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Puthenveetil R, Christenson ET, Vinogradova O. New Horizons in Structural Biology of Membrane Proteins: Experimental Evaluation of the Role of Conformational Dynamics and Intrinsic Flexibility. MEMBRANES 2022; 12:227. [PMID: 35207148 PMCID: PMC8877495 DOI: 10.3390/membranes12020227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
Abstract
A plethora of membrane proteins are found along the cell surface and on the convoluted labyrinth of membranes surrounding organelles. Since the advent of various structural biology techniques, a sub-population of these proteins has become accessible to investigation at near-atomic resolutions. The predominant bona fide methods for structure solution, X-ray crystallography and cryo-EM, provide high resolution in three-dimensional space at the cost of neglecting protein motions through time. Though structures provide various rigid snapshots, only an amorphous mechanistic understanding can be inferred from interpolations between these different static states. In this review, we discuss various techniques that have been utilized in observing dynamic conformational intermediaries that remain elusive from rigid structures. More specifically we discuss the application of structural techniques such as NMR, cryo-EM and X-ray crystallography in studying protein dynamics along with complementation by conformational trapping by specific binders such as antibodies. We finally showcase the strength of various biophysical techniques including FRET, EPR and computational approaches using a multitude of succinct examples from GPCRs, transporters and ion channels.
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Affiliation(s)
- Robbins Puthenveetil
- Section on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 35A Convent Dr., Bethesda, MD 20892, USA
| | | | - Olga Vinogradova
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
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Cheloha RW, Harmand TJ, Wijne C, Schwartz TU, Ploegh HL. Exploring cellular biochemistry with nanobodies. J Biol Chem 2020; 295:15307-15327. [PMID: 32868455 PMCID: PMC7650250 DOI: 10.1074/jbc.rev120.012960] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/27/2020] [Indexed: 12/21/2022] Open
Abstract
Reagents that bind tightly and specifically to biomolecules of interest remain essential in the exploration of biology and in their ultimate application to medicine. Besides ligands for receptors of known specificity, agents commonly used for this purpose are monoclonal antibodies derived from mice, rabbits, and other animals. However, such antibodies can be expensive to produce, challenging to engineer, and are not necessarily stable in the context of the cellular cytoplasm, a reducing environment. Heavy chain-only antibodies, discovered in camelids, have been truncated to yield single-domain antibody fragments (VHHs or nanobodies) that overcome many of these shortcomings. Whereas they are known as crystallization chaperones for membrane proteins or as simple alternatives to conventional antibodies, nanobodies have been applied in settings where the use of standard antibodies or their derivatives would be impractical or impossible. We review recent examples in which the unique properties of nanobodies have been combined with complementary methods, such as chemical functionalization, to provide tools with unique and useful properties.
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Affiliation(s)
- Ross W Cheloha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Thibault J Harmand
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Charlotte Wijne
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA.
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Chen S, Zhang W, Min J, Liu K. Lesson from a Fab-enabled co-crystallization study of TDRD2 and PIWIL1. Methods 2020; 175:72-78. [PMID: 31288074 DOI: 10.1016/j.ymeth.2019.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/30/2019] [Accepted: 07/03/2019] [Indexed: 10/26/2022] Open
Abstract
The interaction of Tudor domain-containing proteins (TDRDs) with P-element-induced wimpy testis (PIWI) proteins plays critical roles in transposon silencing and spermatogenesis. Most human TDRDs recognize PIWI proteins in a methylarginine-dependent manner via their extended Tudor (eTudor) domains, except TDRD2, which prefers an unmethylated PIWI protein. In order to illustrate the recognition of unmethylated PIWI proteins by TDRD2, we extensively tried co-crystallization of the TDRD2 eTudor with different PIWIL1 peptides, but to no avail. Recombinant antigen-binding fragments (Fabs) have been used to crystallize some difficult proteins in the past, so we generated Fab against the TDRD2 eTudor protein using a phage-display antibody library, and one of these Fab fragments indeed facilitated the co-crystallization of TDRD2 and PIWIL1. Structural analysis of Fab, the TDRD2 eTudor domain in complex with an unmethylated PIWIL1-derived peptide revealed that the PIWIL1 residues G3 through R8 bound between the Tudor core and SN domain of TDRD2. The C-terminal residues of the PIWIL1 peptide were not resolved, presumably due to steric competition with the heavy chain of the Fab. We propose Fab-assisted crystallization as a tool not only for structural studies of single proteins, but also for analysis of interactions between proteins and their ligands in cases where co-crystallization of native protein complexes fails.
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Affiliation(s)
- Sizhuo Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Weilian Zhang
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
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Application of antihelix antibodies in protein structure determination. Proc Natl Acad Sci U S A 2019; 116:17786-17791. [PMID: 31371498 DOI: 10.1073/pnas.1910080116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Antibodies are indispensable tools in protein engineering and structural biology. Antibodies suitable for structural studies should recognize the 3-dimensional (3D) conformations of target proteins. Generating such antibodies and characterizing their complexes with antigens take a significant amount of time and effort. Here, we show that we can expand the application of well-characterized antibodies by "transplanting" the epitopes that they recognize to proteins with completely different structures and sequences. Previously, several antibodies have been shown to recognize the alpha-helical conformation of antigenic peptides. We demonstrate that these antibodies can be made to bind to a variety of unrelated "off-target" proteins by modifying amino acids in the preexisting alpha helices of such proteins. Using X-ray crystallography, we determined the structures of the engineered protein-antibody complexes. All of the antibodies bound to the epitope-transplanted proteins, forming accurately predictable structures. Furthermore, we showed that binding of these antihelix antibodies to the engineered target proteins can modulate their catalytic activities by trapping them in selected functional states. Our method is simple and efficient, and it will have applications in protein X-ray crystallography, electron microscopy, and nanotechnology.
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Ereño-Orbea J, Sicard T, Cui H, Carson J, Hermans P, Julien JP. Structural Basis of Enhanced Crystallizability Induced by a Molecular Chaperone for Antibody Antigen-Binding Fragments. J Mol Biol 2017; 430:322-336. [PMID: 29277294 DOI: 10.1016/j.jmb.2017.12.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 11/30/2017] [Accepted: 12/13/2017] [Indexed: 12/20/2022]
Abstract
Monoclonal antibodies constitute one of the largest groups of drugs to treat cancers and immune disorders, and are guiding the design of vaccines against infectious diseases. Fragments antigen-binding (Fabs) have been preferred over monoclonal antibodies for the structural characterization of antibody-antigen complexes due to their relatively low flexibility. Nonetheless, Fabs often remain challenging to crystallize because of the surface characteristics of complementary determining regions and the residual flexibility in the hinge region between the variable and constant domains. Here, we used a variable heavy-chain (VHH) domain specific for the human kappa light chain to assist in the structure determination of three therapeutic Fabs that were recalcitrant to crystallization on their own. We show that this ligand alters the surface properties of the antibody-ligand complex and lowers its aggregation temperature to favor crystallization. The VHH crystallization chaperone also restricts the flexible hinge of Fabs to a narrow range of angles, and so independently of the variable region. Our findings contribute a valuable approach to antibody structure determination and provide biophysical insight into the principles that govern the crystallization of macromolecules.
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Affiliation(s)
- June Ereño-Orbea
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4
| | - Taylor Sicard
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4; Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Hong Cui
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4
| | - Jacob Carson
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4
| | - Pim Hermans
- BAC, BV, part of Thermo Fisher Scientific, Leiden, the Netherlands
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4; Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8; Department of Immunology, University of Toronto, Toronto, ON, Canada M5S 1A8.
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Nilvebrant J, Tessier PM, Sidhu SS. Engineered Autonomous Human Variable Domains. Curr Pharm Des 2016; 22:6527-6537. [PMID: 27655414 PMCID: PMC5326600 DOI: 10.2174/1381612822666160921143011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/16/2016] [Accepted: 09/20/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND The complex multi-chain architecture of antibodies has spurred interest in smaller derivatives that retain specificity but can be more easily produced in bacteria. Domain antibodies consisting of single variable domains are the smallest antibody fragments and have been shown to possess enhanced ability to target epitopes that are difficult to access using multidomain antibodies. However, in contrast to natural camelid antibody domains, human variable domains typically suffer from low stability and high propensity to aggregate. METHODS This review summarizes strategies to improve the biophysical properties of heavy chain variable domains from human antibodies with an emphasis on aggregation resistance. Several protein engineering approaches have targeted antibody frameworks and complementarity determining regions to stabilize the native state and prevent aggregation of the denatured state. CONCLUSION Recent findings enable the construction of highly diverse libraries enriched in aggregation-resistant variants that are expected to provide binders to diverse antigens. Engineered domain antibodies possess unique advantages in expression, epitope preference and flexibility of formatting over conventional immunoreagents and are a promising class of antibody fragments for biomedical development.
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Affiliation(s)
- Johan Nilvebrant
- Division of Protein Technology, School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Peter M. Tessier
- Center for Biotechnology and Interdisciplinary Studies, Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Sachdev S. Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
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Emerging Approaches to GPCR Ligand Screening for Drug Discovery. Trends Mol Med 2015; 21:687-701. [DOI: 10.1016/j.molmed.2015.09.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 09/02/2015] [Accepted: 09/04/2015] [Indexed: 01/07/2023]
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Srivastava A, Gupta B, Gupta C, Shukla AK. Emerging Functional Divergence of β-Arrestin Isoforms in GPCR Function. Trends Endocrinol Metab 2015; 26:628-642. [PMID: 26471844 DOI: 10.1016/j.tem.2015.09.001] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/21/2015] [Accepted: 09/02/2015] [Indexed: 12/22/2022]
Abstract
G protein-coupled receptors (GPCRs) are tightly regulated by multifunctional protein β-arrestins. Two isoforms of β-arrestin sharing more than 70% sequence identity and overall very similar 3D structures, β-arrestins 1 and 2, were originally expected to be functionally redundant. However, in recent years multiple lines of emerging evidence suggest they have distinct roles in various aspects of GPCR regulation and signaling. We summarize selected examples of GPCRs where β-arrestin isoforms are discovered to display non-overlapping and sometimes even antagonistic functions. We also discuss potential mechanistic basis for their functional divergence and highlight new frontiers that are likely to form the focal points of research in this area in coming years.
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Affiliation(s)
- Ashish Srivastava
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Bhagyashri Gupta
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Charu Gupta
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Arun K Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India.
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Shukla AK, Kumari P, Ghosh E, Nidhi K. From Recombinant Expression to Crystals: A Step-by-Step Guide to GPCR Crystallography. Methods Enzymol 2015; 556:549-61. [PMID: 25857799 DOI: 10.1016/bs.mie.2015.01.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
G protein-coupled receptors (GPCRs) are the primary targets of drugs prescribed for many human pathophysiological conditions such as hypertension, allergies, schizophrenia, asthma, and various types of cancer. High-resolution structure determination of GPCRs has been a key focus area in GPCR biology to understand the basic mechanism of their activation and signaling and to materialize the long-standing dream of structure-based drug design on these versatile receptors. There has been tremendous effort at this front in the past two decades and it has culminated into crystal structures of 27 different receptors so far. The recent progress in crystallization and structure determination of GPCRs has been driven by innovation and cutting-edge developments at every step involved in the process of crystallization. Here, we present a step-by-step description of various steps involved in GPCR crystallization starting from recombinant expression to obtaining diffracting crystals. We also discuss the next frontiers in GPCR biology that are likely to be a primary focus for crystallography efforts in the next decade or so.
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Affiliation(s)
- Arun K Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India.
| | - Punita Kumari
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
| | - Eshan Ghosh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
| | - Kumari Nidhi
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
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