1
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Riley TP, Chou HT, Hu R, Bzymek KP, Correia AR, Partin AC, Li D, Gong D, Wang Z, Yu X, Manzanillo P, Garces F. Enhancing the Prefusion Conformational Stability of SARS-CoV-2 Spike Protein Through Structure-Guided Design. Front Immunol 2021; 12:660198. [PMID: 33968063 PMCID: PMC8100506 DOI: 10.3389/fimmu.2021.660198] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/30/2021] [Indexed: 01/08/2023] Open
Abstract
The worldwide pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unprecedented and the impact on public health and the global economy continues to be devastating. Although early therapies such as prophylactic antibodies and vaccines show great promise, there are concerns about the long-term efficacy and universal applicability of these therapies as the virus continues to mutate. Thus, protein-based immunogens that can quickly respond to viral changes remain of continued interest. The Spike protein, the main immunogen of this virus, displays a highly dynamic trimeric structure that presents a challenge for therapeutic development. Here, guided by the structure of the Spike trimer, we rationally design new Spike constructs that show a uniquely high stability profile while simultaneously remaining locked into the immunogen-desirable prefusion state. Furthermore, our approach emphasizes the relationship between the highly conserved S2 region and structurally dynamic Receptor Binding Domains (RBD) to enable vaccine development as well as the generation of antibodies able to resist viral mutation.
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Affiliation(s)
- Timothy P. Riley
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Hui-Ting Chou
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Ruozhen Hu
- Department of Inflammation and Oncology, Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Krzysztof P. Bzymek
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Ana R. Correia
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Alexander C. Partin
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Danqing Li
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Danyang Gong
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Zhulun Wang
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Xinchao Yu
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Paolo Manzanillo
- Department of Inflammation and Oncology, Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Fernando Garces
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
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2
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Gong D, Riley TP, Bzymek KP, Correia AR, Li D, Spahr C, Robinson JH, Case RB, Wang Z, Garces F. Rational selection of building blocks for the assembly of bispecific antibodies. MAbs 2021; 13:1870058. [PMID: 33397191 PMCID: PMC7808324 DOI: 10.1080/19420862.2020.1870058] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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] [Indexed: 01/07/2023] Open
Abstract
Bispecific antibodies, engineered to recognize two targets simultaneously, demonstrate exceptional clinical potential for the therapeutic intervention of complex diseases. However, these molecules are often composed of multiple polypeptide chains of differing sequences. To meet industrial scale productivity, enforcing the correct quaternary assembly of these chains is critical. Here, we describe Chain Selectivity Assessment (CSA), a high-throughput method to rationally select parental monoclonal antibodies (mAbs) to make bispecific antibodies requiring correct heavy/light chain pairing. By deploying CSA, we have successfully identified mAbs that exhibit a native preference toward cognate chain pairing that enables the production of hetero-IgGs without additional engineering. Furthermore, CSA also identified rare light chains (LCs) that permit positive binding of the non-cognate arm in the common LC hetero-IgGs, also without engineering. This rational selection of parental mAbs with favorable developability characteristics is critical to the successful development of bispecific molecules with optimal manufacturability properties.
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Affiliation(s)
- Danyang Gong
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - Timothy P Riley
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - Krzysztof P Bzymek
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - Ana R Correia
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - Danqing Li
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - Christopher Spahr
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - John H Robinson
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - Ryan B Case
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., San Francisco, CA USA
| | - Zhulun Wang
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., San Francisco, CA USA
| | - Fernando Garces
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
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3
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King JD, Ma Y, Kuo YC, Bzymek KP, Goodstein LH, Meyer K, Moore RE, Crow D, Colcher DM, Singh G, Horne DA, Williams JC. Template-Catalyzed, Disulfide Conjugation of Monoclonal Antibodies Using a Natural Amino Acid Tag. Bioconjug Chem 2018; 29:2074-2081. [PMID: 29763554 DOI: 10.1021/acs.bioconjchem.8b00284] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The high specificity and favorable pharmacological properties of monoclonal antibodies (mAbs) have prompted significant interest in re-engineering this class of molecules to add novel functionalities for enhanced therapeutic and diagnostic potential. Here, we used the high affinity, meditope-Fab interaction to template and drive the rapid, efficient, and stable site-specific formation of a disulfide bond. We demonstrate that this template-catalyzed strategy provides a consistent and reproducible means to conjugate fluorescent dyes, cytotoxins, or "click" chemistry handles to meditope-enabled mAbs (memAbs) and memFabs. More importantly, we demonstrate this covalent functionalization is achievable using natural amino acids only, opening up the opportunity to genetically encode cysteine meditope "tags" to biologics. As proof of principle, genetically encoded, cysteine meditope tags were added to the N- and/or C-termini of fluorescent proteins, nanobodies, and affibodies, each expressed in bacteria, purified to homogeneity, and efficiently conjugated to different memAbs and meFabs. We further show that multiple T-cell and Her2-targeting bispecific molecules using this strategy potently activate T-cell signaling pathways in vitro. Finally, the resulting products are highly stable as evidenced by serum stability assays (>14 d at 37 °C) and in vivo imaging of tumor xenographs. Collectively, the platform offers the opportunity to build and exchange an array of functional moieties, including protein biologics, among any cysteine memAb or Fab to rapidly create, test, and optimize stable, multifunctional biologics.
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4
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Bzymek KP, Puckett JW, Zer C, Xie J, Ma Y, King JD, Goodstein LH, Avery KN, Colcher D, Singh G, Horne DA, Williams JC. Mechanically interlocked functionalization of monoclonal antibodies. Nat Commun 2018; 9:1580. [PMID: 29679060 PMCID: PMC5910394 DOI: 10.1038/s41467-018-03976-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 03/27/2018] [Indexed: 01/07/2023] Open
Abstract
Because monoclonal antibodies (mAbs) have exceptional specificity and favorable pharmacology, substantial efforts have been made to functionalize them, either with potent cytotoxins, biologics, radionuclides, or fluorescent groups for therapeutic benefit and/or use as theranostic agents. To exploit our recently discovered meditope-Fab interaction as an alternative means to efficiently functionalize mAbs, we used insights from the structure to enhance the affinity and lifetime of the interaction by four orders of magnitude. To further extend the lifetime of the complex, we created a mechanical bond by incorporating an azide on the meditope, threading the azide through the Fab, and using click chemistry to add a steric group. The mechanically interlocked, meditope-Fab complex retains antigen specificity and is capable of imaging tumors in mice. These studies indicate it is possible to "snap" functionality onto mAbs, opening the possibility of rapidly creating unique combinations of mAbs with an array of cytotoxins, biologics, and imaging agents.
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Affiliation(s)
- Krzysztof P Bzymek
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower St., Duarte, CA, 91010, USA
| | - James W Puckett
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower St., Duarte, CA, 91010, USA
| | - Cindy Zer
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower St., Duarte, CA, 91010, USA
| | - Jun Xie
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower St., Duarte, CA, 91010, USA
| | - Yuelong Ma
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower St., Duarte, CA, 91010, USA
| | - Jeremy D King
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower St., Duarte, CA, 91010, USA
| | - Leah H Goodstein
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower St., Duarte, CA, 91010, USA
| | - Kendra N Avery
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower St., Duarte, CA, 91010, USA.,Xencor, 111W. Lemon Ave., Monrovia, CA, 91016, USA
| | - David Colcher
- Department of Molecular Immunology, Beckman Research Institute of City of Hope, 1710 Flower St., Duarte, CA, 91010, USA
| | - Gagandeep Singh
- Department of Surgery, Beckman Research Institute of City of Hope, 1710 Flower St., Duarte, CA, 91010, USA
| | - David A Horne
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower St., Duarte, CA, 91010, USA
| | - John C Williams
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower St., Duarte, CA, 91010, USA.
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5
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Bzymek KP, Ma Y, Avery KN, Horne DA, Williams JC. Meditope-Fab interaction: threading the hole. Acta Crystallogr F Struct Biol Commun 2017; 73:688-694. [PMID: 29199990 PMCID: PMC5713674 DOI: 10.1107/s2053230x17016272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/10/2017] [Indexed: 05/29/2023]
Abstract
The structure–affinity relationship of complexes of the cetuximab Fab with meditope peptides modified at Arg8 is investigated. Meditope, a cyclic 12-residue peptide, binds to a unique binding side between the light and heavy chains of the cetuximab Fab. In an effort to improve the affinity of the interaction, it was sought to extend the side chain of Arg8 in the meditope, a residue that is accessible from the other side of the meditope binding site, in order to increase the number of interactions. These modifications included an n-butyl and n-octyl extension as well as hydroxyl, amine and carboxyl substitutions. The atomic structures of the complexes and the binding kinetics for each modified meditope indicated that each extension threaded through the Fab ‘hole’ and that the carboxyethylarginine substitution makes a favorable interaction with the Fab, increasing the half-life of the complex by threefold compared with the unmodified meditope. Taken together, these studies provide a basis for the design of additional modifications to enhance the overall affinity of this unique interaction.
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Affiliation(s)
- Krzysztof P Bzymek
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91101, USA
| | - Yuelong Ma
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91101, USA
| | - Kendra N Avery
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91101, USA
| | - David A Horne
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91101, USA
| | - John C Williams
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91101, USA
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6
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Zer C, Avery KN, Meyer K, Goodstein L, Bzymek KP, Singh G, Williams JC. Engineering a high-affinity peptide binding site into the anti-CEA mAb M5A. Protein Eng Des Sel 2017; 30:409-417. [PMID: 28431161 PMCID: PMC5914451 DOI: 10.1093/protein/gzx016] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 03/17/2017] [Accepted: 03/28/2017] [Indexed: 12/27/2022] Open
Abstract
We have previously identified a cyclic peptide called meditope which binds to the central cavity of the Fab portion of cetuximab and shown that this peptide binding site can be grafted, or 'meditope-enabled', onto trastuzumab. This peptide has been shown to act as a hitch for the non-covalent attachment of imaging agents to meditope-enabled antibodies. Herein, we explore the process of grafting this peptide binding site onto M5A, an anti-CEA antibody in clinical trials for cancer diagnostics. In order to explore the contributions of the amino acids, we sequentially introduced pairs of amino acid substitutions into the Fab and then we reverse-substituted key residues in the presence of the other substitutions. We demonstrate that Pro40Thr, Gly41Asn, Phe83Ile and Thr85Asp in the light chain are sufficient to recreate the meditope binding site in M5A with single-digit micromolar affinity. We show that Pro40 abrogates peptide binding in the presence of the other 12 residue substitutions, and that the presence of all 13 substitutions does not interfere with antibody:antigen recognition. Collectively, these studies provide detailed insight for defining and fine-tuning the binding affinity of the meditope binding site within an antibody.
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Affiliation(s)
- Cindy Zer
- Department of Molecular Medicine, Beckman Research Institute at City of Hope
| | - Kendra N. Avery
- Department of Molecular Medicine, Beckman Research Institute at City of Hope
| | - Kassondra Meyer
- Department of Molecular Medicine, Beckman Research Institute at City of Hope
| | - Leah Goodstein
- Department of Molecular Medicine, Beckman Research Institute at City of Hope
| | - Krzysztof P. Bzymek
- Department of Molecular Medicine, Beckman Research Institute at City of Hope
| | - Gagandeep Singh
- Department of Surgery, City of Hope National Medical Center 1500 Duarte Road, Duarte, CA 91010, USA
| | - John C. Williams
- Department of Molecular Medicine, Beckman Research Institute at City of Hope
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7
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Bzymek KP, Avery KA, Ma Y, Horne DA, Williams JC. Natural and non-natural amino-acid side-chain substitutions: affinity and diffraction studies of meditope-Fab complexes. Acta Crystallogr F Struct Biol Commun 2016; 72:820-830. [PMID: 27834791 PMCID: PMC5101583 DOI: 10.1107/s2053230x16016149] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [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: 08/31/2016] [Accepted: 10/11/2016] [Indexed: 12/16/2022] Open
Abstract
Herein, multiple crystal structures of meditope peptide derivatives incorporating natural and unnatural amino acids bound to the cetuximab Fab domain are presented. The affinity of each derivative was determined by surface plasmon resonance and correlated to the atomic structure. Overall, it was observed that the hydrophobic residues in the meditope peptide, Phe3, Leu5 and Leu10, could accommodate a number of moderate substitutions, but these invariably reduced the overall affinity and half-life of the interaction. In one case, the substitution of Phe3 by histidine led to a change in the rotamer conformation, in which the imidazole ring flipped to a solvent-exposed position. Based on this observation, Phe3 was substituted by diphenylalanine and it was found that the phenyl rings in this variant mimic the superposition of the Phe3 and His3 structures, producing a moderate increase, of 1.4-fold, in the half-life of the complex. In addition, it was observed that substitution of Leu5 by tyrosine and glutamate strongly reduced the affinity, whereas the substitution of Leu5 by diphenylalanine moderately reduced the half-life (by approximately fivefold). Finally, it was observed that substitution of Arg8 and Arg9 by citrulline dramatically reduced the overall affinity, presumably owing to lost electrostatic interactions. Taken together, these studies provide insight into the meditope-cetuximab interaction at the atomic level.
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Affiliation(s)
- Krzysztof P. Bzymek
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91010, USA
| | - Kendra A. Avery
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91010, USA
| | - Yuelong Ma
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91010, USA
| | - David A. Horne
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91010, USA
| | - John C. Williams
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91010, USA
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Alontaga AY, Ambaye ND, Li YJ, Vega R, Chen CH, Bzymek KP, Williams JC, Hu W, Chen Y. Observation of an E2 (Ubc9)-homodimer by crystallography. Data Brief 2016; 7:195-200. [PMID: 27408909 PMCID: PMC4927773 DOI: 10.1016/j.dib.2016.02.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 12/19/2015] [Accepted: 02/04/2016] [Indexed: 12/03/2022] Open
Abstract
Post-translational modifications by the small ubiquitin-like modifiers (SUMO), in particular the formation of poly-SUMO-2 and -3 chains, regulates essential cellular functions and its aberration leads to life-threatening diseases (Geoffroy and Hay, 2009) [1]. It was shown previously that the non-covalent interaction between SUMO and the conjugating enzyme (E2) for SUMO, known as Ubc9, is required for poly-SUMO-2/3 chain formation (Knipscheer et al., 2007) [2]. However, the structure of SUMO-Ubc9 non-covalent complex, by itself, could not explain how the poly-SUMO-2/3 chain forms and consequently a Ubc9 homodimer, although never been observed, was proposed for poly-SUMO-2/3 chain formation (Knipscheer et al., 2007) [2]. Here, we solved the crystal structure of a heterotrimer containing a homodimer of Ubc9 and the RWD domain from RWDD3. The asymmetric Ubc9 homodimer is mediated by the N-terminal region of one Ubc9 molecule and a surface near the catalytic Cys of the second Ubc9 molecule (Fig. 1A). This N-terminal surface of Ubc9 that is involved in the homodimer formation also interacts with the RWD domain, the ubiquitin-fold domain of the SUMO activating enzyme (E1), SUMO, and the E3 ligase, RanBP2 (Knipscheer et al., 2007; Tong et al.. 1997; Tatham et al., 2005; Reverter and Lima, 2005; Capili and Lima, 2007; Wang et al., 2009, 2010; Wang and Chen, 2010; Alontaga et al., 2015) [2], [3], [4], [5], [6], [7], [8], [9], [10]. The existence of the Ubc9 homodimer in solution is supported by previously published solution NMR studies of rotational correlation time and chemical shift perturbation (Alontaga et al., 2015; Yuan et al., 1999) [10], [11]. Site-directed mutagenesis and biochemical analysis suggests that this dimeric arrangement of Ubc9 is likely important for poly-SUMO chain formation (Fig. 1B and C). The asymmetric Ubc9 homodimer described for the first time in this work could provide the critical missing link in the poly-SUMO chain formation mechanism. The data presented here are related to the research article entitled, "RWD domain as an E2 (Ubc9) interaction module" (Alontaga et al., 2015) [10]. The data of the crystal structure has been deposited to RCSB protein data bank with identifier: 4Y1L.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Yuan Chen
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope, 1450 East Duarte Road, Duarte, CA 91010, United States
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9
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Bzymek KP, Ma Y, Avery KA, Horne DA, Williams JC. Cyclization strategies of meditopes: affinity and diffraction studies of meditope-Fab complexes. Acta Crystallogr F Struct Biol Commun 2016; 72:434-42. [PMID: 27303895 PMCID: PMC4909242 DOI: 10.1107/s2053230x16007202] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/27/2016] [Indexed: 11/16/2022]
Abstract
An overview of cyclization strategies of a Fab-binding peptide to maximize affinity. Recently, a unique binding site for a cyclic 12-residue peptide was discovered within a cavity formed by the light and heavy chains of the cetuximab Fab domain. In order to better understand the interactions that drive this unique complex, a number of variants including the residues within the meditope peptide and the antibody, as well as the cyclization region of the meditope peptide, were created. Here, multiple crystal structures of meditope peptides incorporating different cyclization strategies bound to the central cavity of the cetuximab Fab domain are presented. The affinity of each cyclic derivative for the Fab was determined by surface plasmon resonance and correlated to structural differences. Overall, it was observed that the disulfide bond used to cyclize the peptide favorably packs against a hydrophobic ‘pocket’ and that amidation and acetylation of the original disulfide meditope increased the overall affinity ∼2.3-fold. Conversely, replacing the terminal cysteines with serines and thus creating a linear peptide reduced the affinity over 50-fold, with much of this difference being reflected in a decrease in the on-rate. Other cyclization methods, including the formation of a lactam, reduced the affinity but not to the extent of the linear peptide. Collectively, the structural and kinetic data presented here indicate that small perturbations introduced by different cyclization strategies can significantly affect the affinity of the meditope–Fab complex.
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Affiliation(s)
- Krzysztof P Bzymek
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91010, USA
| | - Yuelong Ma
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91010, USA
| | - Kendra A Avery
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91010, USA
| | - David A Horne
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91010, USA
| | - John C Williams
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91010, USA
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10
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Alontaga AY, Ambaye ND, Li YJ, Vega R, Chen CH, Bzymek KP, Williams JC, Hu W, Chen Y. RWD Domain as an E2 (Ubc9)-Interaction Module. J Biol Chem 2015; 290:16550-9. [PMID: 25918163 DOI: 10.1074/jbc.m115.644047] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 02/10/2015] [Indexed: 11/06/2022] Open
Abstract
An RWD domain is a well conserved domain found through bioinformatic analysis of the human proteome sequence; however, its function has been unknown. Ubiquitin-like modifications require the catalysis of three enzymes generally known as E1, E2, and E3. We solved the crystal structure of the E2 for the small ubiquitin-like modifiers (SUMO) in complex with an RWD domain and confirmed the structure using solution NMR analysis. The binding surface of RWD on Ubc9 is located near the N terminus of Ubc9 that is known to be involved in noncovalent binding of the proteins in the conjugation machinery, including a domain of E1, SUMO, and an E3 ligase. NMR data indicate that the RWD domain does not bind to SUMO and E1. The interaction between RWD and Ubc9 has a Kd of 32 ± 4 μM. Consistent with the structure and binding affinity and in contrast to a previous report, the RWD domain and RWDD3 have minimal effects on global SUMOylation. The structural and biochemical information presented here forms the basis for further investigation of the functions of RWD-containing proteins.
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Affiliation(s)
| | | | - Yi-Jia Li
- From the Department of Molecular Medicine and
| | - Ramir Vega
- From the Department of Molecular Medicine and
| | | | | | | | - Weidong Hu
- the NMR Core Facility, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - Yuan Chen
- From the Department of Molecular Medicine and
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11
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Avery KN, Zer C, Bzymek KP, Williams JC. Development of a high affinity, non-covalent biologic to add functionality to Fabs. Sci Rep 2015; 5:7817. [PMID: 25588710 PMCID: PMC4295097 DOI: 10.1038/srep07817] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 12/09/2014] [Indexed: 12/31/2022] Open
Abstract
Functionalization of monoclonal antibodies (mAbs) requires chemical derivatization and/or genetic manipulation. Inherent in these methods are challenges with protein heterogeneity, stability and solubility. Such perturbations could potentially be avoided by using a high affinity, non-covalent intermediate to bridge the desired functionality to a stable mAb. Recently, we engineered a binding site for a peptide named “meditope” within the Fab of trastuzumab. Proximity of the meditope site to that of protein L suggested an opportunity to enhance the meditope's moderate affinity. Joined by a peptide linker, the meditope-protein L construct has a KD ~ 180 pM - a 7000-fold increase in affinity. The construct is highly specific to the engineered trastuzumab, as demonstrated by flow cytometry. Moreover, the fusion of a bulky GFP to this construct did not affect the association with cell surface antigens. Collectively, these data indicate this specific, high affinity construct can be developed to rapidly add new functionality to mAbs.
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Affiliation(s)
- Kendra N Avery
- Department of Molecular Medicine, Beckman Research Institute at City of Hope 1710 Flower St, Duarte CA 91010
| | - Cindy Zer
- Department of Molecular Medicine, Beckman Research Institute at City of Hope 1710 Flower St, Duarte CA 91010
| | - Krzysztof P Bzymek
- Department of Molecular Medicine, Beckman Research Institute at City of Hope 1710 Flower St, Duarte CA 91010
| | - John C Williams
- Department of Molecular Medicine, Beckman Research Institute at City of Hope 1710 Flower St, Duarte CA 91010
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12
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Bzymek KP, Hamaoka BY, Ghosh P. Two translation products of Yersinia yscQ assemble to form a complex essential to type III secretion. Biochemistry 2012; 51:1669-77. [PMID: 22320351 PMCID: PMC3289748 DOI: 10.1021/bi201792p] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The bacterial flagellar C-ring is composed of two essential proteins, FliM and FliN. The smaller protein, FliN, is similar to the C-terminus of the larger protein, FliM, both being composed of SpoA domains. While bacterial type III secretion (T3S) systems encode many proteins in common with the flagellum, they mostly have a single protein in place of FliM and FliN. This protein resembles FliM at its N-terminus and is as large as FliM but is more like FliN at its C-terminal SpoA domain. We have discovered that a FliN-sized cognate indeed exists in the Yersinia T3S system to accompany the FliM-sized cognate. The FliN-sized cognate, YscQ-C, is the product of an internal translation initiation site within the locus encoding the FliM-sized cognate YscQ. Both intact YscQ and YscQ-C were found to be required for T3S, indicating that the internal translation initiation site, which is conserved in some but not all YscQ orthologs, is crucial for function. The crystal structure of YscQ-C revealed a SpoA domain that forms a highly intertwined, domain-swapped homodimer, similar to those observed in FliN and the YscQ ortholog HrcQ(B). A single YscQ-C homodimer associated reversibly with a single molecule of intact YscQ, indicating conformational differences between the SpoA domains of intact YscQ and YscQ-C. A "snap-back" mechanism suggested by the structure can account for this. The 1:2 YscQ-YscQ-C complex is a close mimic of the 1:4 FliM-FliN complex and the likely building block of the putative Yersinia T3S system C-ring.
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Affiliation(s)
| | | | - Partho Ghosh
- Corresponding Author: Phone: 858-822-1139. Fax: 858-822-2871.
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Bzymek KP, Newton GL, Ta P, Fahey RC. Mycothiol import by Mycobacterium smegmatis and function as a resource for metabolic precursors and energy production. J Bacteriol 2007; 189:6796-805. [PMID: 17644601 PMCID: PMC2045207 DOI: 10.1128/jb.00644-07] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [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: 12/24/2022] Open
Abstract
Mycothiol ([MSH] AcCys-GlcN-Ins, where Ac is acetyl) is the major thiol produced by Mycobacterium smegmatis and other actinomycetes. Mutants deficient in MshA (strain 49) or MshC (transposon mutant Tn1) of MSH biosynthesis produce no MSH. However, when stationary phase cultures of these mutants were incubated in medium containing MSH, they actively transported it to generate cellular levels of MSH comparable to or greater than the normal content of the wild-type strain. When these MSH-loaded mutants were transferred to MSH-free preconditioned medium, the cellular MSH was catabolized to generate GlcN-Ins and AcCys. The latter was rapidly converted to Cys by a high deacetylase activity assayed in extracts. The Cys could be converted to pyruvate by a cysteine desulfhydrase or used to regenerate MSH in cells with active MshC. Using MSH labeled with [U-(14)C]cysteine or with [6-(3)H]GlcN, it was shown that these residues are catabolized to generate radiolabeled products that are ultimately lost from the cell, indicating extensive catabolism via the glycolytic and Krebs cycle pathways. These findings, coupled with the fact the myo-inositol can serve as a sole carbon source for growth of M. smegmatis, indicate that MSH functions not only as a protective cofactor but also as a reservoir of readily available biosynthetic precursors and energy-generating metabolites potentially important under stress conditions. The half-life of MSH was determined in stationary phase cells to be approximately 50 h in strains with active MshC and 16 +/- 3 h in the MshC-deficient mutant, suggesting that MSH biosynthesis may be a suitable target for drugs to treat dormant tuberculosis.
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Affiliation(s)
- Krzysztof P Bzymek
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0314, USA
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Bzymek KP, Colman RF. Role of alpha-Asp181, beta-Asp192, and gamma-Asp190 in the distinctive subunits of human NAD-specific isocitrate dehydrogenase. Biochemistry 2007; 46:5391-7. [PMID: 17432878 DOI: 10.1021/bi700061t] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [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
Human NAD-dependent isocitrate dehydrogenase (IDH) is allosterically activated by ADP by lowering the Km for isocitrate. The enzyme has three subunit types with distinguishable sequences present in the approximate ratio 2alpha:1beta:1gamma and, per tetramer, binds 2 mol of each ligand. To evaluate whether the subunits also have distinct functions, we replaced equivalent aspartates, one subunit at a time, by asparagines; each expressed, purified enzyme was composed of one mutant and two wild-type subunits. The aspartates were chosen because beta-Asp192 and gamma-Asp190 had previously been affinity labeled by a reactive ADP analogue and alpha-Asp181 is equivalent based on sequence alignments. The alpha-D181N IDH mutant exhibits a 2000-fold decrease in Vmax, with increases of 15-fold in the Kms for Mn(II) and NAD and a much smaller change in the Km for isocitrate. In contrast, the Vmax values of the beta-D192N and gamma-D190N IDHs are only reduced 4-5-fold as compared to wild-type enzyme. The Km for NAD of the beta-D192N enzyme is 9 times that of the normal enzyme with little or no effect on the affinity for Mn(II) or isocitrate, while the Kms for coenzyme and for Mn(II) of the gamma-D190N enzyme are 19 and 72 times, respectively, that of the normal enzyme with a much smaller effect on the Km for isocitrate. Finally, all three mutant enzymes fail to respond to ADP by lowering the Km for isocitrate, although they do bind ADP. Thus, these aspartates are close to but not in the ADP site and are required for communication between the ADP and isocitrate sites. These results demonstrate that alpha-Asp181 is the only one of these aspartates essential for catalysis. Beta-Asp192 is a determinant of the enzyme's affinity for NAD, as is gamma-Asp190, while gamma-Asp190 also influences the enzyme's affinity for metal ion. We conclude that the NAD and ADP sites are shared between alpha- and beta- and alpha- and gamma-subunits, and the Mn(II) site is shared between alpha- and gamma-subunits, while the alpha-subunit is essential for catalysis. Although alpha-Asp181, beta-Asp192, and gamma-Asp190 may have derived from a common progenitor, these aspartates of the three subunits have evolved distinct functions.
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Affiliation(s)
- Krzysztof P Bzymek
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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Abstract
Mycothiol is the major thiol produced by mycobacteria and is required for growth of Mycobacterium tuberculosis. The final three steps in the biosynthesis of mycothiol have been fully elucidated but the initial steps have been unclear. A glycosyltransferase, MshA, is required for production of the mycothiol precursor, 1-O-(2-acetamido-2-deoxy-alpha-D-glucopyranosyl)-D-myo-inositol, but its substrates and immediate products were unknown. In this study, we show that the N-acetylglucosamine donor is UDP-N-acetylglucosamine and that the N-acetylglucosamine acceptor is 1L-myo-inositol 1-phosphate. The reaction generates UDP and 1-O-(2-acetamido-2-deoxy-alpha-D-glucopyranosyl)-D-myo-inositol 3-phosphate. Using cell-free extracts of M. smegmatis mc(2)155, little activity was obtained with myo-inositol, 1D-myo-inositol 1-phosphate, or myo-inositol 2-phosphate as the N-acetylglucosamine acceptor. A phosphatase, designated MshA2, is required to dephosphorylate 1-O-(2-acetamido-2-deoxy-alpha-glucopyranosyl)-D-myo-inositol 3-phosphate to produce 1-O-(2-acetamido-2-deoxy-alpha-D-glucopyranosyl)-D-myo-inositol. The latter is deacetylated, ligated with cysteine, and the cysteinyl amino group acetylated by acetyl-CoA to complete the mycothiol biosynthesis pathway. Uptake and concentration of myo-[14C]inositol is rapid in Mycobacterium smegmatis and leads to production of radiolabeled inositol 1-phosphate and mycothiol. This demonstrates the presence of a myo-inositol transporter and a kinase that generates 1L-myo-inositol 1-phosphate. The biochemical pathway of mycothiol biosynthesis is now fully elucidated.
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Affiliation(s)
- Gerald L Newton
- Department of Chemistry and Biochemistry, University of California, La Jolla, California 92093, USA
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Desmarais W, Bienvenue DL, Bzymek KP, Petsko GA, Ringe D, Holz RC. The high-resolution structures of the neutral and the low pH crystals of aminopeptidase from Aeromonas proteolytica. J Biol Inorg Chem 2006; 11:398-408. [PMID: 16596389 DOI: 10.1007/s00775-006-0093-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [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] [Received: 02/01/2006] [Accepted: 02/10/2006] [Indexed: 10/24/2022]
Abstract
The aminopeptidase from Aeromonas proteolytica (AAP) contains two zinc ions in the active site and catalyzes the degradation of peptides. Herein we report the crystal structures of AAP at 0.95-A resolution at neutral pH and at 1.24-A resolution at low pH. The combination of these structures allowed the precise modeling of atomic positions, the identification of the metal bridging oxygen species, and insight into the physical properties of the metal ions. On the basis of these structures, a new putative catalytic mechanism is proposed for AAP that is likely relevant to all binuclear metalloproteases.
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Affiliation(s)
- William Desmarais
- Program in Biophysics and Structural Biology, Brandeis University, 415 South Street, Waltham, MA 02254-9110, USA
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Bzymek KP, Swierczek SI, Bennett B, Holz RC. Spectroscopic and Thermodynamic Characterization of the E151D and E151A Altered Leucine Aminopeptidases fromAeromonasproteolytica†. Inorg Chem 2005; 44:8574-80. [PMID: 16270998 DOI: 10.1021/ic051034g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [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
Previous kinetic characterization of the glutamate 151 (E151)-substituted forms of the leucine aminopeptidase from Aeromonas proteolytica (Vibrio proteolyticus; AAP) has provided critical evidence that this residue functions as the general acid/base. The close proximity of similar glutamate residues to the bridging water/hydroxide of the dinuclear active sites of metalloenzymes (2.80 and 3.94 angstroms in carboxypeptidase G2 and 3.30 and 3.63 angstroms in AAP), suggests it may also be involved in stabilizing the active-site metal ions. Therefore, the structural perturbations of the dinuclear active site of AAP were examined for two E151-substituted forms, namely E151D-AAP and E151A-AAP, by UV-vis and electron paramagnetic resonance (EPR) spectroscopy. UV-vis spectroscopy of Co(II)-substituted E151A-AAP did not reveal any significant changes in the electronic absorption spectra. However UV-vis spectra of mono- and dicobalt(II) E151D-AAP exhibited a lower molecular absorptivity compared to AAP (23 and 43 M(-1) cm(-1) vs. 56 and 109 M(-1) cm(-1) for E151D-AAP and AAP, respectively) suggesting both Co(II) ions reside in distorted octahedral coordination geometry in E151D-AAP. EPR spectra of [Co_(E151D-AAP)], [ZnCo(E151D-AAP)], and [(CoCo(E151D-AAP)] were identical, with g(perpendicular) = 2.35, g(parallel) = 2.19, and E/D = 0.19, similar to [CoCo(AAP)]. On the other hand, the EPR spectrum of [Co_(E151A-AAP)] was best simulated assuming the presence of two species with (i) g(x,y) = 2.509, g(z) = 2.19, E/D = 0.19, A = 0.0069 cm(-1) and (ii) g(x,y) = 2.565, g(z) = 2.19, E/D = 0.20, A = 0.0082 cm(-1) indicative of a five- or six-coordinate species. Isothermal titration calorimetry experiments revealed a large decrease in Zn(II) affinities, with K(d) values elevated by factors of approximately 850 and approximately 24,000 for the first metal binding events of E151D- and E151A-AAP, respectively. The combination of these data indicates that E151 serves to stabilize the dinuclear active site of AAP.
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Affiliation(s)
- Krzysztof P Bzymek
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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Bzymek KP, Moulin A, Swierczek SI, Ringe D, Petsko GA, Bennett B, Holz RC. Kinetic, Spectroscopic, and X-ray Crystallographic Characterization of the Functional E151H Aminopeptidase from Aeromonas proteolytica,. Biochemistry 2005; 44:12030-40. [PMID: 16142900 DOI: 10.1021/bi0505823] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [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
Glutamate151 (E151) has been shown to be catalytically essential for the aminopeptidase from Vibrio proteolyticus (AAP). E151 acts as the general acid/base during the catalytic mechanism of peptide hydrolysis. However, a glutamate residue is not the only residue capable of functioning as a general acid/base during catalysis for dinuclear metallohydrolases. Recent crystallographic characterization of the D-aminopeptidase from Bacillus subtilis (DppA) revealed a histidine residue that resides in an identical position to E151 in AAP. Because the active-site ligands for DppA and AAP are identical, AAP has been used as a model enzyme to understand the mechanistic role of H115 in DppA. Substitution of E151 with histidine resulted in an active AAP enzyme exhibiting a kcat value of 2.0 min(-1), which is over 2000 times slower than r AAP (4380 min(-1)). ITC experiments revealed that ZnII binds 330 and 3 times more weakly to E151H-AAP compared to r-AAP. UV-vis and EPR spectra of CoII-loaded E151H-AAP indicated that the first metal ion resides in a hexacoordinate/pentacoordinate equilibrium environment, whereas the second metal ion is six-coordinate. pH dependence of the kinetic parameters kcat and K(m) for the hydrolysis of L-leucine p-nitroanilide (L-pNA) revealed a change in an ionization constant in the enzyme-substrate complex from 5.3 in r-AAP to 6.4 in E151H-AAP, consistent with E151 in AAP being the active-site general acid/base. Proton inventory studies at pH 8.50 indicate the transfer of one proton in the rate-limiting step of the reaction. Moreover, the X-ray crystal structure of [ZnZn(E151H-AAP)] has been solved to 1.9 A resolution, and alteration of E151 to histidine does not introduce any major conformational changes to the overall protein structure or the dinuclear ZnII active site. Therefore, a histidine residue can function as the general acid/base in hydrolysis reactions of peptides and, through analogy of the role of E151 in AAP, H115 in DppA likely shuttles a proton to the leaving group of the substrate.
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Affiliation(s)
- Krzysztof P Bzymek
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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Bzymek KP, D'Souza VM, Chen G, Campbell H, Mitchell A, Holz RC. Function of the signal peptide and N- and C-terminal propeptides in the leucine aminopeptidase from Aeromonas proteolytica. Protein Expr Purif 2004; 37:294-305. [PMID: 15358350 DOI: 10.1016/j.pep.2004.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2004] [Revised: 04/29/2004] [Indexed: 10/26/2022]
Abstract
The leucine aminopeptidase from Aeromonas proteolytica (also known as Vibrio proteolyticus) (AAP) is a metalloenzyme with broad substrate specificity. The open reading frame (ORF) for AAP encodes a 54 kDa enzyme, however, the extracellular enzyme has a molecular weight of 43 kDa. This form of AAP is further processed to a mature, thermostable 32 kDa form but the exact nature of this process is unknown. Over-expression of different forms of AAP in Escherichia coli (with AAP's native leader sequence, with and without the N- and/or C-terminal propeptides, and as fusion protein) has allowed a model for the processing of wild-type AAP to be proposed. The role of the A. proteolytica signal peptide in protein secretion as well as comparison to other known signal peptides reveals a close resemblance of the A. proteolytica signal peptide to the outer membrane protein (OmpA) signal peptide. Over-expression of the full 54 kDa AAP enzyme provides an enzyme that is significantly less active, due to a cooperative inhibitory interaction between both propeptides. Over-expression of AAP lacking its C-terminal propeptide provided an enzyme with an identical kcat value to wild-type AAP but exhibited a larger Km value, suggesting competitive inhibition of AAP by the N-terminal propeptide (Ki approximately 0.13 nM). The recombinant 32 kDa form of AAP was characterized by kinetic and spectroscopic methods and was shown to be identical to mature, wild-type AAP. Therefore, the ease of purification and processing of rAAP along with the fact that large quantities can be obtained now allow new detailed mechanistic studies to be performed on AAP through site-directed mutagenesis.
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Affiliation(s)
- Krzysztof P Bzymek
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
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Abstract
Glutamate 151 has been proposed to act as the general acid/base during the peptide hydrolysis reaction catalyzed by the co-catalytic metallohydrolase from Aeromonas proteolytica (AAP). However, to date, no direct evidence has been reported for the role of Glu-151 during catalytic turnover by AAP. In order to elucidate the catalytic role of Glu-151, altered AAP enzymes have been prepared in which Glu-151 has been substituted with a glutamine, an alanine, and an aspartate. The Michaelis constant (K(m)) does not change upon substitution to aspartate or glutamine, but the rate of the reaction changes drastically in the following order: glutamate (100% activity), aspartate (0.05%), glutamine (0.004%), and alanine (0%). Examination of the pH dependence of the kinetic constants k(cat) and K(m) revealed a change in the pK(a) of a group that ionizes at pH 4.8 in recombinant leucine aminopeptidase (rAAP) to 4.2 for E151D-AAP. The remaining pK(a) values at 5.2, 7.5, and 9.9 do not change. Proton inventory studies indicate that one proton is transferred in the rate-limiting step of the reaction at pH 10.50 for both rAAP and E151D-AAP, but at pH 6.50 two protons and general solvation effects are responsible for the observed effects in the reaction catalyzed by rAAP and E151D-AAP, respectively. Based on these data, Glu-151 is intrinsically involved in the peptide hydrolysis reaction catalyzed by AAP and can be assigned the role of a general acid and base.
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Affiliation(s)
- Krzysztof P Bzymek
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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Abstract
Understanding the reaction mechanism of co-catalytic metallopeptidases provides a starting point for the design and synthesis of new molecules that can be screened as potential pharmaceuticals. Many of the enzymes that contain co-catalytic metallo-active sites play important roles in cellular processes such as tissue repair, protein maturation, hormone level regulation, cell-cycle control and protein degradation. Therefore, these enzymes play central roles in several disease states including cancer, HIV, stroke, diabetes, bacterial infections, neurological processes, schizophrenia, seizure disorders, and amyotrophic lateral sclerosis. The mechanism of AAP, an aminopeptidase from Aeromonas proteolytica, is one of the best-characterized examples of a metallopeptidase containing a co-catalytic metallo-active site, although this enzyme is not a specific pharmaceutical target at this time. As a large majority of co-catalytic metallopeptidases contain active sites that are nearly identical to the one observed in AAP, the major steps of their catalytic mechanisms are likely to be very similar. With this in mind, it is possible to propose a general catalytic mechanism for the hydrolysis of amino acid substrates.
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Affiliation(s)
- Richard C Holz
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA.
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Desmarais WT, Bienvenue DL, Bzymek KP, Holz RC, Petsko GA, Ringe D. The 1.20 A resolution crystal structure of the aminopeptidase from Aeromonas proteolytica complexed with tris: a tale of buffer inhibition. Structure 2002; 10:1063-72. [PMID: 12176384 DOI: 10.1016/s0969-2126(02)00810-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [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: 11/26/2022]
Abstract
The aminopeptidase from Aeromonas proteolytica (AAP) is a bridged bimetallic enzyme that removes the N-terminal amino acid from a peptide chain. To fully understand the metal roles in the reaction pathway of AAP we have solved the 1.20 A resolution crystal structure of native AAP (PDB ID = 1LOK). The high-quality electron density maps showed a single Tris molecule chelated to the active site Zn(2+), alternate side chain conformations for some side chains, a sodium ion that mediates a crystal contact, a surface thiocyanate ion, and several potential hydrogen atoms. In addition, the high precision of the atomic positions has led to insight into the protonation states of some of the active site amino acid side chains.
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Affiliation(s)
- William T Desmarais
- Program in Biophysics and Structural Biology, Brandeis University, Waltham, Massachusetts 02454, USA
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