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Ha JH, Presti MF, Loh SN. A Single Protein Disruption Site Results in Efficient Reassembly by Multiple Engineering Methods. Biophys J 2019; 117:56-65. [PMID: 31221439 DOI: 10.1016/j.bpj.2019.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/27/2019] [Accepted: 06/05/2019] [Indexed: 01/03/2023] Open
Abstract
Disrupting a protein's sequence by cleavage or insertion of a hinge domain forms the basis for protein engineering tools, including fragment complementation, circular permutation, and domain swapping. Despite the utility of these designs, their widespread implementation has been limited by the difficulty in choosing where to interrupt the protein sequence: the resulting fragments often aggregate or fail to reassemble. Here, we show that an optimal site exists within ribose binding protein (RBP) that, when disrupted, results in the most efficient formation of fragment-complemented and domain-swapped species. Cleaving RBP at this site also produces a highly stable, cooperatively folded circular permutant. This hot-spot site was identified by an experimental approach involving selection among competing folds. We find that efficiency in the case of RBP is determined by kinetic factors (survival of the first) rather than thermodynamics (survival of the fittest). Together with emerging computational tools, this limited data set defines a pathway for designing robust platforms for molecular switches and biosensors based on the aforementioned protein modifications.
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Affiliation(s)
- Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York.
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2
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DeRosa JR, Moyer BS, Lumen E, Wolfe AJ, Sleeper MB, Bianchi AH, Crawford A, McGuigan C, Wortel D, Fisher C, Moody KJ, Blanden AR. RPtag as an Orally Bioavailable, Hyperstable Epitope Tag and Generalizable Protein Binding Scaffold. Biochemistry 2018; 57:3036-3049. [PMID: 29722979 DOI: 10.1021/acs.biochem.8b00170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antibodies are the most prolific biologics in research and clinical environments because of their ability to bind targets with high affinity and specificity. However, antibodies also carry liabilities. A significant portion of the life-science reproducibility crisis is driven by inconsistent performance of research-grade antibodies, and clinical antibodies are often unstable and require costly cold-chain management to reach their destinations in active form. In biotechnology, antibodies are also limited by difficulty integrating them in many recombinant systems due to their size and structural complexity. A switch to small, stable, sequence-verified binding scaffolds may overcome these barriers. Here we present such a scaffold, RPtag, based on a ribose-binding protein (RBP) from extremophile Caldanaerobacter subterraneus. RPtag binds an optimized peptide with pM affinity, is stable to extreme temperature, pH, and protease treatment, readily refolds after denaturation, is effective in common laboratory applications, was rationally engineered to bind bioactive PDGF-β, and was formulated as a gut-stable orally bioavailable preparation.
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Affiliation(s)
- Jennifer R DeRosa
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Brandon S Moyer
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Ellie Lumen
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Aaron J Wolfe
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Meegan B Sleeper
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Anthony H Bianchi
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Ashleigh Crawford
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Connor McGuigan
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Danique Wortel
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Cheyanne Fisher
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Kelsey J Moody
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Adam R Blanden
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
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Wu I, Arnold FH. Engineered thermostable fungal Cel6A and Cel7A cellobiohydrolases hydrolyze cellulose efficiently at elevated temperatures. Biotechnol Bioeng 2013; 110:1874-83. [PMID: 23404363 DOI: 10.1002/bit.24864] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 01/21/2013] [Accepted: 01/28/2013] [Indexed: 11/05/2022]
Abstract
Thermostability is an important feature in industrial enzymes: it increases biocatalyst lifetime and enables reactions at higher temperatures, where faster rates and other advantages ultimately reduce the cost of biocatalysis. Here we report the thermostabilization of a chimeric fungal family 6 cellobiohydrolase (HJPlus) by directed evolution using random mutagenesis and recombination of beneficial mutations. Thermostable variant 3C6P has a half-life of 280 min at 75°C and a T(50) of 80.1°C, a ~15°C increase over the thermostable Cel6A from Humicola insolens (HiCel6A) and a ~20°C increase over that from Hypocrea jecorina (HjCel6A). Most of the mutations also stabilize the less-stable HjCel6A, the wild-type Cel6A closest in sequence to 3C6P. During a 60-h Avicel hydrolysis, 3C6P released 2.4 times more cellobiose equivalents at its optimum temperature (T(opt)) of 75°C than HiCel6A at its T(opt) of 60°C. The total cellobiose equivalents released by HiCel6A at 60°C after 60 h is equivalent to the total released by 3C6P at 75°C after ~6 h, a 10-fold reduction in hydrolysis time. A binary mixture of thermostable Cel6A and Cel7A hydrolyzes Avicel synergistically and released 1.8 times more cellobiose equivalents than the wild-type mixture, both mixtures assessed at their respective T(opt). Crystal structures of HJPlus and 3C6P, determined at 1.5 and 1.2 Å resolution, indicate that the stabilization comes from improved hydrophobic interactions and restricted loop conformations by introduced proline residues.
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Affiliation(s)
- Indira Wu
- Division of Chemistry and Chemical Engineering, California Institute of Technology 210-41, Pasadena, CA 91125, USA
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Ha JH, Shinsky SA, Loh SN. Stepwise conversion of a binding protein to a fluorescent switch: application to Thermoanaerobacter tengcongensis ribose binding protein. Biochemistry 2013; 52:600-12. [PMID: 23302025 DOI: 10.1021/bi301105u] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Alternate frame folding (AFF) is a protein engineering methodology the purpose of which is to convert an ordinary binding protein into a molecular switch. The AFF modification entails duplicating an amino- or carboxy-terminal segment of the protein and appending it to the opposite end of the molecule. This duplication allows the protein to interconvert, in a ligand-dependent fashion, between two mutually exclusive native folds: the wild-type structure and a circularly permuted form. The fold shift can be detected by placement of extrinsic fluorophores at sites sensitive to the engineered conformational change. Here, we apply the AFF mechanism to create several ribose-sensing proteins derived from Thermoanaerobacter tengcongensis ribose binding protein. Our purpose is to systematically explore the parameters of the AFF design. These considerations include the site of circular permutation, the length and location of the duplicated segment, thermodynamic and kinetic optimization of the switching mechanism, and placement of extrinsic fluorophores. Three of the four AFF variants created here undergo the expected conformational shift and exhibit a ribose-dependent fluorescence change. The fourth construct fails to switch folds upon addition of ribose, likely because the circularly permuted form folds much more slowly than the nonpermuted form. This disparity apparently introduces a kinetic barrier that partitions the refolding molecules to the nonpermuted structure. The results of this study serve as a guideline for applying the AFF modification to other proteins of biomedical, diagnostic, and industrial interest.
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Affiliation(s)
- Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
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Ortega G, Castaño D, Diercks T, Millet O. Carbohydrate Affinity for the Glucose–Galactose Binding Protein Is Regulated by Allosteric Domain Motions. J Am Chem Soc 2012; 134:19869-76. [DOI: 10.1021/ja3092938] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Gabriel Ortega
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Building 800,
48160 Derio, Spain
| | - David Castaño
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Building 800,
48160 Derio, Spain
| | - Tammo Diercks
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Building 800,
48160 Derio, Spain
| | - Oscar Millet
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Building 800,
48160 Derio, Spain
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Bourdès A, Rudder S, East AK, Poole PS. Mining the Sinorhizobium meliloti transportome to develop FRET biosensors for sugars, dicarboxylates and cyclic polyols. PLoS One 2012; 7:e43578. [PMID: 23028462 PMCID: PMC3454389 DOI: 10.1371/journal.pone.0043578] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 07/24/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Förster resonance energy transfer (FRET) biosensors are powerful tools to detect biologically important ligands in real time. Currently FRET bisosensors are available for twenty-two compounds distributed in eight classes of chemicals (two pentoses, two hexoses, two disaccharides, four amino acids, one nucleobase, two nucleotides, six ions and three phytoestrogens). To expand the number of available FRET biosensors we used the induction profile of the Sinorhizobium meliloti transportome to systematically screen for new FRET biosensors. METHODOLOGY/PRINCIPAL FINDINGS Two new vectors were developed for cloning genes for solute-binding proteins (SBPs) between those encoding FRET partner fluorescent proteins. In addition to a vector with the widely used cyan and yellow fluorescent protein FRET partners, we developed a vector using orange (mOrange2) and red fluorescent protein (mKate2) FRET partners. From the sixty-nine SBPs tested, seven gave a detectable FRET signal change on binding substrate, resulting in biosensors for D-quinic acid, myo-inositol, L-rhamnose, L-fucose, β-diglucosides (cellobiose and gentiobiose), D-galactose and C4-dicarboxylates (malate, succinate, oxaloacetate and fumarate). To our knowledge, we describe the first two FRET biosensor constructs based on SBPs from Tripartite ATP-independent periplasmic (TRAP) transport systems. CONCLUSIONS/SIGNIFICANCE FRET based on orange (mOrange2) and red fluorescent protein (mKate2) partners allows the use of longer wavelength light, enabling deeper penetration of samples at lower energy and increased resolution with reduced back-ground auto-fluorescence. The FRET biosensors described in this paper for four new classes of compounds; (i) cyclic polyols, (ii) L-deoxy sugars, (iii) β-linked disaccharides and (iv) C4-dicarboxylates could be developed to study metabolism in vivo.
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Affiliation(s)
- Alexandre Bourdès
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Steven Rudder
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Alison K. East
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Philip S. Poole
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
- * E-mail:
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Sooriyaarachchi S, Ubhayasekera W, Park C, Mowbray SL. Conformational changes and ligand recognition of Escherichia coli D-xylose binding protein revealed. J Mol Biol 2010; 402:657-68. [PMID: 20678502 DOI: 10.1016/j.jmb.2010.07.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 07/17/2010] [Accepted: 07/20/2010] [Indexed: 10/19/2022]
Abstract
ATP binding cassette transport systems account for most import of necessary nutrients in bacteria. The periplasmic binding component (or an equivalent membrane-anchored protein) is critical to recognizing cognate ligand and directing it to the appropriate membrane permease. Here we report the X-ray structures of D-xylose binding protein from Escherichia coli in ligand-free open form, ligand-bound open form, and ligand-bound closed form at 2.15 Å, 2.2 Å, and 2.2 Å resolutions, respectively. The ligand-bound open form is the first such structure to be reported at high resolution; the combination of the three different forms from the same protein furthermore gives unprecedented details concerning the conformational changes involved in binding protein function. As is typical of the structural family, the protein has two similar globular domains, which are connected by a three-stranded hinge region. The open liganded structure shows that xylose binds first to the C-terminal domain, with only very small conformational changes resulting. After a 34° closing motion, additional interactions are formed with the N-terminal domain; changes in this domain are larger and serve to make the structure more ordered near the ligand. An analysis of the interactions suggests why xylose is the preferred ligand. Furthermore, a comparison with the most closely related proteins in the structural family shows that the conformational changes are distinct in each type of binding protein, which may have implications for how the individual proteins act in concert with their respective membrane permeases.
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Affiliation(s)
- Sanjeewani Sooriyaarachchi
- Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Cuneo MJ, Beese LS, Hellinga HW. Ligand-induced conformational changes in a thermophilic ribose-binding protein. BMC STRUCTURAL BIOLOGY 2008; 8:50. [PMID: 19019243 PMCID: PMC2630998 DOI: 10.1186/1472-6807-8-50] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Accepted: 11/19/2008] [Indexed: 01/07/2023]
Abstract
BACKGROUND Members of the periplasmic binding protein (PBP) superfamily are involved in transport and signaling processes in both prokaryotes and eukaryotes. Biological responses are typically mediated by ligand-induced conformational changes in which the binding event is coupled to a hinge-bending motion that brings together two domains in a closed form. In all PBP-mediated biological processes, downstream partners recognize the closed form of the protein. This motion has also been exploited in protein engineering experiments to construct biosensors that transduce ligand binding to a variety of physical signals. Understanding the mechanistic details of PBP conformational changes, both global (hinge bending, twisting, shear movements) and local (rotamer changes, backbone motion), therefore is not only important for understanding their biological function but also for protein engineering experiments. RESULTS Here we present biochemical characterization and crystal structure determination of the periplasmic ribose-binding protein (RBP) from the hyperthermophile Thermotoga maritima in its ribose-bound and unliganded state. The T. maritima RBP (tmRBP) has 39% sequence identity and is considerably more resistant to thermal denaturation (app Tm value is 108 degrees C) than the mesophilic Escherichia coli homolog (ecRBP) (app Tm value is 56 degrees C). Polar ligand interactions and ligand-induced global conformational changes are conserved among ecRBP and tmRBP; however local structural rearrangements involving side-chain motions in the ligand-binding site are not conserved. CONCLUSION Although the large-scale ligand-induced changes are mediated through similar regions, and are produced by similar backbone movements in tmRBP and ecRBP, the small-scale ligand-induced structural rearrangements differentiate the mesophile and thermophile. This suggests there are mechanistic differences in the manner by which these two proteins bind their ligands and are an example of how two structurally similar proteins utilize different mechanisms to form a ligand-bound state.
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Affiliation(s)
- Matthew J Cuneo
- The Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - Lorena S Beese
- The Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - Homme W Hellinga
- The Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710, USA
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