1
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Roy S, Fitzgerald K, Lalani A, Lai CW, Kim A, Kim J, Ou P, Mirsoian A, Liu X, Ramrakhiani A, Zhao H, Zhou H, Xu H, Meisen H, Li CM, Lugt BV, Thibault S, Tinberg CE, DeVoss J, Egen J, Wu LC, Noubade R. Autonomous IL-36R signaling in neutrophils activates potent antitumor effector functions. J Clin Invest 2023; 133:e162088. [PMID: 37317970 DOI: 10.1172/jci162088] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 04/19/2023] [Indexed: 06/16/2023] Open
Abstract
While the rapid advancement of immunotherapies has revolutionized cancer treatment, only a small fraction of patients derive clinical benefit. Eradication of large, established tumors appears to depend on engaging and activating both innate and adaptive immune system components to mount a rigorous and comprehensive immune response. Identifying such agents is a high unmet medical need, because they are sparse in the therapeutic landscape of cancer treatment. Here, we report that IL-36 cytokine can engage both innate and adaptive immunity to remodel an immune-suppressive tumor microenvironment (TME) and mediate potent antitumor immune responses via signaling in host hematopoietic cells. Mechanistically, IL-36 signaling modulates neutrophils in a cell-intrinsic manner to greatly enhance not only their ability to directly kill tumor cells but also promote T and NK cell responses. Thus, while poor prognostic outcomes are typically associated with neutrophil enrichment in the TME, our results highlight the pleiotropic effects of IL-36 and its therapeutic potential to modify tumor-infiltrating neutrophils into potent effector cells and engage both the innate and adaptive immune system to achieve durable antitumor responses in solid tumors.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Haoda Xu
- Therapeutic Discovery, Amgen, South San Francisco, California, USA
| | | | | | | | - Steve Thibault
- Therapeutic Discovery, Amgen, South San Francisco, California, USA
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2
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Sun H, Wang S, Lu M, Tinberg CE, Alba BM. Protein production from HEK293 cell line-derived stable pools with high protein quality and quantity to support discovery research. PLoS One 2023; 18:e0285971. [PMID: 37267316 DOI: 10.1371/journal.pone.0285971] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 05/07/2023] [Indexed: 06/04/2023] Open
Abstract
Antibody-based therapeutics and recombinant protein reagents are often produced in mammalian expression systems, which provide human-like post-translational modifications. Among the available mammalian cell lines used for recombinant protein expression, Chinese hamster ovary (CHO)-derived suspension cells are generally utilized because they are easy to culture and tend to produce proteins in high yield. However, some proteins purified from CHO cell overexpression suffer from clipping and display undesired non-human post translational modifications (PTMs). In addition, CHO cell lines are often not suitable for producing proteins with many glycosylation motifs for structural biology studies, as N-linked glycosylation of proteins poses challenges for structure determination by X-ray crystallography. Hence, alternative and complementary cell lines are required to address these issues. Here, we present a robust method for expressing proteins in human embryonic kidney 293 (HEK293)-derived stable pools, leading to recombinant protein products with much less clipped species compared to those expressed in CHO cells and with higher yield compared to those expressed in transiently-transfected HEK293 cells. Importantly, the stable pool generation protocol is also applicable to HEK293S GnTI- (N-acetylglucosaminyltransferase I-negative) and Expi293F GnTI- suspension cells, facilitating production of high yields of proteins with less complex glycans for use in structural biology projects. Compared to HEK293S GnTI- stable pools, Expi293F GnTI- stable pools consistently produce proteins with similar or higher expression levels. HEK293-derived stable pools can lead to a significant cost reduction and greatly promote the production of high-quality proteins for diverse research projects.
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Affiliation(s)
- Hong Sun
- Biologic Therapeutic Discovery, Amgen Research, South San Francisco, California, United States of America
| | - Songyu Wang
- Biologic Therapeutic Discovery, Amgen Research, South San Francisco, California, United States of America
| | - Mei Lu
- Biologic Therapeutic Discovery, Amgen Research, South San Francisco, California, United States of America
| | - Christine E Tinberg
- Biologic Therapeutic Discovery, Amgen Research, South San Francisco, California, United States of America
| | - Benjamin M Alba
- Biologic Therapeutic Discovery, Amgen Research, South San Francisco, California, United States of America
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3
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Biswas R, Belouski E, Graham K, Hortter M, Mock M, Tinberg CE, Russell AJ. VERITAS: Harnessing the power of nomenclature in biologic discovery. MAbs 2023; 15:2207232. [PMID: 37162235 PMCID: PMC10173791 DOI: 10.1080/19420862.2023.2207232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
We are entering an era in which therapeutic proteins are assembled using building block-like strategies, with no standardized schema to discuss these formats. Existing nomenclatures, like AbML, sacrifice human readability for precision. Therefore, considering even a dozen such formats, in combination with hundreds of possible targets, can create confusion and increase the complexity of drug discovery. To address this challenge, we introduce Verified Taxonomy for Antibodies (VERITAS). This classification and nomenclature scheme is extensible to multispecific therapeutic formats and beyond. VERITAS names are easy to understand while drawing direct connections to the structure of a given format, with or without specific target information, making these names useful to adopt in scientific discourse and as inputs to machine learning algorithms for drug development.
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Affiliation(s)
- Riti Biswas
- Biologic Therapeutic Discovery, Amgen Research, South San Francisco, CA, USA
| | - Ed Belouski
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Kevin Graham
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Michelle Hortter
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Marissa Mock
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Christine E Tinberg
- Biologic Therapeutic Discovery, Amgen Research, South San Francisco, CA, USA
| | - Alan J Russell
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
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4
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Harmalkar A, Rao R, Richard Xie Y, Honer J, Deisting W, Anlahr J, Hoenig A, Czwikla J, Sienz-Widmann E, Rau D, Rice AJ, Riley TP, Li D, Catterall HB, Tinberg CE, Gray JJ, Wei KY. Toward generalizable prediction of antibody thermostability using machine learning on sequence and structure features. MAbs 2023; 15:2163584. [PMID: 36683173 PMCID: PMC9872953 DOI: 10.1080/19420862.2022.2163584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/14/2022] [Accepted: 12/26/2022] [Indexed: 01/24/2023] Open
Abstract
Over the last three decades, the appeal for monoclonal antibodies (mAbs) as therapeutics has been steadily increasing as evident with FDA's recent landmark approval of the 100th mAb. Unlike mAbs that bind to single targets, multispecific biologics (msAbs) have garnered particular interest owing to the advantage of engaging distinct targets. One important modular component of msAbs is the single-chain variable fragment (scFv). Despite the exquisite specificity and affinity of these scFv modules, their relatively poor thermostability often hampers their development as a potential therapeutic drug. In recent years, engineering antibody sequences to enhance their stability by mutations has gained considerable momentum. As experimental methods for antibody engineering are time-intensive, laborious and expensive, computational methods serve as a fast and inexpensive alternative to conventional routes. In this work, we show two machine learning approaches - one with pre-trained language models (PTLM) capturing functional effects of sequence variation, and second, a supervised convolutional neural network (CNN) trained with Rosetta energetic features - to better classify thermostable scFv variants from sequence. Both of these models are trained over temperature-specific data (TS50 measurements) derived from multiple libraries of scFv sequences. On out-of-distribution (refers to the fact that the out-of-distribution sequnes are blind to the algorithm) sequences, we show that a sufficiently simple CNN model performs better than general pre-trained language models trained on diverse protein sequences (average Spearman correlation coefficient, ρ , of 0.4 as opposed to 0.15). On the other hand, an antibody-specific language model performs comparatively better than the CNN model on the same task (ρ = 0.52). Further, we demonstrate that for an independent mAb with available thermal melting temperatures for 20 experimentally characterized thermostable mutations, these models trained on TS50 data could identify 18 residue positions and 5 identical amino-acid mutations showing remarkable generalizability. Our results suggest that such models can be broadly applicable for improving the biological characteristics of antibodies. Further, transferring such models for alternative physicochemical properties of scFvs can have potential applications in optimizing large-scale production and delivery of mAbs or bsAbs.
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Affiliation(s)
- Ameya Harmalkar
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, USA
| | - Roshan Rao
- Electrical Engineering and Computer Science, University of California, Berkeley, CA, USA
| | - Yuxuan Richard Xie
- Department of Bioengineering and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jonas Honer
- Therapeutic Discovery, Amgen Research (Munich) GmbH, Munich, Germany
| | - Wibke Deisting
- Therapeutic Discovery, Amgen Research (Munich) GmbH, Munich, Germany
| | - Jonas Anlahr
- Therapeutic Discovery, Amgen Research (Munich) GmbH, Munich, Germany
| | - Anja Hoenig
- Therapeutic Discovery, Amgen Research (Munich) GmbH, Munich, Germany
| | - Julia Czwikla
- Therapeutic Discovery, Amgen Research (Munich) GmbH, Munich, Germany
| | - Eva Sienz-Widmann
- Therapeutic Discovery, Amgen Research (Munich) GmbH, Munich, Germany
| | - Doris Rau
- Therapeutic Discovery, Amgen Research (Munich) GmbH, Munich, Germany
| | - Austin J. Rice
- Therapeutic Discovery, Amgen Research, Amgen Inc, Thousand Oaks, CA, USA
| | - Timothy P. Riley
- Therapeutic Discovery, Amgen Research, Amgen Inc, Thousand Oaks, CA, USA
| | - Danqing Li
- Therapeutic Discovery, Amgen Research, Amgen Inc, Thousand Oaks, CA, USA
| | | | | | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, USA
| | - Kathy Y. Wei
- Therapeutic Discovery, Amgen Research, Amgen Inc, South San Francisco, CA, USA
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Abstract
Biosensors are important components of many synthetic biology and metabolic engineering applications. Here, we report a second generation of Saccharomyces cerevisiae digoxigenin and progesterone biosensors based on destabilized dimeric ligand-binding domains that undergo ligand-induced stabilization. The biosensors, comprising one ligand-binding domain monomer fused to a DNA-binding domain and another fused to a transcriptional activation domain, activate reporter gene expression in response to steroid binding and receptor dimerization. The introduction of a destabilizing mutation to the dimer interface increased biosensor dynamic range by an order of magnitude. Computational redesign of the dimer interface and functional selections were used to create heterodimeric pairs with further improved dynamic range. A heterodimeric biosensor built from the digoxigenin and progesterone ligand-binding domains functioned as a synthetic "AND"-gate, with 20-fold stronger response to the two ligands in combination than to either one alone. We also identified mutations that increase the sensitivity or selectivity of the biosensors to chemically similar ligands. These dimerizing biosensors provide additional flexibility for the construction of logic gates and other applications.
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Affiliation(s)
- Benjamin W. Jester
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Christine E. Tinberg
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Matthew S. Rich
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - David Baker
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Stanley Fields
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
- Department of Medicine, University of Washington, Seattle, Washington 98195, United States
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6
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Van Patten WJ, Walder R, Adhikari A, Okoniewski SR, Ravichandran R, Tinberg CE, Baker D, Perkins TT. Front Cover: Improved Free-Energy Landscape Quantification Illustrated with a Computationally Designed Protein-Ligand Interaction (ChemPhysChem 1/2018). Chemphyschem 2017. [DOI: 10.1002/cphc.201701341] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- William J. Van Patten
- JILA; National Institute of Standards and Technology and the University of Colorado, Department of Physics and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder; 440 UCB Boulder CO 80309-0440 USA
| | - Robert Walder
- JILA; National Institute of Standards and Technology and the University of Colorado, Department of Physics and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder; 440 UCB Boulder CO 80309-0440 USA
| | - Ayush Adhikari
- JILA; National Institute of Standards and Technology and the University of Colorado, Department of Physics and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder; 440 UCB Boulder CO 80309-0440 USA
| | - Stephen R. Okoniewski
- JILA; National Institute of Standards and Technology and the University of Colorado, Department of Physics and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder; 440 UCB Boulder CO 80309-0440 USA
| | - Rashmi Ravichandran
- University of Washington, Seattle; Department of Biochemistry, Institute for Protein Design and Howard Hughes Medical Institute; Seattle Washington 98195 USA
| | - Christine E. Tinberg
- University of Washington, Seattle; Department of Biochemistry, Institute for Protein Design and Howard Hughes Medical Institute; Seattle Washington 98195 USA
| | - David Baker
- University of Washington, Seattle; Department of Biochemistry, Institute for Protein Design and Howard Hughes Medical Institute; Seattle Washington 98195 USA
| | - Thomas T. Perkins
- JILA; National Institute of Standards and Technology and the University of Colorado, Department of Physics and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder; 440 UCB Boulder CO 80309-0440 USA
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7
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Van Patten WJ, Walder R, Adhikari A, Okoniewski SR, Ravichandran R, Tinberg CE, Baker D, Perkins TT. Improved Free-Energy Landscape Quantification Illustrated with a Computationally Designed Protein-Ligand Interaction. Chemphyschem 2017. [DOI: 10.1002/cphc.201701340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- William J. Van Patten
- JILA; National Institute of Standards and Technology and the University of Colorado, Department of Physics and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder; 440 UCB Boulder CO 80309-0440 USA
| | - Robert Walder
- JILA; National Institute of Standards and Technology and the University of Colorado, Department of Physics and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder; 440 UCB Boulder CO 80309-0440 USA
| | - Ayush Adhikari
- JILA; National Institute of Standards and Technology and the University of Colorado, Department of Physics and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder; 440 UCB Boulder CO 80309-0440 USA
| | - Stephen R. Okoniewski
- JILA; National Institute of Standards and Technology and the University of Colorado, Department of Physics and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder; 440 UCB Boulder CO 80309-0440 USA
| | - Rashmi Ravichandran
- University of Washington, Seattle; Department of Biochemistry, Institute for Protein Design and Howard Hughes Medical Institute; Seattle Washington 98195 USA
| | - Christine E. Tinberg
- University of Washington, Seattle; Department of Biochemistry, Institute for Protein Design and Howard Hughes Medical Institute; Seattle Washington 98195 USA
| | - David Baker
- University of Washington, Seattle; Department of Biochemistry, Institute for Protein Design and Howard Hughes Medical Institute; Seattle Washington 98195 USA
| | - Thomas T. Perkins
- JILA; National Institute of Standards and Technology and the University of Colorado, Department of Physics and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder; 440 UCB Boulder CO 80309-0440 USA
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8
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Van Patten WJ, Walder R, Adhikari A, Okoniewski SR, Ravichandran R, Tinberg CE, Baker D, Perkins TT. Improved Free-Energy Landscape Quantification Illustrated with a Computationally Designed Protein-Ligand Interaction. Chemphyschem 2017; 19:19-23. [PMID: 29069529 DOI: 10.1002/cphc.201701147] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Indexed: 11/09/2022]
Abstract
Quantifying the energy landscape underlying protein-ligand interactions leads to an enhanced understanding of molecular recognition. A powerful yet accessible single-molecule technique is atomic force microscopy (AFM)-based force spectroscopy, which generally yields the zero-force dissociation rate constant (koff ) and the distance to the transition state (Δx≠ ). Here, we introduce an enhanced AFM assay and apply it to probe the computationally designed protein DIG10.3 binding to its target ligand, digoxigenin. Enhanced data quality enabled an analysis that yielded the height of the transition state (ΔG≠ =6.3±0.2 kcal mol-1 ) and the shape of the energy barrier at the transition state (linear-cubic) in addition to the traditional parameters [koff (=4±0.1×10-4 s-1 ) and Δx≠ (=8.3±0.1 Å)]. We expect this automated and relatively rapid assay to provide a more complete energy landscape description of protein-ligand interactions and, more broadly, the diverse systems studied by AFM-based force spectroscopy.
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Affiliation(s)
- William J Van Patten
- JILA, National Institute of Standards and Technology and the University of Colorado, Department of Physics and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, 440 UCB, Boulder, CO, 80309-0440, USA
| | - Robert Walder
- JILA, National Institute of Standards and Technology and the University of Colorado, Department of Physics and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, 440 UCB, Boulder, CO, 80309-0440, USA
| | - Ayush Adhikari
- JILA, National Institute of Standards and Technology and the University of Colorado, Department of Physics and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, 440 UCB, Boulder, CO, 80309-0440, USA
| | - Stephen R Okoniewski
- JILA, National Institute of Standards and Technology and the University of Colorado, Department of Physics and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, 440 UCB, Boulder, CO, 80309-0440, USA
| | - Rashmi Ravichandran
- University of Washington, Seattle, Department of Biochemistry, Institute for Protein Design and Howard Hughes Medical Institute, Seattle, Washington, 98195, USA
| | - Christine E Tinberg
- University of Washington, Seattle, Department of Biochemistry, Institute for Protein Design and Howard Hughes Medical Institute, Seattle, Washington, 98195, USA
| | - David Baker
- University of Washington, Seattle, Department of Biochemistry, Institute for Protein Design and Howard Hughes Medical Institute, Seattle, Washington, 98195, USA
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology and the University of Colorado, Department of Physics and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, 440 UCB, Boulder, CO, 80309-0440, USA
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9
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Hasegawa H, Hsu A, Tinberg CE, Siegler KE, Nazarian AA, Tsai MM. Single amino acid substitution in LC-CDR1 induces Russell body phenotype that attenuates cellular protein synthesis through eIF2α phosphorylation and thereby downregulates IgG secretion despite operational secretory pathway traffic. MAbs 2017; 9:854-873. [PMID: 28379093 DOI: 10.1080/19420862.2017.1314875] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Amino acid sequence differences in the variable region of immunoglobulin (Ig) cause wide variations in secretion outputs. To address how a primary sequence difference comes to modulate Ig secretion, we investigated the biosynthetic process of 2 human IgG2κ monoclonal antibodies (mAbs) that differ only by one amino acid in the light chain complementarity-determining region 1 while showing ∼20-fold variance in secretion titer. Although poorly secreted, the lower-secreting mAb of the 2 was by no means defective in terms of its folding stability, antigen binding, and in vitro biologic activity. However, upon overexpression in HEK293 cells, the low-secreting mAb revealed a high propensity to aggregate into enlarged globular structures called Russell bodies (RBs) in the endoplasmic reticulum. While Golgi morphology was affected by the formation of RBs, secretory pathway membrane traffic remained operational in those cells. Importantly, cellular protein synthesis was severely suppressed in RB-positive cells through the phosphorylation of eIF2α. PERK-dependent signaling was implicated in this event, given the upregulation and nuclear accumulation of downstream effectors such as ATF4 and CHOP. These findings illustrated that the underlining process of poor Ig secretion in RB-positive cells was due to downregulation of Ig synthesis instead of a disruption or blockade of secretory pathway trafficking. Therefore, RB formation signifies an end of active Ig production at the protein translation level. Consequently, depending on how soon and how severely an antibody-expressing cell develops the RB phenotype, the productive window of Ig secretion can vary widely among the cells expressing different mAbs.
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Affiliation(s)
- Haruki Hasegawa
- a Department of Therapeutic Discovery , Amgen Inc. , South San Francisco , CA , USA
| | - Ann Hsu
- b Department of Therapeutic Discovery , Amgen Inc. , Thousand Oaks , CA , USA
| | - Christine E Tinberg
- a Department of Therapeutic Discovery , Amgen Inc. , South San Francisco , CA , USA
| | - Karen E Siegler
- c Department of Cardiometabolic Disorders , Amgen Inc. , South San Francisco , CA , USA
| | - Aaron A Nazarian
- b Department of Therapeutic Discovery , Amgen Inc. , Thousand Oaks , CA , USA
| | - Mei-Mei Tsai
- b Department of Therapeutic Discovery , Amgen Inc. , Thousand Oaks , CA , USA
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10
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Van Pattten WJ, Walder R, Adhikari A, Ravichandran R, Tinberg CE, Baker D, Perkins TT. A Computationally Designed Protein-Ligand Interaction is Mechanically Robust. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.2440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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11
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Abstract
The ability to design novel small-molecule binding sites in proteins is a stringent test of our understanding of the principles of molecular recognition, and would have many practical applications, in synthetic biology and medicine. Here, we describe a computational method in the context of the macromolecular modeling suite Rosetta to designing proteins with sites featuring predetermined interactions to ligands of choice. The required inputs for the method are a model of the small molecule and the desired interactions (e.g., hydrogen bonding, electrostatics, steric packing), and a set of crystallographic structures of proteins containing existing or predicted binding pockets. Constellations of backbones surrounding the putative pocket are searched for compatibility with the desired binding site conception using RosettaMatch and surrounding amino acid side chain identities are optimized using RosettaDesign. Validation of the design is performed using metrics that evaluate the interface energy of the predicted binding pose, the preformation of key binding site features in the apo-state, and the local compatibility of the designed sequence changes with the wild type backbone structure, and top-ranking candidate designs are generated for experimental validation. This approach can allow for the creation of novel binding sites and for the rational tuning of specificity for congeneric ligands by altering the programmed interactions by design, thus offering a general computational protocol for construction and modulation of protein-small molecule interfaces.
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Affiliation(s)
- Christine E Tinberg
- Department of Biochemistry, University of Washington, Seattle, WA, 98109, USA
| | - Sagar D Khare
- Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine at Rutgers, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA.
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12
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Abstract
The ability to de novo design proteins that can bind small molecules has wide implications for synthetic biology and medicine. Combining computational protein design with the high-throughput screening of mutagenic libraries of computationally designed proteins is emerging as a general approach for creating binding proteins with programmable binding modes, affinities, and selectivities. The computational step enables the creation of a binding site in a protein that otherwise does not (measurably) bind the intended ligand, and targeted mutagenic screening allows for validation and refinement of the computational model as well as provides orders-of-magnitude increases in the binding affinity. Deep sequencing of mutagenic libraries can provide insights into the mutagenic binding landscape and enable further affinity improvements. Moreover, in such a combined computational-experimental approach where the binding mode is preprogrammed and iteratively refined, selectivity can be achieved (and modulated) by the placement of specified amino acid side chain groups around the ligand in defined orientations. Here, we describe the experimental aspects of a combined computational-experimental approach for designing-using the software suite Rosetta-proteins that bind a small molecule of choice and engineering, using fluorescence-activated cell sorting and high-throughput yeast surface display, high affinity and ligand selectivity. We illustrated the utility of this approach by performing the design of a selective digoxigenin (DIG)-binding protein that, after affinity maturation, binds DIG with picomolar affinity and high selectivity over structurally related steroids.
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Affiliation(s)
- Christine E Tinberg
- Department of Biochemistry, University of Washington, Seattle, WA, 98109, USA.
- Amgen, South San Francisco, CA, 94080, USA.
| | - Sagar D Khare
- Department of Chemistry and Chemical Biology, Rutgers State University of New Jersey, Piscataway, NJ, 08854, USA
- Center for Integrative Proteomics Research, Rutgers State University of New Jersey, Piscataway, NJ, 08854, USA
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13
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Feng J, Jester BW, Tinberg CE, Mandell DJ, Antunes MS, Chari R, Morey KJ, Rios X, Medford JI, Church GM, Fields S, Baker D. A general strategy to construct small molecule biosensors in eukaryotes. eLife 2015; 4. [PMID: 26714111 PMCID: PMC4739774 DOI: 10.7554/elife.10606] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 12/17/2015] [Indexed: 12/22/2022] Open
Abstract
Biosensors for small molecules can be used in applications that range from metabolic engineering to orthogonal control of transcription. Here, we produce biosensors based on a ligand-binding domain (LBD) by using a method that, in principle, can be applied to any target molecule. The LBD is fused to either a fluorescent protein or a transcriptional activator and is destabilized by mutation such that the fusion accumulates only in cells containing the target ligand. We illustrate the power of this method by developing biosensors for digoxin and progesterone. Addition of ligand to yeast, mammalian, or plant cells expressing a biosensor activates transcription with a dynamic range of up to ~100-fold. We use the biosensors to improve the biotransformation of pregnenolone to progesterone in yeast and to regulate CRISPR activity in mammalian cells. This work provides a general methodology to develop biosensors for a broad range of molecules in eukaryotes. DOI:http://dx.doi.org/10.7554/eLife.10606.001 Small molecules play essential roles in organisms, and so methods to sense these molecules within living cells could have wide-ranging uses in both biology and biotechnology. However, current methods for making new “biosensors” are limited and only a narrow range of small molecules can be detected. One approach to biosensor design in yeast and other eukaryotic organisms uses proteins called ligand-binding domains, which bind to small molecules. Here, Feng, Jester, Tinberg, Mandell et al. have developed a new method to make biosensors from ligand-binding domains that could, in principle, be applied to any target small molecule. The new method involves taking a ligand-binding domain that is either engineered or occurs in nature and linking it to something that can be readily detected, such as a protein that fluoresces or that controls gene expression. This combined biosensor protein is then engineered, via mutations, such that it is unstable unless it binds to the small molecule. This means that, in the absence of the small molecule, these proteins are destroyed inside living cells. However, the binding of a target molecule to one of these proteins protects it from degradation, which allows the signal to be detected. Feng, Jester, Tinberg, Mandell et al. use this method to create biosensors for a human hormone called progesterone and a drug called digoxin, which is used to treat heart disease. Further experiments used the biosensors to optimize the production of progesterone in yeast and to regulate the activity of a gene editing protein called Cas9 in human cells. The biosensors can be also used to produce long-term environmental sensors in plant cells. This approach makes it possible to produce a wide variety of biosensors for different organisms. The next step is to continue to explore the ability of various proteins to be converted into biosensors, and to find out how easy it is to transfer a biosensor produced in one species to another. DOI:http://dx.doi.org/10.7554/eLife.10606.002
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Affiliation(s)
- Justin Feng
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States
| | - Benjamin W Jester
- Department of Genome Sciences, University of Washington, Seattle, United States.,Howard Hughes Medical Institute, University of Washington, Seattle, United States
| | - Christine E Tinberg
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Daniel J Mandell
- Department of Genetics, Harvard Medical School, Boston, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, United States
| | - Mauricio S Antunes
- Department of Biology, Colorado State University, Fort Collins, United States
| | - Raj Chari
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Kevin J Morey
- Department of Biology, Colorado State University, Fort Collins, United States
| | - Xavier Rios
- Department of Genetics, Harvard Medical School, Boston, United States
| | - June I Medford
- Department of Biology, Colorado State University, Fort Collins, United States
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, United States
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, United States.,Howard Hughes Medical Institute, University of Washington, Seattle, United States.,Department of Medicine, University of Washington, Seattle, United States
| | - David Baker
- Howard Hughes Medical Institute, University of Washington, Seattle, United States.,Department of Biochemistry, University of Washington, Seattle, United States
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14
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Smith RD, Damm-Ganamet KL, Dunbar JB, Ahmed A, Chinnaswamy K, Delproposto JE, Kubish GM, Tinberg CE, Khare SD, Dou J, Doyle L, Stuckey JA, Baker D, Carlson HA. CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge. J Chem Inf Model 2015; 56:1022-31. [PMID: 26419257 DOI: 10.1021/acs.jcim.5b00387] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Community Structure-Activity Resource (CSAR) conducted a benchmark exercise to evaluate the current computational methods for protein design, ligand docking, and scoring/ranking. The exercise consisted of three phases. The first phase required the participants to identify and rank order which designed sequences were able to bind the small molecule digoxigenin. The second phase challenged the community to select a near-native pose of digoxigenin from a set of decoy poses for two of the designed proteins. The third phase investigated the ability of current methods to rank/score the binding affinity of 10 related steroids to one of the designed proteins (pKd = 4.1 to 6.7). We found that 11 of 13 groups were able to correctly select the sequence that bound digoxigenin, with most groups providing the correct three-dimensional structure for the backbone of the protein as well as all atoms of the active-site residues. Eleven of the 14 groups were able to select the appropriate pose from a set of plausible decoy poses. The ability to predict absolute binding affinities is still a difficult task, as 8 of 14 groups were able to correlate scores to affinity (Pearson-r > 0.7) of the designed protein for congeneric steroids and only 5 of 14 groups were able to correlate the ranks of the 10 related ligands (Spearman-ρ > 0.7).
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Affiliation(s)
- Richard D Smith
- Department of Medicinal Chemistry, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Kelly L Damm-Ganamet
- Department of Medicinal Chemistry, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - James B Dunbar
- Department of Medicinal Chemistry, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Aqeel Ahmed
- Department of Medicinal Chemistry, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Krishnapriya Chinnaswamy
- Life Sciences Institute, University of Michigan , 210 Washtenaw Ave, Ann Arbor, Michigan 48109-2216, United States
| | - James E Delproposto
- Life Sciences Institute, University of Michigan , 210 Washtenaw Ave, Ann Arbor, Michigan 48109-2216, United States
| | - Ginger M Kubish
- Life Sciences Institute, University of Michigan , 210 Washtenaw Ave, Ann Arbor, Michigan 48109-2216, United States
| | | | | | | | - Lindsey Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center , 1100 Fairview Ave. N., Seattle, Washington 98109, United States
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan , 210 Washtenaw Ave, Ann Arbor, Michigan 48109-2216, United States
| | | | - Heather A Carlson
- Department of Medicinal Chemistry, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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15
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Heinisch T, Pellizzoni M, Dürrenberger M, Tinberg CE, Köhler V, Klehr J, Häussinger D, Baker D, Ward TR. Improving the Catalytic Performance of an Artificial Metalloenzyme by Computational Design. J Am Chem Soc 2015; 137:10414-9. [DOI: 10.1021/jacs.5b06622] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Tillmann Heinisch
- Department
of Chemistry, University of Basel, 4056 Basel, Switzerland
| | | | - Marc Dürrenberger
- Department
of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Christine E. Tinberg
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Valentin Köhler
- Department
of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Juliane Klehr
- Department
of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Daniel Häussinger
- Department
of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - David Baker
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Howard
Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
| | - Thomas R. Ward
- Department
of Chemistry, University of Basel, 4056 Basel, Switzerland
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16
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Griss R, Schena A, Reymond L, Patiny L, Werner D, Tinberg CE, Baker D, Johnsson K. Bioluminescent sensor proteins for point-of-care therapeutic drug monitoring. Nat Chem Biol 2014; 10:598-603. [DOI: 10.1038/nchembio.1554] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 05/15/2014] [Indexed: 02/05/2023]
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17
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Tinberg CE, Khare SD, Dou J, Doyle L, Nelson JW, Schena A, Jankowski W, Kalodimos CG, Johnsson K, Stoddard BL, Baker D. Computational design of ligand-binding proteins with high affinity and selectivity. Nature 2013; 501:212-216. [PMID: 24005320 DOI: 10.1038/nature12443] [Citation(s) in RCA: 293] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 07/11/2013] [Indexed: 01/27/2023]
Abstract
The ability to design proteins with high affinity and selectivity for any given small molecule is a rigorous test of our understanding of the physiochemical principles that govern molecular recognition. Attempts to rationally design ligand-binding proteins have met with little success, however, and the computational design of protein-small-molecule interfaces remains an unsolved problem. Current approaches for designing ligand-binding proteins for medical and biotechnological uses rely on raising antibodies against a target antigen in immunized animals and/or performing laboratory-directed evolution of proteins with an existing low affinity for the desired ligand, neither of which allows complete control over the interactions involved in binding. Here we describe a general computational method for designing pre-organized and shape complementary small-molecule-binding sites, and use it to generate protein binders to the steroid digoxigenin (DIG). Of seventeen experimentally characterized designs, two bind DIG; the model of the higher affinity binder has the most energetically favourable and pre-organized interface in the design set. A comprehensive binding-fitness landscape of this design, generated by library selections and deep sequencing, was used to optimize its binding affinity to a picomolar level, and X-ray co-crystal structures of two variants show atomic-level agreement with the corresponding computational models. The optimized binder is selective for DIG over the related steroids digitoxigenin, progesterone and β-oestradiol, and this steroid binding preference can be reprogrammed by manipulation of explicitly designed hydrogen-bonding interactions. The computational design method presented here should enable the development of a new generation of biosensors, therapeutics and diagnostics.
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Affiliation(s)
- Christine E Tinberg
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sagar D Khare
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jiayi Dou
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.,Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195, USA
| | - Lindsey Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jorgen W Nelson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Alberto Schena
- Institute of Chemical Sciences and Engineering, Institute of Bioengineering, National Centre of Competence in Research (NCCR) of Chemical Biology, École Polytechnique Fédérale de Laussane (EPFL), Laussane, Switzerland
| | - Wojciech Jankowski
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | | | - Kai Johnsson
- Institute of Chemical Sciences and Engineering, Institute of Bioengineering, National Centre of Competence in Research (NCCR) of Chemical Biology, École Polytechnique Fédérale de Laussane (EPFL), Laussane, Switzerland
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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18
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Pan E, Zhang XA, Huang Z, Krezel A, Zhao M, Tinberg CE, Lippard SJ, McNamara JO. Vesicular zinc promotes presynaptic and inhibits postsynaptic long-term potentiation of mossy fiber-CA3 synapse. Neuron 2011; 71:1116-26. [PMID: 21943607 DOI: 10.1016/j.neuron.2011.07.019] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2011] [Indexed: 01/05/2023]
Abstract
The presence of zinc in glutamatergic synaptic vesicles of excitatory neurons of mammalian cerebral cortex suggests that zinc might regulate plasticity of synapses formed by these neurons. Long-term potentiation (LTP) is a form of synaptic plasticity that may underlie learning and memory. We tested the hypothesis that zinc within vesicles of mossy fibers (mf) contributes to mf-LTP, a classical form of presynaptic LTP. We synthesized an extracellular zinc chelator with selectivity and kinetic properties suitable for study of the large transient of zinc in the synaptic cleft induced by mf stimulation. We found that vesicular zinc is required for presynaptic mf-LTP. Unexpectedly, vesicular zinc also inhibits a form of postsynaptic mf-LTP. Because the mf-CA3 synapse provides a major source of excitatory input to the hippocampus, regulating its efficacy by these dual actions, vesicular zinc is critical to proper function of hippocampal circuitry in health and disease.
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Affiliation(s)
- Enhui Pan
- Department of Medicine (Neurology), Duke University Medical Center, Durham, NC 27710, USA
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19
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Do LH, Wang H, Tinberg CE, Dowty E, Yoda Y, Cramer SP, Lippard SJ. Characterization of a synthetic peroxodiiron(III) protein model complex by nuclear resonance vibrational spectroscopy. Chem Commun (Camb) 2011; 47:10945-7. [PMID: 21897991 DOI: 10.1039/c1cc13836g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The vibrational spectrum of an η(1),η(1)-1,2-peroxodiiron(III) complex was measured by nuclear resonance vibrational spectroscopy and fit using an empirical force field analysis. Isotopic (18)O(2) labelling studies revealed a feature involving motion of the {Fe(2)(O(2))}(4+) core that was not previously observed by resonance Raman spectroscopy.
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Affiliation(s)
- Loi H Do
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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20
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Abstract
The controlled oxidation of methane to methanol is a chemical transformation of great value, particularly in the pursuit of alternative fuels, but the reaction remains underutilized industrially because of inefficient and costly synthetic procedures. In contrast, methane monooxygenase enzymes (MMOs) from methanotrophic bacteria achieve this chemistry efficiently under ambient conditions. In this Account, we discuss the first observable step in the oxidation of methane at the carboxylate-bridged diiron active site of the soluble MMO (sMMO), namely, the reductive activation of atmospheric O(2). The results provide benchmarks against which the dioxygen activation mechanisms of other bacterial multicomponent monooxygenases can be measured. Molecular oxygen reacts rapidly with the reduced diiron(II) cen-ter of the hydroxylase component of sMMO (MMOH). The first spectroscopically characterized intermediate that results from this process is a peroxodiiron(III) species, P*, in which the iron atoms have identical environments. P* converts to a second peroxodiiron(III) unit, H(peroxo), in a process accompanied by the transfer of a proton, probably with the assistance of a residue near the active site. Proton-promoted O-O bond scission and rearrangement of the diiron core then leads to a diiron(IV) unit, termed Q, that is directly responsible for the oxidation of methane to methanol. In one section of this Account, we provide a detailed discussion of these processes, with particular emphasis on possible structures of the intermediates. The geometries of P* and H(peroxo) are currently unknown, and recent synthetic modeling chemistry has highlighted the need for further structural characterization of Q, currently assigned as a di(μ-oxo)diiron(IV) "diamond core." In another section of the Account, we discuss in detail proton transfer during the O(2) activation events. The role of protons in promoting O-O bond cleavage, thereby initiating the conversion of H(peroxo) to Q, was previously a controversial topic. Recent studies of the mechanism, covering a range of pH values and in D(2)O instead of H(2)O, confirmed conclusively that the transfer of protons, possibly at or near the active site, is necessary for both P*-to-H(peroxo) and H(peroxo)-to-Q conversions. Specific mechanistic insights into these processes are provided. In the final section of the Account, we present our view of experiments that need to be done to further define crucial aspects of sMMO chemistry. Here our goal is to detail the challenges that we and others face in this research, particularly with respect to some long-standing questions about the system, as well as approaches that might be used to solve them.
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Affiliation(s)
- Christine E. Tinberg
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Stephen J. Lippard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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21
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Tinberg CE, Song WJ, Izzo V, Lippard SJ. Multiple roles of component proteins in bacterial multicomponent monooxygenases: phenol hydroxylase and toluene/o-xylene monooxygenase from Pseudomonas sp. OX1. Biochemistry 2011; 50:1788-98. [PMID: 21366224 PMCID: PMC3059347 DOI: 10.1021/bi200028z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phenol hydroxylase (PH) and toluene/o-xylene monooxygenase (ToMO) from Pseudomonas sp. OX1 require three or four protein components to activate dioxygen for the oxidation of aromatic substrates at a carboxylate-bridged diiron center. In this study, we investigated the influence of the hydroxylases, regulatory proteins, and electron-transfer components of these systems on substrate (phenol; NADH) consumption and product (catechol; H(2)O(2)) generation. Single-turnover experiments revealed that only complete systems containing all three or four protein components are capable of oxidizing phenol, a major substrate for both enzymes. Under ideal conditions, the hydroxylated product yield was ∼50% of the diiron centers for both systems, suggesting that these enzymes operate by half-sites reactivity mechanisms. Single-turnover studies indicated that the PH and ToMO electron-transfer components exert regulatory effects on substrate oxidation processes taking place at the hydroxylase actives sites, most likely through allostery. Steady state NADH consumption assays showed that the regulatory proteins facilitate the electron-transfer step in the hydrocarbon oxidation cycle in the absence of phenol. Under these conditions, electron consumption is coupled to H(2)O(2) formation in a hydroxylase-dependent manner. Mechanistic implications of these results are discussed.
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Affiliation(s)
- Christine E. Tinberg
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Woon Ju Song
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Viviana Izzo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Stephen J. Lippard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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22
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Tinberg CE, Tonzetich ZJ, Wang H, Do LH, Yoda Y, Cramer SP, Lippard SJ. Characterization of iron dinitrosyl species formed in the reaction of nitric oxide with a biological Rieske center. J Am Chem Soc 2010; 132:18168-76. [PMID: 21133361 DOI: 10.1021/ja106290p] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Reactions of nitric oxide with cysteine-ligated iron-sulfur cluster proteins typically result in disassembly of the iron-sulfur core and formation of dinitrosyl iron complexes (DNICs). Here we report the first evidence that DNICs also form in the reaction of NO with Rieske-type [2Fe-2S] clusters. Upon treatment of a Rieske protein, component C of toluene/o-xylene monooxygenase from Pseudomonas sp. OX1, with an excess of NO(g) or NO-generators S-nitroso-N-acetyl-D,L-pencillamine and diethylamine NONOate, the absorbance bands of the [2Fe-2S] cluster are extinguished and replaced by a new feature that slowly grows in at 367 nm. Analysis of the reaction products by electron paramagnetic resonance, Mössbauer, and nuclear resonance vibrational spectroscopy reveals that the primary product of the reaction is a thiolate-bridged diiron tetranitrosyl species, [Fe(2)(μ-SCys)(2)(NO)(4)], having a Roussin's red ester (RRE) formula, and that mononuclear DNICs account for only a minor fraction of nitrosylated iron. Reduction of this RRE reaction product with sodium dithionite produces the one-electron-reduced RRE, having absorptions at 640 and 960 nm. These results demonstrate that NO reacts readily with a Rieske center in a protein and suggest that dinuclear RRE species, not mononuclear DNICs, may be the primary iron dinitrosyl species responsible for the pathological and physiological effects of nitric oxide in such systems in biology.
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Affiliation(s)
- Christine E Tinberg
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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23
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Tinberg CE, Lippard SJ. Oxidation reactions performed by soluble methane monooxygenase hydroxylase intermediates H(peroxo) and Q proceed by distinct mechanisms. Biochemistry 2010; 49:7902-12. [PMID: 20681546 PMCID: PMC2935519 DOI: 10.1021/bi1009375] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Soluble methane monooxygenase is a bacterial enzyme that converts methane to methanol at a carboxylate-bridged diiron center with exquisite control. Because the oxidizing power required for this transformation is demanding, it is not surprising that the enzyme is also capable of hydroxylating and epoxidizing a broad range of hydrocarbon substrates in addition to methane. In this work we took advantage of this promiscuity of the enzyme to gain insight into the mechanisms of action of H(peroxo) and Q, two oxidants that are generated sequentially during the reaction of reduced protein with O(2). Using double-mixing stopped-flow spectroscopy, we investigated the reactions of the two intermediate species with a panel of substrates of varying C-H bond strength. Three classes of substrates were identified according to the rate-determining step in the reaction. We show for the first time that an inverse trend exists between the rate constant of reaction with H(peroxo) and the C-H bond strength of the hydrocarbon examined for those substrates in which C-H bond activation is rate-determining. Deuterium kinetic isotope effects revealed that reactions performed by Q, but probably not H(peroxo), involve extensive quantum mechanical tunneling. This difference sheds light on the observation that H(peroxo) is not a sufficiently potent oxidant to hydroxylate methane, whereas Q can perform this reaction in a facile manner. In addition, the reaction of H(peroxo) with acetonitrile appears to proceed by a distinct mechanism in which a cyanomethide anionic intermediate is generated, bolstering the argument that H(peroxo) is an electrophilic oxidant that operates via two-electron transfer chemistry.
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Affiliation(s)
- Christine E. Tinberg
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Stephen J. Lippard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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24
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Tonzetich ZJ, Wang H, Mitra D, Tinberg CE, Do LH, Jenney FE, Adams MWW, Cramer SP, Lippard SJ. Identification of protein-bound dinitrosyl iron complexes by nuclear resonance vibrational spectroscopy. J Am Chem Soc 2010; 132:6914-6. [PMID: 20429508 DOI: 10.1021/ja101002f] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We have applied (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to identify protein-bound dinitrosyl iron complexes. Intense NRVS peaks due to vibrations of the N-Fe-N unit can be observed between 500 and 700 cm(-1) and are diagnostic indicators of the type of iron dinitrosyl species present. NRVS spectra for four iron dinitrosyl model compounds are presented and used as benchmarks for the identification of species formed in the reaction of Pyrococcus furiosus ferredoxin D14C with nitric oxide.
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Affiliation(s)
- Zachary J Tonzetich
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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25
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Tinberg CE, Lippard SJ. Revisiting the mechanism of dioxygen activation in soluble methane monooxygenase from M. capsulatus (Bath): evidence for a multi-step, proton-dependent reaction pathway. Biochemistry 2009; 48:12145-58. [PMID: 19921958 PMCID: PMC2797563 DOI: 10.1021/bi901672n] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Stopped-flow kinetic investigations of soluble methane monooxygenase (sMMO) from M. capsulatus (Bath) have clarified discrepancies that exist in the literature regarding several aspects of catalysis by this enzyme. The development of thorough kinetic analytical techniques has led to the discovery of two novel oxygenated iron species that accumulate in addition to the well-established intermediates H(peroxo) and Q. The first intermediate, P*, is a precursor to H(peroxo) and was identified when the reaction of reduced MMOH and MMOB with O(2) was carried out in the presence of >or=540 microM methane to suppress the dominating absorbance signal due to Q. The optical properties of P* are similar to those of H(peroxo), with epsilon(420) = 3500 M(-1) cm(-1) and epsilon(720) = 1250 M(-1) cm(-1). These values are suggestive of a peroxo-to-iron(III) charge-transfer transition and resemble those of peroxodiiron(III) intermediates characterized in other carboxylate-bridged diiron proteins and synthetic model complexes. The second identified intermediate, Q*, forms on the pathway of Q decay when reactions are performed in the absence of hydrocarbon substrate. Q* does not react with methane, forms independently of buffer composition, and displays a unique shoulder at 455 nm in its optical spectrum. Studies conducted at different pH values reveal that rate constants corresponding to P* decay/H(peroxo) formation and H(peroxo) decay/Q formation are both significantly retarded at high pH and indicate that both events require proton transfer. The processes exhibit normal kinetic solvent isotope effects (KSIEs) of 2.0 and 1.8, respectively, when the reactions are performed in D(2)O. Mechanisms are proposed to account for the observations of these novel intermediates and the proton dependencies of P* to H(peroxo) and H(peroxo) to Q conversion.
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Affiliation(s)
| | - Stephen J. Lippard
- To whom correspondence should be addressed.
. Telephone: (617) 253-1892. Fax: (617)
258-8150
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26
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Hakemian AS, Tinberg CE, Kondapalli KC, Telser J, Hoffman BM, Stemmler TL, Rosenzweig AC. The copper chelator methanobactin from Methylosinus trichosporium OB3b binds copper(I). J Am Chem Soc 2006; 127:17142-3. [PMID: 16332035 PMCID: PMC2864604 DOI: 10.1021/ja0558140] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oxidation state of copper bound to methanobactin, a small siderophore-like molecule from the methanotroph Methylosinus trichosporium OB3b, was investigated. Purified methanobactin loaded with Cu(II) exhibits a weak EPR signal probably due to adventitious Cu(II). The EPR signal intensity increases significantly upon addition of the strong oxidant nitric acid. Features of the X-ray absorption near edge spectrum, including a 1s --> 4p transition at 8985 eV, further indicate the presence of Cu(I). EXAFS data were best fit using a multiple scattering model generated from previously reported crystallographic parameters. These results establish definitively that M. trichosporium OB3b methanobactin binds Cu(I) and suggest that methanobactin itself reduces Cu(II) to Cu(I).
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