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Adra HJ, Jeong KB, You SM, Seo DH, Baik MY, Park CS, Kim YR. Palmitic acid-mediated modulation of crystallization dynamics in amylose microparticle formation: From spherical to macaron and disc shapes. Food Chem 2024; 460:140804. [PMID: 39137578 DOI: 10.1016/j.foodchem.2024.140804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/04/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024]
Abstract
Here, we investigated the complexation of short chain amylose (SCAs) and palmitic acid (PA), serving as polymeric building blocks that alter the selectivity and directionality of particle growth. This alteration affects the shape anisotropy of the particles, broadening their applications due to the increased surface area. By modifying the concentration of PA, we were able to make spherical, macaron, and disc-shaped particles, demonstrating that PA acts as a structure-directing agent. We further illustrated the lateral and longitudinal stacking kinetics between PA-SCA inclusion complexes during self-assembly, leading to anisotropy. Transmission electron microscope (TEM) and scanning electron microscope (SEM) revealed the structural difference between the initial and final morphologies of palmitic acid-short chain amylose particles (PA-SCAPs) compared to those of short-chain amylose particle (SCAPs). The presence of PA-SCA inclusion complex in the anisotropic particles was confirmed using nuclear magnetic resonance (NMR) and powder x-ray diffraction (XRD) analysis.
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Affiliation(s)
- Hazzel Joy Adra
- Institute of Life Sciences and Resources & Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea; Department of Food Technology, College of Education, University of Santo Tomas, Espana Blvd, Sampaloc, Manila 1008, Philippines
| | - Ki-Baek Jeong
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Sang-Mook You
- Institute of Life Sciences and Resources & Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Dong-Ho Seo
- Institute of Life Sciences and Resources & Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Moo-Yeol Baik
- Institute of Life Sciences and Resources & Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Cheon-Seok Park
- Institute of Life Sciences and Resources & Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Young-Rok Kim
- Institute of Life Sciences and Resources & Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea.
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2
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Han K, Zhang Z, Tezcan FA. Spatially Patterned, Porous Protein Crystals as Multifunctional Materials. J Am Chem Soc 2023; 145:19932-19944. [PMID: 37642457 DOI: 10.1021/jacs.3c06348] [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: 08/31/2023]
Abstract
While the primary use of protein crystals has historically been in crystallographic structure determination, they have recently emerged as promising materials with many advantageous properties such as high porosity, biocompatibility, stability, structural and functional versatility, and genetic/chemical tailorability. Here, we report that the utility of protein crystals as functional materials can be further augmented through their spatial patterning and control of their morphologies. To this end, we took advantage of the chemically and kinetically controllable nature of ferritin self-assembly and constructed core-shell crystals with chemically distinct domains, tunable structural patterns, and morphologies. The spatial organization within ferritin crystals enabled the generation of patterned, multi-enzyme frameworks with cooperative catalytic behavior. We further exploited the differential growth kinetics of ferritin crystal facets to assemble Janus-type architectures with an anisotropic arrangement of chemically distinct domains. These examples represent a step toward using protein crystals as reaction vessels for complex multi-step reactions and broadening their utility as functional, solid-state materials. Our results demonstrate that morphology control and spatial patterning, which are key concepts in materials science and nanotechnology, can also be applied for engineering protein crystals.
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Affiliation(s)
- Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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3
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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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4
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Han K, Na Y, Zhang L, Tezcan FA. Dynamic, Polymer-Integrated Crystals for Efficient, Reversible Protein Encapsulation. J Am Chem Soc 2022; 144:10139-10144. [PMID: 35666988 DOI: 10.1021/jacs.2c02584] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crystalline materials are increasingly being used as platforms for encapsulating proteins to create stable, functional materials. However, the uptake efficiencies and stimuli-responsiveness of crystalline frameworks are limited by their rigidities. We have recently reported a new form of materials, polymer-integrated crystals (PIX), which combine the structural order of protein crystals with the dynamic, stimuli-responsive properties of synthetic polymers. Here we show that the crystallinity, flexibility, and chemical tunability of PIX can be exploited to encapsulate guest proteins with high loading efficiencies (up to 46% w/w). The electrostatic host-guest interactions enable reversible, pH-controlled uptake/release of guest proteins as well as the mutual stabilization of the host and the guest, thus creating a uniquely synergistic platform toward the development of functional biomaterials and the controlled delivery of biological macromolecules.
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Affiliation(s)
- Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Ling Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States.,Materials Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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Domínguez-Zotes S, Fuertes MA, Rodríguez-Huete A, Valbuena A, Mateu MG. A Genetically Engineered, Chain Mail-Like Nanostructured Protein Material with Increased Fatigue Resistance and Enhanced Self-Healing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2105456. [PMID: 35060301 DOI: 10.1002/smll.202105456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Protein-based nanostructured materials are being developed for many biomedical and nanotechnological applications. Despite their many desirable features, protein materials are highly susceptible to disruption by mechanical stress and fatigue. This study is aimed to increase fatigue resistance and enhance self-healing of a natural protein-based supramolecular nanomaterial through permanent genetic modification. The authors envisage the conversion of a model nanosheet, formed by a regular array of noncovalently bound human immunodeficiency virus capsid protein molecules, into a supramolecular "chain mail." Rationally engineered mutations allow the formation of a regular network of disulfide bridges in the protein lattice. This network links each molecule in the lattice to each adjacent molecule through one covalent bond, analogous to the rivetting of interlinked iron rings in the chain mail of a medieval knight. The engineered protein nanosheet shows greatly increased thermostability and resistance to mechanical stress and fatigue in particular, as well as enhanced self-healing, without undesirable stiffening compared to the original material. The results provide proof of concept for a genetic design to permanently increase fatigue resistance and enhance self-healing of protein-based nanostructured materials. They also provide insights into the molecular basis for fatigue of protein materials.
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Affiliation(s)
- Santos Domínguez-Zotes
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, Madrid, 28049, Spain
| | - Miguel Angel Fuertes
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, Madrid, 28049, Spain
| | - Alicia Rodríguez-Huete
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, Madrid, 28049, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, Madrid, 28049, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, Madrid, 28049, Spain
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Kojima M, Abe S, Ueno T. Engineering of protein crystals for use as solid biomaterials. Biomater Sci 2021; 10:354-367. [PMID: 34928275 DOI: 10.1039/d1bm01752g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein crystals have attracted a great deal of attention as solid biomaterials because they have porous structures created by regular assemblies of proteins. The lattice structures of protein crystals are controlled by designing molecular interfacial interactions via covalent bonds and non-covalent bonds. Protein crystals have been functionalized as templates to immobilize foreign molecules such as metal nanoparticles, metal complexes, and proteins. These hybrid crystals are used as functional materials for catalytic reactions and structural analysis. Furthermore, in-cell protein crystals have been studied extensively, providing progress in rapid protein crystallization and crystallography. This review highlights recent advances in crystal engineering for protein crystallization and generation of solid functional materials both in vitro and within cells.
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Affiliation(s)
- Mariko Kojima
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
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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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Selivanovitch E, Uchida M, Lee B, Douglas T. Substrate Partitioning into Protein Macromolecular Frameworks for Enhanced Catalytic Turnover. ACS NANO 2021; 15:15687-15699. [PMID: 34473481 PMCID: PMC9136710 DOI: 10.1021/acsnano.1c05004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Spatial partitioning of chemical processes is an important attribute of many biological systems, the effect of which is reflected in the high efficiency of enzymes found within otherwise chaotic cellular environments. Barriers, often provided through the formation of compartments or phase segregation, gate the access of macromolecules and small molecules within the cell and provide an added level of metabolic control. Taking inspiration from nature, we have designed virus-like particles (VLPs) as nanoreactor compartments that sequester enzyme catalysts and have used these as building blocks to construct 3D protein macromolecular framework (PMF) materials, which are structurally characterized using small-angle X-ray scattering (SAXS). The highly charged PMFs form a separate phase in suspension, and by tuning the ionic strength, we show positively charged molecules preferentially partition into the PMF, while negatively charged molecules are excluded. This molecular partitioning was exploited to tune the catalytic activity of enzymes enclosed within the individual particles in the PMF, the results of which showed that positively charged substrates had turnover rates that were 8500× faster than their negatively charged counterparts. Moreover, the catalytic PMF led to cooperative behavior resulting in charge dependent trends opposite to those observed with individual P22 nanoreactor particles.
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Affiliation(s)
- Ekaterina Selivanovitch
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Masaki Uchida
- Department of Chemistry and Biochemistry, California State University Fresno, Fresno, California 93740, Unites States
| | - Byeongdu Lee
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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Sun R, Lim S. Protein cages as building blocks for superstructures. ENGINEERING BIOLOGY 2021; 5:35-42. [PMID: 36969478 PMCID: PMC9996708 DOI: 10.1049/enb2.12010] [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: 04/27/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 11/20/2022] Open
Abstract
Proteins naturally self-assemble to function. Protein cages result from the self-assembly of multiple protein subunits that interact to form hollow symmetrical structures with functions that range from cargo storage to catalysis. Driven by self-assembly, building elegant higher-order superstructures with protein cages as building blocks has been an increasingly attractive field in recent years. It presents an engineering challenge not only at the molecular level but also at the supramolecular level. The higher-order constructs are proposed to provide access to diverse functional materials. Focussing on design strategy as a perspective, current work on protein cage supramolecular self-assembly are reviewed from three principles that are electrostatic, metal-ligand coordination and inherent symmetry. The review also summarises possible applications of the superstructure architecture built using modified protein cages.
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Affiliation(s)
- Ruoxuan Sun
- School of Chemical and Biomedical EngineeringNanyang Technological UniversitySingapore
| | - Sierin Lim
- School of Chemical and Biomedical EngineeringNanyang Technological UniversitySingapore
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