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Meng Q, Ramírez-Palacios C, Capra N, Hooghwinkel ME, Thallmair S, Rozeboom HJ, Thunnissen AMWH, Wijma HJ, Marrink SJ, Janssen DB. Computational Redesign of an ω-Transaminase from Pseudomonas jessenii for Asymmetric Synthesis of Enantiopure Bulky Amines. ACS Catal 2021; 11:10733-10747. [PMID: 34504735 PMCID: PMC8419838 DOI: 10.1021/acscatal.1c02053] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/26/2021] [Indexed: 01/19/2023]
Abstract
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ω-Transaminases
(ω-TA) are attractive biocatalysts
for the production of chiral amines from prochiral ketones via asymmetric synthesis. However, the substrate scope of
ω-TAs is usually limited due to steric hindrance at the active
site pockets. We explored a protein engineering strategy using computational
design to expand the substrate scope of an (S)-selective
ω-TA from Pseudomonas jessenii (PjTA-R6) toward the production of bulky amines. PjTA-R6 is attractive for use in applied biocatalysis due
to its thermostability, tolerance to organic solvents, and acceptance
of high concentrations of isopropylamine as amino donor. PjTA-R6 showed no detectable activity for the synthesis of six bicyclic
or bulky amines targeted in this study. Six small libraries composed
of 7–18 variants each were separately designed via computational methods and tested in the laboratory for ketone to
amine conversion. In each library, the vast majority of the variants
displayed the desired activity, and of the 40 different designs, 38
produced the target amine in good yield with >99% enantiomeric
excess.
This shows that the substrate scope and enantioselectivity of PjTA mutants could be predicted in silico with high accuracy. The single mutant W58G showed the best performance
in the synthesis of five structurally similar bulky amines containing
the indan and tetralin moieties. The best variant for the other bulky
amine, 1-phenylbutylamine, was the triple mutant W58M + F86L + R417L,
indicating that Trp58 is a key residue in the large binding pocket
for PjTA-R6 redesign. Crystal structures of the two
best variants confirmed the computationally predicted structures.
The results show that computational design can be an efficient approach
to rapidly expand the substrate scope of ω-TAs to produce enantiopure
bulky amines.
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Affiliation(s)
- Qinglong Meng
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
| | - Carlos Ramírez-Palacios
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, AG Groningen 9747, Groningen, The Netherlands
| | - Nikolas Capra
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
| | - Mattijs E. Hooghwinkel
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
| | - Sebastian Thallmair
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, AG Groningen 9747, Groningen, The Netherlands
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Str. 1, Frankfurt am Main 60438, Germany
| | - Henriëtte J. Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
| | - Andy-Mark W. H. Thunnissen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
| | - Hein J. Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
| | - Siewert J. Marrink
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, AG Groningen 9747, Groningen, The Netherlands
| | - Dick B. Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
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Hayes RL, Vilseck JZ, Brooks CL. Approaching protein design with multisite λ dynamics: Accurate and scalable mutational folding free energies in T4 lysozyme. Protein Sci 2019; 27:1910-1922. [PMID: 30175503 DOI: 10.1002/pro.3500] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/06/2018] [Accepted: 08/15/2018] [Indexed: 12/14/2022]
Abstract
The estimation of changes in free energy upon mutation is central to the problem of protein design. Modern protein design methods have had remarkable success over a wide range of design targets, but are reaching their limits in ligand binding and enzyme design due to insufficient accuracy in mutational free energies. Alchemical free energy calculations have the potential to supplement modern design methods through more accurate molecular dynamics based prediction of free energy changes, but suffer from high computational cost. Multisite λ dynamics (MSλD) is a particularly efficient and scalable free energy method with potential to explore combinatorially large sequence spaces inaccessible with other free energy methods. This work aims to quantify the accuracy of MSλD and demonstrate its scalability. We apply MSλD to the classic problem of calculating folding free energies in T4 lysozyme, a system with a wealth of experimental measurements. Single site mutants considering 32 mutations show remarkable agreement with experiment with a Pearson correlation of 0.914 and mean unsigned error of 1.19 kcal/mol. Multisite mutants in systems with up to five concurrent mutations spanning 240 different sequences show comparable agreement with experiment. These results demonstrate the promise of MSλD in exploring large sequence spaces for protein design.
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Affiliation(s)
- Ryan L Hayes
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Jonah Z Vilseck
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Charles L Brooks
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109.,Biophysics Program, University of Michigan, Ann Arbor, Michigan, 48109
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3
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An Evaluation of the Potential of NMR Spectroscopy and Computational Modelling Methods to Inform Biopharmaceutical Formulations. Pharmaceutics 2018; 10:pharmaceutics10040165. [PMID: 30248922 PMCID: PMC6320905 DOI: 10.3390/pharmaceutics10040165] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/11/2018] [Accepted: 09/17/2018] [Indexed: 12/22/2022] Open
Abstract
Protein-based therapeutics are considered to be one of the most important classes of pharmaceuticals on the market. The growing need to prolong stability of high protein concentrations in liquid form has proven to be challenging. Therefore, significant effort is being made to design formulations which can enable the storage of these highly concentrated protein therapies for up to 2 years. Currently, the excipient selection approach involves empirical high-throughput screening, but does not reveal details on aggregation mechanisms or the molecular-level effects of the formulations under storage conditions. Computational modelling approaches have the potential to elucidate such mechanisms, and rapidly screen in silico prior to experimental testing. Nuclear Magnetic Resonance (NMR) spectroscopy can also provide complementary insights into excipient–protein interactions. This review will highlight the underpinning principles of molecular modelling and NMR spectroscopy. It will also discuss the advancements in the applications of computational and NMR approaches in investigating excipient–protein interactions.
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4
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Childers MC, Daggett V. Insights from molecular dynamics simulations for computational protein design. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2017; 2:9-33. [PMID: 28239489 PMCID: PMC5321087 DOI: 10.1039/c6me00083e] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.
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Affiliation(s)
| | - Valerie Daggett
- Corresponding author: , Phone: 1.206.685.7420, Fax: 1.206.685.3300
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5
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Pakulska MM, Miersch S, Shoichet MS. Designer protein delivery: From natural to engineered affinity-controlled release systems. Science 2016; 351:aac4750. [PMID: 26989257 DOI: 10.1126/science.aac4750] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Exploiting binding affinities between molecules is an established practice in many fields, including biochemical separations, diagnostics, and drug development; however, using these affinities to control biomolecule release is a more recent strategy. Affinity-controlled release takes advantage of the reversible nature of noncovalent interactions between a therapeutic protein and a binding partner to slow the diffusive release of the protein from a vehicle. This process, in contrast to degradation-controlled sustained-release formulations such as poly(lactic-co-glycolic acid) microspheres, is controlled through the strength of the binding interaction, the binding kinetics, and the concentration of binding partners. In the context of affinity-controlled release--and specifically the discovery or design of binding partners--we review advances in in vitro selection and directed evolution of proteins, peptides, and oligonucleotides (aptamers), aided by computational design.
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Affiliation(s)
- Malgosia M Pakulska
- Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, and Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Shane Miersch
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Molly S Shoichet
- Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, and Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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6
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Abstract
Proteins that bind small molecules (ligands) can be used as biosensors, signal modulators, and sequestering agents. When naturally occurring proteins for a particular target ligand are not available, artificial proteins can be computationally designed. We present a protocol based on RosettaLigand to redesign an existing protein pocket to bind a target ligand. Starting with a protein structure and the structure of the ligand, Rosetta can optimize both the placement of the ligand in the pocket and the identity and conformation of the surrounding sidechains, yielding proteins that bind the target compound.
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7
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Ai H, Zheng F, Deng F, Zhu C, Gu Y, Zhang L, Li X, Chang AK, Zhao J, Zhu J, Liu H. Structure-Based Virtual Screening for Potential Inhibitors of Influenza A Virus RNA Polymerase PA Subunit. Int J Pept Res Ther 2014. [DOI: 10.1007/s10989-014-9442-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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8
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Yang XQ, Liu JY, Li XC, Chen MH, Zhang YL. Key Amino Acid Associated with Acephate Detoxification by Cydia pomonella Carboxylesterase Based on Molecular Dynamics with Alanine Scanning and Site-Directed Mutagenesis. J Chem Inf Model 2014; 54:1356-70. [DOI: 10.1021/ci500159q] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
| | | | - Xian Chun Li
- Department
of Entomology, The University of Arizona, Tucson, Arizona 85721, United States
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9
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An accurate binding interaction model in de novo computational protein design of interactions: If you build it, they will bind. J Struct Biol 2014; 185:136-46. [DOI: 10.1016/j.jsb.2013.03.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 03/15/2013] [Accepted: 03/21/2013] [Indexed: 01/07/2023]
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10
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Wijma HJ, Janssen DB. Computational design gains momentum in enzyme catalysis engineering. FEBS J 2013; 280:2948-60. [DOI: 10.1111/febs.12324] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 04/19/2013] [Accepted: 04/24/2013] [Indexed: 01/19/2023]
Affiliation(s)
- Hein J. Wijma
- Department of Biochemistry; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; The Netherlands
| | - Dick B. Janssen
- Department of Biochemistry; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; The Netherlands
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11
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Malisi C, Schumann M, Toussaint NC, Kageyama J, Kohlbacher O, Höcker B. Binding pocket optimization by computational protein design. PLoS One 2012; 7:e52505. [PMID: 23300688 PMCID: PMC3531388 DOI: 10.1371/journal.pone.0052505] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/14/2012] [Indexed: 01/19/2023] Open
Abstract
Engineering specific interactions between proteins and small molecules is extremely useful for biological studies, as these interactions are essential for molecular recognition. Furthermore, many biotechnological applications are made possible by such an engineering approach, ranging from biosensors to the design of custom enzyme catalysts. Here, we present a novel method for the computational design of protein-small ligand binding named PocketOptimizer. The program can be used to modify protein binding pocket residues to improve or establish binding of a small molecule. It is a modular pipeline based on a number of customizable molecular modeling tools to predict mutations that alter the affinity of a target protein to its ligand. At its heart it uses a receptor-ligand scoring function to estimate the binding free energy between protein and ligand. We compiled a benchmark set that we used to systematically assess the performance of our method. It consists of proteins for which mutational variants with different binding affinities for their ligands and experimentally determined structures exist. Within this test set PocketOptimizer correctly predicts the mutant with the higher affinity in about 69% of the cases. A detailed analysis of the results reveals that the strengths of PocketOptimizer lie in the correct introduction of stabilizing hydrogen bonds to the ligand, as well as in the improved geometric complemetarity between ligand and binding pocket. Apart from the novel method for binding pocket design we also introduce a much needed benchmark data set for the comparison of affinities of mutant binding pockets, and that we use to asses programs for in silico design of ligand binding.
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Affiliation(s)
- Christoph Malisi
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Marcel Schumann
- Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Nora C. Toussaint
- Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Jorge Kageyama
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Oliver Kohlbacher
- Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Birte Höcker
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- * E-mail:
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12
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Chang SS, Huang HJ, Chen CYC. Two birds with one stone? Possible dual-targeting H1N1 inhibitors from traditional Chinese medicine. PLoS Comput Biol 2011; 7:e1002315. [PMID: 22215997 PMCID: PMC3245300 DOI: 10.1371/journal.pcbi.1002315] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 11/03/2011] [Indexed: 12/20/2022] Open
Abstract
The H1N1 influenza pandemic of 2009 has claimed over 18,000 lives. During this pandemic, development of drug resistance further complicated efforts to control and treat the widespread illness. This research utilizes traditional Chinese medicine Database@Taiwan (TCM Database@Taiwan) to screen for compounds that simultaneously target H1 and N1 to overcome current difficulties with virus mutations. The top three candidates were de novo derivatives of xylopine and rosmaricine. Bioactivity of the de novo derivatives against N1 were validated by multiple machine learning prediction models. Ability of the de novo compounds to maintain CoMFA/CoMSIA contour and form key interactions implied bioactivity within H1 as well. Addition of a pyridinium fragment was critical to form stable interactions in H1 and N1 as supported by molecular dynamics (MD) simulation. Results from MD, hydrophobic interactions, and torsion angles are consistent and support the findings of docking. Multiple anchors and lack of binding to residues prone to mutation suggest that the TCM de novo derivatives may be resistant to drug resistance and are advantageous over conventional H1N1 treatments such as oseltamivir. These results suggest that the TCM de novo derivatives may be suitable candidates of dual-targeting drugs for influenza.
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Affiliation(s)
- Su-Sen Chang
- Laboratory of Computational and Systems Biology, China Medical University, Taichung, Taiwan
| | - Hung-Jin Huang
- Sciences and Chinese Medicine Resources, China Medical University, Taichung, Taiwan
| | - Calvin Yu-Chian Chen
- Laboratory of Computational and Systems Biology, China Medical University, Taichung, Taiwan
- Department of Bioinformatics, Asia University, Taichung, Taiwan
- China Medical University Beigang Hospital, Yunlin, Taiwan
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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13
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Soteropulos CE, Hunt HK, Armani AM. Determination of binding kinetics using whispering gallery mode microcavities. APPLIED PHYSICS LETTERS 2011; 99:103703-1037033. [PMID: 21990943 PMCID: PMC3189252 DOI: 10.1063/1.3634023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 08/16/2011] [Indexed: 05/08/2023]
Abstract
Silica optical microcavity sensors show great promise in the kinetic evaluation of binding pairs, fundamental in understanding biomolecular interactions. Here, we develop and demonstrate a novel platform, based on bioconjugated silica microsphere resonators, to study the binding kinetics of the biotin-streptavidin system. We characterize the optical performance, verify the covalent attachment of biotin to the surface, and perform streptavidin detection experiments. We perform preliminary kinetic analysis of the detection data which shows the potential of whispering gallery mode resonators in the determination of the dissociation constant of the binding pair, which is in good agreement with previously published values.
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