1
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Duan M, Lv C, Zang J, Leng X, Zhao G, Zhang T. Metals at the Helm: Revolutionizing Protein Assembly and Applications. Macromol Biosci 2024:e2400126. [PMID: 39239781 DOI: 10.1002/mabi.202400126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/23/2024] [Indexed: 09/07/2024]
Abstract
Protein assembly is an essential process in biological systems, where proteins self-assemble into complex structures with diverse functions. Inspired by the exquisite control over protein assembly in nature, scientists have been exploring ways to design and assemble protein structures with precise control over their topologies and functions. One promising approach for achieving this goal is through metal coordination, which utilizes metal-binding motifs to mediate protein-protein interactions and assemble protein complexes with controlled stoichiometry and geometry. Metal coordination provides a modular and tunable approach for protein assembly and de novo structure design, where the metal ion acts as a molecular glue that holds the protein subunits together in a specific orientation. Metal-coordinated protein assemblies have shown great potential for developing functional metalloproteinase, novel biomaterials and integrated drug delivery systems. In this review, an overview of the recent advances in protein assemblies benefited from metal coordination is provided, focusing on various protein arrangements in different dimensions including protein oligomers, protein nanocage and higher-order protein architectures. Moreover, the key metal-binding motifs and strategies used to assemble protein structures with precise control over their properties are highlighted. The potential applications of metal-mediated protein assemblies in biotechnology and biomedicine are also discussed.
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Affiliation(s)
- Maoping Duan
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Chenyan Lv
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Jiachen Zang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Xiaojing Leng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Guanghua Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Tuo Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Center of Food Colloids and Delivery for Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
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2
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Zhu S, Niu Y, Zhou W, Liu Y, Liu J, Liu X, Lu L, Yu C. Mitochondrial copper overload promotes renal fibrosis via inhibiting pyruvate dehydrogenase activity. Cell Mol Life Sci 2024; 81:340. [PMID: 39120696 PMCID: PMC11335263 DOI: 10.1007/s00018-024-05358-1] [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: 02/13/2024] [Revised: 06/15/2024] [Accepted: 07/09/2024] [Indexed: 08/10/2024]
Abstract
Copper is a trace element essential for numerous biological activities, whereas the mitochondria serve as both major sites of intracellular copper utilization and copper reservoir. Here, we investigated the impact of mitochondrial copper overload on the tricarboxylic acid cycle, renal senescence and fibrosis. We found that copper ion levels are significantly elevated in the mitochondria in fibrotic kidney tissues, which are accompanied by reduced pyruvate dehydrogenase (PDH) activity, mitochondrial dysfunction, cellular senescence and renal fibrosis. Conversely, lowering mitochondrial copper levels effectively restore PDH enzyme activity, improve mitochondrial function, mitigate cellular senescence and renal fibrosis. Mechanically, we found that mitochondrial copper could bind directly to lipoylated dihydrolipoamide acetyltransferase (DLAT), the E2 component of the PDH complex, thereby changing the interaction between the subunits of lipoylated DLAT, inducing lipoylated DLAT protein dimerization, and ultimately inhibiting PDH enzyme activity. Collectively, our study indicates that mitochondrial copper overload could inhibit PDH activity, subsequently leading to mitochondrial dysfunction, cellular senescence and renal fibrosis. Reducing mitochondrial copper overload might therefore serve as a strategy to rescue renal fibrosis.
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Affiliation(s)
- Saiya Zhu
- Department of Nephrology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yangyang Niu
- Department of Nephrology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Wenqian Zhou
- Department of Nephrology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yuqing Liu
- Department of Nephrology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Jing Liu
- Department of Nephrology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Xi Liu
- Department of Nephrology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Limin Lu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Yixueyuan Road, Shanghai, 200032, China.
| | - Chen Yu
- Department of Nephrology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
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3
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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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4
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Ledesma‐Fernandez A, Velasco‐Lozano S, Campos‐Muelas P, Madrid R, López‐Gallego F, Cortajarena AL. Engineering bio-brick protein scaffolds for organizing enzyme assemblies. Protein Sci 2024; 33:e4984. [PMID: 38607190 PMCID: PMC11010954 DOI: 10.1002/pro.4984] [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: 01/10/2024] [Revised: 03/11/2024] [Accepted: 03/23/2024] [Indexed: 04/13/2024]
Abstract
Enzyme scaffolding is an emerging approach for enhancing the catalytic efficiency of multi-enzymatic cascades by controlling their spatial organization and stoichiometry. This study introduces a novel family of engineered SCAffolding Bricks, named SCABs, utilizing the consensus tetratricopeptide repeat (CTPR) domain for organized multi-enzyme systems. Two SCAB systems are developed, one employing head-to-tail interactions with reversible covalent disulfide bonds, the other relying on non-covalent metal-driven assembly via engineered metal coordinating interfaces. Enzymes are directly fused to SCAB modules, triggering assembly in a non-reducing environment or by metal presence. A proof-of-concept with formate dehydrogenase (FDH) and L-alanine dehydrogenase (AlaDH) shows enhanced specific productivity by 3.6-fold compared to free enzymes, with the covalent stapling outperforming the metal-driven assembly. This enhancement likely stems from higher-order supramolecular assembly and improved NADH cofactor regeneration, resulting in more efficient cascades. This study underscores the potential of protein engineering to tailor scaffolds, leveraging supramolecular spatial-organizing tools, for more efficient enzymatic cascade reactions.
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Affiliation(s)
- Alba Ledesma‐Fernandez
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology Alliance (BRTA)Donostia‐San SebastiánSpain
- University of the Basque Country (UPV/EHU)LeioaSpain
| | - Susana Velasco‐Lozano
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology Alliance (BRTA)Donostia‐San SebastiánSpain
- Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH‐CSIC)University of ZaragozaZaragozaSpain
- Aragonese Foundation for Research and Development (ARAID)ZaragozaSpain
| | | | - Ricardo Madrid
- BioAssays S.L.MadridSpain
- Complutense University of MadridMadridSpain
| | - Fernando López‐Gallego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology Alliance (BRTA)Donostia‐San SebastiánSpain
- IkerbasqueBasque Foundation for ScienceBilbaoSpain
| | - Aitziber L. Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology Alliance (BRTA)Donostia‐San SebastiánSpain
- IkerbasqueBasque Foundation for ScienceBilbaoSpain
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5
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Guo Z, Liu J, Wang Y, Chen M, Wang D, Xu D, Cheng J. Diffusion models in bioinformatics and computational biology. NATURE REVIEWS BIOENGINEERING 2024; 2:136-154. [PMID: 38576453 PMCID: PMC10994218 DOI: 10.1038/s44222-023-00114-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/25/2023] [Indexed: 04/06/2024]
Abstract
Denoising diffusion models embody a type of generative artificial intelligence that can be applied in computer vision, natural language processing and bioinformatics. In this Review, we introduce the key concepts and theoretical foundations of three diffusion modelling frameworks (denoising diffusion probabilistic models, noise-conditioned scoring networks and score stochastic differential equations). We then explore their applications in bioinformatics and computational biology, including protein design and generation, drug and small-molecule design, protein-ligand interaction modelling, cryo-electron microscopy image data analysis and single-cell data analysis. Finally, we highlight open-source diffusion model tools and consider the future applications of diffusion models in bioinformatics.
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Affiliation(s)
- Zhiye Guo
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, USA
| | - Jian Liu
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, USA
| | - Yanli Wang
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, USA
| | - Mengrui Chen
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, USA
| | - Duolin Wang
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, USA
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, USA
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6
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Chen X, Zhang T, Liu H, Zang J, Lv C, Du M, Zhao G. Shape-Anisotropic Assembly of Protein Nanocages with Identical Building Blocks by Designed Intermolecular π-π Interactions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2305398. [PMID: 37870198 PMCID: PMC10724428 DOI: 10.1002/advs.202305398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/12/2023] [Indexed: 10/24/2023]
Abstract
Protein lattices that shift the structure and shape anisotropy in response to environmental cues are closely coupled to potential functionality. However, to design and construct shape-anisotropic protein arrays from the same building blocks in response to different external stimuli remains challenging. Here, by a combination of the multiple, symmetric interaction sites on the outer surface of protein nanocages and the tunable features of phenylalanine-phenylalanine interactions, a protein engineering approach is reported to construct a variety of superstructures with shape anisotropy, including 3D cubic, 2D hexagonal layered, and 1D rod-like crystalline protein nanocage arrays by using one single protein building block. Notably, the assembly of these crystalline protein arrays is reversible, which can be tuned by external stimuli (pH and ionic strength). The anisotropic morphologies of the fabricated macroscopic crystals can be correlated with the Å-to-nm scale protein arrangement details by crystallographic elucidation. These results enhance the understanding of the freedom offered by an object's symmetry and inter-object π-π stacking interactions for protein building blocks to assemble into direction- and shape-anisotropic biomaterials.
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Affiliation(s)
- Xuemin Chen
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
| | - Tuo Zhang
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
| | - Hanxiong Liu
- School of Food Science and TechnologyNational Engineering Research Center of SeafoodDalian Polytechnic UniversityDalian116034China
| | - Jiachen Zang
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
| | - Chenyan Lv
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
| | - Ming Du
- School of Food Science and TechnologyNational Engineering Research Center of SeafoodDalian Polytechnic UniversityDalian116034China
| | - Guanghua Zhao
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
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7
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Watson JL, Juergens D, Bennett NR, Trippe BL, Yim J, Eisenach HE, Ahern W, Borst AJ, Ragotte RJ, Milles LF, Wicky BIM, Hanikel N, Pellock SJ, Courbet A, Sheffler W, Wang J, Venkatesh P, Sappington I, Torres SV, Lauko A, De Bortoli V, Mathieu E, Ovchinnikov S, Barzilay R, Jaakkola TS, DiMaio F, Baek M, Baker D. De novo design of protein structure and function with RFdiffusion. Nature 2023; 620:1089-1100. [PMID: 37433327 PMCID: PMC10468394 DOI: 10.1038/s41586-023-06415-8] [Citation(s) in RCA: 258] [Impact Index Per Article: 258.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 07/07/2023] [Indexed: 07/13/2023]
Abstract
There has been considerable recent progress in designing new proteins using deep-learning methods1-9. Despite this progress, a general deep-learning framework for protein design that enables solution of a wide range of design challenges, including de novo binder design and design of higher-order symmetric architectures, has yet to be described. Diffusion models10,11 have had considerable success in image and language generative modelling but limited success when applied to protein modelling, probably due to the complexity of protein backbone geometry and sequence-structure relationships. Here we show that by fine-tuning the RoseTTAFold structure prediction network on protein structure denoising tasks, we obtain a generative model of protein backbones that achieves outstanding performance on unconditional and topology-constrained protein monomer design, protein binder design, symmetric oligomer design, enzyme active site scaffolding and symmetric motif scaffolding for therapeutic and metal-binding protein design. We demonstrate the power and generality of the method, called RoseTTAFold diffusion (RFdiffusion), by experimentally characterizing the structures and functions of hundreds of designed symmetric assemblies, metal-binding proteins and protein binders. The accuracy of RFdiffusion is confirmed by the cryogenic electron microscopy structure of a designed binder in complex with influenza haemagglutinin that is nearly identical to the design model. In a manner analogous to networks that produce images from user-specified inputs, RFdiffusion enables the design of diverse functional proteins from simple molecular specifications.
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Affiliation(s)
- Joseph L Watson
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - David Juergens
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA
| | - Nathaniel R Bennett
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA
| | - Brian L Trippe
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Columbia University, Department of Statistics, New York, NY, USA
- Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA
| | - Jason Yim
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helen E Eisenach
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Woody Ahern
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Andrew J Borst
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Robert J Ragotte
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lukas F Milles
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Basile I M Wicky
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Nikita Hanikel
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Samuel J Pellock
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alexis Courbet
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- National Centre for Scientific Research, École Normale Supérieure rue d'Ulm, Paris, France
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jue Wang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Preetham Venkatesh
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA
| | - Isaac Sappington
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA
| | - Susana Vázquez Torres
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA
| | - Anna Lauko
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA
| | - Valentin De Bortoli
- National Centre for Scientific Research, École Normale Supérieure rue d'Ulm, Paris, France
| | - Emile Mathieu
- Department of Engineering, University of Cambridge, Cambridge, UK
| | - Sergey Ovchinnikov
- Faculty of Applied Sciences, Harvard University, Cambridge, MA, USA
- John Harvard Distinguished Science Fellowship, Harvard University, Cambridge, MA, USA
| | | | | | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Minkyung Baek
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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8
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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: 3] [Impact Index Per Article: 3.0] [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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9
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Hoffnagle AM, Tezcan FA. Atomically Accurate Design of Metalloproteins with Predefined Coordination Geometries. J Am Chem Soc 2023; 145:14208-14214. [PMID: 37352018 PMCID: PMC10439731 DOI: 10.1021/jacs.3c04047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2023]
Abstract
We report a new computational protein design method for the construction of oligomeric protein assemblies around metal centers with predefined coordination geometries. We apply this method to design two homotrimeric assemblies, Tet4 and TP1, with tetrahedral and trigonal-pyramidal tris(histidine) metal coordination geometries, respectively, and demonstrate that both assemblies form the targeted metal centers with ≤0.2 Å accuracy. Although Tet4 and TP1 are constructed from the same parent protein building block, they are distinct in terms of their overall architectures, the environment surrounding the metal centers, and their metal-based reactivities, illustrating the versatility of our approach.
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Affiliation(s)
- Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
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10
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Oohora K. Supramolecular assembling systems of hemoproteins using chemical modifications. J INCL PHENOM MACRO 2023. [DOI: 10.1007/s10847-023-01181-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2023]
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11
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Zhu W, Yang DT, Gronenborn AM. Ligand-Capped Cobalt(II) Multiplies the Value of the Double-Histidine Motif for PCS NMR Studies. J Am Chem Soc 2023; 145:4564-4569. [PMID: 36786809 PMCID: PMC10032564 DOI: 10.1021/jacs.2c12021] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Indexed: 02/15/2023]
Abstract
In structural studies by NMR, pseudocontact shifts (PCSs) provide both angular and distance information. For proteins, incorporation of a di-histidine (diHis) motif, coordinated to Co2+, has emerged as an important tool to measure PCS. Here, we show that using different Co(II)-chelating ligands, such as nitrilotriacetic acid (NTA) and iminodiacetic acid (IDA), resolves the isosurface ambiguity of Co2+-diHis and yields orthogonal PCS data sets with different Δχ-tensors for the same diHis-bearing protein. Importantly, such capping ligands effectively eliminate undesired intermolecular interactions, which can be detrimental to PCS studies. Devising and employing ligand-capping strategies afford versatile and powerful means to obtain multiple orthogonal PCS data sets, significantly extending the use of the diHis motif for structural studies by NMR.
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Affiliation(s)
- Wenkai Zhu
- Department
of Structural Biology, University of Pittsburgh,
School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Darian T. Yang
- Department
of Structural Biology, University of Pittsburgh,
School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
- Department
of Chemistry, University of Pittsburgh,
Dietrich School of Arts and Sciences, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Angela M. Gronenborn
- Department
of Structural Biology, University of Pittsburgh,
School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
- Department
of Chemistry, University of Pittsburgh,
Dietrich School of Arts and Sciences, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
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12
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Hoffnagle AM, Eng VH, Markel U, Tezcan F. Computationally Guided Redesign of a Heme-free Cytochrome with Native-like Structure and Stability. Biochemistry 2022; 61:2063-2072. [PMID: 36106943 PMCID: PMC9949987 DOI: 10.1021/acs.biochem.2c00369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metals can play key roles in stabilizing protein structures, but ensuring their proper incorporation is a challenge when a metalloprotein is overexpressed in a non-native cellular environment. Here, we have used computational protein design tools to redesign cytochrome b562 (cyt b562), which relies on the binding of its heme cofactor to achieve its proper fold, into a stable, heme-free protein. The resulting protein, ApoCyt, features only four mutations and no metal-ligand or covalent bonds, yet displays improved stability over cyt b562. Mutagenesis studies and X-ray crystal structures reveal that the increase in stability is due to the computationally prescribed mutations, which stabilize the protein fold through a combination of hydrophobic packing interactions, hydrogen bonds, and cation-π interactions. Upon installation of the relevant mutations, ApoCyt is capable of assembling into previously reported, cytochrome-based trimeric and tetrameric assemblies, demonstrating that ApoCyt retains the structure and assembly properties of cyt b562. The successful design of ApoCyt therefore enables further functional diversification of cytochrome-based assemblies and demonstrates that structural metal cofactors can be replaced by a small number of well-designed, non-covalent interactions.
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Affiliation(s)
| | | | | | - F.Akif Tezcan
- Corresponding Author: F. Akif Tezcan, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States.
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13
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Oranges M, Wort JL, Fukushima M, Fusco E, Ackermann K, Bode BE. Pulse Dipolar Electron Paramagnetic Resonance Spectroscopy Reveals Buffer-Modulated Cooperativity of Metal-Templated Protein Dimerization. J Phys Chem Lett 2022; 13:7847-7852. [PMID: 35976741 PMCID: PMC9421889 DOI: 10.1021/acs.jpclett.2c01719] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/10/2022] [Indexed: 05/26/2023]
Abstract
Self-assembly of protein monomers directed by metal ion coordination constitutes a promising strategy for designing supramolecular architectures complicated by the noncovalent interaction between monomers. Herein, two pulse dipolar electron paramagnetic resonance spectroscopy (PDS) techniques, pulse electron-electron double resonance and relaxation-induced dipolar modulation enhancement, were simultaneously employed to study the CuII-templated dimerization behavior of a model protein (Streptococcus sp. group G, protein G B1 domain) in both phosphate and Tris-HCl buffers. A cooperative binding model could simultaneously fit all data and demonstrate that the cooperativity of protein dimerization across α-helical double-histidine motifs in the presence of CuII is strongly modulated by the buffer, representing a platform for highly tunable buffer-switchable templated dimerization. Hence, PDS enriches the family of techniques for monitoring binding processes, supporting the development of novel strategies for bioengineering structures and stable architectures assembled by an initial metal-templated dimerization.
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14
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Kerns S, Biswas A, Minnetian NM, Borovik AS. Artificial Metalloproteins: At the Interface between Biology and Chemistry. JACS AU 2022; 2:1252-1265. [PMID: 35783165 PMCID: PMC9241007 DOI: 10.1021/jacsau.2c00102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 05/22/2023]
Abstract
Artificial metalloproteins (ArMs) have recently gained significant interest due to their potential to address issues in a broad scope of applications, including biocatalysis, biotechnology, protein assembly, and model chemistry. ArMs are assembled by the incorporation of a non-native metallocofactor into a protein scaffold. This can be achieved by a number of methods that apply tools of chemical biology, computational de novo design, and synthetic chemistry. In this Perspective, we highlight select systems in the hope of demonstrating the breadth of ArM design strategies and applications and emphasize how these systems address problems that are otherwise difficult to do so with strictly biochemical or synthetic approaches.
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Affiliation(s)
- Spencer
A. Kerns
- Department of Chemistry, University of California, 1102 Natural
Science II, Irvine, California 92797, United States
| | - Ankita Biswas
- Department of Chemistry, University of California, 1102 Natural
Science II, Irvine, California 92797, United States
| | - Natalie M. Minnetian
- Department of Chemistry, University of California, 1102 Natural
Science II, Irvine, California 92797, United States
| | - A. S. Borovik
- Department of Chemistry, University of California, 1102 Natural
Science II, Irvine, California 92797, United States
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15
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Kakkis A, Golub E, Choi TS, Tezcan FA. Redox- and metal-directed structural diversification in designed metalloprotein assemblies. Chem Commun (Camb) 2022; 58:6958-6961. [PMID: 35642584 DOI: 10.1039/d2cc02440c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we describe a designed protein building block whose self-assembly behaviour is dually gated by the redox state of disulphide bonds and the identity of exogenous metal ions. This protein construct is shown - through extensive structural and biophysical characterization - to access five distinct oligomeric states, exemplifying how the complex interplay between hydrophobic, metal-ligand, and reversible covalent interactions could be harnessed to obtain multiple, responsive protein architectures from a single building block.
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Affiliation(s)
- Albert Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - Eyal Golub
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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16
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Li X, Bai Y, Luo Q, Xu J, Chen T, Liu J. Morphological Selectivity of a Protein Self-Assembly System with a Repertoire of Diverse Interaction Modes. ACS Macro Lett 2022; 11:675-679. [PMID: 35570806 DOI: 10.1021/acsmacrolett.2c00154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multiple metal chelating sites were incorporated onto the second mitochondria-derived activator of caspase (SMAC) building blocks. The combination of different binding sites generated a repertoire of diverse binding modes, among which two different microfilament types (small and large) with distinct patterns were selected under thermodynamic control. Furthermore, the two microfilaments exhibited a pronounced secondary assembly trend due to the potential noncovalent interactions on the protein surfaces. Coupled with stereoselectivity, they presented a strong self-recognition effect and underwent two distinct reassembly patterns. That is, the large filaments self-associated in pairs to form "interlocked chain" structures, while the small ones twisted to form protein helical bundles. This work represents one of the few studies of selective self-assembly of self-assembled protein assemblies. Such an idea may provide inspiration for constructing more sophisticated protein architectures in the future.
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Affiliation(s)
- Xiumei Li
- Department of Chemistry, Jinan University, Guangzhou 510632, P. R. China
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, P. R. China
| | - Yushi Bai
- Department of Preventative and Restorative Dental Sciences, School of Dentistry, University of California, San Francisco, California 94143, United States
| | - Quan Luo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Jiayun Xu
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, P. R. China
| | - Tianfeng Chen
- Department of Chemistry, Jinan University, Guangzhou 510632, P. R. China
| | - Junqiu Liu
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, P. R. China
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17
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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: 107] [Impact Index Per Article: 35.7] [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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18
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Hirota S, Mashima T, Kobayashi N. Use of 3D domain swapping in constructing supramolecular metalloproteins. Chem Commun (Camb) 2021; 57:12074-12086. [PMID: 34714300 DOI: 10.1039/d1cc04608j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Supramolecules, which are formed by assembling multiple molecules by noncovalent intermolecular interactions instead of covalent bonds, often show additional properties that cannot be exhibited by a single molecule. Supramolecules have evolved into molecular machines in the field of chemistry, and various supramolecular proteins are responsible for life activities in the field of biology. The design and creation of supramolecular proteins will lead to development of new enzymes, functional biomaterials, drug delivery systems, etc.; thus, the number of studies on the regulation of supramolecular proteins is increasing year by year. Several methods, including disulfide bond, metal coordination, and surface-surface interaction, have been utilized to construct supramolecular proteins. In nature, proteins have been shown to form oligomers by 3D domain swapping (3D-DS), a phenomenon in which a structural region is exchanged between molecules of the same protein. We have been studying the mechanism of 3D-DS and utilizing 3D-DS to construct supramolecular metalloproteins. Cytochrome c forms cyclic oligomers and polymers by 3D-DS, whereas other metalloproteins, such as various c-type cytochromes and azurin form small oligomers and myoglobin forms a compact dimer. We have also utilized 3D-DS to construct heterodimers with different active sites, a protein nanocage encapsulating a Zn-SO4 cluster in the internal cavity, and a tetrahedron with a designed building block protein. Protein oligomer formation was controlled for the 3D-DS dimer of a dimer-monomer transition protein. This article reviews our research on supramolecular metalloproteins.
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Affiliation(s)
- Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
| | - Tsuyoshi Mashima
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
| | - Naoya Kobayashi
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
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19
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Subramanian RH, Zhu J, Bailey JB, Chiong JA, Li Y, Golub E, Tezcan FA. Design of metal-mediated protein assemblies via hydroxamic acid functionalities. Nat Protoc 2021; 16:3264-3297. [PMID: 34050338 DOI: 10.1038/s41596-021-00535-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/15/2021] [Indexed: 02/05/2023]
Abstract
The self-assembly of proteins into sophisticated multicomponent assemblies is a hallmark of all living systems and has spawned extensive efforts in the construction of novel synthetic protein architectures with emergent functional properties. Protein assemblies in nature are formed via selective association of multiple protein surfaces through intricate noncovalent protein-protein interactions, a challenging task to accurately replicate in the de novo design of multiprotein systems. In this protocol, we describe the application of metal-coordinating hydroxamate (HA) motifs to direct the metal-mediated assembly of polyhedral protein architectures and 3D crystalline protein-metal-organic frameworks (protein-MOFs). This strategy has been implemented using an asymmetric cytochrome cb562 monomer through selective, concurrent association of Fe3+ and Zn2+ ions to form polyhedral cages. Furthermore, the use of ditopic HA linkers as bridging ligands with metal-binding protein nodes has allowed the construction of crystalline 3D protein-MOF lattices. The protocol is divided into two major sections: (1) the development of a Cys-reactive HA molecule for protein derivatization and self-assembly of protein-HA conjugates into polyhedral cages and (2) the synthesis of ditopic HA bridging ligands for the construction of ferritin-based protein-MOFs using symmetric metal-binding protein nodes. Protein cages are analyzed using analytical ultracentrifugation, transmission electron microscopy and single-crystal X-ray diffraction techniques. HA-mediated protein-MOFs are formed in sitting-drop vapor diffusion crystallization trays and are probed via single-crystal X-ray diffraction and multi-crystal small-angle X-ray scattering measurements. Ligand synthesis, construction of HA-mediated assemblies, and post-assembly analysis as described in this protocol can be performed by a graduate-level researcher within 6 weeks.
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Affiliation(s)
- Rohit H Subramanian
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Jie Zhu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Jake B Bailey
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Jerika A Chiong
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Eyal Golub
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA. .,Materials Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
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20
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Selecting Subpopulations of High-Quality Protein Conformers among Conformational Mixtures of Recombinant Bovine MMP-9 Solubilized from Inclusion Bodies. Int J Mol Sci 2021; 22:ijms22063020. [PMID: 33809594 PMCID: PMC8001920 DOI: 10.3390/ijms22063020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/03/2021] [Accepted: 03/12/2021] [Indexed: 12/30/2022] Open
Abstract
A detailed workflow to analyze the physicochemical characteristics of mammalian matrix metalloproteinase (MMP-9) protein species obtained from protein aggregates (inclusion bodies-IBs) was followed. MMP-9 was recombinantly produced in the prokaryotic microbial cell factories Clearcoli (an engineered form of Escherichia coli) and Lactococcus lactis, mainly forming part of IBs and partially recovered under non-denaturing conditions. After the purification by affinity chromatography of solubilized MMP-9, four protein peaks were obtained. However, so far, the different conformational protein species forming part of IBs have not been isolated and characterized. Therefore, with the aim to link the physicochemical characteristics of the isolated peaks with their biological activity, we set up a methodological approach that included dynamic light scattering (DLS), circular dichroism (CD), and spectrofluorometric analysis confirming the separation of subpopulations of conformers with specific characteristics. In protein purification procedures, the detailed analysis of the individual physicochemical properties and the biological activity of protein peaks separated by chromatographic techniques is a reliable source of information to select the best-fitted protein populations.
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21
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Kakkis A, Gagnon D, Esselborn J, Britt RD, Tezcan FA. Metal‐Templated Design of Chemically Switchable Protein Assemblies with High‐Affinity Coordination Sites. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Albert Kakkis
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Derek Gagnon
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Julian Esselborn
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - R. David Britt
- Department of Chemistry University of California, Davis 1 Shields Avenue Davis CA 95616 USA
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 USA
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22
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Ghanbarpour A, Santos EM, Pinger C, Assar Z, Hossaini Nasr S, Vasileiou C, Spence D, Borhan B, Geiger JH. Human Cellular Retinol Binding Protein II Forms a Domain-Swapped Trimer Representing a Novel Fold and a New Template for Protein Engineering. Chembiochem 2020; 21:3192-3196. [PMID: 32608180 PMCID: PMC8220890 DOI: 10.1002/cbic.202000405] [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: 06/24/2020] [Revised: 06/29/2020] [Indexed: 11/07/2022]
Abstract
Domain-swapping is a mechanism for evolving new protein structure from extant scaffolds, and has been an efficient protein-engineering strategy for tailoring functional diversity. However, domain swapping can only be exploited if it can be controlled, especially in cases where various folds can coexist. Herein, we describe the structure of a domain-swapped trimer of the iLBP family member hCRBPII, and suggest a mechanism for domain-swapped trimerization. It is further shown that domain-swapped trimerization can be favored by strategic installation of a disulfide bond, thus demonstrating a strategy for fold control. We further show the domain-swapped trimer to be a useful protein design template by installing a high-affinity metal binding site through the introduction of a single mutation, taking advantage of its threefold symmetry. Together, these studies show how nature can promote oligomerization, stabilize a specific oligomer, and generate new function with minimal changes to the protein sequence.
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Affiliation(s)
- Alireza Ghanbarpour
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
- Yale University Medical School, Department of Cell Biology, 333 S. Cedar Street, New Haven, CT 06510, USA
| | - Elizabeth M Santos
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
- Dow Performance Silicones, 2200W Salzburg Road, Midland, MI 48686, USA
| | - Cody Pinger
- Department of Biomedical Engineering, Michigan State University, 775 Woodlot Drive, East Lansing, MI 48823, USA
| | - Zahra Assar
- Cayman Chemical, 1180 East Ellsworth Road, Ann Arbor, MI 48108, USA
| | - Seyedmehdi Hossaini Nasr
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - Chrysoula Vasileiou
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - Dana Spence
- Department of Biomedical Engineering, Michigan State University, 775 Woodlot Drive, East Lansing, MI 48823, USA
| | - Babak Borhan
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - James H Geiger
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
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23
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Kakkis A, Gagnon D, Esselborn J, Britt RD, Tezcan FA. Metal-Templated Design of Chemically Switchable Protein Assemblies with High-Affinity Coordination Sites. Angew Chem Int Ed Engl 2020; 59:21940-21944. [PMID: 32830423 DOI: 10.1002/anie.202009226] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/13/2020] [Indexed: 11/09/2022]
Abstract
To mimic a hypothetical pathway for protein evolution, we previously tailored a monomeric protein (cyt cb562 ) for metal-mediated self-assembly, followed by re-design of the resulting oligomers for enhanced stability and metal-based functions. We show that a single hydrophobic mutation on the cyt cb562 surface drastically alters the outcome of metal-directed oligomerization to yield a new trimeric architecture, (TriCyt1)3. This nascent trimer was redesigned into second and third-generation variants (TriCyt2)3 and (TriCyt3)3 with increased structural stability and preorganization for metal coordination. The three TriCyt variants combined furnish a unique platform to 1) provide tunable coupling between protein quaternary structure and metal coordination, 2) enable the construction of metal/pH-switchable protein oligomerization motifs, and 3) generate a robust metal coordination site that can coordinate all mid-to-late first-row transition-metal ions with high affinity.
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Affiliation(s)
- Albert Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Derek Gagnon
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Julian Esselborn
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - R David Britt
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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24
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Korpi A, Anaya-Plaza E, Välimäki S, Kostiainen M. Highly ordered protein cage assemblies: A toolkit for new materials. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 12:e1578. [PMID: 31414574 DOI: 10.1002/wnan.1578] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/19/2019] [Accepted: 06/28/2019] [Indexed: 12/16/2022]
Abstract
Protein capsids are specialized and versatile natural macromolecules with exceptional properties. Their homogenous, spherical, rod-like or toroidal geometry, and spatially directed functionalities make them intriguing building blocks for self-assembled nanostructures. High degrees of functionality and modifiability allow for their assembly via non-covalent interactions, such as electrostatic and coordination bonding, enabling controlled self-assembly into higher-order structures. These assembly processes are sensitive to the molecules used and the surrounding conditions, making it possible to tune the chemical and physical properties of the resultant material and generate multifunctional and environmentally sensitive systems. These materials have numerous potential applications, including catalysis and drug delivery. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
- Antti Korpi
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
| | - Eduardo Anaya-Plaza
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
| | - Salla Välimäki
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
| | - Mauri Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
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25
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Miyamoto T, Hayashi Y, Yoshida K, Watanabe H, Uchihashi T, Yonezawa K, Shimizu N, Kamikubo H, Hirota S. Construction of a Quadrangular Tetramer and a Cage-Like Hexamer from Three-Helix Bundle-Linked Fusion Proteins. ACS Synth Biol 2019; 8:1112-1120. [PMID: 30966743 DOI: 10.1021/acssynbio.9b00019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Self-assembled protein nanostructures have gained interest, owing to their potential applications in biomaterials; however, successful design and construction of protein nanostructures are limited. Herein, we constructed fusion protein 1 by linking the C-terminus of a dimerization domain and the N-terminus of another dimerization domain with a three-helix bundle protein, where it self-assembled mainly into tetramers. By replacing the C-terminal dimerization domain of 1 with a trimerization domain (fusion protein 2), hexamers were mainly obtained. According to ab initio structural models reconstructed from the small-angle X-ray scattering data, the tetramer of 1 and hexamer of 2 adopted quadrangle and cage-like structures, respectively, although they were combinations of different conformations. High-speed atomic force microscopy observations indicated that the tetramer and hexamer exhibit conformational dynamics. These results show that the present method utilizing three-helix bundle-linked fusion proteins is useful in the construction of protein nanostructures.
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Affiliation(s)
- Takaaki Miyamoto
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Yugo Hayashi
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Keito Yoshida
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hiroki Watanabe
- Exploratory Research Center on Life and Living Systems, Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Takayuki Uchihashi
- Exploratory Research Center on Life and Living Systems, Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
- Department of Physics, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Kento Yonezawa
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Nobutaka Shimizu
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Hironari Kamikubo
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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26
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Churchfield LA, Tezcan FA. Design and Construction of Functional Supramolecular Metalloprotein Assemblies. Acc Chem Res 2019; 52:345-355. [PMID: 30698941 DOI: 10.1021/acs.accounts.8b00617] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nature puts to use only a small fraction of metal ions in the periodic table. Yet, when incorporated into protein scaffolds, this limited set of metal ions carry out innumerable cellular functions and execute essential biochemical transformations such as photochemical H2O oxidation, O2 or CO2 reduction, and N2 fixation, highlighting the outsized importance of metalloproteins in biology. Not surprisingly, elucidating the intricate interplay between metal ions and protein structures has been the focus of extensive structural and mechanistic scrutiny over the last several decades. As a result of such top-down efforts, we have gained a reasonably detailed understanding of how metal ions shape protein structures and how protein structures in turn influence metal reactivity. It is fair to say that we now have some idea-and in some cases, a good idea-about how most known metalloproteins function and we possess enough insight to quickly assess the modus operandi of newly discovered ones. However, translating this knowledge into an ability to construct functional metalloproteins from scratch represents a challenge at a whole different level: it is one thing to know how an automobile works; it is another to build one. In our quest to build new metalloproteins, we have taken an original approach in which folded, monomeric proteins are used as ligands or synthons for building supramolecular complexes through metal-mediated self-assembly (MDPSA, Metal-Directed Protein Self-Assembly). The interfaces in the resulting protein superstructures are subsequently tailored with covalent, noncovalent, or additional metal-coordination interactions for stabilization and incorporation of new functionalities (MeTIR, Metal Templated Interface Redesign). In an earlier Account, we had described the proof-of-principle studies for MDPSA and MeTIR, using a four-helix bundle, heme protein cytochrome cb562 (cyt cb562), as a model building block. By the end of those studies, we were able to demonstrate that a tetrameric, Zn-directed cyt cb562 complex (Zn4:M14) could be stabilized through computationally prescribed noncovalent interactions inserted into the nascent protein-protein interfaces. In this Account, we first describe the rationale and motivation for our particular metalloprotein engineering strategy and a brief summary of our earlier work. We then describe the next steps in the "evolution" of bioinorganic complexity on the Zn4:M14 scaffold, namely, (a) the generation of a self-standing protein assembly that can stably and selectively bind metal ions, (b) the creation of reactive metal centers within the protein assembly, and (c) the coupling of metal coordination and reactivity to external stimuli through allosteric effects.
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Affiliation(s)
- Lewis A. Churchfield
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0356, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0356, United States
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27
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Markel U, Sauer DF, Schiffels J, Okuda J, Schwaneberg U. Towards the Evolution of Artificial Metalloenzymes—A Protein Engineer's Perspective. Angew Chem Int Ed Engl 2019; 58:4454-4464. [DOI: 10.1002/anie.201811042] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Ulrich Markel
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Daniel F. Sauer
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Johannes Schiffels
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Jun Okuda
- Institute of Inorganic Chemistry RWTH Aachen University Landoltweg 1 52056 Aachen Germany
| | - Ulrich Schwaneberg
- DWI Leibniz-Institute for Interactive Materials Forckenbeckstrasse 50 52074 Aachen Germany
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
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28
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Markel U, Sauer DF, Schiffels J, Okuda J, Schwaneberg U. Auf dem Weg zur Evolution artifizieller Metalloenzyme – aus einem Protein‐Engineering‐Blickwinkel. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201811042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ulrich Markel
- Institut für Biotechnologie RWTH Aachen Worringer Weg 3 52074 Aachen Deutschland
| | - Daniel F. Sauer
- Institut für Biotechnologie RWTH Aachen Worringer Weg 3 52074 Aachen Deutschland
| | - Johannes Schiffels
- Institut für Biotechnologie RWTH Aachen Worringer Weg 3 52074 Aachen Deutschland
| | - Jun Okuda
- Institut für Anorganische Chemie RWTH Aachen Landoltweg 1 52056 Aachen Deutschland
| | - Ulrich Schwaneberg
- DWI Leibniz-Institut für Interaktive Materialien Forckenbeckstraße 50 52074 Aachen Deutschland
- Institut für Biotechnologie RWTH Aachen Worringer Weg 3 52074 Aachen Deutschland
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29
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Kuan SL, Bergamini FRG, Weil T. Functional protein nanostructures: a chemical toolbox. Chem Soc Rev 2018; 47:9069-9105. [PMID: 30452046 PMCID: PMC6289173 DOI: 10.1039/c8cs00590g] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Indexed: 01/08/2023]
Abstract
Nature has evolved an optimal synthetic factory in the form of translational and posttranslational processes by which millions of proteins with defined primary sequences and 3D structures can be built. Nature's toolkit gives rise to protein building blocks, which dictates their spatial arrangement to form functional protein nanostructures that serve a myriad of functions in cells, ranging from biocatalysis, formation of structural networks, and regulation of biochemical processes, to sensing. With the advent of chemical tools for site-selective protein modifications and recombinant engineering, there is a rapid development to develop and apply synthetic methods for creating structurally defined, functional protein nanostructures for a broad range of applications in the fields of catalysis, materials and biomedical sciences. In this review, design principles and structural features for achieving and characterizing functional protein nanostructures by synthetic approaches are summarized. The synthetic customization of protein building blocks, the design and introduction of recognition units and linkers and subsequent assembly into structurally defined protein architectures are discussed herein. Key examples of these supramolecular protein nanostructures, their unique functions and resultant impact for biomedical applications are highlighted.
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Affiliation(s)
- Seah Ling Kuan
- Max-Planck Institute for Polymer Research
,
Ackermannweg 10
, 55128 Mainz
, Germany
.
;
- Institute of Inorganic Chemistry I – Ulm University
,
Albert-Einstein-Allee 11
, 89081 Ulm
, Germany
| | - Fernando R. G. Bergamini
- Institute of Chemistry
, Federal University of Uberlândia – UFU
,
38400-902 Uberlândia
, MG
, Brazil
| | - Tanja Weil
- Max-Planck Institute for Polymer Research
,
Ackermannweg 10
, 55128 Mainz
, Germany
.
;
- Institute of Inorganic Chemistry I – Ulm University
,
Albert-Einstein-Allee 11
, 89081 Ulm
, Germany
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30
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Dhillon A, Sharma K, Rajulapati V, Goyal A. The multi-ligand binding first family 35 Carbohydrate Binding Module (CBM35) of Clostridium thermocellum targets rhamnogalacturonan I. Arch Biochem Biophys 2018; 654:194-208. [PMID: 30080990 DOI: 10.1016/j.abb.2018.07.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/25/2018] [Accepted: 07/27/2018] [Indexed: 11/24/2022]
Abstract
Carbohydrate Binding Modules (CBMs) targeting cellulose, xylan and mannan have been reported, however, a CBM targeting rhamnogalacturonan I (RG I) has never been identified. We had studied earlier a rhamnogalacturonan lyase (CtRGL) from Clostridium thermocellum that was associated with a family 35 CBM, Rgl-CBM35. In this study we show that Rgl-CBM35 displays binding with β-d-glucuronic acid (β-D-GlcpA), Δ4,5-anhydro-d-galactopyranosyluronic acid (Δ4,5-GalpA), rhamnogalacturonan I, arabinan, galactan, glucuronoxylans and arabinoxylans. Rgl-CBM35 contains a conserved ligand binding site in the loops known for binding β-D-GlcpA and Δ4,5-GalpA moiety of unsaturated RG I and pectic-oligosaccharides. Mutagenesis revealed that Asn118 plays an important role in binding β-D-GlcpA, Δ4,5-GalpA, sugarbeet arabinan and potato galactan at its conserved ligand binding site present in surface exposed loops. EDTA-treated Rgl-CBM35 showed no affinity towards β-D-GlcpA and Δ4,5-GalpA underscoring Ca2+ mediated ligand recognition. Contrastingly, the EDTA-treated Rgl-CBM35 and its mutant N118A displayed affinity for sugarbeet arabinan and potato galactan. The curtailed affinity of Y37A/N118A and R69A/N118A double mutants towards sugarbeet arabinan emphasized the presence of a second ligand binding site. Rgl-CBM35 is the first CBM reported to primarily target RG I and also is the first member of family 35 CBM possessing at least two ligand binding sites.
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Affiliation(s)
- Arun Dhillon
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Kedar Sharma
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Vikky Rajulapati
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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31
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Alcala-Torano R, Walther M, Sommer DJ, Park CK, Ghirlanda G. Rational design of a hexameric protein assembly stabilized by metal chelation. Biopolymers 2018; 109:e23233. [PMID: 30191549 DOI: 10.1002/bip.23233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 06/15/2018] [Accepted: 07/05/2018] [Indexed: 12/27/2022]
Abstract
Protein-based self-assembled nanostructures hold tremendous promise as smart materials. One strategy to control the assembly of individual protein modules takes advantage of the directionality and high affinity bonding afforded by metal chelation. Here, we describe the use of 2,2'-bipyridine units (Bpy) as side chains to template the assembly of large structures (MW approx. 35 000 Da) in a metal-dependent manner. The structures are trimers of independently folded 3-helix bundles, and are held together by 2 Me(Bpy)3 complexes. The assemblies are stable to thermal denaturation, and are more than 90% helical at 90°C. Circular dichroism spectroscopy shows that one of the 2 possible (Bpy)3 enantiomers is favored over the other. Because of the sequence pliability of the starting peptides, these constructs could find use to organize functional groups at controlled positions within a supramolecular assembly.
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Affiliation(s)
| | - Mathieu Walther
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
| | - Dayn J Sommer
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
| | - Chad K Park
- Department of Biochemistry, University of Arizona, Tucson, Arizona
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Nakashige TG, Bowman SEJ, Zygiel EM, Drennan CL, Nolan EM. Biophysical Examination of the Calcium-Modulated Nickel-Binding Properties of Human Calprotectin Reveals Conformational Change in the EF-Hand Domains and His 3Asp Site. Biochemistry 2018; 57:4155-4164. [PMID: 29890074 PMCID: PMC6050108 DOI: 10.1021/acs.biochem.8b00415] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Calprotectin (CP, S100A8/S100A9 oligomer, MRP-8/MRP-14 oligomer) is a host-defense protein that sequesters nutrient transition metals from microbes. Each S100A8/S100A9 heterodimer contains four EF-hand domains and two transition-metal-binding sites. We investigate the effect of Ca(II) ions on the structure and Ni(II)-binding properties of human CP. By employing energy dispersive X-ray (EDX) spectroscopy, we evaluate the metal content of Ni(II)-bound CP-Ser [oligomer of S100A8(C42S) and S100A9(C3S)] crystals obtained in the absence and presence of Ca(II). We present a 2.1 Å resolution crystal structure of Ni(II)-bound CP-Ser and compare this structure to a reported Ni(II)- and Ca(II)-bound CP-Ser structure [Nakashige, T. G., et al. (2017) J. Am. Chem. Soc. 139, 8828-8836]. This analysis reveals conformational changes associated with coordination of Ca(II) to the EF-hands of S100A9 and that Ca(II) binding affects the coordination number and geometry of the Ni(II) ion bound to the His3Asp site. In contrast, negligible differences are observed for the Ni(II)-His6 site in the absence and presence of Ca(II). Biochemical studies show that, whereas the His6 site has a thermodynamic preference for Ni(II) over Zn(II), the His3Asp site selects for Zn(II) over Ni(II), and relatively rapid metal exchange occurs at this site. These observations inform the working model for how CP withholds nutrient metals in the extracellular space.
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33
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Yang G, Wu L, Chen G, Jiang M. Precise protein assembly of array structures. Chem Commun (Camb) 2018; 52:10595-605. [PMID: 27384233 DOI: 10.1039/c6cc04190f] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The assembly of proteins into various nano-objects with regular and periodic microstructures, i.e. protein arrays, is a fast-growing field in materials science. Due to the structural complexity of proteins, reports in this field are still quite limited. In this review, we summarize the recent developments in protein array construction by different driving forces, including electrostatic interactions, metal-ligand interactions, molecular recognition and protein-protein interactions. In line with our particular interest, assemblies driven by molecular recognition are particularly explored. Finally, functionalities of the obtained protein arrays are briefly discussed.
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Affiliation(s)
- Guang Yang
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
| | - Libin Wu
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
| | - Guosong Chen
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
| | - Ming Jiang
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
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34
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Knight AS, Larsson J, Ren JM, Zerdan RB, Seguin S, Vrahas R, Liu J, Ren G, Hawker CJ. Control of Amphiphile Self-Assembly via Bioinspired Metal Ion Coordination. J Am Chem Soc 2018; 140:1409-1414. [PMID: 29338205 PMCID: PMC10546914 DOI: 10.1021/jacs.7b11005] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Inspired by marine siderophores that exhibit a morphological shift upon metal coordination, hybrid peptide-polymer conjugates that assemble into different morphologies based on the nature of the metal ion coordination have been designed. Coupling of a peptide chelator, hexahistidine, with hydrophobic oligostyrene allows a modular strategy to be established for the efficient synthesis and purification of these tunable amphiphiles (oSt(His)6). Remarkably, in the presence of different divalent transition metal ions (Mn, Co, Ni, Cu, Zn, and Cd) a variety of morphologies were observed. Zinc(II), cobalt(II), and copper(II) led to aggregated micelles. Nickel(II) and cadmium(II) produced micelles, and multilamellar vesicles were obtained in the presence of manganese(II). This work highlights the significant potential for transition metal ion coordination as a tool for directing the assembly of synthetic nanomaterials.
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Affiliation(s)
- Abigail S. Knight
- California NanoSystems Institute and Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States
| | - Josefin Larsson
- California NanoSystems Institute and Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States
| | - Jing M. Ren
- California NanoSystems Institute and Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States
| | - Raghida Bou Zerdan
- California NanoSystems Institute and Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States
| | - Shay Seguin
- California NanoSystems Institute and Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States
| | - Remy Vrahas
- California NanoSystems Institute and Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Craig J. Hawker
- California NanoSystems Institute and Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States
- Materials Department and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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35
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Wang Z, Dai Y, Wang Z, Jacobson O, Zhang F, Yung BC, Zhang P, Gao H, Niu G, Liu G, Chen X. Metal ion assisted interface re-engineering of a ferritin nanocage for enhanced biofunctions and cancer therapy. NANOSCALE 2018; 10:1135-1144. [PMID: 29271453 PMCID: PMC5812362 DOI: 10.1039/c7nr08188j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The bottom-up self-assembly of protein subunits into supramolecular nanoarchitectures is ubiquitously exploited to recapitulate and expand the features of natural proteins to advance nanoscience in medicine. Various chemical and biological re-engineering approaches are available to render diverse functions in the given proteins. They are, unfortunately, capable of compromising protein integrity and stability after extensive modifications. In this study, we introduce a new protein re-engineering method, metal ion assisted interface re-engineering (MAIR), to serve as a robust and universal strategy to extend the functions of self-assembly proteins by boosting structural features to advance their diverse biomedical applications. In particular, the MAIR strategy was applied to a widely used natural protein, ferritin, as a model protein to coordinate with copper ions in its mutagenic artificial metal binding domain. Structure directed rational protein mutagenesis was carried out at the C2 interface amino acid residues of the ferritin subunit for metal ion coordination site optimization. Copper binding at the artificial binding pocket was highly specific over the other divalent ions present in physiological fluids, and the structurally embedded copper ion in turn strengthened the overall protein integrity and stability. In the presence of isotopic copper-64, the interface re-engineered ferritin worked as a chelator-free molecular nanoprobe with an extraordinarily high specific activity to allow PET imaging of tumors in live animals. We also found that the re-engineered ferritin coordinating with copper ions demonstrates high drug loading capacity of a widely used anti-cancer agent, doxorubicin (DOX), to achieve significant drug retention at the tumor site and enhance tumor regression for improved anti-cancer effects. The MAIR approach, thus, exploited the copper ion to facilitate efficient one-step labeling of mutant ferritin derivatives for simultaneous molecular imaging and drug delivery. The reported interface re-engineering strategy provides an unparalleled opportunity to expand protein biofunctions to serve as a new theranostic agent in cancer research.
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Affiliation(s)
- Zhantong Wang
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, USA.
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36
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Nakashige TG, Zygiel EM, Drennan CL, Nolan EM. Nickel Sequestration by the Host-Defense Protein Human Calprotectin. J Am Chem Soc 2017; 139:8828-8836. [PMID: 28573847 PMCID: PMC5754018 DOI: 10.1021/jacs.7b01212] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The human innate immune protein calprotectin (CP, S100A8/S100A9 oligomer, calgranulin A/calgranulin B oligomer, MRP-8/MRP-14 oligomer) chelates a number of first-row transition metals, including Mn(II), Fe(II), and Zn(II), and can withhold these essential nutrients from microbes. Here we elucidate the Ni(II) coordination chemistry of human CP. We present a 2.6-Å crystal structure of Ni(II)- and Ca(II)-bound CP, which reveals that CP binds Ni(II) ions at both its transition-metal-binding sites: the His3Asp motif (site 1) and the His6 motif (site 2). Further biochemical studies establish that coordination of Ni(II) at the hexahistidine site is thermodynamically preferred over Zn(II). We also demonstrate that CP can sequester Ni(II) from two human pathogens, Staphylococcus aureus and Klebsiella pneumoniae, that utilize this metal nutrient during infection, and inhibit the activity of the Ni(II)-dependent enzyme urease in bacterial cultures. In total, our findings expand the biological coordination chemistry of Ni(II)-chelating proteins in nature and provide a foundation for evaluating putative roles of CP in Ni(II) homeostasis at the host-microbe interface and beyond.
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Affiliation(s)
- Toshiki G. Nakashige
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Emily M. Zygiel
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Catherine L. Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Elizabeth M. Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
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37
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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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38
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Repurposing proteins for new bioinorganic functions. Essays Biochem 2017; 61:245-258. [DOI: 10.1042/ebc20160068] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/17/2017] [Accepted: 01/23/2017] [Indexed: 02/06/2023]
Abstract
Inspired by the remarkable sophistication and complexity of natural metalloproteins, the field of protein design and engineering has traditionally sought to understand and recapitulate the design principles that underlie the interplay between metals and protein scaffolds. Yet, some recent efforts in the field demonstrate that it is possible to create new metalloproteins with structural, functional and physico-chemical properties that transcend evolutionary boundaries. This essay aims to highlight some of these efforts and draw attention to the ever-expanding scope of bioinorganic chemistry and its new connections to synthetic biology, biotechnology, supramolecular chemistry and materials engineering.
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39
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40
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Design of Redox-Active Peptides: Towards Functional Materials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [PMID: 27677515 DOI: 10.1007/978-3-319-39196-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
In nature, the majority of processes that occur in the cell involve the cycling of electrons and protons, changing the reduction and oxidation state of substrates to alter their chemical reactivity and usefulness in vivo. One of the most relevant examples of these processes is the electron transport chain, a series of oxidoreductase proteins that shuttle electrons through well-defined pathways, concurrently moving protons across the cell membrane. Inspired by these processes, researchers have sought to develop materials to mimic natural systems for a number of applications, including fuel production. The most common cofactors found in proteins to carry out electron transfer are iron sulfur clusters and porphyrin-like molecules. Both types have been studied within natural proteins, such as in photosynthetic machinery or soluble electron carriers; in parallel, an extensive literature has developed over recent years attempting to model and study these cofactors within peptide-based materials. This chapter will focus on major designs that have significantly advanced the field.
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Luo Q, Hou C, Bai Y, Wang R, Liu J. Protein Assembly: Versatile Approaches to Construct Highly Ordered Nanostructures. Chem Rev 2016; 116:13571-13632. [PMID: 27587089 DOI: 10.1021/acs.chemrev.6b00228] [Citation(s) in RCA: 357] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Nature endows life with a wide variety of sophisticated, synergistic, and highly functional protein assemblies. Following Nature's inspiration to assemble protein building blocks into exquisite nanostructures is emerging as a fascinating research field. Dictating protein assembly to obtain highly ordered nanostructures and sophisticated functions not only provides a powerful tool to understand the natural protein assembly process but also offers access to advanced biomaterials. Over the past couple of decades, the field of protein assembly has undergone unexpected and rapid developments, and various innovative strategies have been proposed. This Review outlines recent advances in the field of protein assembly and summarizes several strategies, including biotechnological strategies, chemical strategies, and combinations of these approaches, for manipulating proteins to self-assemble into desired nanostructures. The emergent applications of protein assemblies as versatile platforms to design a wide variety of attractive functional materials with improved performances have also been discussed. The goal of this Review is to highlight the importance of this highly interdisciplinary field and to promote its growth in a diverse variety of research fields ranging from nanoscience and material science to synthetic biology.
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Affiliation(s)
- Quan Luo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Chunxi Hou
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Yushi Bai
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Ruibing Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Taipa, Macau SAR 999078, China
| | - Junqiu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
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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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Bailey JB, Subramanian RH, Churchfield LA, Tezcan FA. Metal-Directed Design of Supramolecular Protein Assemblies. Methods Enzymol 2016; 580:223-50. [PMID: 27586336 PMCID: PMC5131729 DOI: 10.1016/bs.mie.2016.05.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Owing to their central roles in cellular signaling, construction, and biochemistry, protein-protein interactions (PPIs) and protein self-assembly have become a major focus of molecular design and synthetic biology. In order to circumvent the complexity of constructing extensive noncovalent interfaces, which are typically involved in natural PPIs and protein self-assembly, we have developed two design strategies, metal-directed protein self-assembly (MDPSA) and metal-templated interface redesign (MeTIR). These strategies, inspired by both the proposed evolutionary roles of metals and their prevalence in natural PPIs, take advantage of the favorable properties of metal coordination (bonding strength, directionality, and reversibility) to guide protein self-assembly with minimal design and engineering. Using a small, monomeric protein (cytochrome cb562) as a model building block, we employed MDPSA and MeTIR to create a diverse array of functional supramolecular architectures which range from structurally tunable oligomers to metalloprotein complexes that can properly self-assemble in living cells into novel metalloenzymes. The design principles and strategies outlined herein should be readily applicable to other protein systems with the goal of creating new PPIs and protein assemblies with structures and functions not yet produced by natural evolution.
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Affiliation(s)
- J B Bailey
- University of California, San Diego, La Jolla, CA, United States
| | - R H Subramanian
- University of California, San Diego, La Jolla, CA, United States
| | - L A Churchfield
- University of California, San Diego, La Jolla, CA, United States
| | - F A Tezcan
- University of California, San Diego, La Jolla, CA, United States.
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Determining the N-terminal orientations of recombinant transmembrane proteins in the Escherichia coli plasma membrane. Sci Rep 2015; 5:15086. [PMID: 26462555 PMCID: PMC4604451 DOI: 10.1038/srep15086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/11/2015] [Indexed: 11/08/2022] Open
Abstract
In silico algorithms have been the common approach for transmembrane (TM) protein topology prediction. However, computational tools may produce questionable results and experimental validation has proven difficult. Although biochemical strategies are available to determine the C-terminal orientation of TM proteins, experimental strategies to determine the N-terminal orientation are still limited but needed because the N-terminal end is essential for membrane targeting. Here, we describe a new and easy method to effectively determine the N-terminal orientation of the target TM proteins in Escherichia coli plasma membrane environment. D94N, the mutant of bacteriorhodopsin from Haloarcula marismortui, can be a fusion partner to increase the production of the target TM proteins if their N-termini are in cytoplasm (Nin orientation). To create a suitable linker for orientating the target TM proteins with the periplasmic N-termini (Nout orientation) correctly, we designed a three-TM-helix linker fused at the C-terminus of D94N fusion partner (termed D94N-3TM) and found that D94N-3TM can specifically improve the production of the Nout target TM proteins. In conclusion, D94N and D94N-3TM fusion partners can be applied to determine the N-terminal end of the target TM proteins oriented either Nin or Nout by evaluating the net expression of the fusion proteins.
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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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Lai YT, Jiang L, Chen W, Yeates TO. On the predictability of the orientation of protein domains joined by a spanning alpha-helical linker. Protein Eng Des Sel 2015; 28:491-9. [DOI: 10.1093/protein/gzv035] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 07/08/2015] [Indexed: 11/14/2022] Open
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Bullen GA, Tucker JHR, Peacock AFA. Exploiting anthracene photodimerization within peptides: light induced sequence-selective DNA binding. Chem Commun (Camb) 2015; 51:8130-3. [DOI: 10.1039/c5cc01618e] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Here we detail the first example of anthracene photodimerisation in peptides, and use it to trigger a selective biomolecular recognition event.
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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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Luo Q, Dong Z, Hou C, Liu J. Protein-based supramolecular polymers: progress and prospect. Chem Commun (Camb) 2014; 50:9997-10007. [DOI: 10.1039/c4cc03143a] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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50
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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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