The cost and performance of the approaches were studied using a tight-binding model to maximize the static first electronic hyperpolarizability of molecules. Our analysis shows that discrete branch and bound methods provide robust strategies for inverse chemical design involving diverse chemical structures. Based on the linear combination of atomic potentials, a hybrid discrete-gradient optimization strategy significantly improves the performance of the gradient methods. The hybrid method performs better than dead-end elimination and competes with branch and bound and genetic algorithms. The branch and bound methods for these model Hamiltonians are more cost effective than genetic algorithms for moderate-sized molecular optimization.
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Affiliation(s)
- D Balamurugan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
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Vasileiou C, Vaezeslami S, Crist RM, Rabago-Smith M, Geiger JH, Borhan B. Protein design: reengineering cellular retinoic acid binding protein II into a rhodopsin protein mimic. J Am Chem Soc 2007; 129:6140-8. [PMID: 17447762 DOI: 10.1021/ja067546r] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rational redesign of the binding pocket of Cellular Retinoic Acid Binding Protein II (CRABPII) has provided a mutant that can bind retinal as a protonated Schiff base, mimicking the binding observed in rhodopsin. The reengineering was accomplished through a series of choreographed manipulations to ultimately orient the reactive species (the epsilon-amino group of Lys132 and the carbonyl of retinal) in the proper geometry for imine formation. The guiding principle was to achieve the appropriate Bürgi-Dunitz trajectory for the reaction to ensue. Through crystallographic analysis of protein mutants incapable of forming the requisite Schiff base, a highly ordered water molecule was identified as a key culprit in orienting retinal in a nonconstructive manner. Removal of the ordered water, along with placing reinforcing mutations to favor the desired orientation of retinal, led to a triple mutant CRABPII protein capable of nanomolar binding of retinal as a protonated Schiff base. The high-resolution crystal structure of all-trans-retinal bound to the CRABPII triple mutant (1.2 A resolution) unequivocally illustrates the imine formed between retinal and the protein.
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Affiliation(s)
- Chrysoula Vasileiou
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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Abstract
An increasing attention has been dedicated to the characterization of complex networks within the protein world. This work is reporting how we uncovered networked structures that reflected the structural similarities among protein binding sites. First, a 211 binding sites dataset has been compiled by removing the redundant proteins in the Protein Ligand Database (PLD) (http://www-mitchell.ch.cam.ac.uk/pld/). Using a clique detection algorithm we have performed all-against-all binding site comparisons among the 211 available ones. Within the set of nodes representing each binding site an edge was added whenever a pair of binding sites had a similarity higher than a threshold value. The generated similarity networks revealed that many nodes had few links and only few were highly connected, but due to the limited data available it was not possible to definitively prove a scale-free architecture. Within the same dataset, the binding site similarity networks were compared with the networks of sequence and fold similarity networks. In the protein world, indications were found that structure is better conserved than sequence, but on its own, sequence was better conserved than the subset of functional residues forming the binding site. Because a binding site is strongly linked with protein function, the identification of protein binding site similarity networks could accelerate the functional annotation of newly identified genes. In view of this we have discussed several potential applications of binding site similarity networks, such as the construction of novel binding site classification databases, as well as the implications for protein molecular design in general and computational chemogenomics in particular.
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Affiliation(s)
- Ziding Zhang
- Nestlé Research Center, Nestec Ltd, BioAnalytical Science, CH-1000 Lausanne 26, Switzerland
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Sterner R, Höcker B. Catalytic Versatility, Stability, and Evolution of the (βα)8-Barrel Enzyme Fold. Chem Rev 2005; 105:4038-55. [PMID: 16277370 DOI: 10.1021/cr030191z] [Citation(s) in RCA: 166] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Reinhard Sterner
- Institut für Biophysik und physikalische Biochemie, Universität Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany.
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Minshull J, Ness JE, Gustafsson C, Govindarajan S. Predicting enzyme function from protein sequence. Curr Opin Chem Biol 2005; 9:202-9. [PMID: 15811806 DOI: 10.1016/j.cbpa.2005.02.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There are two main reasons to try to predict an enzyme's function from its sequence. The first is to identify the components and thus the functional capabilities of an organism, the second is to create enzymes with specific properties. Genomics, expression analysis, proteomics and metabonomics are largely directed towards understanding how information flows from DNA sequence to protein functions within an organism. This review focuses on information flow in the opposite direction: the applicability of what is being learned from natural enzymes to improve methods for catalyst design.
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Norgren AS, Arvidsson PI. Functionalized foldamers: synthesis and characterization of a glycosylated beta-peptide 314-helix conveying the TN-antigen. Org Biomol Chem 2005; 3:1359-61. [PMID: 15827626 DOI: 10.1039/b503237g] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we describe the design, synthesis, and solution structure of a novel type of conjugate composed of a naturally occurring bio-active ligand bound to an artificial peptidomimetic backbone; in this first report on such functionalized foldamers we utilized a beta-peptide as backbone and a GalNAc carbohydrate residue as ligand.
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Affiliation(s)
- Anna S Norgren
- Department of Chemistry, Organic Chemistry, Uppsala University, Sweden
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