1
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Kalra S, Donnelly A, Singh N, Matthews D, Del Villar-Guerra R, Bemmer V, Dominguez C, Allcock N, Cherny D, Revyakin A, Rusling DA. Functionalizing DNA Origami by Triplex-Directed Site-Specific Photo-Cross-Linking. J Am Chem Soc 2024; 146:13617-13628. [PMID: 38695163 PMCID: PMC11100008 DOI: 10.1021/jacs.4c03413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Here, we present a cross-linking approach to covalently functionalize and stabilize DNA origami structures in a one-pot reaction. Our strategy involves adding nucleotide sequences to adjacent staple strands, so that, upon assembly of the origami structure, the extensions form short hairpin duplexes targetable by psoralen-labeled triplex-forming oligonucleotides bearing other functional groups (pso-TFOs). Subsequent irradiation with UVA light generates psoralen adducts with one or both hairpin staples leading to site-specific attachment of the pso-TFO (and attached group) to the origami with ca. 80% efficiency. Bis-adduct formation between strands in proximal hairpins further tethers the TFO to the structure and generates "superstaples" that improve the structural integrity of the functionalized complex. We show that directing cross-linking to regions outside of the origami core dramatically reduces sensitivity of the structures to thermal denaturation and disassembly by T7 RNA polymerase. We also show that the underlying duplex regions of the origami core are digested by DNase I and thus remain accessible to read-out by DNA-binding proteins. Our strategy is scalable and cost-effective, as it works with existing DNA origami structures, does not require scaffold redesign, and can be achieved with just one psoralen-modified oligonucleotide.
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Affiliation(s)
- Shantam Kalra
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Amber Donnelly
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Nishtha Singh
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Daniel Matthews
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Rafael Del Villar-Guerra
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Victoria Bemmer
- Centre
for Enzyme Innovation, School of Biological Sciences, University of Portsmouth, Portsmouth, Hampshire PO1 2DY, U.K.
| | - Cyril Dominguez
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Natalie Allcock
- Core
Biotechnology Services Electron Microscopy Facility, University of Leicester, Leicester LE1 7RH, U.K.
| | - Dmitry Cherny
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Andrey Revyakin
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - David A. Rusling
- School
of Medicine, Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, U.K.
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2
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Obeng EM, Steer DL, Fulcher AJ, Wagstaff KM. Sortase A transpeptidation produces seamless, unbranched biotinylated nanobodies for multivalent and multifunctional applications. NANOSCALE ADVANCES 2023; 5:2251-2260. [PMID: 37056610 PMCID: PMC10089078 DOI: 10.1039/d3na00014a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
Exploitation of the biotin-streptavidin interaction for advanced protein engineering is used in many bio-nanotechnology applications. As such, researchers have used diverse techniques involving chemical and enzyme reactions to conjugate biotin to biomolecules of interest for subsequent docking onto streptavidin-associated molecules. Unfortunately, the biotin-streptavidin interaction is susceptible to steric hindrance and conformational malformation, leading to random orientations that ultimately impair the function of the displayed biomolecule. To minimize steric conflicts, we employ sortase A transpeptidation to produce quantitative, seamless, and unbranched nanobody-biotin conjugates for efficient display on streptavidin-associated nanoparticles. We further characterize the protein-nanoparticle complex and demonstrate its usefulness in optical microscopy and multivalent severe acute respiratory syndrome coronavirus (SARS-CoV-2) antigen interaction. The approach reported here provides a template for making novel multivalent and multifunctional protein complexes for avidity-inspired technologies.
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Affiliation(s)
- Eugene M Obeng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University Clayton VIC 3800 Australia
| | - David L Steer
- Monash Proteomics and Metabolomics Facility, Monash University Clayton VIC 3800 Australia
| | - Alex J Fulcher
- Monash Micro Imaging, Monash University Clayton VIC 3800 Australia
| | - Kylie M Wagstaff
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University Clayton VIC 3800 Australia
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3
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L. Mpye K, Gildenhuys S, Mosebi S. The effects of temperature on streptavidin-biotin binding using affinity isothermal titration calorimetry. AIMS BIOPHYSICS 2020. [DOI: 10.3934/biophy.2020018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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4
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Cooperativity of hydrogen bonding network in microsolvated biotin, the ligand of avidin class proteins. J Mol Model 2019; 25:361. [DOI: 10.1007/s00894-019-4253-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 11/12/2019] [Indexed: 10/25/2022]
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5
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Waner MJ, Hiznay JM, Mustovich AT, Patton W, Ponyik C, Mascotti DP. Streptavidin cooperative allosterism upon binding biotin observed by differential changes in intrinsic fluorescence. Biochem Biophys Rep 2019; 17:127-131. [PMID: 30805560 PMCID: PMC6372923 DOI: 10.1016/j.bbrep.2018.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/12/2018] [Accepted: 12/25/2018] [Indexed: 12/02/2022] Open
Abstract
While the binding of biotin by streptavidin does not appear to be cooperative in the traditional sense of altered binding strength, it has been suggested that it may be cooperative in terms of differential structural changes in the protein. In this work we present intrinsic tryptophan fluorescence data as evidence of a cooperative structural change. The technique involves examination of the differences in fluorescence emission corresponding to distinct tryptophan populations accompanying protein-ligand binding. Specifically we note that the 335 nm emission population (i.e. more hydrophobic) saturates prior to the saturation of the 350 nm emission population commonly used in the standard binding activity assay. We also note that the wavelength of maximum emission, total integrated fluorescence emission and full width at half maximum during the titration of ligand into streptavidin also reach saturation before the expected 4:1 stoichiometric end point. This suggests that the binding of the first 3 biotins effect greater structural changes in the protein than the final ligand.
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Affiliation(s)
- Mark J. Waner
- Department of Chemistry, John Carroll University, 1 John Carroll Blvd., University Heights, OH 44118, USA
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6
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Perry TN, Souabni H, Rapisarda C, Fronzes R, Giusti F, Popot JL, Zoonens M, Gubellini F. BAmSA: Visualising transmembrane regions in protein complexes using biotinylated amphipols and electron microscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:466-477. [DOI: 10.1016/j.bbamem.2018.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/06/2018] [Accepted: 11/08/2018] [Indexed: 12/30/2022]
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7
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Friedrich NO, Simsir M, Kirchmair J. How Diverse Are the Protein-Bound Conformations of Small-Molecule Drugs and Cofactors? Front Chem 2018; 6:68. [PMID: 29637066 PMCID: PMC5880911 DOI: 10.3389/fchem.2018.00068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/05/2018] [Indexed: 12/19/2022] Open
Abstract
Knowledge of the bioactive conformations of small molecules or the ability to predict them with theoretical methods is of key importance to the design of bioactive compounds such as drugs, agrochemicals, and cosmetics. Using an elaborate cheminformatics pipeline, which also evaluates the support of individual atom coordinates by the measured electron density, we compiled a complete set ("Sperrylite Dataset") of high-quality structures of protein-bound ligand conformations from the PDB. The Sperrylite Dataset consists of a total of 10,936 high-quality structures of 4,548 unique ligands. Based on this dataset, we assessed the variability of the bioactive conformations of 91 small molecules-each represented by a minimum of ten structures-and found it to be largely independent of the number of rotatable bonds. Sixty-nine molecules had at least two distinct conformations (defined by an RMSD greater than 1 Å). For a representative subset of 17 approved drugs and cofactors we observed a clear trend for the formation of few clusters of highly similar conformers. Even for proteins that share a very low sequence identity, ligands were regularly found to adopt similar conformations. For cofactors, a clear trend for extended conformations was measured, although in few cases also coiled conformers were observed. The Sperrylite Dataset is available for download from http://www.zbh.uni-hamburg.de/sperrylite_dataset.
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Affiliation(s)
- Nils-Ole Friedrich
- Department of Informatics, Center for Bioinformatics, Universität Hamburg, Hamburg, Germany
| | - Méliné Simsir
- Department of Informatics, Center for Bioinformatics, Universität Hamburg, Hamburg, Germany.,Molécules Thérapeutiques In Silico, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Johannes Kirchmair
- Department of Informatics, Center for Bioinformatics, Universität Hamburg, Hamburg, Germany
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8
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Abstract
Virus-like particle (VLP) technologies are based on virus-inspired artificial structures and the intrinsic ability of viral proteins to self-assemble at controlled conditions. Therefore, the basic knowledge about the mechanisms of viral particle formation is highly important for designing of industrial applications. As an alternative to genetic and chemical processes, different physical methods are frequently used for VLP construction, including well characterized protein complexes for introduction of foreign molecules in VLP structures.This chapter shortly discusses the mechanisms how the viruses form their perfectly ordered structures as well as the principles and most interesting application examples, how to exploit the structural and assembly/disassembly properties of viral structures for creation of new nanomaterials.
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Affiliation(s)
- Andris Zeltins
- Latvian Biomedical Research and Study Centre, Riga, Latvia.
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9
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Milioni D, Tsortos A, Velez M, Gizeli E. Extracting the Shape and Size of Biomolecules Attached to a Surface as Suspended Discrete Nanoparticles. Anal Chem 2017; 89:4198-4203. [DOI: 10.1021/acs.analchem.7b00206] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Dimitra Milioni
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Achilleas Tsortos
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Marisela Velez
- Instituto de Catálisis y Petroleoquímica, CSIC, C/Marie Curie 2, 28049 Madrid, Spain
| | - Electra Gizeli
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
- Department
of Biology, University of Crete, Heraklion 71110, Greece
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10
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Arcila-Lozano LS, Ríos-Corripio MA, García-Pérez BE, Jaramillo-Flores ME, González CA, Rocha-Gracia RC, Gracia-Jiménez JM, Rojas-López M. Fluorescent Bioconjugate Based on Gold Nanoparticles for the Determination of Staphylococcus aureus. ANAL LETT 2016. [DOI: 10.1080/00032719.2016.1212204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
| | | | - B. E. García-Pérez
- Instituto Politécnico Nacional, ENCB-Depto. de Inmunología, Ciudad de México, México
| | - M. E. Jaramillo-Flores
- Instituto Politécnico Nacional, ENCB-Depto. de Ingeniería Bioquímica, Ciudad de México, México
| | - C. A. González
- Instituto Politécnico Nacional, ESM, Ciudad de México, México
| | - R. C. Rocha-Gracia
- Benemérita Universidad Autónoma de Puebla, Instituto de Ciencias, Centro de Investigaciones en Ciencias Microbiológicas, Puebla, Puebla, México
| | - J. M. Gracia-Jiménez
- Benemérita Universidad Autónoma de Puebla, Instituto de Física, Puebla, Puebla, México
| | - M. Rojas-López
- Instituto Politécnico Nacional, CIBA-Tlaxcala, Tepetitla, Tlaxcala, México
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11
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Macchia E, Alberga D, Manoli K, Mangiatordi GF, Magliulo M, Palazzo G, Giordano F, Lattanzi G, Torsi L. Organic bioelectronics probing conformational changes in surface confined proteins. Sci Rep 2016; 6:28085. [PMID: 27312768 PMCID: PMC4911579 DOI: 10.1038/srep28085] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/31/2016] [Indexed: 02/07/2023] Open
Abstract
The study of proteins confined on a surface has attracted a great deal of attention due to its relevance in the development of bio-systems for laboratory and clinical settings. In this respect, organic bio-electronic platforms can be used as tools to achieve a deeper understanding of the processes involving protein interfaces. In this work, biotin-binding proteins have been integrated in two different organic thin-film transistor (TFT) configurations to separately address the changes occurring in the protein-ligand complex morphology and dipole moment. This has been achieved by decoupling the output current change upon binding, taken as the transducing signal, into its component figures of merit. In particular, the threshold voltage is related to the protein dipole moment, while the field-effect mobility is associated with conformational changes occurring in the proteins of the layer when ligand binding occurs. Molecular Dynamics simulations on the whole avidin tetramer in presence and absence of ligands were carried out, to evaluate how the tight interactions with the ligand affect the protein dipole moment and the conformation of the loops surrounding the binding pocket. These simulations allow assembling a rather complete picture of the studied interaction processes and support the interpretation of the experimental results.
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Affiliation(s)
- Eleonora Macchia
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro - Bari (Italy)
| | - Domenico Alberga
- Dipartimento Interateneo di Fisica "M. Merlin" dell'Università e del Politecnico di Bari - Bari (Italy)
| | - Kyriaki Manoli
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro - Bari (Italy)
| | - Giuseppe F Mangiatordi
- Dipartimento di Farmacia - Scienze del Farmaco, Università degli Studi di Bari Aldo Moro - Bari (Italy)
| | - Maria Magliulo
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro - Bari (Italy)
| | - Gerardo Palazzo
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro - Bari (Italy)
| | - Francesco Giordano
- Dipartimento Interateneo di Fisica "M. Merlin" dell'Università e del Politecnico di Bari - Bari (Italy)
| | - Gianluca Lattanzi
- Dipartimento di Medicina Clinica e Sperimentale -Università degli Studi di Foggia - Foggia (Italy)
| | - Luisa Torsi
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro - Bari (Italy)
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12
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Müller JM, Bruhn S, Flaschel E, Friehs K, Risse JM. GAP promoter-based fed-batch production of highly bioactive core streptavidin byPichia pastoris. Biotechnol Prog 2016; 32:855-64. [DOI: 10.1002/btpr.2283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/02/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Jakob Michael Müller
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
| | - Simon Bruhn
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
| | - Erwin Flaschel
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
| | - Karl Friehs
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
| | - Joe Max Risse
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
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13
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Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakas DT, Lang PT, Case DA, Kuntz ID, Rizzo RC. DOCK 6: Impact of new features and current docking performance. J Comput Chem 2015; 36:1132-56. [PMID: 25914306 DOI: 10.1002/jcc.23905] [Citation(s) in RCA: 445] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 03/01/2015] [Accepted: 03/07/2015] [Indexed: 12/11/2022]
Abstract
This manuscript presents the latest algorithmic and methodological developments to the structure-based design program DOCK 6.7 focused on an updated internal energy function, new anchor selection control, enhanced minimization options, a footprint similarity scoring function, a symmetry-corrected root-mean-square deviation algorithm, a database filter, and docking forensic tools. An important strategy during development involved use of three orthogonal metrics for assessment and validation: pose reproduction over a large database of 1043 protein-ligand complexes (SB2012 test set), cross-docking to 24 drug-target protein families, and database enrichment using large active and decoy datasets (Directory of Useful Decoys [DUD]-E test set) for five important proteins including HIV protease and IGF-1R. Relative to earlier versions, a key outcome of the work is a significant increase in pose reproduction success in going from DOCK 4.0.2 (51.4%) → 5.4 (65.2%) → 6.7 (73.3%) as a result of significant decreases in failure arising from both sampling 24.1% → 13.6% → 9.1% and scoring 24.4% → 21.1% → 17.5%. Companion cross-docking and enrichment studies with the new version highlight other strengths and remaining areas for improvement, especially for systems containing metal ions. The source code for DOCK 6.7 is available for download and free for academic users at http://dock.compbio.ucsf.edu/.
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Affiliation(s)
- William J Allen
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York, 11794
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14
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Fu J, Yu C, Li L, Yao SQ. Intracellular Delivery of Functional Proteins and Native Drugs by Cell-Penetrating Poly(disulfide)s. J Am Chem Soc 2015; 137:12153-60. [DOI: 10.1021/jacs.5b08130] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jiaqi Fu
- Department
of Chemistry, National University of Singapore, 117543 Singapore
| | - Changmin Yu
- Department
of Chemistry, National University of Singapore, 117543 Singapore
| | - Lin Li
- Department
of Chemistry, National University of Singapore, 117543 Singapore
- Key
Laboratory of Flexible Electronics and Institute of Advanced Materials,
National Jiangsu Synergistic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, P. R. China
| | - Shao Q. Yao
- Department
of Chemistry, National University of Singapore, 117543 Singapore
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15
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Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking. Methods 2015; 93:72-83. [PMID: 26165956 DOI: 10.1016/j.ymeth.2015.07.004] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 07/06/2015] [Accepted: 07/08/2015] [Indexed: 11/22/2022] Open
Abstract
Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of protein-peptide interactions is usually divided into two stages: prediction of the binding site at a protein receptor surface, and then docking (and modeling) the peptide structure into the known binding site. This paper presents a comprehensive CABS-dock method for the simultaneous search of binding sites and flexible protein-peptide docking, available as a user's friendly web server. We present example CABS-dock results obtained in the default CABS-dock mode and using its advanced options that enable the user to increase the range of flexibility for chosen receptor fragments or to exclude user-selected binding modes from docking search. Furthermore, we demonstrate a strategy to improve CABS-dock performance by assessing the quality of models with classical molecular dynamics. Finally, we discuss the promising extensions and applications of the CABS-dock method and provide a tutorial appendix for the convenient analysis and visualization of CABS-dock results. The CABS-dock web server is freely available at http://biocomp.chem.uw.edu.pl/CABSdock/.
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16
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Müller JM, Risse JM, Friehs K, Flaschel E. Model-based development of an assay for the rapid detection of biotin-blocked binding sites of streptavidin. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Jakob M. Müller
- Chair of Fermentation Engineering; Faculty of Technology; Bielefeld University; Bielefeld Germany
| | - Joe M. Risse
- Chair of Fermentation Engineering; Faculty of Technology; Bielefeld University; Bielefeld Germany
| | - Karl Friehs
- Chair of Fermentation Engineering; Faculty of Technology; Bielefeld University; Bielefeld Germany
| | - Erwin Flaschel
- Chair of Fermentation Engineering; Faculty of Technology; Bielefeld University; Bielefeld Germany
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17
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Taskinen B, Zauner D, Lehtonen SI, Koskinen M, Thomson C, Kähkönen N, Kukkurainen S, Määttä JAE, Ihalainen TO, Kulomaa MS, Gruber HJ, Hytönen VP. Switchavidin: Reversible Biotin–Avidin–Biotin Bridges with High Affinity and Specificity. Bioconjug Chem 2014; 25:2233-43. [DOI: 10.1021/bc500462w] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Barbara Taskinen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu
4, FI-33520 Tampere, Finland
| | - Dominik Zauner
- Institute
of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020 Linz, Austria
| | - Soili I. Lehtonen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Tampere University Hospital, PL 2000, FI-33521 Tampere, Finland
| | - Masi Koskinen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu
4, FI-33520 Tampere, Finland
| | - Chloe Thomson
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu
4, FI-33520 Tampere, Finland
| | - Niklas Kähkönen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Tampere University Hospital, PL 2000, FI-33521 Tampere, Finland
| | - Sampo Kukkurainen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu
4, FI-33520 Tampere, Finland
| | - Juha A. E. Määttä
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu
4, FI-33520 Tampere, Finland
| | - Teemu O. Ihalainen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
| | - Markku S. Kulomaa
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Tampere University Hospital, PL 2000, FI-33521 Tampere, Finland
| | - Hermann J. Gruber
- Institute
of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020 Linz, Austria
| | - Vesa P. Hytönen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu
4, FI-33520 Tampere, Finland
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18
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Dauter Z, Wlodawer A, Minor W, Jaskolski M, Rupp B. Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining. IUCRJ 2014; 1:179-93. [PMID: 25075337 PMCID: PMC4086436 DOI: 10.1107/s2052252514005442] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/10/2014] [Indexed: 05/20/2023]
Abstract
Whereas the vast majority of the more than 85 000 crystal structures of macromolecules currently deposited in the Protein Data Bank are of high quality, some suffer from a variety of imperfections. Although this fact has been pointed out in the past, it is still worth periodic updates so that the metadata obtained by global analysis of the available crystal structures, as well as the utilization of the individual structures for tasks such as drug design, should be based on only the most reliable data. Here, selected abnormal deposited structures have been analysed based on the Bayesian reasoning that the correctness of a model must be judged against both the primary evidence as well as prior knowledge. These structures, as well as information gained from the corresponding publications (if available), have emphasized some of the most prevalent types of common problems. The errors are often perfect illustrations of the nature of human cognition, which is frequently influenced by preconceptions that may lead to fanciful results in the absence of proper validation. Common errors can be traced to negligence and a lack of rigorous verification of the models against electron density, creation of non-parsimonious models, generation of improbable numbers, application of incorrect symmetry, illogical presentation of the results, or violation of the rules of chemistry and physics. Paying more attention to such problems, not only in the final validation stages but during the structure-determination process as well, is necessary not only in order to maintain the highest possible quality of the structural repositories and databases but most of all to provide a solid basis for subsequent studies, including large-scale data-mining projects. For many scientists PDB deposition is a rather infrequent event, so the need for proper training and supervision is emphasized, as well as the need for constant alertness of reason and critical judgment as absolutely necessary safeguarding measures against such problems. Ways of identifying more problematic structures are suggested so that their users may be properly alerted to their possible shortcomings.
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Affiliation(s)
- Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, NCI, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, NCI at Frederick, Frederick, MD 21702, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
- Midwest Center for Structural Genomics, USA
- New York Structural Genomics Consortium, USA
- Center for Structural Genomics of Infectious Diseases, USA
- Enzyme Function Initiative, USA
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Bernhard Rupp
- k.-k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084, USA
- Department of Genetic Epidemiology, Innsbruck Medical University, Schöpfstrasse 41, A-6020 Innsbruck, Austria
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Panwar P, Deniaud A, Pebay-Peyroula E. Contamination from an affinity column: an encounter with a new villain in the world of membrane-protein crystallization. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1272-7. [DOI: 10.1107/s090744491202639x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 06/11/2012] [Indexed: 11/10/2022]
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Development of a tetrameric streptavidin mutein with reversible biotin binding capability: engineering a mobile loop as an exit door for biotin. PLoS One 2012; 7:e35203. [PMID: 22536357 PMCID: PMC3334968 DOI: 10.1371/journal.pone.0035203] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 03/10/2012] [Indexed: 12/01/2022] Open
Abstract
A novel form of tetrameric streptavidin has been engineered to have reversible biotin binding capability. In wild-type streptavidin, loop3–4 functions as a lid for the entry and exit of biotin. When biotin is bound, interactions between biotin and key residues in loop3–4 keep this lid in the closed state. In the engineered mutein, a second biotin exit door is created by changing the amino acid sequence of loop7–8. This door is mobile even in the presence of the bound biotin and can facilitate the release of biotin from the mutein. Since loop7–8 is involved in subunit interactions, alteration of this loop in the engineered mutein results in an 11° rotation between the two dimers in reference to wild-type streptavidin. The tetrameric state of the engineered mutein is stabilized by a H127C mutation, which leads to the formation of inter-subunit disulfide bonds. The biotin binding kinetic parameters (koff of 4.28×10−4 s−1 and Kd of 1.9×10−8 M) make this engineered mutein a superb affinity agent for the purification of biotinylated biomolecules. Affinity matrices can be regenerated using gentle procedures, and regenerated matrices can be reused at least ten times without any observable reduction in binding capacity. With the combination of both the engineered mutein and wild-type streptavidin, biotinylated biomolecules can easily be affinity purified to high purity and immobilized to desirable platforms without any leakage concerns. Other potential biotechnological applications, such as development of an automated high-throughput protein purification system, are feasible.
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Hong Lim K, Hwang I, Park S. Biotin-assisted folding of streptavidin on the yeast surface. Biotechnol Prog 2011; 28:276-83. [DOI: 10.1002/btpr.721] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 07/31/2011] [Indexed: 01/28/2023]
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Lim KH, Huang H, Pralle A, Park S. Engineered Streptavidin Monomer and Dimer with Improved Stability and Function. Biochemistry 2011; 50:8682-91. [DOI: 10.1021/bi2010366] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kok Hong Lim
- Department
of Chemical and Biological Engineering and ‡Department of Physics, University at Buffalo, State University of New York, Buffalo, New York 14260, United States
| | - Heng Huang
- Department
of Chemical and Biological Engineering and ‡Department of Physics, University at Buffalo, State University of New York, Buffalo, New York 14260, United States
| | - Arnd Pralle
- Department
of Chemical and Biological Engineering and ‡Department of Physics, University at Buffalo, State University of New York, Buffalo, New York 14260, United States
| | - Sheldon Park
- Department
of Chemical and Biological Engineering and ‡Department of Physics, University at Buffalo, State University of New York, Buffalo, New York 14260, United States
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How the biotin-streptavidin interaction was made even stronger: investigation via crystallography and a chimaeric tetramer. Biochem J 2011; 435:55-63. [PMID: 21241253 PMCID: PMC3062853 DOI: 10.1042/bj20101593] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The interaction between SA (streptavidin) and biotin is one of the strongest non-covalent interactions in Nature. SA is a widely used tool and a paradigm for protein–ligand interactions. We previously developed a SA mutant, termed Tr (traptavidin), possessing a 10-fold lower off-rate for biotin, with increased mechanical and thermal stability. In the present study, we determined the crystal structures of apo-Tr and biotin–Tr at 1.5 Å resolution. In apo-SA the loop (L3/4), near biotin's valeryl tail, is typically disordered and open, but closes upon biotin binding. In contrast, L3/4 was shut in both apo-Tr and biotin–Tr. The reduced flexibility of L3/4 and decreased conformational change on biotin binding provide an explanation for Tr's reduced biotin off- and on-rates. L3/4 includes Ser45, which forms a hydrogen bond to biotin consistently in Tr, but erratically in SA. Reduced breakage of the biotin–Ser45 hydrogen bond in Tr is likely to inhibit the initiating event in biotin's dissociation pathway. We generated a Tr with a single biotin-binding site rather than four, which showed a simi-larly low off-rate, demonstrating that Tr's low off-rate was governed by intrasubunit effects. Understanding the structural features of this tenacious interaction may assist the design of even stronger affinity tags and inhibitors.
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Computational and mutagenesis studies of the streptavidin native dimer interface. J Mol Graph Model 2010; 29:295-308. [DOI: 10.1016/j.jmgm.2010.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2010] [Revised: 08/08/2010] [Accepted: 09/15/2010] [Indexed: 11/20/2022]
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Panek JJ, Ward TR, Jezierska-Mazzarello A, Novic M. Flexibility of a biotinylated ligand in artificial metalloenzymes based on streptavidin--an insight from molecular dynamics simulations with classical and ab initio force fields. J Comput Aided Mol Des 2010; 24:719-32. [PMID: 20526651 PMCID: PMC2918797 DOI: 10.1007/s10822-010-9369-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Accepted: 05/24/2010] [Indexed: 11/19/2022]
Abstract
In the field of enzymatic catalysis, creating activity from a non catalytic scaffold is a daunting task. Introduction of a catalytically active moiety within a protein scaffold offers an attractive means for the creation of artificial metalloenzymes. With this goal in mind, introduction of a biotinylated d(6)-piano-stool complex within streptavidin (SAV) affords enantioselective artificial transfer-hydrogenases for the reduction of prochiral ketones. Based on an X-ray crystal structure of a highly selective hybrid catalyst, displaying significant disorder around the biotinylated catalyst [eta(6)-(p-cymene)Ru(Biot-p-L)Cl], we report on molecular dynamics simulations to shed light on the protein-cofactor interactions and contacts. The results of these simulations with classical force field indicate that the SAV-biotin and SAV-catalyst complexes are more stable than ligand-free SAV. The point mutations introduced did not affect significantly the overall behavior of SAV and, unexpectedly, the P64G substitution did not provide additional flexibility to the protein scaffold. The metal-cofactor proved to be conformationally flexible, and the S112K or P64G mutants proved to enhance this effect in the most pronounced way. The network of intermolecular hydrogen bonds is efficient at stabilizing the position of biotin, but much less at fixing the conformation of an extended biotinylated ligand. This leads to a relative conformational freedom of the metal-cofactor, and a poorly localized catalytic metal moiety. MD calculations with ab initio potential function suggest that the hydrogen bonds alone are not sufficient factors for full stabilization of the biotin. The hydrophobic biotin-binding pocket (and generally protein scaffold) maintains the hydrogen bonds between biotin and protein.
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Affiliation(s)
- Jarosław J Panek
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland.
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Reconsideration of dynamic force spectroscopy analysis of streptavidin-biotin interactions. Int J Mol Sci 2010; 11:2134-51. [PMID: 20559507 PMCID: PMC2885099 DOI: 10.3390/ijms11052134] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 05/03/2010] [Accepted: 05/06/2010] [Indexed: 11/29/2022] Open
Abstract
To understand and design molecular functions on the basis of molecular recognition processes, the microscopic probing of the energy landscapes of individual interactions in a molecular complex and their dependence on the surrounding conditions is of great importance. Dynamic force spectroscopy (DFS) is a technique that enables us to study the interaction between molecules at the single-molecule level. However, the obtained results differ among previous studies, which is considered to be caused by the differences in the measurement conditions. We have developed an atomic force microscopy technique that enables the precise analysis of molecular interactions on the basis of DFS. After verifying the performance of this technique, we carried out measurements to determine the landscapes of streptavidin-biotin interactions. The obtained results showed good agreement with theoretical predictions. Lifetimes were also well analyzed. Using a combination of cross-linkers and the atomic force microscope that we developed, site-selective measurement was carried out, and the steps involved in bonding due to microscopic interactions are discussed using the results obtained by site-selective analysis.
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27
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Muta H, Hirayama N. Alpha sphere filter method: Application of pseudomolecular descriptors in virtual screening of 2D chemical structures. J Comput Chem 2010; 31:2225-32. [DOI: 10.1002/jcc.21517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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Taninaka A, Takeuchi O, Shigekawa H. Hidden variety of biotin–streptavidin/avidin local interactions revealed by site-selective dynamic force spectroscopy. Phys Chem Chem Phys 2010; 12:12578-83. [DOI: 10.1039/c0cp00259c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Panek JJ, Ward TR, Jezierska A, Novič M. Effects of tryptophan residue fluorination on streptavidin stability and biotin–streptavidin interactions via molecular dynamics simulations. J Mol Model 2008; 15:257-66. [DOI: 10.1007/s00894-008-0382-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Accepted: 10/27/2008] [Indexed: 11/29/2022]
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Cerutti DS, Le Trong I, Stenkamp RE, Lybrand TP. Simulations of a protein crystal: explicit treatment of crystallization conditions links theory and experiment in the streptavidin-biotin complex. Biochemistry 2008; 47:12065-77. [PMID: 18950193 DOI: 10.1021/bi800894u] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A 250 ns molecular dynamics simulation of the biotin-liganded streptavidin crystal lattice, including cryoprotectant molecules and crystallization salts, is compared to a 250 ns simulation of the lattice solvated with pure water. The simulation using detailed crystallization conditions preserves the initial X-ray structure better than the simulation using pure water, even though the protein molecules display comparable mobility in either simulation. Atomic fluctuations computed from the simulation with crystallization conditions closely reproduce fluctuations derived from experimental temperature factors (correlation coefficient of 0.88, omitting two N-terminal residues with very high experimental B-factors). In contrast, fluctuations calculated from the simulation with pure water were less accurate, particularly for two of the streptavidin loops exposed to solvent in the crystal lattice. Finally, we obtain good agreement between the water and cryoprotectant densities obtained from the simulated crystallization conditions and the electron density due to solvent molecules in the X-ray structure. Our results suggest that detailed lattice simulations with realistic crystallization conditions can be used to assess potential function parameters, validate simulation protocols, and obtain valuable insights that solution-phase simulations do not easily provide. We anticipate that this will prove to be a powerful strategy for molecular dynamics simulations of biomolecules.
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Affiliation(s)
- David S Cerutti
- Center for Structural Biology, Department of Chemistry, Vanderbilt University, 5142 Medical Research Building III, 465 21st Avenue South, Nashville, Tennessee 37232-8725, USA
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31
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Cerutti DS, Duke R, Freddolino PL, Fan H, Lybrand TP. Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics. J Chem Theory Comput 2008; 4:1669-1680. [PMID: 19180249 DOI: 10.1021/ct8002173] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a serious problem associated with a number of current implementations of Andersen and Langevin dynamics algorithms. When long simulations are run in many segments, it is sometimes possible to have a repeating sequence of pseudorandom numbers enter the calcuation. We show that, if the sequence repeats rapidly, the resulting artifacts can quickly denature biomolecules and are then easily detectable. However, if the sequence repeats less frequently, the artifacts become subtle and easily overlooked. We derive a formula for the underlying cause of artifacts in the case of the Langevin thermostat, and find it vanishes slowly as the inverse square root of the number of time steps per simulation segment. Numerous examples of simulation artifacts are presented, including dissociation of a tetrameric protein after 110 ns of dynamics, reductions in atomic fluctuations for a small protein in implicit solvent, altered thermodynamic properties of a box of water molecules, and changes in the transition free energies between dihedral angle conformations. Finally, in the case of strong thermocoupling, we link the observed artifacts to previous work in nonlinear dynamics and show that it is possible to drive a 20-residue, implicitly solvated protein into periodic trajectories if the thermostat is not used properly. Our findings should help other investigators re-evaluate simulations that may have been corrupted and obtain more accurate results.
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Affiliation(s)
- David S Cerutti
- Center for Structural Biology, Department of Chemistry, Vanderbilt University, 5140 Medical Research Building III, 465 21st Avenue South, Nashville, Tennessee 37232-8725
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32
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Tanrikulu Y, Schneider G. Pseudoreceptor models in drug design: bridging ligand- and receptor-based virtual screening. Nat Rev Drug Discov 2008; 7:667-77. [DOI: 10.1038/nrd2615] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Hassen WM, Angnes L, Abdelghani A, Bessueille F, Leonard D, Jaffrezic-Renault N. Under flow impedimetric measurements using magnetic particles for label-free detection affinity target. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2008. [DOI: 10.1016/j.msec.2007.10.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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34
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Pordea A, Creus M, Panek J, Duboc C, Mathis D, Novic M, Ward TR. Artificial Metalloenzyme for Enantioselective Sulfoxidation Based on Vanadyl-Loaded Streptavidin. J Am Chem Soc 2008; 130:8085-8. [DOI: 10.1021/ja8017219] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anca Pordea
- Institute of Chemistry, University of Neuchâtel, Avenue Bellevaux 51, CP 158,2009 Neuchâtel, Switzerland, Laboratory of Chemometrics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, and Département de Chimie Moléculaire UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
| | - Marc Creus
- Institute of Chemistry, University of Neuchâtel, Avenue Bellevaux 51, CP 158,2009 Neuchâtel, Switzerland, Laboratory of Chemometrics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, and Département de Chimie Moléculaire UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
| | - Jaroslaw Panek
- Institute of Chemistry, University of Neuchâtel, Avenue Bellevaux 51, CP 158,2009 Neuchâtel, Switzerland, Laboratory of Chemometrics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, and Département de Chimie Moléculaire UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
| | - Carole Duboc
- Institute of Chemistry, University of Neuchâtel, Avenue Bellevaux 51, CP 158,2009 Neuchâtel, Switzerland, Laboratory of Chemometrics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, and Département de Chimie Moléculaire UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
| | - Déborah Mathis
- Institute of Chemistry, University of Neuchâtel, Avenue Bellevaux 51, CP 158,2009 Neuchâtel, Switzerland, Laboratory of Chemometrics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, and Département de Chimie Moléculaire UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
| | - Marjana Novic
- Institute of Chemistry, University of Neuchâtel, Avenue Bellevaux 51, CP 158,2009 Neuchâtel, Switzerland, Laboratory of Chemometrics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, and Département de Chimie Moléculaire UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
| | - Thomas R. Ward
- Institute of Chemistry, University of Neuchâtel, Avenue Bellevaux 51, CP 158,2009 Neuchâtel, Switzerland, Laboratory of Chemometrics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, and Département de Chimie Moléculaire UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
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Li P, Huey-Tubman KE, Gao T, Li X, West AP, Bennett MJ, Bjorkman PJ. The structure of a polyQ-anti-polyQ complex reveals binding according to a linear lattice model. Nat Struct Mol Biol 2007; 14:381-7. [PMID: 17450152 DOI: 10.1038/nsmb1234] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Accepted: 03/14/2007] [Indexed: 11/09/2022]
Abstract
Huntington and related neurological diseases result from expansion of a polyglutamine (polyQ) tract. The linear lattice model for the structure and binding properties of polyQ proposes that both expanded and normal polyQ tracts in the preaggregation state are random-coil structures but that an expanded polyQ repeat contains a larger number of epitopes recognized by antibodies or other proteins. The crystal structure of polyQ bound to MW1, an antibody against polyQ, reveals that polyQ adopts an extended, coil-like structure. Consistent with the linear lattice model, multimeric MW1 Fvs bind more tightly to longer than to shorter polyQ tracts and, compared with monomeric Fv, bind expanded polyQ repeats with higher apparent affinities. These results suggest a mechanism for the toxicity of expanded polyQ and a strategy to link anti-polyQ compounds to create high-avidity therapeutics.
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Affiliation(s)
- Pingwei Li
- Division of Biology 114-96, California Institute of Technology, Pasadena, California 91125, USA.
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36
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Gotoh H, Matsumoto Y. Cell-surface streptavidin fusion protein for rapid selection of transfected mammalian cells. Gene 2007; 389:146-53. [PMID: 17175122 DOI: 10.1016/j.gene.2006.10.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Revised: 10/22/2006] [Accepted: 10/28/2006] [Indexed: 10/23/2022]
Abstract
We developed a series of eight mammalian cell surface marker fusion genes by using the streptavidin gene from Streptomyces avidinii. These fusion genes are useful and non-growth-toxic selection markers for rapid-harvest transfected mammalian cells. Two streptavidin constructs were used; the longer fragment contains the native bacterial signal sequence, which the shorter fragment lacks. For expression of the streptavidin antigen on the surface of mammalian cells, streptavidin was flanked by a mammalian signal sequence and a transmembrane domain (from mouse H2-K or Kit); some constructs also contained the gene for enhanced green fluorescent protein (EGFP). We transfected a series of plasmids encoding the fusion proteins into HeLa cells and determined that the transfected cells produced the fusion protein on their cell surfaces. To separate transfected cells from nontransfected cells, we incubated cells with a polyclonal antibody against streptavidin, and antibody-bound cells were harvested by the use of paramagnetic beads coupled with the corresponding secondary antibody. We obtained highly pure populations of transfected cells; this result also confirmed the production of the fusion protein on the cell surface. Cell growth assays revealed that none of the transfected fusion genes or their products adversely affected the proliferation of HeLa cells. Our results indicate that the fusion constructs we developed and the immunomagnetic separation protocol we used are valuable tools for various transfection applications. In particular, the constructs containing EGFP are advantageous because transfection efficiency can be assessed without additional treatment of cells.
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Affiliation(s)
- Hideo Gotoh
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.
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37
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de Araújo AD, Palomo JM, Cramer J, Köhn M, Schröder H, Wacker R, Niemeyer C, Alexandrov K, Waldmann H. Diels-Alder Ligation and Surface Immobilization of Proteins. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200502266] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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38
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de Araújo AD, Palomo JM, Cramer J, Köhn M, Schröder H, Wacker R, Niemeyer C, Alexandrov K, Waldmann H. Diels-Alder Ligation and Surface Immobilization of Proteins. Angew Chem Int Ed Engl 2006; 45:296-301. [PMID: 16315328 DOI: 10.1002/anie.200502266] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Aline Dantas de Araújo
- Department of Chemical Biology, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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Choresh O, Loya Y, Müller WEG, Wiedenmann J, Azem A. The mitochondrial 60-kDa heat shock protein in marine invertebrates: biochemical purification and molecular characterization. Cell Stress Chaperones 2005; 9:38-48. [PMID: 15270076 PMCID: PMC1065304 DOI: 10.1379/469.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Sessile marine invertebrates undergo constant direct exposure to the surrounding environmental conditions, including local and global environmental fluctuations that may lead to fatal protein damage. Induction of heat shock proteins (Hsps) constitutes an important defense mechanism that protects these organisms from deleterious stress conditions. In a previous study, we reported the immunological detection of a 60-kDa Hsp (Hsp60) in the sea anemone Anemonia viridis (formerly called Anemonia sulcata) and studied its expression under a variety of stress conditions. In the present study, we show that the sponge Tetilla sp. from tidal habitats with a highly variable temperature regime is characterized by an increased level of Hsp60. Moreover, we show the expression of Hsp60 in various species among Porifera and Cnidaria, suggesting a general importance of this protein among marine invertebrates. We further cloned the hsp60 gene from A viridis, using a combination of conventional protein isolation methods and screening of a complementary deoxyribonucleic acid library by polymerase chain reaction. The cloned sequence (1764 bp) encodes for a protein of 62.8 kDa (588 amino acids). The 62.8-kDa protein, which contains an amino terminal extension that may serve as a mitochondrial targeting signal, shares a significant identity with mitochondrial Hsp60s from several animals but less identity with Hsp60s from either bacteria or plants.
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Affiliation(s)
- Omer Choresh
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
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Waner MJ, Navrotskaya I, Bain A, Oldham ED, Mascotti DP. Thermal and sodium dodecylsulfate induced transitions of streptavidin. Biophys J 2004; 87:2701-13. [PMID: 15298874 PMCID: PMC1304689 DOI: 10.1529/biophysj.104.047266] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Accepted: 07/28/2004] [Indexed: 11/18/2022] Open
Abstract
The strong specific binding of streptavidin (SA) to biotin is utilized in numerous biotechnological applications. The SA tetramer is also known to exhibit significant stability, even in the presence of sodium dodecylsulfate (SDS). Despite its importance, relatively little is known about the nature of the thermal denaturation pathway for SA. This work uses a homogeneous SA preparation to expand on the data of previous literature reports, leading to the proposal of a model for temperature induced structural changes in SA. Temperature dependent data were obtained by SDS and native polyacrylamide gel electrophoresis (PAGE), differential scanning calorimetry (DSC), and fluorescence and ultraviolet (UV)-visible spectroscopy in the presence and absence of SDS. In addition to the development of this model, it is found that the major thermal transition of SA in 1% SDS is reversible. Finally, although SA exhibits significant precipitation at elevated temperatures in aqueous solution, inclusion of SDS acts to prevent SA aggregation.
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Affiliation(s)
- Mark J Waner
- Department of Chemistry, John Carroll University, University Heights, Ohio 44118, USA
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41
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Xia N, Shumaker-Parry JS, Zareie MH, Campbell CT, Castner DG. A streptavidin linker layer that functions after drying. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2004; 20:3710-6. [PMID: 15875404 DOI: 10.1021/la035864n] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The ability of streptavidin (SA) to simultaneously bind four biotins is often used in linker layers, where a biotinylated molecule is linked to a biotin-functionalized surface via SA. For biosensor and array applications, it is desirable that the SA linker layer be stable to drying and rehydration. In this study it was observed that a significant decrease in binding capacity of a SA layer occurred when that layer was dried. For this study a SA linker layer was constructed by binding SA to a biotin-containing alkylthiolate monolayer (BAT/OEG) self-assembled onto gold. Its stability after drying was investigated using surface plasmon resonance (SPR). Approximately a quarter of the SA layer was removed from the BAT/OEG surface upon drying and rehydration, suggesting disruption of SA-biotin binding when dry. This resulted in the dried SA layer losing approximately 40% of its biotinylated ferritin (BF) binding capacity. Coating the layer with trehalose before drying was found to inhibit the loss of SA from the BAT/OEG surface. SPR showed that the trehalose-protected SA linker layer retained approximately 91% of its original BF binding capacity after drying and rehydration. Atomic force microscopy, which was used to image individual surface-bound SA and BF molecules, qualitatively confirmed these observations.
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Affiliation(s)
- Nan Xia
- National ESCA and Surface Analysis Center for Biomedical Problems, Department of Chemical Engineering, University of Washington, Box 351750, Seattle, Washington 98195-1750, USA
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42
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Choresh O, Loya Y, Müller WE, Wiedenmann J, Azem A. The mitochondrial 60-kDa heat shock protein in marine invertebrates: biochemical purification and molecular characterization. Cell Stress Chaperones 2004. [DOI: 10.1379/1466-1268(2004)009<0038:tmkhsp>2.0.co;2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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43
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Pazy Y, Eisenberg-Domovich Y, Laitinen OH, Kulomaa MS, Bayer EA, Wilchek M, Livnah O. Dimer-tetramer transition between solution and crystalline states of streptavidin and avidin mutants. J Bacteriol 2003; 185:4050-6. [PMID: 12837778 PMCID: PMC164866 DOI: 10.1128/jb.185.14.4050-4056.2003] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The biotin-binding tetrameric proteins, streptavidin from Streptomyces avidinii and chicken egg white avidin, are excellent models for the study of subunit-subunit interactions of a multimeric protein. Efforts are thus being made to prepare mutated forms of streptavidin and avidin, which would form monomers or dimers, in order to examine their effect on quaternary structure and assembly. In the present communication, we compared the crystal structures of binding site W-->K mutations in streptavidin and avidin. In solution, both mutant proteins are known to form dimers, but upon crystallization, both formed tetramers with the same parameters as the native proteins. All of the intersubunit bonds were conserved, except for the hydrophobic interaction between biotin and the tryptophan that was replaced by lysine. In the crystal structure, the binding site of the mutated apo-avidin contains 3 molecules of structured water instead of the 5 contained in the native protein. The lysine side chain extends in a direction opposite that of the native tryptophan, the void being partially filled by an adjacent lysine residue. Nevertheless, the binding-site conformation observed for the mutant tetramer is an artificial consequence of crystal packing that would not be maintained in the solution-phase dimer. It appears that the dimer-tetramer transition may be concentration dependent, and the interaction among subunits obeys the law of mass action.
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Affiliation(s)
- Yael Pazy
- Department of Biological Chemistry, The Institute of Life Sciences, The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
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44
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Katz BA, Elrod K, Verner E, Mackman RL, Luong C, Shrader WD, Sendzik M, Spencer JR, Sprengeler PA, Kolesnikov A, Tai VWF, Hui HC, Breitenbucher JG, Allen D, Janc JW. Elaborate manifold of short hydrogen bond arrays mediating binding of active site-directed serine protease inhibitors. J Mol Biol 2003; 329:93-120. [PMID: 12742021 DOI: 10.1016/s0022-2836(03)00399-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
An extensive structural manifold of short hydrogen bond-mediated, active site-directed, serine protease inhibition motifs is revealed in a set of over 300 crystal structures involving a large suite of small molecule inhibitors (2-(2-phenol)-indoles and 2-(2-phenol)-benzimidazoles) determined over a wide range of pH (3.5-11.4). The active site hydrogen-bonding mode was found to vary markedly with pH, with the steric and electronic properties of the inhibitor, and with the type of protease (trypsin, thrombin or urokinase type plasminogen activator (uPA)). The pH dependence of the active site hydrogen-bonding motif is often intricate, constituting a distinct fingerprint of each complex. Isosteric replacements or minor substitutions within the inhibitor that modulate the pK(a) of the phenol hydroxyl involved in short hydrogen bonding, or that affect steric interactions distal to the active site, can significantly shift the pH-dependent structural profile characteristic of the parent scaffold, or produce active site-binding motifs unique to the bound analog. Ionization equilibria at the active site associated with inhibitor binding are probed in a series of the protease-inhibitor complexes through analysis of the pH dependence of the structure and environment of the active site-binding groups involved in short hydrogen bond arrays. Structures determined at high pH (>11), suggest that the pK(a) of His57 is dramatically elevated, to a value as high as approximately 11 in certain complexes. K(i) values involving uPA and trypsin determined as a function of pH for a set of inhibitors show pronounced parabolic pH dependence, the pH for optimal inhibition governed by the pK(a) of the inhibitor phenol involved in short hydrogen bonds. Comparison of structures of trypsin, thrombin and uPA, each bound by the same inhibitor, highlights important structural variations in the S1 and active sites accessible for engineering notable selectivity into remarkably small molecules with low nanomolar K(i) values.
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Affiliation(s)
- Bradley A Katz
- Celera, 180 Kimball Way, South San Francisco, CA 94080, USA.
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45
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Marttila AT, Hytönen VP, Laitinen OH, Bayer EA, Wilchek M, Kulomaa MS. Mutation of the important Tyr-33 residue of chicken avidin: functional and structural consequences. Biochem J 2003; 369:249-54. [PMID: 12358604 PMCID: PMC1223082 DOI: 10.1042/bj20020886] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2002] [Revised: 08/09/2002] [Accepted: 10/02/2002] [Indexed: 11/17/2022]
Abstract
The strong interaction between avidin and biotin is so tight (dissociation constant 10(-15) M) that conditions usually sufficient for protein denaturing fail to dislodge biotin from the avidin-biotin complex. This kind of irreversible binding hinders the use of avidin in applications such as affinity purification or protein immobilization. To address this concern, we have constructed a series of mutants of the strategically positioned Tyr-33 in order to study the role of this residue in biotin binding, and to create avidin variants with more reversible ligand-binding properties. Unexpectedly, an avidin mutant in which Tyr-33 was replaced with phenylalanine (Avm-Y33F) displayed similar biotin-binding characteristics to the native avidin, indicating that the hydrogen bond formed between the hydroxy group of Tyr-33 and the carbonyl oxygen of biotin is not as important for the tight binding of biotin as previously suggested. In terms of the reversibility of biotin binding, Avm-Y33H was the most successful substitution constructed in this study. Interestingly, the binding of this mutant exhibited clear pH-dependence, since at neutral pH it bound to the biotin surface in an irreversible fashion, whereas, at pH 9, 50% of the bound protein could be released with free biotin. Furthermore, although Tyr-33 is located relatively distant from the monomer-monomer interfaces, the mutagenesis of this residue also weakened the quaternary structure of avidin, indicating that the high ligand binding and the high stability of avidin have evolved together and it is difficult to modify one without affecting the other.
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Affiliation(s)
- Ari T Marttila
- Department of Biological and Environmental Science, FIN-40014 University of Jyväskylä, Finland
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46
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Pazy Y, Kulik T, Bayer EA, Wilchek M, Livnah O. Ligand exchange between proteins. Exchange of biotin and biotin derivatives between avidin and streptavidin. J Biol Chem 2002; 277:30892-900. [PMID: 12055191 DOI: 10.1074/jbc.m202874200] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have studied the structural elements that affect ligand exchange between the two high affinity biotin-binding proteins, egg white avidin and its bacterial analogue, streptavidin. For this purpose, we have developed a simple assay based on the antipodal behavior of the two proteins toward hydrolysis of biotinyl p-nitrophenyl ester (BNP). The assay provided the experimental basis for these studies. It was found that biotin migrates unidirectionally from streptavidin to avidin. Conversely, the biotin derivative, BNP, is transferred in the opposite direction, from avidin to streptavidin. A previous crystallographic study (Huberman, T., Eisenberg-Domovich, Y., Gitlin, G., Kulik, T., Bayer, E. A., Wilchek, M., and Livnah, O. (2001) J. Biol. Chem. 276, 32031-32039) provided insight into a plausible explanation for these results. These data revealed that the non-hydrolyzable BNP analogue, biotinyl p-nitroanilide, was almost completely sheltered in streptavidin as opposed to avidin in which the disordered conformation of a critical loop resulted in the loss of several hydrogen bonds and concomitant exposure of the analogue to the solvent. In order to determine the minimal modification of the biotin molecule required to cause the disordered loop conformation, the structures of avidin and streptavidin were determined with norbiotin, homobiotin, and a common long-chain biotin derivative, biotinyl epsilon-aminocaproic acid. Six new crystal structures of the avidin and streptavidin complexes with the latter biotin analogues and derivatives were thus elucidated. It was found that extending the biotin side chain by a single CH(2) group (i.e. homobiotin) is sufficient to result in this remarkable conformational change in the loop of avidin. These results bear significant biotechnological importance, suggesting that complexes containing biotinylated probes with streptavidin would be more stable than those with avidin. These findings should be heeded when developing new drugs based on lead compounds because it is difficult to predict the structural and conformational consequences on the resultant protein-ligand interactions.
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Affiliation(s)
- Yael Pazy
- Department of Biological Chemistry, The Institute of Life Sciences, The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
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47
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Korndörfer IP, Skerra A. Improved affinity of engineered streptavidin for the Strep-tag II peptide is due to a fixed open conformation of the lid-like loop at the binding site. Protein Sci 2002; 11:883-93. [PMID: 11910031 PMCID: PMC2373521 DOI: 10.1110/ps.4150102] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
The Strep-tag II is a nine-amino acid peptide that was developed as an affinity tool for the purification of corresponding fusion proteins on streptavidin columns. The peptide recognizes the same pocket of streptavidin where the natural ligand is normally bound so that biotin or its chemical derivatives can be used for competitive elution. We report here the crystal structures of the streptavidin mutants '1' and '2,' which had been engineered for 10-fold higher affinity towards the Strep-tag II. Both streptavidin mutants carry mutations at positions 44, 45, and 47, that is, in a flexible loop region close to the binding site. The crystal structures of the two apo-proteins and their complexes with the Strep-tag II peptide were refined at resolutions below 2 A. Both in the presence and absence of the peptide, the lid-like loop next to the ligand pocket--comprising residues 45 through 52--adopts an 'open' conformation in all four subunits within the asymmetric unit. The same loop was previously described to be disordered in the wild-type apo-streptavidin and to close over the pocket upon complexation of the natural ligand biotin. Our findings suggest that stabilization of the 'open' loop conformation in the absence of a ligand abolishes the need for conformational rearrangement prior to the docking of the voluminous peptide. Because no direct contacts between the flexible part of the loop and the peptide ligand were detected, it seems likely that the higher affinity of the two streptavidin mutants for the Strep-tag II is caused by a predominantly entropic mechanism.
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Affiliation(s)
- Ingo P Korndörfer
- Lehrstuhl für Biologische Chemie, Technische Universität München, Freising-Weihenstephan, Germany
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48
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Neish CS, Martin IL, Henderson RM, Edwardson JM. Direct visualization of ligand-protein interactions using atomic force microscopy. Br J Pharmacol 2002; 135:1943-50. [PMID: 11959797 PMCID: PMC1573323 DOI: 10.1038/sj.bjp.0704660] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
1. Streptavidin is a 60-kDa tetramer which binds four molecules of biotin with extremely high affinity (K(A) approximately 10(14) M(-1)). We have used atomic force microscopy (AFM) to visualize this ligand-protein interaction directly. 2. Biotin was tagged with a short (152-basepair; 50-nm) DNA rod and incubated with streptavidin. The resulting complexes were then imaged by AFM. The molecular volume of streptavidin calculated from the dimensions of the protein particles (105+/-3 nm(3)) was in close agreement with the value calculated from its molecular mass (114 nm(3)). Biotinylation increased the apparent size of streptavidin (to 133+/-2 nm(3)), concomitant with an increase in the thermal stability of the tetramer. 3. Images of streptavidin with one to four molecules of DNA-biotin bound were obtained. When two ligands were bound, the angle between the DNA rods was either acute or obtuse, as expected from the relative orientations of the biotin binding sites. The ratio of acute : obtuse angles (1 : 3) was lower than the expected value (1 : 2), indicating a degree of steric hindrance in the binding of the DNA-biotin. The slight under-representation of higher occupancy states supported this idea. 4. Streptavidin with a single molecule of DNA-biotin bound was used to tag biotinylated beta-galactosidase, a model multimeric enzyme. 5. The ability to image directly the binding of a ligand to its protein target by AFM provides useful information about the nature of the interaction, and about the effect of complex formation on the structure of the protein. Furthermore, the use of DNA-biotin/streptavidin tags could potentially shed light on the architecture of multi-subunit proteins.
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Affiliation(s)
- Calum S Neish
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD
| | - Ian L Martin
- Pharmaceutical Sciences Research Institute, School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET
| | | | - J Michael Edwardson
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD
- Author for correspondence:
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49
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Huberman T, Eisenberg-Domovich Y, Gitlin G, Kulik T, Bayer EA, Wilchek M, Livnah O. Chicken avidin exhibits pseudo-catalytic properties. Biochemical, structural, and electrostatic consequences. J Biol Chem 2001; 276:32031-9. [PMID: 11395489 DOI: 10.1074/jbc.m102018200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Avidin and its bacterial analogue streptavidin exhibit similarly high affinities toward the vitamin biotin. The extremely high affinity of these two proteins has been utilized as a powerful tool in many biotechnological applications. Although avidin and streptavidin have similar tertiary and quaternary structures, they differ in many of their properties. Here we show that avidin enhances the alkaline hydrolysis of biotinyl p-nitrophenyl ester, whereas streptavidin protects this reaction even under extreme alkaline conditions (pH > 12). Unlike normal enzymatic catalysis, the hydrolysis reaction proceeds as a single cycle with no turnover because of the extremely high affinity of the protein for one of the reaction products (i.e. free biotin). The three-dimensional crystal structures of avidin (2 A) and streptavidin (2.4 A) complexed with the amide analogue, biotinyl p-nitroanilide, as a model for the p-nitrophenyl ester, revealed structural insights into the factors that enhance or protect the hydrolysis reaction. The data demonstrate that several molecular features of avidin are responsible for the enhanced hydrolysis of biotinyl p-nitrophenyl ester. These include the nature of a decisive flexible loop, the presence of an obtrusive arginine 114, and a newly formed critical interaction between lysine 111 and the nitro group of the substrate. The open conformation of the loop serves to expose the substrate to the solvent, and the arginine shifts the p-nitroanilide moiety toward the interacting lysine, which increases the electron withdrawing characteristics and consequent electrophilicity of the carbonyl group of the substrate. Streptavidin lacked such molecular properties, and analogous interactions with the substrate were consequently absent. The information derived from these structures may provide insight into the action of artificial protein catalysts and the evolution of catalytic sites in general.
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Affiliation(s)
- T Huberman
- Department of Biological Chemistry, The Institute of Life Sciences, Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
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50
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Katz BA, Elrod K, Luong C, Rice MJ, Mackman RL, Sprengeler PA, Spencer J, Hataye J, Janc J, Link J, Litvak J, Rai R, Rice K, Sideris S, Verner E, Young W. A novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site. J Mol Biol 2001; 307:1451-86. [PMID: 11292354 DOI: 10.1006/jmbi.2001.4516] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We describe a new serine protease inhibition motif in which binding is mediated by a cluster of very short hydrogen bonds (<2.3 A) at the active site. This protease-inhibitor binding paradigm is observed at high resolution in a large set of crystal structures of trypsin, thrombin, and urokinase-type plasminogen activator (uPA) bound with a series of small molecule inhibitors (2-(2-phenol)indoles and 2-(2-phenol)benzimidazoles). In each complex there are eight enzyme-inhibitor or enzyme-water-inhibitor hydrogen bonds at the active site, three of which are very short. These short hydrogen bonds connect a triangle of oxygen atoms comprising O(gamma)(Ser195), a water molecule co-bound in the oxyanion hole (H(2)O(oxy)), and the phenolate oxygen atom of the inhibitor (O6'). Two of the other hydrogen bonds between the inhibitor and active site of the trypsin and uPA complexes become short in the thrombin counterparts, extending the three-centered short hydrogen-bonding array into a tetrahedral array of atoms (three oxygen and one nitrogen) involved in short hydrogen bonds. In the uPA complexes, the extensive hydrogen-bonding interactions at the active site prevent the inhibitor S1 amidine from forming direct hydrogen bonds with Asp189 because the S1 site is deeper in uPA than in trypsin or thrombin. Ionization equilibria at the active site associated with inhibitor binding are probed through determination and comparison of structures over a wide range of pH (3.5 to 11.4) of thrombin complexes and of trypsin complexes in three different crystal forms. The high-pH trypsin-inhibitor structures suggest that His57 is protonated at pH values as high as 9.5. The pH-dependent inhibition of trypsin, thrombin, uPA and factor Xa by 2-(2-phenol)benzimidazole analogs in which the pK(a) of the phenol group is modulated is shown to be consistent with a binding process involving ionization of both the inhibitor and the enzyme. These data further suggest that the pK(a) of His57 of each protease in the unbound state in solution is about the same, approximately 6.8. By comparing inhibition constants (K(i) values), inhibitor solubilities, inhibitor conformational energies and corresponding structures of short and normal hydrogen bond-mediated complexes, we have estimated the contribution of the short hydrogen bond networks to inhibitor affinity ( approximately 1.7 kcal/mol). The structures and K(i) values associated with the short hydrogen-bonding motif are compared with those corresponding to an alternate, Zn(2+)-mediated inhibition motif at the active site. Structural differences among apo-enzymes, enzyme-inhibitor and enzyme-inhibitor-Zn(2+) complexes are discussed in the context of affinity determinants, selectivity development, and structure-based inhibitor design.
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Affiliation(s)
- B A Katz
- Axys Pharmaceuticals Corporation, 385 Oyster Point Boulevard, Suite 3, South San Francisco, CA, 94080, USA.
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