1
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Stover L, Bahramimoghaddam H, Wang L, Schrecke S, Yadav GP, Zhou M, Laganowsky A. Grafting the ALFA tag for structural studies of aquaporin Z. J Struct Biol X 2024; 9:100097. [PMID: 38361954 PMCID: PMC10867769 DOI: 10.1016/j.yjsbx.2024.100097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Aquaporin Z (AqpZ), a bacterial water channel, forms a tetrameric complex and, like many other membrane proteins, activity is regulated by lipids. Various methods have been developed to facilitate structure determination of membrane proteins, such as the use of antibodies. Here, we graft onto AqpZ the ALFA tag (AqpZ-ALFA), an alpha helical epitope, to make use of the high-affinity anti-ALFA nanobody (nB). Native mass spectrometry reveals the AqpZ-ALFA fusion forms a stable, 1:1 complex with nB. Single-particle cryogenic electron microscopy studies reveal the octameric (AqpZ-ALFA)4(nB)4 complex forms a dimeric assembly and the structure was determined to 1.9 Å resolution. Dimerization of the octamer is mediated through stacking of the symmetrically bound nBs. Tube-like density is also observed, revealing a potential cardiolipin binding site. Grafting of the ALFA tag, or other epitope, along with binding and association of nBs to promote larger complexes will have applications in structural studies and protein engineering.
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Affiliation(s)
- Lauren Stover
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
| | | | - Lie Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Samantha Schrecke
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
| | - Gaya P. Yadav
- Laboratory for Biomolecular Structure and Dynamics (LBSD), Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
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2
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Liutkus M, Sasselli IR, Rojas AL, Cortajarena AL. Diverse crystalline protein scaffolds through metal-dependent polymorphism. Protein Sci 2024; 33:e4971. [PMID: 38591647 PMCID: PMC11002994 DOI: 10.1002/pro.4971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 04/10/2024]
Abstract
As protein crystals are increasingly finding diverse applications as scaffolds, controlled crystal polymorphism presents a facile strategy to form crystalline assemblies with controllable porosity with minimal to no protein engineering. Polymorphs of consensus tetratricopeptide repeat proteins with varying porosity were obtained through co-crystallization with metal salts, exploiting the innate metal ion geometric requirements. A single structurally exposed negative amino acid cluster was responsible for metal coordination, despite the abundance of negatively charged residues. Density functional theory calculations showed that while most of the crystals were the most thermodynamically stable assemblies, some were kinetically trapped states. Thus, crystalline porosity diversity is achieved and controlled with metal coordination, opening a new scope in the application of proteins as biocompatible protein-metal-organic frameworks (POFs). In addition, metal-dependent polymorphic crystals allow direct comparison of metal coordination preferences.
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Affiliation(s)
- Mantas Liutkus
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology AllianceSan SebastianSpain
| | - Ivan R. Sasselli
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology AllianceSan SebastianSpain
- Present address:
Centro de Física de Materiales (CFM)CSIC‐UPV/EHUSan SebastiánSpain
| | - Adriana L. Rojas
- Centre for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceBilbaoSpain
| | - Aitziber L. Cortajarena
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology AllianceSan SebastianSpain
- IkerbasqueBasque Foundation for ScienceBilbaoSpain
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3
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Zhu S, Fan S, Tang T, Huang J, Zhou H, Huang C, Chen Y, Qian F. Polymorphic nanobody crystals as long-acting intravitreal therapy for wet age-related macular degeneration. Bioeng Transl Med 2023; 8:e10523. [PMID: 38023710 PMCID: PMC10658565 DOI: 10.1002/btm2.10523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/23/2023] [Accepted: 03/29/2023] [Indexed: 12/01/2023] Open
Abstract
Wet age-related macular degeneration (wet AMD) is the most common cause of blindness, and chronic intravitreal injection of anti-vascular endothelial growth factor (VEGF) proteins has been the dominant therapeutic approach. Less intravitreal injection and a prolonged inter-injection interval are the main drivers behind new wet AMD drug innovations. By rationally engineering the surface residues of a model anti-VEGF nanobody, we obtained a series of anti-VEGF nanobodies with identical protein structures and VEGF binding affinities, while drastically different crystallization propensities and crystal lattice structures. Among these nanobody crystals, the P212121 lattice appeared to be denser and released protein slower than the P1 lattice, while nanobody crystals embedding zinc coordination further slowed the protein release rate. The polymorphic protein crystals could be a potentially breakthrough strategy for chronic intravitreal administration of anti-VEGF proteins.
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Affiliation(s)
- Shuqian Zhu
- School of Pharmaceutical Sciences, Beijing Advanced Innovation Center for Structural Biology, and Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Tsinghua UniversityBeijingPeople's Republic of China
| | - Shilong Fan
- Beijing Frontier Research Center for Biological StructureTsinghua UniversityBeijingPeople's Republic of China
| | - Tianxin Tang
- School of Pharmaceutical Sciences, Beijing Advanced Innovation Center for Structural Biology, and Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Tsinghua UniversityBeijingPeople's Republic of China
| | - Jinliang Huang
- Quaerite Biopharm ResearchBeijingPeople's Republic of China
| | - Heng Zhou
- Shuimu BioSciences Co. Ltd.BeijingPeople's Republic of China
| | - Chengnan Huang
- School of Pharmaceutical Sciences, Beijing Advanced Innovation Center for Structural Biology, and Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Tsinghua UniversityBeijingPeople's Republic of China
| | - Youxin Chen
- Peking Union Medical College HospitalBeijingPeople's Republic of China
| | - Feng Qian
- School of Pharmaceutical Sciences, Beijing Advanced Innovation Center for Structural Biology, and Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Tsinghua UniversityBeijingPeople's Republic of China
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4
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Yang Y, Wang P, Ji Z, Xu X, Zhang H, Wang Y. Polysaccharide‑platinum complexes for cancer theranostics. Carbohydr Polym 2023; 315:120997. [PMID: 37230639 DOI: 10.1016/j.carbpol.2023.120997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/21/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023]
Abstract
Platinum anticancer drugs have been explored and developed in recent years to reduce systematic toxicities and resist drug resistance. Polysaccharides derived from nature have abundant structures as well as pharmacological activities. The review provides insights on the design, synthesis, characterization and associating therapeutic application of platinum complexes with polysaccharides that are classified by electronic charge. The complexes give birth to multifunctional properties with enhanced drug accumulation, improved tumor selectivity and achieved synergistic antitumor effect in cancer therapy. Several techniques developing polysaccharides-based carriers newly are also discussed. Moreover, the lasted immunoregulatory activities of innate immune reactions triggered by polysaccharides are summarized. Finally, we discuss the current shortcomings and outline potential strategies for improving platinum-based personalized cancer treatment. Using platinum-polysaccharides complexes for improving the immunotherapy efficiency represents a promising framework in future.
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Affiliation(s)
- Yunxia Yang
- School of Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng 224007, China; Jiangsu Province Engineering Research Center of Agricultural Breeding Pollution Control and Resource, Yancheng Teachers University, Yancheng 224007, China; Jiangsu Key Laboratory for Bioresources of Saline Soils, Yancheng Teachers University, Yancheng 224007, China.
| | - Pengge Wang
- School of Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng 224007, China
| | - Zengrui Ji
- School of Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng 224007, China
| | - Xi Xu
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing 210094, China.
| | - Hongmei Zhang
- School of Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng 224007, China
| | - Yanqing Wang
- School of Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng 224007, China.
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5
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Mallik BB, Stanislaw J, Alawathurage TM, Khmelinskaia A. De Novo Design of Polyhedral Protein Assemblies: Before and After the AI Revolution. Chembiochem 2023; 24:e202300117. [PMID: 37014094 DOI: 10.1002/cbic.202300117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 04/05/2023]
Abstract
Self-assembling polyhedral protein biomaterials have gained attention as engineering targets owing to their naturally evolved sophisticated functions, ranging from protecting macromolecules from the environment to spatially controlling biochemical reactions. Precise computational design of de novo protein polyhedra is possible through two main types of approaches: methods from first principles, using physical and geometrical rules, and more recent data-driven methods based on artificial intelligence (AI), including deep learning (DL). Here, we retrospect first principle- and AI-based approaches for designing finite polyhedral protein assemblies, as well as advances in the structure prediction of such assemblies. We further highlight the possible applications of these materials and explore how the presented approaches can be combined to overcome current challenges and to advance the design of functional protein-based biomaterials.
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Affiliation(s)
- Bhoomika Basu Mallik
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Jenna Stanislaw
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Tharindu Madhusankha Alawathurage
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Alena Khmelinskaia
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
- Current address: Department of Chemistry, Ludwig Maximillian University, 80539, Munich, Germany
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6
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Dixit H, Kulharia M, Verma SK. Metalloproteome of human-infective RNA viruses: a study towards understanding the role of metal ions in virology. Pathog Dis 2023; 81:ftad020. [PMID: 37653445 DOI: 10.1093/femspd/ftad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/07/2023] [Accepted: 08/29/2023] [Indexed: 09/02/2023] Open
Abstract
Metalloproteins and metal-based inhibitors have been shown to effectively combat infectious diseases, particularly those caused by RNA viruses. In this study, a diverse set of bioinformatics methods was employed to identify metal-binding proteins of human RNA viruses. Seventy-three viral proteins with a high probability of being metal-binding proteins were identified. These proteins included 40 zinc-, 47 magnesium- and 14 manganese-binding proteins belonging to 29 viral species and eight significant viral families, including Coronaviridae, Flaviviridae and Retroviridae. Further functional characterization has revealed that these proteins play a critical role in several viral processes, including viral replication, fusion and host viral entry. They fall under the essential categories of viral proteins, including polymerase and protease enzymes. Magnesium ion is abundantly predicted to interact with these viral enzymes, followed by zinc. In addition, this study also examined the evolutionary aspects of predicted viral metalloproteins, offering essential insights into the metal utilization patterns among different viral species. The analysis indicates that the metal utilization patterns are conserved within the functional classes of the proteins. In conclusion, the findings of this study provide significant knowledge on viral metalloproteins that can serve as a valuable foundation for future research in this area.
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Affiliation(s)
- Himisha Dixit
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra 176206, Himachal Pradesh, India
| | - Mahesh Kulharia
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra 176206, Himachal Pradesh, India
| | - Shailender Kumar Verma
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra 176206, Himachal Pradesh, India
- Department of Environmental Studies, University of Delhi 110007, Delhi, India
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7
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Aptekmann AA, Buongiorno J, Giovannelli D, Glamoclija M, Ferreiro DU, Bromberg Y. mebipred: identifying metal binding potential in protein sequence. Bioinformatics 2022; 38:3532-3540. [PMID: 35639953 PMCID: PMC9272798 DOI: 10.1093/bioinformatics/btac358] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 03/27/2022] [Accepted: 05/22/2022] [Indexed: 11/23/2022] Open
Abstract
Motivation metal-binding proteins have a central role in maintaining life processes. Nearly one-third of known protein structures contain metal ions that are used for a variety of needs, such as catalysis, DNA/RNA binding, protein structure stability, etc. Identifying metal-binding proteins is thus crucial for understanding the mechanisms of cellular activity. However, experimental annotation of protein metal-binding potential is severely lacking, while computational techniques are often imprecise and of limited applicability. Results we developed a novel machine learning-based method, mebipred, for identifying metal-binding proteins from sequence-derived features. This method is over 80% accurate in recognizing proteins that bind metal ion-containing ligands; the specific identity of 11 ubiquitously present metal ions can also be annotated. mebipred is reference-free, i.e. no sequence alignments are involved, and is thus faster than alignment-based methods; it is also more accurate than other sequence-based prediction methods. Additionally, mebipred can identify protein metal-binding capabilities from short sequence stretches, e.g. translated sequencing reads, and, thus, may be useful for the annotation of metal requirements of metagenomic samples. We performed an analysis of available microbiome data and found that ocean, hot spring sediments and soil microbiomes use a more diverse set of metals than human host-related ones. For human microbiomes, physiological conditions explain the observed metal preferences. Similarly, subtle changes in ocean sample ion concentration affect the abundance of relevant metal-binding proteins. These results highlight mebipred’s utility in analyzing microbiome metal requirements. Availability and implementation mebipred is available as a web server at services.bromberglab.org/mebipred and as a standalone package at https://pypi.org/project/mymetal/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- A A Aptekmann
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ, 08873, USA.,Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | | | - D Giovannelli
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA.,Department of Biology, University of Naples Federico II, Naples, Italy.,Institute for Marine Biological Resources and Biotechnology-IRBIM, National Research Council of Italy, CNR, Ancona, Italy
| | - M Glamoclija
- Department of Earth and Environmental Sciences, Rutgers University, New Brunswick, NJ, 07102, USA
| | - D U Ferreiro
- Protein Physiology Lab, Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires-CONICET-IQUIBICEN, Buenos Aires, 1428, Argentina
| | - Y Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ, 08873, USA
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8
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Curtis RW, Scrudders KL, Ulcickas JRW, Simpson GJ, Low-Nam ST, Chmielewski J. Supramolecular Assembly of His-Tagged Fluorescent Protein Guests within Coiled-Coil Peptide Crystal Hosts: Three-Dimensional Ordering and Protein Thermal Stability. ACS Biomater Sci Eng 2022; 8:1860-1866. [PMID: 35377599 PMCID: PMC9840175 DOI: 10.1021/acsbiomaterials.2c00155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The use of biomaterials for the inclusion and stabilization of biopolymers is an ongoing challenge. Herein, we disclose three-dimensional (3D) coiled-coil peptide crystals with metal ions that include and overgrow His-tagged fluorescent proteins within the crystal. The protein guests are found within two symmetry-related growth sectors of the crystalline host that are associated with faces of the growing crystal that display ligands for metal ions. The fluorescent proteins are included within this "hourglass" region of the crystals at a notably high level, display order within the crystal hosts, and demonstrate sufficiently tight packing to enable energy transfer between a donor-acceptor pair. His-tagged fluorescent proteins display remarkable thermal stability to denaturation over extended periods of time (days) at high temperatures when within the crystals. Ultimately, this strategy may prove useful for the prolonged storage of thermally sensitive biopolymer guests within a 3D crystalline matrix.
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Affiliation(s)
- Ryan W. Curtis
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Kevin L. Scrudders
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - James R. W. Ulcickas
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Garth J. Simpson
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Shalini T. Low-Nam
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Jean Chmielewski
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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9
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Kojima M, Abe S, Ueno T. Engineering of protein crystals for use as solid biomaterials. Biomater Sci 2021; 10:354-367. [PMID: 34928275 DOI: 10.1039/d1bm01752g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein crystals have attracted a great deal of attention as solid biomaterials because they have porous structures created by regular assemblies of proteins. The lattice structures of protein crystals are controlled by designing molecular interfacial interactions via covalent bonds and non-covalent bonds. Protein crystals have been functionalized as templates to immobilize foreign molecules such as metal nanoparticles, metal complexes, and proteins. These hybrid crystals are used as functional materials for catalytic reactions and structural analysis. Furthermore, in-cell protein crystals have been studied extensively, providing progress in rapid protein crystallization and crystallography. This review highlights recent advances in crystal engineering for protein crystallization and generation of solid functional materials both in vitro and within cells.
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Affiliation(s)
- Mariko Kojima
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
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10
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Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
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Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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11
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Transfer of a Rational Crystal Contact Engineering Strategy between Diverse Alcohol Dehydrogenases. CRYSTALS 2021. [DOI: 10.3390/cryst11080975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein crystallization can serve as a purification step in biotechnological processes but is often limited by the non-crystallizability of proteins. Enabling or improving crystallization is mostly achieved by high-throughput screening of crystallization conditions and, more recently, by rational crystal contact engineering. Two selected rational crystal contact mutations, Q126K and T102E, were transferred from the alcohol dehydrogenases of Lactobacillus brevis (LbADH) to Lactobacillus kefir (LkADH). Proteins were expressed in E. coli and batch protein crystallization was performed in stirred crystallizers. Highly similar crystal packing of LkADH wild type compared to LbADH, which is necessary for the transfer of crystal contact engineering strategies, was achieved by aligning purification tag and crystallization conditions, as shown by X-ray diffraction. After comparing the crystal sizes after crystallization of LkADH mutants with the wild type, the mean protein crystal size of LkADH mutants was reduced by 40–70% in length with a concomitant increase in the total amount of crystals (higher number of nucleation events). Applying this measure to the LkADH variants studied results in an order of crystallizability T102E > Q126K > LkADH wild type, which corresponds to the results with LbADH mutants and shows, for the first time, the successful transfer of crystal contact engineering strategies.
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12
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Partridge BE, Winegar PH, Han Z, Mirkin CA. Redefining Protein Interfaces within Protein Single Crystals with DNA. J Am Chem Soc 2021; 143:8925-8934. [PMID: 34096291 PMCID: PMC8381744 DOI: 10.1021/jacs.1c04191] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Proteins are exquisite nanoscale building blocks: molecularly pure, chemically addressable, and inherently selective for their evolved function. The organization of proteins into single crystals with high positional, orientational, and translational order results in materials where the location of every atom can be known. However, controlling the organization of proteins is challenging due to the myriad interactions that define protein interfaces within native single crystals. Recently, we discovered that introducing a single DNA-DNA interaction between protein surfaces leads to changes in the packing of proteins within single crystals and the protein-protein interactions (PPIs) that arise. However, modifying specific PPIs to effect deliberate changes to protein packing is an unmet challenge. In this work, we hypothesized that disrupting and replacing a highly conserved PPI with a DNA-DNA interaction would enable protein packing to be modulated by exploiting the programmability of the introduced oligonucleotides. Using concanavalin A (ConA) as a model protein, we circumvent potentially deleterious mutagenesis and exploit the selective binding of ConA toward mannose to noncovalently attach DNA to the protein surface. We show that DNA association eliminates the major PPI responsible for crystallization of native ConA, thereby allowing subtle changes to DNA design (length, complementarity, and attachment position) to program distinct changes to ConA packing, including the realization of three novel crystal structures and the deliberate expansion of ConA packing along a single crystallographic axis. These findings significantly enhance our understanding of how DNA can supersede native PPIs to program protein packing within ordered materials.
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Affiliation(s)
- Benjamin E Partridge
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Peter H Winegar
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Zhenyu Han
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Chad A Mirkin
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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13
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Chesterman C, Arnold E. Co-crystallization with diabodies: A case study for the introduction of synthetic symmetry. Structure 2021; 29:598-605.e3. [PMID: 33636101 PMCID: PMC8178225 DOI: 10.1016/j.str.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 10/05/2020] [Accepted: 02/08/2021] [Indexed: 01/09/2023]
Abstract
This work presents a method for introducing synthetic symmetry into protein crystallization samples using an antibody fragment termed a diabody (Dab). These Dabs contain two target binding sites, and engineered disulfide bonds have been included to modulate Dab flexibility. The impacts of Dab engineering have been observed through assessment of thermal stability, small-angle X-ray scattering, and high-resolution crystal structures. Complexes between the engineered Dabs and HIV-1 reverse transcriptase (RT) bound to a high-affinity DNA aptamer were also generated to explore the capacity of engineered Dabs to enable the crystallization of bound target proteins. This strategy increased the crystallization hit frequency obtained for RT-aptamer, and the structure of a Dab-RT-aptamer complex was determined to 3.0-Å resolution. Introduction of synthetic symmetry using a Dab could be a broadly applicable strategy, especially when monoclonal antibodies for a target have previously been identified.
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Affiliation(s)
- Chelsy Chesterman
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA; GSK, Rockville, MD 20850, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
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14
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Rationally designed protein cross-linked hydrogel for bone regeneration via synergistic release of magnesium and zinc ions. Biomaterials 2021; 274:120895. [PMID: 34020269 DOI: 10.1016/j.biomaterials.2021.120895] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/29/2021] [Accepted: 05/09/2021] [Indexed: 12/20/2022]
Abstract
The development of recombinant protein cross-linked injectable hydrogels with good mechanical strength and effective drug loading capacity for bone regeneration is extremely attractive and rarely reported. Here, we report the fabrication of a smart hydrogel delivery system by incorporating a rationally designed T4 lysozyme mutant (T4M) to mediate the localized delivery and synergistic release of Mg2+ and Zn2+ for bone repair. Apart from its intrinsic antibacterial properties, T4M bears abundant free amine groups on its surface to function as effective covalent crosslinkers to strengthen the hydrogel network as well as exhibits specific binding affinity to multivalent cations such as Zn2+. Moreover, the integrin receptor-binding Arg-Gly-Asp (RGD) sequence was introduced onto the C-terminus of T4 lysozyme to improve its cellular affinity and further facilitate rapid tissue regeneration. The final composite hydrogel displays excellent injectability, improved mechanical properties, antibacterial activity, and unique bioactivities. The effective loading of Mg2+/Zn2+ in the hydrogels could mediate the sequential and sustained release of Mg2+ and Zn2+, thereby resulting in synergistic enhancement on bone regeneration through modulation of the MAPK signaling pathway. We believe that the strategy proposed in this paper opens up a new route for developing protein cross-linked smart delivery systems for tissue regeneration.
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15
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Mehr A, Henneberg F, Chari A, Görlich D, Huyton T. The copper(II)-binding tripeptide GHK, a valuable crystallization and phasing tag for macromolecular crystallography. Acta Crystallogr D Struct Biol 2020; 76:1222-1232. [PMID: 33263328 PMCID: PMC7709198 DOI: 10.1107/s2059798320013741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/13/2020] [Indexed: 12/04/2022] Open
Abstract
The growth of diffraction-quality crystals and experimental phasing remain two of the main bottlenecks in protein crystallography. Here, the high-affinity copper(II)-binding tripeptide GHK was fused to the N-terminus of a GFP variant and an MBP-FG peptide fusion. The GHK tag promoted crystallization, with various residues (His, Asp, His/Pro) from symmetry molecules completing the copper(II) square-pyramidal coordination sphere. Rapid structure determination by copper SAD phasing could be achieved, even at a very low Bijvoet ratio or after significant radiation damage. When collecting highly redundant data at a wavelength close to the copper absorption edge, residual S-atom positions could also be located in log-likelihood-gradient maps and used to improve the phases. The GHK copper SAD method provides a convenient way of both crystallizing and phasing macromolecular structures, and will complement the current trend towards native sulfur SAD and MR-SAD phasing.
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Affiliation(s)
- Alexander Mehr
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Fabian Henneberg
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ashwin Chari
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Trevor Huyton
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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16
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Byrne NJ, Lee AC, Kostas J, Reid JC, Partridge AT, So SS, Cowan JE, Abeywickrema P, Huang H, Zebisch M, Barker JJ, Soisson SM, Brooun A, Su HP. Development of a robust crystallization platform for immune receptor TREM2 using a crystallization chaperone strategy. Protein Expr Purif 2020; 179:105796. [PMID: 33221505 DOI: 10.1016/j.pep.2020.105796] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/15/2020] [Accepted: 11/13/2020] [Indexed: 11/18/2022]
Abstract
TREM2 has been identified by genomic analysis as a potential and novel target for the treatment of Alzheimer's disease. To enable structure-based screening of potential small molecule therapeutics, we sought to develop a robust crystallization platform for the TREM2 Ig-like domain. A systematic set of constructs containing the structural chaperone, maltose binding protein (MBP), fused to the Ig domain of TREM2, were evaluated in parallel expression and purification, followed by crystallization studies. Using protein crystallization and high-resolution diffraction as a readout, a MBP-TREM2 Ig fusion construct was identified that generates reproducible protein crystals diffracting at 2.0 Å, which makes it suitable for soaking of potential ligands. Importantly, analysis of crystal packing interfaces indicates that most of the surface of the TREM2 Ig domain is available for small molecule binding. A proof of concept co-crystallization study with a small library of fragments validated potential utility of this system for the discovery of new TREM2 therapeutics.
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Affiliation(s)
- Noel J Byrne
- Department of Computational and Structural Sciences, Merck & Co., Inc., West Point, PA, USA.
| | - Amy C Lee
- Department of Computational and Structural Sciences, Merck & Co., Inc., West Point, PA, USA
| | - James Kostas
- Department of Computational and Structural Sciences, Merck & Co., Inc., West Point, PA, USA
| | - John C Reid
- Department of Computational and Structural Sciences, Merck & Co., Inc., West Point, PA, USA
| | - Andrea T Partridge
- Department of Computational and Structural Sciences, Merck & Co., Inc., West Point, PA, USA
| | - Sung-Sau So
- Department of Computational and Structural Sciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Joseph E Cowan
- Department of Discovery Sample Management, Merck & Co., Inc., Rahway, NJ, USA
| | - Pravien Abeywickrema
- Department of Computational and Structural Sciences, Merck & Co., Inc., West Point, PA, USA
| | | | | | | | - Stephen M Soisson
- Department of Computational and Structural Sciences, Merck & Co., Inc., West Point, PA, USA
| | - Alexei Brooun
- Department of Computational and Structural Sciences, Merck & Co., Inc., West Point, PA, USA
| | - Hua-Poo Su
- Department of Computational and Structural Sciences, Merck & Co., Inc., West Point, PA, USA
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17
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Abstract
Five small protein domains, the CC-domains, at the N terminus of the RECK protein, play essential roles in signaling by WNT7A and WNT7B in the context of central nervous system angiogenesis and blood-brain barrier formation and maintenance. We have determined the structure of CC domain 4 (CC4) at 1.65-Å resolution and find that it folds into a compact four-helix bundle with three disulfide bonds. The CC4 structure, together with homology modeling of CC1, reveals the surface locations of critical residues that were shown in previous mutagenesis studies to mediate GPR124 binding and WNT7A/WNT7B recognition and signaling. Surprisingly, sequence and structural homology searches reveal no other cell-surface or secreted domains in vertebrates that resemble the CC domain, a pattern that is in striking contrast to other ancient and similarly sized domains, such as Epidermal Growth Factor, Fibronectin Type 3, Immunoglobulin, and Thrombospondin type 1 domains, which are collectively present in hundreds of proteins.
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18
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Structural underpinnings of Ric8A function as a G-protein α-subunit chaperone and guanine-nucleotide exchange factor. Nat Commun 2019; 10:3084. [PMID: 31300652 PMCID: PMC6625990 DOI: 10.1038/s41467-019-11088-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 06/21/2019] [Indexed: 02/03/2023] Open
Abstract
Resistance to inhibitors of cholinesterase 8A (Ric8A) is an essential regulator of G protein α-subunits (Gα), acting as a guanine nucleotide exchange factor and a chaperone. We report two crystal structures of Ric8A, one in the apo form and the other in complex with a tagged C-terminal fragment of Gα. These structures reveal two principal domains of Ric8A: an armadillo-fold core and a flexible C-terminal tail. Additionally, they show that the Gα C-terminus binds to a highly-conserved patch on the concave surface of the Ric8A armadillo-domain, with selectivity determinants residing in the Gα sequence. Biochemical analysis shows that the Ric8A C-terminal tail is critical for its stability and function. A model of the Ric8A/Gα complex derived from crosslinking mass spectrometry and molecular dynamics simulations suggests that the Ric8A C-terminal tail helps organize the GTP-binding site of Gα. This study lays the groundwork for understanding Ric8A function at the molecular level. Ric8A regulates G protein α-subunits (Gα) by acting as a guanine nucleotide exchange factor (GEF) and a Gα chaperone. Here, the authors solve the crystal structures of free and Gα fragment bound Ric8A, and provide insights into the structural basis for Ric8A’s GEF and chaperone functions.
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19
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Cui P, Lin S, Han W, Jiang P, Zhu B, Sun N. The formation mechanism of a sea cucumber ovum derived heptapeptide–calcium nanocomposite and its digestion/absorption behavior. Food Funct 2019; 10:8240-8249. [DOI: 10.1039/c9fo01335k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Calcium coordination induced the self-assembly of the sea cucumber ovum derived heptapeptide (NDEELNK), resulting in the formation of the nanocomposite with potential function to transport calcium through the gastrointestinal system.
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Affiliation(s)
- Pengbo Cui
- National Engineering Research Center of Seafood
- School of Food Science and Technology
- Dalian Polytechnic University
- Dalian 116034
- P. R. China
| | - Songyi Lin
- National Engineering Research Center of Seafood
- School of Food Science and Technology
- Dalian Polytechnic University
- Dalian 116034
- P. R. China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
- School of Life Science
- Jilin University
- Changchun 130012
- P. R. China
| | - Pengfei Jiang
- National Engineering Research Center of Seafood
- School of Food Science and Technology
- Dalian Polytechnic University
- Dalian 116034
- P. R. China
| | - Beiwei Zhu
- National Engineering Research Center of Seafood
- School of Food Science and Technology
- Dalian Polytechnic University
- Dalian 116034
- P. R. China
| | - Na Sun
- National Engineering Research Center of Seafood
- School of Food Science and Technology
- Dalian Polytechnic University
- Dalian 116034
- P. R. China
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20
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Hartje LF, Snow CD. Protein crystal based materials for nanoscale applications in medicine and biotechnology. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2018; 11:e1547. [DOI: 10.1002/wnan.1547] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/28/2018] [Accepted: 10/12/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Luke F. Hartje
- Department of Biochemistry and Molecular Biology Colorado State University Fort Collins Colorado
| | - Christopher D. Snow
- Department of Chemical and Biological Engineering Colorado State University Fort Collins Colorado
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21
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Kubitza C, Ginsel C, Bittner F, Havemeyer A, Clement B, Scheidig AJ. T4 lysozyme-facilitated crystallization of the human molybdenum cofactor-dependent enzyme mARC. Acta Crystallogr F Struct Biol Commun 2018; 74:337-344. [PMID: 29870017 PMCID: PMC5987741 DOI: 10.1107/s2053230x18006921] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/04/2018] [Indexed: 12/12/2022] Open
Abstract
The human mitochondrial amidoxime reducing component (hmARC) is a molybdenum cofactor-dependent enzyme that is involved in the reduction of a diverse range of N-hydroxylated compounds of either physiological or xenobiotic origin. In this study, the use of a fusion-protein approach with T4 lysozyme (T4L) to determine the structure of this hitherto noncrystallizable enzyme by X-ray crystallography is described. A set of four different hmARC-T4L fusion proteins were designed. Two of them contained either an N-terminal or a C-terminal T4L moiety fused to hmARC, while the other two contained T4L as an internal fusion partner tethered to the hmARC enzyme between two predicted secondary-structure elements. One of these internal fusion constructs could be expressed and crystallized successfully. The hmARC-T4L crystals diffracted to 1.7 Å resolution using synchrotron radiation and belonged to space group P212121 with one molecule in the asymmetric unit. Initial attempts to solve the structure by molecular replacement using T4L did not result in electron-density distributions that were sufficient for model building and interpretation of the hmARC moiety. However, this study emphasizes the utility of the T4L fusion-protein approach, which can be used for the crystallization and structure determination of membrane-bound proteins as well as soluble proteins.
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Affiliation(s)
- Christian Kubitza
- Structural Biology, Zoological Institute, Kiel University, Am Botanischen Garten 1–9, 24118 Kiel, Germany
| | - Carsten Ginsel
- Pharmaceutical Institute, Kiel University, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Florian Bittner
- Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Erwin-Baur-Strasse 27, 06484 Quedlinburg, Germany
| | - Antje Havemeyer
- Pharmaceutical Institute, Kiel University, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Bernd Clement
- Pharmaceutical Institute, Kiel University, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Axel J. Scheidig
- Structural Biology, Zoological Institute, Kiel University, Am Botanischen Garten 1–9, 24118 Kiel, Germany
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22
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Bozkurt E, Perez MAS, Hovius R, Browning NJ, Rothlisberger U. Genetic Algorithm Based Design and Experimental Characterization of a Highly Thermostable Metalloprotein. J Am Chem Soc 2018; 140:4517-4521. [DOI: 10.1021/jacs.7b10660] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Esra Bozkurt
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Marta A. S. Perez
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Ruud Hovius
- Laboratory of Protein Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Nicholas J. Browning
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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23
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Functionalization of protein crystals with metal ions, complexes and nanoparticles. Curr Opin Chem Biol 2017; 43:68-76. [PMID: 29245143 DOI: 10.1016/j.cbpa.2017.11.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/09/2017] [Accepted: 11/26/2017] [Indexed: 01/08/2023]
Abstract
Self-assembled proteins have specific functions in biology. With inspiration provided by natural protein systems, several artificial protein assemblies have been constructed via site-specific mutations or metal coordination, which have important applications in catalysis, material and bio-supramolecular chemistry. Similar to natural protein assemblies, protein crystals have been recognized as protein assemblies formed of densely-packed monomeric proteins. Protein crystals can be functionalized with metal ions, metal complexes or nanoparticles via soaking, co-crystallization, creating new metal binding sites by site-specific mutations. The field of protein crystal engineering with metal coordination is relatively new and has gained considerable attention for developing solid biomaterials as well as structural investigations of enzymatic reactions, growth of nanoparticles and catalysis. This review highlights recent and significant research on functionalization of protein crystals with metal coordination and future prospects.
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24
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Park WM, Bedewy M, Berggren KK, Keating AE. Modular assembly of a protein nanotriangle using orthogonally interacting coiled coils. Sci Rep 2017; 7:10577. [PMID: 28874805 PMCID: PMC5585338 DOI: 10.1038/s41598-017-10918-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/16/2017] [Indexed: 12/30/2022] Open
Abstract
Synthetic protein assemblies that adopt programmed shapes would support many applications in nanotechnology. We used a rational design approach that exploits the modularity of orthogonally interacting coiled coils to create a self-assembled protein nanotriangle. Coiled coils have frequently been used to construct nanoassemblies and materials, but rarely with successful prior specification of the resulting structure. We designed a heterotrimer from three pairs of heterodimeric coiled coils that mediate specific interactions while avoiding undesired crosstalk. Non-associating pairs of coiled-coil units were strategically fused to generate three chains that were predicted to preferentially form the heterotrimer, and a rational annealing process led to the desired oligomer. Extensive biophysical characterization and modeling support the formation of a molecular triangle, which is a shape distinct from naturally occurring supramolecular nanostructures. Our approach can be extended to design more complex nanostructures using additional coiled-coil modules, other protein parts, or templated surfaces.
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Affiliation(s)
- Won Min Park
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
| | - Mostafa Bedewy
- Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
- Department of Industrial Engineering, University of Pittsburgh, 3700 O'Hara Street, Pittsburgh, Pennsylvania, 15261, USA
| | - Karl K Berggren
- Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA.
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25
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Hansen WA, Khare SD. Benchmarking a computational design method for the incorporation of metal ion-binding sites at symmetric protein interfaces. Protein Sci 2017; 26:1584-1594. [PMID: 28513090 PMCID: PMC5521545 DOI: 10.1002/pro.3194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 04/07/2017] [Accepted: 05/06/2017] [Indexed: 11/12/2022]
Abstract
The design of novel metal-ion binding sites along symmetric axes in protein oligomers could provide new avenues for metalloenzyme design, construction of protein-based nanomaterials and novel ion transport systems. Here, we describe a computational design method, symmetric protein recursive ion-cofactor sampling (SyPRIS), for locating constellations of backbone positions within oligomeric protein structures that are capable of supporting desired symmetrically coordinated metal ion(s) chelated by sidechains (chelant model). Using SyPRIS on a curated benchmark set of protein structures with symmetric metal binding sites, we found high recovery of native metal coordinating rotamers: in 65 of the 67 (97.0%) cases, native rotamers featured in the best scoring model while in the remaining cases native rotamers were found within the top three scoring models. In a second test, chelant models were crossmatched against protein structures with identical cyclic symmetry. In addition to recovering all native placements, 10.4% (8939/86013) of the non-native placements, had acceptable geometric compatibility scores. Discrimination between native and non-native metal site placements was further enhanced upon constrained energy minimization using the Rosetta energy function. Upon sequence design of the surrounding first-shell residues, we found further stabilization of native placements and a small but significant (1.7%) number of non-native placement-based sites with favorable Rosetta energies, indicating their designability in existing protein interfaces. The generality of the SyPRIS approach allows design of novel symmetric metal sites including with non-natural amino acid sidechains, and should enable the predictive incorporation of a variety of metal-containing cofactors at symmetric protein interfaces.
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Affiliation(s)
- William A. Hansen
- Institute for Quantitative Biomedicine at Rutgers610 Taylor RoadPiscatawayNew Jersey08854
- Center for integrative Proteomics Research610 Taylor RoadPiscatawayNew Jersey08854
| | - Sagar D. Khare
- Institute for Quantitative Biomedicine at Rutgers610 Taylor RoadPiscatawayNew Jersey08854
- Center for integrative Proteomics Research610 Taylor RoadPiscatawayNew Jersey08854
- Chemistry and Chemical Biology at Rutgers610 Taylor RoadPiscatawayNew Jersey08854
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26
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Yekwa E, Khourieh J, Canard B, Papageorgiou N, Ferron F. Activity inhibition and crystal polymorphism induced by active-site metal swapping. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:641-649. [PMID: 28777079 DOI: 10.1107/s205979831700866x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 06/10/2017] [Indexed: 11/11/2022]
Abstract
The Arenaviridae family is one of the two RNA viral families that encode a 3'-5' exonuclease in their genome. An exonuclease domain is found in the Arenaviridae nucleoprotein and targets dsRNA specifically. This domain is directly involved in suppression of innate immunity in the host cell. Like most phosphate-processing enzymes, it requires a divalent metal ion such as Mg2+ (or Mn2+) as a cofactor to catalyse nucleotide-cleavage and nucleotide-transfer reactions. On the other hand, calcium (Ca2+) inhibits this enzymatic activity, in spite of the fact that Mg2+ and Ca2+ present comparable binding affinities and biological availabilities. Here, the molecular and structural effects of the replacement of magnesium by calcium and its inhibition mechanism for phosphodiester cleavage, an essential reaction in the viral process of innate immunity suppression, are studied. Biochemical data and high-resolution structures of the Mopeia virus exonuclease domain complexed with each ion are reported for the first time. The consequences of the ion swap for the stability of the protein, the catalytic site and the functional role of a specific metal ion in enabling the catalytic cleavage of a dsRNA substrate are outlined.
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Affiliation(s)
- Elsie Yekwa
- CNRS, AFMB UMR 7257, 13288 Marseille, France
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27
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Giegé R. What macromolecular crystallogenesis tells us - what is needed in the future. IUCRJ 2017; 4:340-349. [PMID: 28875021 PMCID: PMC5571797 DOI: 10.1107/s2052252517006595] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 05/02/2017] [Indexed: 05/05/2023]
Abstract
Crystallogenesis is a longstanding topic that has transformed into a discipline that is mainly focused on the preparation of crystals for practising crystallo-graphers. Although the idiosyncratic features of proteins have to be taken into account, the crystallization of proteins is governed by the same physics as the crystallization of inorganic materials. At present, a diversified panel of crystallization methods adapted to proteins has been validated, and although only a few methods are in current practice, the success rate of crystallization has increased constantly, leading to the determination of ∼105 X-ray structures. These structures reveal a huge repertoire of protein folds, but they only cover a restricted part of macromolecular diversity across the tree of life. In the future, crystals representative of missing structures or that will better document the structural dynamics and functional steps underlying biological processes need to be grown. For the pertinent choice of biologically relevant targets, computer-guided analysis of structural databases is needed. From another perspective, crystallization is a self-assembly process that can occur in the bulk of crowded fluids, with crystals being supramolecular assemblies. Life also uses self-assembly and supramolecular processes leading to transient, or less often stable, complexes. An integrated view of supramolecularity implies that proteins crystallizing either in vitro or in vivo or participating in cellular processes share common attributes, notably determinants and antideterminants that favour or disfavour their correct or incorrect associations. As a result, under in vivo conditions proteins show a balance between features that favour or disfavour association. If this balance is broken, disorders/diseases occur. Understanding crystallization under in vivo conditions is a challenge for the future. In this quest, the analysis of packing contacts and contacts within oligomers will be crucial in order to decipher the rules governing protein self-assembly and will guide the engineering of novel biomaterials. In a wider perspective, understanding such contacts will open the route towards supramolecular biology and generalized crystallogenesis.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l’ARN, UPR 9002, Université de Strasbourg and CNRS, F-67084 Strasbourg, France
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28
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Hegde RP, Pavithra GC, Dey D, Almo SC, Ramakumar S, Ramagopal UA. Can the propensity of protein crystallization be increased by using systematic screening with metals? Protein Sci 2017. [PMID: 28643473 DOI: 10.1002/pro.3214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein crystallization is one of the major bottlenecks in protein structure elucidation with new strategies being constantly developed to improve the chances of crystallization. Generally, well-ordered epitopes possessing complementary surface and capable of producing stable inter-protein interactions generate a regular three-dimensional arrangement of protein molecules which eventually results in a crystal lattice. Metals, when used for crystallization, with their various coordination numbers and geometries, can generate such epitopes mediating protein oligomerization and/or establish crystal contacts. Some examples of metal-mediated oligomerization and crystallization together with our experience on metal-mediated crystallization of a putative rRNA methyltransferase from Sinorhizobium meliloti are presented. Analysis of crystal structures from protein data bank (PDB) using a non-redundant data set with a 90% identity cutoff, reveals that around 67% of proteins contain at least one metal ion, with ∼14% containing combination of metal ions. Interestingly, metal containing conditions in most commercially available and popular crystallization kits generally contain only a single metal ion, with combinations of metals only in a very few conditions. Based on the results presented in this review, it appears that the crystallization screens need expansion with systematic screening of metal ions that could be crucial for stabilizing the protein structure or for establishing crystal contact and thereby aiding protein crystallization.
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Affiliation(s)
- Raghurama P Hegde
- Division of Biological Sciences, Poornaprajna Institute of Scientific Research, Bangalore, 560080, India
| | - Gowribidanur C Pavithra
- Division of Biological Sciences, Poornaprajna Institute of Scientific Research, Bangalore, 560080, India
- Manipal University, Manipal, 576104, India
| | - Debayan Dey
- Division of Biological Sciences, Poornaprajna Institute of Scientific Research, Bangalore, 560080, India
- Department of Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, 10461
- Department of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, New York, 10461
| | - S Ramakumar
- Department of Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Udupi A Ramagopal
- Division of Biological Sciences, Poornaprajna Institute of Scientific Research, Bangalore, 560080, India
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, 10461
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29
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Jin T, Chuenchor W, Jiang J, Cheng J, Li Y, Fang K, Huang M, Smith P, Xiao TS. Design of an expression system to enhance MBP-mediated crystallization. Sci Rep 2017; 7:40991. [PMID: 28112203 PMCID: PMC5256280 DOI: 10.1038/srep40991] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/13/2016] [Indexed: 11/09/2022] Open
Abstract
Crystallization chaperones have been used to facilitate the crystallization of challenging proteins. Even though the maltose-binding protein (MBP) is one of the most commonly used crystallization chaperones, the design of optimal expression constructs for crystallization of MBP fusion proteins remains a challenge. To increase the success rate of MBP-facilitated crystallization, a series of expression vectors have been designed with either a short flexible linker or a set of rigid helical linkers. Seven death domain superfamily members were tested for crystallization with this set of vectors, six of which had never been crystallized before. All of the seven targets were crystallized, and their structures were determined using at least one of the vectors. Our successful crystallization of all of the targets demonstrates the validity of our approach and expands the arsenal of the crystallization chaperone toolkit, which may be applicable to crystallization of other difficult protein targets, as well as to other crystallization chaperones.
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Affiliation(s)
- Tengchuan Jin
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Diseases, CAS Center for Excellence in Molecular Cell Sciences, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei 230027 China.,Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Watchalee Chuenchor
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Jiansheng Jiang
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Jinbo Cheng
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Diseases, CAS Center for Excellence in Molecular Cell Sciences, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei 230027 China
| | - Yajuan Li
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Diseases, CAS Center for Excellence in Molecular Cell Sciences, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei 230027 China
| | - Kang Fang
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Diseases, CAS Center for Excellence in Molecular Cell Sciences, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei 230027 China
| | - Mo Huang
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Patrick Smith
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Tsan Sam Xiao
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106 USA
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The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability. Methods Mol Biol 2017; 1607:77-115. [PMID: 28573570 DOI: 10.1007/978-1-4939-7000-1_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Crystallization of macromolecules has long been perceived as a stochastic process, which cannot be predicted or controlled. This is consistent with another popular notion that the interactions of molecules within the crystal, i.e., crystal contacts, are essentially random and devoid of specific physicochemical features. In contrast, functionally relevant surfaces, such as oligomerization interfaces and specific protein-protein interaction sites, are under evolutionary pressures so their amino acid composition, structure, and topology are distinct. However, current theoretical and experimental studies are significantly changing our understanding of the nature of crystallization. The increasingly popular "sticky patch" model, derived from soft matter physics, describes crystallization as a process driven by interactions between select, specific surface patches, with properties thermodynamically favorable for cohesive interactions. Independent support for this model comes from various sources including structural studies and bioinformatics. Proteins that are recalcitrant to crystallization can be modified for enhanced crystallizability through chemical or mutational modification of their surface to effectively engineer "sticky patches" which would drive crystallization. Here, we discuss the current state of knowledge of the relationship between the microscopic properties of the target macromolecule and its crystallizability, focusing on the "sticky patch" model. We discuss state-of-the-art in silico methods that evaluate the propensity of a given target protein to form crystals based on these relationships, with the objective to design variants with modified molecular surface properties and enhanced crystallization propensity. We illustrate this discussion with specific cases where these approaches allowed to generate crystals suitable for structural analysis.
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31
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Yeates TO, Liu Y, Laniado J. The design of symmetric protein nanomaterials comes of age in theory and practice. Curr Opin Struct Biol 2016; 39:134-143. [DOI: 10.1016/j.sbi.2016.07.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 07/02/2016] [Accepted: 07/03/2016] [Indexed: 12/25/2022]
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Zhang Y, Ren H, Wang Y, Chen K, Fang B, Wang S. Bioinspired Immobilization of Glycerol Dehydrogenase by Metal Ion-Chelated Polyethyleneimines as Artificial Polypeptides. Sci Rep 2016; 6:24163. [PMID: 27053034 PMCID: PMC4823755 DOI: 10.1038/srep24163] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 03/16/2016] [Indexed: 01/09/2023] Open
Abstract
In this study, a novel, simple and generally applicable strategy for multimeric oxidoreductase immobilization with multi-levels interactions was developed and involved activity and stability enhancements. Linear polyethyleneimines (PEIs) are flexible cationic polymers with molecular weights that span a wide range and are suitable biomimic polypeptides for biocompatible frameworks for enzyme immobilization. Metal ion-chelated linear PEIs were applied as a heterofunctional framework for glycerol dehydrogenase (GDH) immobilization by hydrogen bonds, electrostatic forces and coordination bonds interactions. Nanoparticles with diameters from 250-650 nm were prepared that exhibited a 1.4-fold enhancement catalytic efficiency. Importantly, the half-life of the immobilized GDH was enhanced by 5.6-folds in aqueous phase at 85 °C. A mechanistic illustration of the formation of multi-level interactions in the PEI-metal-GDH complex was proposed based on morphological and functional studies of the immobilized enzyme. This generally applicable strategy offers a potential technique for multimeric enzyme immobilization with the advantages of low cost, easy operation, high activity reservation and high stability.
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Affiliation(s)
- Yonghui Zhang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Hong Ren
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yali Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Kainan Chen
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Baishan Fang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, Fujian, 361005, P. R. China
| | - Shizhen Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, Fujian, 361005, P. R. China
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Bokhove M, Sadat Al Hosseini H, Saito T, Dioguardi E, Gegenschatz-Schmid K, Nishimura K, Raj I, de Sanctis D, Han L, Jovine L. Easy mammalian expression and crystallography of maltose-binding protein-fused human proteins. J Struct Biol 2016; 194:1-7. [PMID: 26850170 PMCID: PMC4771870 DOI: 10.1016/j.jsb.2016.01.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/28/2016] [Accepted: 01/31/2016] [Indexed: 01/19/2023]
Abstract
We present a strategy to obtain milligrams of highly post-translationally modified eukaryotic proteins, transiently expressed in mammalian cells as rigid or cleavable fusions with a mammalianized version of bacterial maltose-binding protein (mMBP). This variant was engineered to combine mutations that enhance MBP solubility and affinity purification, as well as provide crystal-packing interactions for increased crystallizability. Using this cell type-independent approach, we could increase the expression of secreted and intracellular human proteins up to 200-fold. By molecular replacement with MBP, we readily determined five novel high-resolution structures of rigid fusions of targets that otherwise defied crystallization.
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Affiliation(s)
- Marcel Bokhove
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Hamed Sadat Al Hosseini
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Takako Saito
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Elisa Dioguardi
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Katharina Gegenschatz-Schmid
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Kaoru Nishimura
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Isha Raj
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | | | - Ling Han
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Luca Jovine
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden.
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A structured interdomain linker directs self-polymerization of human uromodulin. Proc Natl Acad Sci U S A 2016; 113:1552-7. [PMID: 26811476 DOI: 10.1073/pnas.1519803113] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Uromodulin (UMOD)/Tamm-Horsfall protein, the most abundant human urinary protein, plays a key role in chronic kidney diseases and is a promising therapeutic target for hypertension. Via its bipartite zona pellucida module (ZP-N/ZP-C), UMOD forms extracellular filaments that regulate kidney electrolyte balance and innate immunity, as well as protect against renal stones. Moreover, salt-dependent aggregation of UMOD filaments in the urine generates a soluble molecular net that captures uropathogenic bacteria and facilitates their clearance. Despite the functional importance of its homopolymers, no structural information is available on UMOD and how it self-assembles into filaments. Here, we report the crystal structures of polymerization regions of human UMOD and mouse ZP2, an essential sperm receptor protein that is structurally related to UMOD but forms heteropolymers. The structure of UMOD reveals that an extensive hydrophobic interface mediates ZP-N domain homodimerization. This arrangement is required for filament formation and is directed by an ordered ZP-N/ZP-C linker that is not observed in ZP2 but is conserved in the sequence of deafness/Crohn's disease-associated homopolymeric glycoproteins α-tectorin (TECTA) and glycoprotein 2 (GP2). Our data provide an example of how interdomain linker plasticity can modulate the function of structurally similar multidomain proteins. Moreover, the architecture of UMOD rationalizes numerous pathogenic mutations in both UMOD and TECTA genes.
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35
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Munch HK, Nygaard J, Christensen NJ, Engelbrekt C, Østergaard M, Porsgaard T, Hoeg-Jensen T, Zhang J, Arleth L, Thulstrup PW, Jensen KJ. Construction of Insulin 18-mer Nanoassemblies Driven by Coordination to Iron(II) and Zinc(II) Ions at Distinct Sites. Angew Chem Int Ed Engl 2016; 55:2378-81. [DOI: 10.1002/anie.201509088] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/01/2015] [Indexed: 11/06/2022]
Affiliation(s)
| | - Jesper Nygaard
- MAX-lab; Lund University; Sweden
- Niels Bohr Institute; University of Copenhagen; Denmark
| | | | | | | | | | | | - Jingdong Zhang
- Department of Chemistry; Technical University of Denmark; Kgs. Lyngby Denmark
| | - Lise Arleth
- Niels Bohr Institute; University of Copenhagen; Denmark
| | | | - Knud J. Jensen
- Department of Chemistry; University of Copenhagen; Denmark
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36
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Munch HK, Nygaard J, Christensen NJ, Engelbrekt C, Østergaard M, Porsgaard T, Hoeg-Jensen T, Zhang J, Arleth L, Thulstrup PW, Jensen KJ. Construction of Insulin 18-mer Nanoassemblies Driven by Coordination to Iron(II) and Zinc(II) Ions at Distinct Sites. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Jesper Nygaard
- MAX-lab; Lund University; Sweden
- Niels Bohr Institute; University of Copenhagen; Denmark
| | | | | | | | | | | | - Jingdong Zhang
- Department of Chemistry; Technical University of Denmark; Kgs. Lyngby Denmark
| | - Lise Arleth
- Niels Bohr Institute; University of Copenhagen; Denmark
| | | | - Knud J. Jensen
- Department of Chemistry; University of Copenhagen; Denmark
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37
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Hou C, Tsodikov OV. Structural Basis for Dimerization and DNA Binding of Transcription Factor FLI1. Biochemistry 2015; 54:7365-74. [PMID: 26618620 DOI: 10.1021/acs.biochem.5b01121] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
FLI1 (Friend leukemia integration 1) is a metazoan transcription factor that is upregulated in a number of cancers. In addition, rearrangements of the fli1 gene cause sarcomas, leukemias, and lymphomas. These rearrangements encode oncogenic transcription factors, in which the DNA binding domain (DBD or ETS domain) of FLI1 on the C-terminal side is fused to a part of an another protein on the N-terminal side. Such abnormal cancer cell-specific fusions retain the DNA binding properties of FLI1 and acquire non-native protein-protein or protein-nucleic acid interactions of the substituted region. As a result, these fusions trigger oncogenic transcriptional reprogramming of the host cell. Interactions of FLI1 fusions with other proteins and with itself play a critical role in the oncogenic regulatory functions, and they are currently under intense scrutiny, mechanistically and as potential novel anticancer drug targets. We report elusive crystal structures of the FLI1 DBD, alone and in complex with cognate DNA containing a GGAA recognition sequence. Both structures reveal a previously unrecognized dimer of this domain, consistent with its dimerization in solution. The homodimerization interface is helix-swapped and dominated by hydrophobic interactions, including those between two interlocking Phe362 residues. A mutation of Phe362 to an alanine disrupted the propensity of this domain to dimerize without perturbing its structure or the DNA binding function, consistent with the structural observations. We propose that FLI1 DBD dimerization plays a role in transcriptional activation and repression by FLI1 and its fusions at promoters containing multiple FLI1 binding sites.
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Affiliation(s)
- Caixia Hou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
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38
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Miyamoto T, Kuribayashi M, Nagao S, Shomura Y, Higuchi Y, Hirota S. Domain-swapped cytochrome cb562 dimer and its nanocage encapsulating a Zn-SO 4 cluster in the internal cavity. Chem Sci 2015; 6:7336-7342. [PMID: 28791095 PMCID: PMC5519777 DOI: 10.1039/c5sc02428e] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/22/2015] [Indexed: 01/01/2023] Open
Abstract
Three domain-swapped cytochrome cb562 dimers formed a unique cage structure with a Zn–SO4 cluster inside the cavity.
Protein nanostructures have been gaining in interest, along with developments in new methods for construction of novel nanostructures. We have previously shown that c-type cytochromes and myoglobin form oligomers by domain swapping. Herein, we show that a four-helix bundle protein cyt cb562, with the cyt b562 heme attached to the protein moiety by two Cys residues insertion, forms a domain-swapped dimer. Dimeric cyt cb562 did not dissociate to monomers at 4 °C, whereas dimeric cyt b562 dissociated under the same conditions, showing that heme attachment to the protein moiety stabilizes the domain-swapped structure. According to X-ray crystallographic analysis of dimeric cyt cb562, the two helices in the N-terminal region of one protomer interacted with the other two helices in the C-terminal region of the other protomer, where Lys51–Asp54 served as a hinge loop. The heme coordination structure of the dimer was similar to that of the monomer. In the crystal, three domain-swapped cyt cb562 dimers formed a unique cage structure with a Zn–SO4 cluster inside the cavity. The Zn–SO4 cluster consisted of fifteen Zn2+ and seven SO42– ions, whereas six additional Zn2+ ions were detected inside the cavity. The cage structure was stabilized by coordination of the amino acid side chains of the dimers to the Zn2+ ions and connection of two four-helix bundle units through the conformation-adjustable hinge loop. These results show that domain swapping can be applied in the construction of unique protein nanostructures.
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Affiliation(s)
- Takaaki Miyamoto
- Graduate School of Materials Science , Nara Institute of Science and Technology , 8916-5 Takayama, Ikoma , Nara 630-0192 , Japan .
| | - Mai Kuribayashi
- Graduate School of Materials Science , Nara Institute of Science and Technology , 8916-5 Takayama, Ikoma , Nara 630-0192 , Japan .
| | - Satoshi Nagao
- Graduate School of Materials Science , Nara Institute of Science and Technology , 8916-5 Takayama, Ikoma , Nara 630-0192 , Japan .
| | - Yasuhito Shomura
- Graduate School of Science and Engineering , Ibaraki University , 4-12-1, Nakanarusawa , Hitachi , Ibaraki 316-8511 , Japan
| | - Yoshiki Higuchi
- Department of Life Science , Graduate School of Life Science , University of Hyogo , 3-2-1 Koto, Kamigori-cho, Ako-gun , Hyogo 678-1297 , Japan.,RIKEN SPring-8 Center , 1-1-1 Koto, Sayo-cho, Sayo-gun , Hyogo 679-5148 , Japan
| | - Shun Hirota
- Graduate School of Materials Science , Nara Institute of Science and Technology , 8916-5 Takayama, Ikoma , Nara 630-0192 , Japan .
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Leibly DJ, Arbing MA, Pashkov I, DeVore N, Waldo GS, Terwilliger TC, Yeates TO. A Suite of Engineered GFP Molecules for Oligomeric Scaffolding. Structure 2015; 23:1754-1768. [PMID: 26278175 DOI: 10.1016/j.str.2015.07.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 06/08/2015] [Accepted: 07/07/2015] [Indexed: 10/23/2022]
Abstract
Applications ranging from synthetic biology to protein crystallization could be advanced by facile systems for connecting multiple proteins together in predefined spatial relationships. One approach to this goal is to engineer many distinct assembly forms of a single carrier protein or scaffold, to which other proteins of interest can then be readily attached. In this work we chose GFP as a scaffold and engineered many alternative oligomeric forms, driven by either specific disulfide bond formation or metal ion addition. We generated a wide range of spatial arrangements of GFP subunits from 11 different oligomeric variants, and determined their X-ray structures in a total of 33 distinct crystal forms. Some of the oligomeric GFP variants show geometric polymorphism depending on conditions, while others show considerable geometric rigidity. Potential future applications of this system are discussed.
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Affiliation(s)
- David J Leibly
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Mark A Arbing
- UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Inna Pashkov
- UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Natasha DeVore
- Bioscience Division, Los Alamos National Laboratory, MS M888, Los Alamos, NM 87545, USA
| | - Geoffrey S Waldo
- Bioscience Division, Los Alamos National Laboratory, MS M888, Los Alamos, NM 87545, USA
| | - Thomas C Terwilliger
- Bioscience Division, Los Alamos National Laboratory, MS M888, Los Alamos, NM 87545, USA
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA.
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40
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Little DJ, Milek S, Bamford NC, Ganguly T, DiFrancesco BR, Nitz M, Deora R, Howell PL. The protein BpsB is a poly-β-1,6-N-acetyl-D-glucosamine deacetylase required for biofilm formation in Bordetella bronchiseptica. J Biol Chem 2015. [PMID: 26203190 DOI: 10.1074/jbc.m115.672469] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Bordetella pertussis and Bordetella bronchiseptica are the causative agents of whooping cough in humans and a variety of respiratory diseases in animals, respectively. Bordetella species produce an exopolysaccharide, known as the Bordetella polysaccharide (Bps), which is encoded by the bpsABCD operon. Bps is required for Bordetella biofilm formation, colonization of the respiratory tract, and confers protection from complement-mediated killing. In this report, we have investigated the role of BpsB in the biosynthesis of Bps and biofilm formation by B. bronchiseptica. BpsB is a two-domain protein that localizes to the periplasm and outer membrane. BpsB displays metal- and length-dependent deacetylation on poly-β-1,6-N-acetyl-d-glucosamine (PNAG) oligomers, supporting previous immunogenic data that suggests Bps is a PNAG polymer. BpsB can use a variety of divalent metal cations for deacetylase activity and showed highest activity in the presence of Ni(2+) and Co(2+). The structure of the BpsB deacetylase domain is similar to the PNAG deacetylases PgaB and IcaB and contains the same circularly permuted family four carbohydrate esterase motifs. Unlike PgaB from Escherichia coli, BpsB is not required for polymer export and has unique structural differences that allow the N-terminal deacetylase domain to be active when purified in isolation from the C-terminal domain. Our enzymatic characterizations highlight the importance of conserved active site residues in PNAG deacetylation and demonstrate that the C-terminal domain is required for maximal deacetylation of longer PNAG oligomers. Furthermore, we show that BpsB is critical for the formation and complex architecture of B. bronchiseptica biofilms.
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Affiliation(s)
- Dustin J Little
- From the Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Sonja Milek
- the Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, and
| | - Natalie C Bamford
- From the Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Tridib Ganguly
- the Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, and
| | | | - Mark Nitz
- the Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Rajendar Deora
- the Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, and
| | - P Lynne Howell
- From the Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada,
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Mooers BHM. Fusion RNAs in crystallographic studies of double-stranded RNA from trypanosome RNA editing. Methods Mol Biol 2015; 1240:191-216. [PMID: 25352146 DOI: 10.1007/978-1-4939-1896-6_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Head-to-head fusions of two identical double-stranded fragments of RNA can be designed to self-assemble from a single RNA species and form a double-stranded helix with a twofold rotation axis relating the two strands. These symmetrical RNA molecules are more likely to crystallize without end-on-end statistical packing disorder because the two halves of the molecule are identical. This approach can be used to study many fragments of double-stranded RNA or many isolated helical domains from large single-stranded RNAs that may not yet be amenable to high-resolution studies by crystallography or NMR. We used fusion RNAs to study one (the U-helix) of three functional domains formed when guide RNA binds to its cognate pre-edited mRNA from the trypanosome RNA editing system. The U-helix forms when the 3' oligo(U) tail of the guide RNA (gRNA) binds to the purine-rich, pre-edited mRNA upstream from the current RNA editing site. Fusion RNAs 16-and 32-base pairs in length formed crystals that gave diffraction to 1.37 and 1.05 Å respectively. We provide the composition of a fusion RNA crystallization screen and describe the X-ray data collection, structure determination, and refinement of the crystal structures of fusion RNAs.
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Affiliation(s)
- Blaine H M Mooers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, 975 NE 10th St., Stanton L. Young Biomedical Research Center Rm. 466, Oklahoma City, OK, 73104-5419, USA,
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Abe-Ohya R, Ishikawa T, Shiozawa H, Suda K, Nara F. Identification of metals from osteoblastic ST-2 cell supernatants as novel OGR1 agonists. J Recept Signal Transduct Res 2015; 35:485-92. [DOI: 10.3109/10799893.2015.1015736] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Johnson JL, Entzminger KC, Hyun J, Kalyoncu S, Heaner DP, Morales IA, Sheppard A, Gumbart JC, Maynard JA, Lieberman RL. Structural and biophysical characterization of an epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:896-906. [PMID: 25849400 PMCID: PMC4388267 DOI: 10.1107/s1399004715001856] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 01/28/2015] [Indexed: 12/22/2022]
Abstract
Crystallization chaperones are attracting increasing interest as a route to crystal growth and structure elucidation of difficult targets such as membrane proteins. While strategies to date have typically employed protein-specific chaperones, a peptide-specific chaperone to crystallize multiple cognate peptide epitope-containing client proteins is envisioned. This would eliminate the target-specific chaperone-production step and streamline the co-crystallization process. Previously, protein engineering and directed evolution were used to generate a single-chain variable (scFv) antibody fragment with affinity for the peptide sequence EYMPME (scFv/EE). This report details the conversion of scFv/EE to an anti-EE Fab format (Fab/EE) followed by its biophysical characterization. The addition of constant chains increased the overall stability and had a negligible impact on the antigen affinity. The 2.0 Å resolution crystal structure of Fab/EE reveals contacts with larger surface areas than those of scFv/EE. Surface plasmon resonance, an enzyme-linked immunosorbent assay, and size-exclusion chromatography were used to assess Fab/EE binding to EE-tagged soluble and membrane test proteins: namely, the β-barrel outer membrane protein intimin and α-helical A2a G protein-coupled receptor (A2aR). Molecular-dynamics simulation of the intimin constructs with and without Fab/EE provides insight into the energetic complexities of the co-crystallization approach.
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Affiliation(s)
- Jennifer L. Johnson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
| | - Kevin C. Entzminger
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712, USA
| | - Jeongmin Hyun
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712, USA
| | - Sibel Kalyoncu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
| | - David P. Heaner
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
| | - Ivan A. Morales
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
| | - Aly Sheppard
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
| | - James C. Gumbart
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
- School of Physics, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
| | - Jennifer A. Maynard
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712, USA
| | - Raquel L. Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
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Role of the unfolded protein response in regulating the mucin-dependent filamentous-growth mitogen-activated protein kinase pathway. Mol Cell Biol 2015; 35:1414-32. [PMID: 25666509 DOI: 10.1128/mcb.01501-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Signaling mucins are evolutionarily conserved regulators of signal transduction pathways. The signaling mucin Msb2p regulates the Cdc42p-dependent mitogen-activated protein kinase (MAPK) pathway that controls filamentous growth in yeast. The cleavage and release of the glycosylated inhibitory domain of Msb2p is required for MAPK activation. We show here that proteolytic processing of Msb2p was induced by underglycosylation of its extracellular domain. Cleavage of underglycosylated Msb2p required the unfolded protein response (UPR), a quality control (QC) pathway that operates in the endoplasmic reticulum (ER). The UPR regulator Ire1p, which detects misfolded/underglycosylated proteins in the ER, controlled Msb2p cleavage by regulating transcriptional induction of Yps1p, the major protease that processes Msb2p. Accordingly, the UPR was required for differentiation to the filamentous cell type. Cleavage of Msb2p occurred in conditional trafficking mutants that trap secretory cargo in the endomembrane system. Processed Msb2p was delivered to the plasma membrane, and its turnover by the ubiquitin ligase Rsp5p and ESCRT attenuated the filamentous-growth pathway. We speculate that the QC pathways broadly regulate signaling glycoproteins and their cognate pathways by recognizing altered glycosylation patterns that can occur in response to extrinsic cues.
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Abstract
Protein crystals have been functionalized for applications in preparation of inorganic materials, asymmetric catalysis and accumulation of functional compounds.
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Affiliation(s)
- Satoshi Abe
- Department of Biomolecular Engineering
- Graduate School of Bioscience and Biotechnology
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Takafumi Ueno
- Department of Biomolecular Engineering
- Graduate School of Bioscience and Biotechnology
- Tokyo Institute of Technology
- Midori-ku
- Japan
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47
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Abstract
From the catalytic reactions that sustain the global oxygen, nitrogen, and carbon cycles to the stabilization of DNA processing proteins, transition metal ions and metallocofactors play key roles in biology. Although the exquisite interplay between metal ions and protein scaffolds has been studied extensively, the fact that the biological roles of the metals often stem from their placement in the interfaces between proteins and protein subunits is not always recognized. Interfacial metal ions stabilize permanent or transient protein-protein interactions, enable protein complexes involved in cellular signaling to adopt distinct conformations in response to environmental stimuli, and catalyze challenging chemical reactions that are uniquely performed by multisubunit protein complexes. This review provides a structural survey of transition metal ions and metallocofactors found in protein-protein interfaces, along with a series of selected examples that illustrate their diverse biological utility and significance.
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Affiliation(s)
- Woon Ju Song
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093; emails: , ,
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48
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Abstract
The construction of crystalline arrays allows proteins to be presented in a dense, oriented and functional way that also facilitates determination of their structure. Rational design of these supramolecular structures is becoming increasingly tractable with recent successes exploiting both innate protein symmetry and advances in protein–protein interface design. Pre-existing symmetry minimizes the number of non-native interfaces that must be produced, and the use of symmetric interfaces facilitates protein alignment. Arrays in which metal coordination or peptide binding are responsible for the inter-particle associations show particular promise due to the malleable and reversible nature of these interactions. Cross-pollination of the principles that underlie successful strategies is likely to produce rapid advances in this field and consequent benefits to both nanotechnology and structural biology.
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Oohora K, Hayashi T. Hemoprotein-based supramolecular assembling systems. Curr Opin Chem Biol 2014; 19:154-61. [PMID: 24658057 DOI: 10.1016/j.cbpa.2014.02.014] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 02/11/2014] [Accepted: 02/13/2014] [Indexed: 12/11/2022]
Abstract
Hemoproteins are metalloproteins which include iron porphyrin as a cofactor. These proteins have received much attention as promising building blocks for development of new types of biomaterials. This review summarizes recent efforts in the rational design of supramolecular hemoprotein assemblies using myoglobin, horseradish peroxidase, cytochrome b562 and cytochrome c as a monomer unit. The processes of coordination bond-mediated assembly or domain swapping-mediated assembly provide defined oligomers, while hemoprotein reconstitution with synthetic heme derivatives provides submicrometer-sized structures such as fibrils, vesicles/micelles, or networks. Interestingly, several of these assembled structures maintain the intrinsic functions of monomer units. The chemical and/or biological strategies described in this review will lead to the creation of unique hemoprotein-based functional biomaterials.
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Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University Suita, 565-0871, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University Suita, 565-0871, Japan.
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Nakabayashi M, Kataoka M, Mishima Y, Maeno Y, Ishikawa K. Structural analysis of β-glucosidase mutants derived from a hyperthermophilic tetrameric structure. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:877-88. [PMID: 24598756 PMCID: PMC3949513 DOI: 10.1107/s1399004713032276] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 11/26/2013] [Indexed: 11/11/2022]
Abstract
Substitutive mutations that convert a tetrameric β-glucosidase into a dimeric state lead to improvement of its crystal quality. β-Glucosidase from Pyrococcus furiosus (BGLPf) is a hyperthermophilic tetrameric enzyme which can degrade cellooligosaccharides to glucose under hyperthermophilic conditions and thus holds promise for the saccharification of lignocellulosic biomass at high temperature. Prior to the production of large amounts of this enzyme, detailed information regarding the oligomeric structure of the enzyme is required. Several crystals of BGLPf have been prepared over the past ten years, but its crystal structure had not been solved until recently. In 2011, the first crystal structure of BGLPf was solved and a model was constructed at somewhat low resolution (2.35 Å). In order to obtain more detailed structural data on BGLPf, the relationship between its tetrameric structure and the quality of the crystal was re-examined. A dimeric form of BGLPf was constructed and its crystal structure was solved at a resolution of 1.70 Å using protein-engineering methods. Furthermore, using the high-resolution crystal structural data for the dimeric form, a monomeric form of BGLPf was constructed which retained the intrinsic activity of the tetrameric form. The thermostability of BGLPf is affected by its oligomeric structure. Here, the biophysical and biochemical properties of engineered dimeric and monomeric BGLPfs are reported, which are promising prototype models to apply to the saccharification reaction. Furthermore, details regarding the oligomeric structures of BGLPf and the reasons why the mutations yielded improved crystal structures are discussed.
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Affiliation(s)
- Makoto Nakabayashi
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science, 3-11-32, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Misumi Kataoka
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science, 3-11-32, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Yumiko Mishima
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science, 3-11-32, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Yuka Maeno
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science, 3-11-32, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Kazuhiko Ishikawa
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science, 3-11-32, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
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