1
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Patkar SS, Wang B, Mosquera AM, Kiick KL. Genetically Fusing Order-Promoting and Thermoresponsive Building Blocks to Design Hybrid Biomaterials. Chemistry 2024; 30:e202400582. [PMID: 38501912 DOI: 10.1002/chem.202400582] [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: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 03/20/2024]
Abstract
The unique biophysical and biochemical properties of intrinsically disordered proteins (IDPs) and their recombinant derivatives, intrinsically disordered protein polymers (IDPPs) offer opportunities for producing multistimuli-responsive materials; their sequence-encoded disorder and tendency for phase separation facilitate the development of multifunctional materials. This review highlights the strategies for enhancing the structural diversity of elastin-like polypeptides (ELPs) and resilin-like polypeptides (RLPs), and their self-assembled structures via genetic fusion to ordered motifs such as helical or beta sheet domains. In particular, this review describes approaches that harness the synergistic interplay between order-promoting and thermoresponsive building blocks to design hybrid biomaterials, resulting in well-structured, stimuli-responsive supramolecular materials ordered on the nanoscale.
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Affiliation(s)
- Sai S Patkar
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware, 19716, United States
- Eli Lilly and Company, 450 Kendall Street, Cambridge, MA, 02142, United States
| | - Bin Wang
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware, 19716, United States
| | - Ana Maria Mosquera
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware, 19716, United States
| | - Kristi L Kiick
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware, 19716, United States
- Department of Biomedical Engineering, University of Delaware, Newark, Delaware, 19716, United States
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2
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Christians LF, Halingstad EV, Kram E, Okolovitch EM, Pak AJ. Formalizing Coarse-Grained Representations of Anisotropic Interactions at Multimeric Protein Interfaces Using Virtual Sites. J Phys Chem B 2024; 128:1394-1406. [PMID: 38316012 DOI: 10.1021/acs.jpcb.3c07023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Molecular simulations of biomacromolecules that assemble into multimeric complexes remain a challenge due to computationally inaccessible length and time scales. Low-resolution and implicit-solvent coarse-grained modeling approaches using traditional nonbonded interactions (both pairwise and spherically isotropic) have been able to partially address this gap. However, these models may fail to capture the complex anisotropic interactions present at macromolecular interfaces unless higher-order interaction potentials are incorporated at the expense of the computational cost. In this work, we introduce an alternate and systematic approach to represent directional interactions at protein-protein interfaces by using virtual sites restricted to pairwise interactions. We show that virtual site interaction parameters can be optimized within a relative entropy minimization framework by using only information from known statistics between coarse-grained sites. We compare our virtual site models to traditional coarse-grained models using two case studies of multimeric protein assemblies and find that the virtual site models predict pairwise correlations with higher fidelity and, more importantly, assembly behavior that is morphologically consistent with experiments. Our study underscores the importance of anisotropic interaction representations and paves the way for more accurate yet computationally efficient coarse-grained simulations of macromolecular assembly in future research.
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Affiliation(s)
- Luc F Christians
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Ethan V Halingstad
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Emiel Kram
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Evan M Okolovitch
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Alexander J Pak
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
- Quantitative Biosciences and Engineering Program, Colorado School of Mines, Golden, Colorado 80401, United States
- Materials Science Program, Colorado School of Mines, Golden, Colorado 80401, United States
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3
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Britton D, Christians LF, Liu C, Legocki J, Xiao Y, Meleties M, Yang L, Cammer M, Jia S, Zhang Z, Mahmoudinobar F, Kowalski Z, Renfrew PD, Bonneau R, Pochan DJ, Pak AJ, Montclare JK. Computational Prediction of Coiled-Coil Protein Gelation Dynamics and Structure. Biomacromolecules 2024; 25:258-271. [PMID: 38110299 PMCID: PMC10777397 DOI: 10.1021/acs.biomac.3c00968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023]
Abstract
Protein hydrogels represent an important and growing biomaterial for a multitude of applications, including diagnostics and drug delivery. We have previously explored the ability to engineer the thermoresponsive supramolecular assembly of coiled-coil proteins into hydrogels with varying gelation properties, where we have defined important parameters in the coiled-coil hydrogel design. Using Rosetta energy scores and Poisson-Boltzmann electrostatic energies, we iterate a computational design strategy to predict the gelation of coiled-coil proteins while simultaneously exploring five new coiled-coil protein hydrogel sequences. Provided this library, we explore the impact of in silico energies on structure and gelation kinetics, where we also reveal a range of blue autofluorescence that enables hydrogel disassembly and recovery. As a result of this library, we identify the new coiled-coil hydrogel sequence, Q5, capable of gelation within 24 h at 4 °C, a more than 2-fold increase over that of our previous iteration Q2. The fast gelation time of Q5 enables the assessment of structural transition in real time using small-angle X-ray scattering (SAXS) that is correlated to coarse-grained and atomistic molecular dynamics simulations revealing the supramolecular assembling behavior of coiled-coils toward nanofiber assembly and gelation. This work represents the first system of hydrogels with predictable self-assembly, autofluorescent capability, and a molecular model of coiled-coil fiber formation.
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Affiliation(s)
- Dustin Britton
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Luc F. Christians
- Department
of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Chengliang Liu
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Jakub Legocki
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Yingxin Xiao
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Michael Meleties
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Lin Yang
- National
Synchrotron Light Source-II, Brookhaven
National Laboratory, Upton, New York 11973, United States
| | - Michael Cammer
- Microscopy
Laboratory, New York University Langone
Health, New York, New York 10016, United States
| | - Sihan Jia
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Zihan Zhang
- Department
of Materials Science and Engineering, University
of Delaware, Newark, Delaware 19716, United States
| | - Farbod Mahmoudinobar
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Center for
Computational Biology, Flatiron Institute, Simons Foundation, New York, New York 10010, United States
| | - Zuzanna Kowalski
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - P. Douglas Renfrew
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Richard Bonneau
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Center
for Genomics and Systems Biology, New York
University, New York, New York 10003, United States
- Courant
Institute of Mathematical Sciences, Computer Science Department, New York University, New York, New York 10009, United States
| | - Darrin J. Pochan
- Department
of Materials Science and Engineering, University
of Delaware, Newark, Delaware 19716, United States
| | - Alexander J. Pak
- Department
of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
- Quantitative
Biosciences and Engineering, Colorado School
of Mines, Golden, Colorado 80401, United States
| | - Jin Kim Montclare
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Department
of Chemistry, New York University, New York, New York 10012, United States
- Department of Biomedical Engineering, New
York University, New York, New York 11201, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department
of Radiology, New York University School
of Medicine, New York, New York 10016, United States
- Department of Biomaterials, New York University
College of Dentistry, New York, New York 10010, United States
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4
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Chen X, Xia C, Guo P, Wang C, Zuo X, Jiang YB, Jiang T. Preserving Structurally Labile Peptide Nanosheets After Molecular Functionalization of the Self-Assembling Peptides. Angew Chem Int Ed Engl 2024; 63:e202315296. [PMID: 38009674 DOI: 10.1002/anie.202315296] [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: 10/10/2023] [Revised: 11/14/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
A significant challenge in creating supramolecular materials is that conjugating molecular functionalities to building blocks often results in dissociation or undesired morphological transformation of their assemblies. Here we present a facile strategy to preserve structurally labile peptide assemblies after molecular modification of the self-assembling peptides. Sheet-forming peptides are designed to afford a staggered alignment with the segments bearing chemical modification sites protruding from the sheet surfaces. The staggered assembly allows for simultaneous separation of attached molecules from each other and from the underlying assembly motifs. Strikingly, using PEGs as the external molecules, PEG400 - and PEG700 -peptide conjugates directly self-associate into nanosheets with the PEG chains localized on the sheet surfaces. In contrast, the sheet formation based on in-register lateral packing of peptides does not recur upon the peptide PEGylation. This strategy allows for fabrication of densely modified assemblies with a variety of molecules, as demonstrated using biotin (hydrophobic molecule), c(RGDfK) (cyclic pentapeptide), and nucleic acid aptamer (negatively charged ssDNA). The staggered co-assembly also enables extended tunability of the amount/density of surface molecules, as exemplified by screening ligand-appended assemblies for cell targeting. This study paves the way for functionalization of historically challenging fragile assemblies while maintaining their overall morphology.
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Affiliation(s)
- Xin Chen
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen, 361005, China
| | - Cai Xia
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen, 361005, China
| | - Pan Guo
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen, 361005, China
| | - Chenru Wang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen, 361005, China
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Yun-Bao Jiang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen, 361005, China
| | - Tao Jiang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen, 361005, China
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5
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Gaspar-Morales EA, Waterston A, Sadqi M, Diaz-Parga P, Smith AM, Gopinath A, Andresen Eguiluz RC, de Alba E. Natural and Engineered Isoforms of the Inflammasome Adaptor ASC Form Noncovalent, pH-Responsive Hydrogels. Biomacromolecules 2023; 24:5563-5577. [PMID: 37930828 DOI: 10.1021/acs.biomac.3c00409] [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: 11/08/2023]
Abstract
The protein ASC polymerizes into intricate filament networks to assemble the inflammasome, a filamentous multiprotein complex that triggers the inflammatory response. ASC carries two Death Domains integrally involved in protein self-association for filament assembly. We have leveraged this behavior to create noncovalent, pH-responsive hydrogels of full-length, folded ASC by carefully controlling the pH as a critical factor in the polymerization process. We show that natural variants of ASC (ASC isoforms) involved in inflammasome regulation also undergo hydrogelation. To further demonstrate this general capability, we engineered proteins inspired by the ASC structure that also form hydrogels. We analyzed the structural network of the natural and engineered protein hydrogels using transmission and scanning electron microscopy and studied their viscoelastic behavior using shear rheology. Our results reveal one of the very few examples of hydrogels created by the self-assembly of globular proteins and domains in their native conformation and show that Death Domains can be used alone or as building blocks to engineer bioinspired hydrogels.
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6
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Britton D, Legocki J, Aristizabal O, Mishkit O, Liu C, Jia S, Renfrew PD, Bonneau R, Wadghiri YZ, Montclare JK. Protein-Engineered Fibers For Drug Encapsulation Traceable via 19F Magnetic Resonance. ACS APPLIED NANO MATERIALS 2023; 6:21245-21257. [PMID: 38037605 PMCID: PMC10682962 DOI: 10.1021/acsanm.3c04357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 12/02/2023]
Abstract
Theranostic materials research is experiencing rapid growth driven by the interest in integrating both therapeutic and diagnostic modalities. These materials offer the unique capability to not only provide treatment but also track the progression of a disease. However, to create an ideal theranostic biomaterial without compromising drug encapsulation, diagnostic imaging must be optimized for improved sensitivity and spatial localization. Herein, we create a protein-engineered fluorinated coiled-coil fiber, Q2TFL, capable of improved sensitivity to 19F magnetic resonance spectroscopy (MRS) detection. Leveraging residue-specific noncanonical amino acid incorporation of trifluoroleucine (TFL) into the coiled-coil, Q2, which self-assembles into nanofibers, we generate Q2TFL. We demonstrate that fluorination results in a greater increase in thermostability and 19F magnetic resonance detection compared to the nonfluorinated parent, Q2. Q2TFL also exhibits linear ratiometric 19F MRS thermoresponsiveness, allowing it to act as a temperature probe. Furthermore, we explore the ability of Q2TFL to encapsulate the anti-inflammatory small molecule, curcumin (CCM), and its impact on the coiled-coil structure. Q2TFL also provides hyposignal contrast in 1H MRI, echogenic signal with high-frequency ultrasound and sensitive detection by 19F MRS in vivo illustrating fluorination of coiled-coils for supramolecular assembly and their use with 1H MRI, 19F MRS and high frequency ultrasound as multimodal theranostic agents.
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Affiliation(s)
- Dustin Britton
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Jakub Legocki
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Orlando Aristizabal
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
| | - Orin Mishkit
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
| | - Chengliang Liu
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Sihan Jia
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Paul Douglas Renfrew
- Center
for Computational Biology, Flatiron Institute,
Simons Foundation, New York, New York 10010, United States
| | - Richard Bonneau
- Center
for Computational Biology, Flatiron Institute,
Simons Foundation, New York, New York 10010, United States
- Center for
Genomics and Systems Biology, New York University, New York, New York 10003, United States
- Courant
Institute
of Mathematical Sciences, Computer Science Department, New York University, New York, New York 10009, United States
| | - Youssef Z. Wadghiri
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
| | - Jin Kim Montclare
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
- Department
of Chemistry, New York University, New York, New York 10012, United States
- Department
of Biomaterials, New York University College
of Dentistry, New York, New York 10010, United States
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7
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Agrahari A, Lipton M, Chmielewski J. Metal-Promoted Higher-Order Assembly of Disulfide-Stapled Helical Barrels. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2645. [PMID: 37836285 PMCID: PMC10574645 DOI: 10.3390/nano13192645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023]
Abstract
Peptide-based helical barrels are a noteworthy building block for hierarchical assembly, with a hydrophobic cavity that can serve as a host for cargo. In this study, disulfide-stapled helical barrels were synthesized containing ligands for metal ions on the hydrophilic face of each amphiphilic peptide helix. The major product of the disulfide-stapling reaction was found to be composed of five amphiphilic peptides, thereby going from a 16-amino-acid peptide to a stapled 80-residue protein in one step. The structure of this pentamer, 5HB1, was optimized in silico, indicating a significant hydrophobic cavity of ~6 Å within a helical barrel. Metal-ion-promoted assembly of the helical barrel building blocks generated higher order assemblies with a three-dimensional (3D) matrix morphology. The matrix was decorated with hydrophobic dyes and His-tagged proteins both before and after assembly, taking advantage of the hydrophobic pocket within the helical barrels and coordination sites within the metal ion-peptide framework. As such, this peptide-based biomaterial has potential for a number of biotechnology applications, including supplying small molecule and protein growth factors during cell and tissue growth within the matrix.
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Affiliation(s)
| | - Mark Lipton
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA;
| | - Jean Chmielewski
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA;
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8
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Guo P, Wang D, Zhang S, Cheng D, Wu S, Zuo X, Jiang YB, Jiang T. Reassembly of Peptide Nanofibrils on Live Cell Surfaces Promotes Cell-Cell Interactions. NANO LETTERS 2023. [PMID: 37399537 DOI: 10.1021/acs.nanolett.3c01100] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Nature regulates cellular interactions through the cell-surface molecules and plasma membranes. Despite advances in cell-surface engineering with diverse ligands and reactive groups, modulating cell-cell interactions through scaffolds of the cell-binding cues remains a challenging endeavor. Here, we assembled peptide nanofibrils on live cell surfaces to present the ligands that bind to the target cells. Surprisingly, with the same ligands, reducing the thermal stability of the nanofibrils promoted cellular interactions. Characterizations of the system revealed a thermally induced fibril disassembly and reassembly pathway that facilitated the complexation of the fibrils with the cells. Using the nanofibrils of varied stabilities, the cell-cell interaction was promoted to different extents with free-to-bound cell conversion ratios achieved at low (31%), medium (54%), and high (93%) levels. This study expands the toolbox to generate desired cell behaviors for applications in many areas and highlights the merits of thermally less stable nanoassemblies in designing functional materials.
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Affiliation(s)
- Pan Guo
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China
| | - Di Wang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China
| | - Shumin Zhang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China
| | - Dan Cheng
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China
| | - Siyu Wu
- X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Yun-Bao Jiang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Tao Jiang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
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9
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Gaspar-Morales EA, Waterston A, Diaz-Parga P, Smith AM, Sadqi M, Gopinath A, Andresen Eguiluz RC, de Alba E. Natural and engineered isoforms of the inflammasome adaptor ASC form non-covalent, pH-responsive hydrogels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539154. [PMID: 37205378 PMCID: PMC10187214 DOI: 10.1101/2023.05.03.539154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The protein ASC polymerizes into intricate filament networks to assemble the inflammasome, a filamentous multiprotein complex that triggers the inflammatory response. ASC carries two Death Domains integrally involved in protein self-association for filament assembly. We have leveraged this behavior to create non-covalent, pH-responsive hydrogels of full-length, folded ASC by carefully controlling the pH as a critical factor in the polymerization process. We show that natural variants of ASC (ASC isoforms) involved in inflammasome regulation also undergo hydrogelation. To further demonstrate this general capability, we engineered proteins inspired in the ASC structure that successfully form hydrogels. We analyzed the structural network of the natural and engineered protein hydrogels using transmission and scanning electron microscopy, and studied their viscoelastic behavior by shear rheology. Our results reveal one of the very few examples of hydrogels created by the self-assembly of globular proteins and domains in their native conformation and show that Death Domains can be used alone or as building blocks to engineer bioinspired hydrogels.
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10
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Punia K, Britton D, Hüll K, Yin L, Wang Y, Renfrew PD, Gilchrist ML, Bonneau R, Trauner D, Montclare JK. Fluorescent azobenzene-confined coiled-coil mesofibers. SOFT MATTER 2023; 19:497-501. [PMID: 36538008 DOI: 10.1039/d2sm01578a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Fluorescent protein biomaterials have important applications such as bioimaging in pharmacological studies. Self-assembly of proteins, especially into fibrils, is known to produce fluorescence in the blue band. Capable of self-assembly into nanofibers, we have shown we can modulate its aggregation into mesofibers by encapsulation of a small hydrophobic molecule. Conversely, azobenzenes are hydrophobic small molecules that are virtually non-fluorescent in solution due to their highly efficient photoisomerization. However, they demonstrate fluorogenic properties upon confinement in nanoscale assemblies by reducing the non-radiative photoisomerization. Here, we report the fluorescence of a hybrid protein-small molecule system in which azobenzene is confined in our protein assembly leading to fiber thickening and increased fluorescence. We show our engineered protein Q encapsulates AzoCholine, bearing a photoswitchable azobenzene moiety, in the hydrophobic pore to produce fluorescent mesofibers. This study further investigates the photocontrol of protein conformation as well as fluorescence of an azobenze-containing biomaterial.
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Affiliation(s)
- Kamia Punia
- Departments of Chemical and Biomolecular Engineering, Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, New York 11201, USA.
| | - Dustin Britton
- Departments of Chemical and Biomolecular Engineering, Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, New York 11201, USA.
| | - Katharina Hüll
- Department of Chemistry, New York University, New York, New York 10003, USA
- Department of Chemistry, Ludwig Maximilian University, München, Germany
| | - Liming Yin
- Departments of Chemical and Biomolecular Engineering, Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, New York 11201, USA.
| | - Yifei Wang
- Departments of Chemical and Biomolecular Engineering, Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, New York 11201, USA.
| | - P Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - M Lane Gilchrist
- Department of Chemical Engineering and Biomedical Engineering, The City College of the City University of New York, New York, New York 10031, USA
| | - Richard Bonneau
- Center for Genomics and Systems Biology, Department of Biology, New York University New York, New York 10003, USA
| | - Dirk Trauner
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jin K Montclare
- Departments of Chemical and Biomolecular Engineering, Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, New York 11201, USA.
- Department of Chemistry, New York University, New York, New York 10003, USA
- Department of Biomaterials, NYU College of Dentistry, New York, NY, 10010, USA
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11
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Haq-Siddiqi NA, Britton D, Kim Montclare J. Protein-engineered biomaterials for cartilage therapeutics and repair. Adv Drug Deliv Rev 2023; 192:114647. [PMID: 36509172 DOI: 10.1016/j.addr.2022.114647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 10/17/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
Cartilage degeneration and injury are major causes of pain and disability that effect millions, and yet treatment options for conditions like osteoarthritis (OA) continue to be mainly palliative or involve complete replacement of injured joints. Several biomaterial strategies have been explored to address cartilage repair either by the delivery of therapeutics or as support for tissue repair, however the complex structure of cartilage tissue, its mechanical needs, and lack of regenerative capacity have hindered this goal. Recent advances in synthetic biology have opened new possibilities for engineered proteins to address these unique needs. Engineered protein and peptide-based materials benefit from inherent biocompatibility and nearly unlimited tunability as they utilize the body's natural building blocks to fabricate a variety of supramolecular structures. The pathophysiology and needs of OA cartilage are presented here, along with an overview of the current state of the art and next steps for protein-engineered repair strategies for cartilage.
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Affiliation(s)
- Nada A Haq-Siddiqi
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, NY 11201, United States
| | - Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, NY 11201, United States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, NY 11201, United States; Department of Chemistry, New York University, New York 10003, United States; Department of Radiology, New York University Grossman School of Medicine, New York 10016, United States; Department of Biomaterials, NYU College of Dentistry, New York, NY 10010, United States; Department of Biomedical Engineering, New York University Tandon School of Engineering, Brooklyn, NY 11201, United States.
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12
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Britton D, Monkovic J, Jia S, Liu C, Mahmoudinobar F, Meleties M, Renfrew PD, Bonneau R, Montclare JK. Supramolecular Assembly and Small-Molecule Binding by Protein-Engineered Coiled-Coil Fibers. Biomacromolecules 2022; 23:4851-4859. [PMID: 36227640 DOI: 10.1021/acs.biomac.2c01031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability to engineer a solvent-exposed surface of self-assembling coiled coils allows one to achieve a higher-order hierarchical assembly such as nano- or microfibers. Currently, these materials are being developed for a range of biomedical applications, including drug delivery systems; however, ways to mechanistically optimize the coiled-coil structure for drug binding are yet to be explored. Our laboratory has previously leveraged the functional properties of the naturally occurring cartilage oligomeric matrix protein coiled coil (C), not only for its favorable motif but also for the presence of a hydrophobic pore to allow for small-molecule binding. This includes the development of Q, a rationally designed pentameric coiled coil derived from C. Here, we present a small library of protein microfibers derived from the parent sequences of C and Q bearing various electrostatic potentials with the aim to investigate the influence of higher-order assembly and encapsulation of candidate small molecule, curcumin. The supramolecular fiber size appears to be well-controlled by sequence-imbued electrostatic surface potential, and protein stability upon curcumin binding is well correlated to relative structure loss, which can be predicted by in silico docking.
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Affiliation(s)
- Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - Julia Monkovic
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - Sihan Jia
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - Chengliang Liu
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - Farbod Mahmoudinobar
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States.,Center for Computational Biology, Flatiron Institute, New York, New York10010, United States
| | - Michael Meleties
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - P Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, New York, New York10010, United States
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, New York, New York10010, United States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States.,Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York10016, United States.,Department of Chemistry, New York University, New York, New York10012, United States.,Department of Biomaterials, New York University College of Dentistry, New York, New York10010, United States
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13
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Jorgensen MD, Chmielewski J. Recent advances in coiled-coil peptide materials and their biomedical applications. Chem Commun (Camb) 2022; 58:11625-11636. [PMID: 36172799 DOI: 10.1039/d2cc04434j] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extensive research has gone into deciphering the sequence requirements for peptides to fold into coiled-coils of varying oligomeric states. More recently, additional signals have been introduced within coiled-coils to promote higher order assembly into biomaterials with a rich distribution of morphologies. Herein we describe these strategies for association of coiled-coil building blocks and biomedical applications. With many of the systems described herein having proven use in protein storage, cargo binding and delivery, three dimensional cell culturing and vaccine development, the future potential of coiled-coil materials to have significant biomedical impact is highly promising.
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Affiliation(s)
- Michael D Jorgensen
- Purdue University, Department of Chemistry, 560 Oval Drive, West Lafayette, Indiana, USA.
| | - Jean Chmielewski
- Purdue University, Department of Chemistry, 560 Oval Drive, West Lafayette, Indiana, USA.
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14
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Hill LK, Britton D, Jihad T, Punia K, Xie X, Delgado-Fukushima E, Liu CF, Mishkit O, Liu C, Hu C, Meleties M, Renfrew PD, Bonneau R, Wadghiri YZ, Montclare JK. Engineered Protein-Iron Oxide Hybrid Biomaterial for MRI-traceable Drug Encapsulation. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2022; 7:915-932. [PMID: 37274761 PMCID: PMC10237276 DOI: 10.1039/d2me00002d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Labeled protein-based biomaterials have become a popular for various biomedical applications such as tissue-engineered, therapeutic, or diagnostic scaffolds. Labeling of protein biomaterials, including with ultrasmall super-paramagnetic iron oxide (USPIO) nanoparticles, has enabled a wide variety of imaging techniques. These USPIO-based biomaterials are widely studied in magnetic resonance imaging (MRI), thermotherapy, and magnetically-driven drug delivery which provide a method for direct and non-invasive monitoring of implants or drug delivery agents. Where most developments have been made using polymers or collagen hydrogels, shown here is the use of a rationally designed protein as the building block for a meso-scale fiber. While USPIOs have been chemically conjugated to antibodies, glycoproteins, and tissue-engineered scaffolds for targeting or improved biocompatibility and stability, these constructs have predominantly served as diagnostic agents and often involve harsh conditions for USPIO synthesis. Here, we present an engineered protein-iron oxide hybrid material comprised of an azide-functionalized coiled-coil protein with small molecule binding capacity conjugated via bioorthogonal azide-alkyne cycloaddition to an alkyne-bearing iron oxide templating peptide, CMms6, for USPIO biomineralization under mild conditions. The coiled-coil protein, dubbed Q, has been previously shown to form nanofibers and, upon small molecule binding, further assembles into mesofibers via encapsulation and aggregation. The resulting hybrid material is capable of doxorubicin encapsulation as well as sensitive T2*-weighted MRI darkening for strong imaging capability that is uniquely derived from a coiled-coil protein.
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Affiliation(s)
- Lindsay K. Hill
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
- Department of Biomedical Engineering, SUNY Downstate Medical Center, Brooklyn, New York, 11203, USA
- Center for Advanced Imaging Innovation and Research (CAIR), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
| | - Teeba Jihad
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
| | - Kamia Punia
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
| | - Xuan Xie
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
| | - Erika Delgado-Fukushima
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
| | - Che Fu Liu
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
| | - Orin Mishkit
- Center for Advanced Imaging Innovation and Research (CAIR), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Chengliang Liu
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
| | - Chunhua Hu
- Department of Chemistry, New York University, New York, New York, 10012, USA
| | - Michael Meleties
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
| | - P. Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, 10010, USA
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, 10010, USA
- Center for Genomics and Systems Biology, New York University, New York, New York, 10003, USA
- Courant Institute of Mathematical Sciences, Computer Science Department, New York University, New York, New York, 10009, USA
| | - Youssef Z. Wadghiri
- Center for Advanced Imaging Innovation and Research (CAIR), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
- Department of Chemistry, New York University, New York, New York, 10012, USA
- Department of Biomaterials, New York University College of Dentistry, New York, New York, 10010, USA
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15
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Palamà IE, Maiorano G, Di Maria F, Zangoli M, Candini A, Zanelli A, D’Amone S, Fabiano E, Gigli G, Barbarella G. Spontaneous Coassembly of the Protein Terthiophene into Fluorescent Electroactive Microfibers in 2D and 3D Cell Cultures. ACS OMEGA 2022; 7:12624-12636. [PMID: 35474798 PMCID: PMC9026133 DOI: 10.1021/acsomega.1c06677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
Protein-based microfibers are biomaterials of paramount importance in materials science, nanotechnology, and medicine. Here we describe the spontaneous in situ formation and secretion of nanostructured protein microfibers in 2D and 3D cell cultures of 3T3 fibroblasts and B104 neuroblastoma cells upon treatment with a micromolar solution of either unmodified terthiophene or terthiophene modified by mono-oxygenation (thiophene → thiophene S-oxide) or dioxygenation (thiophene → thiophene S,S-dioxide) of the inner ring. We demonstrate via metabolic cytotoxicity tests that modification to the S-oxide leads to a severe drop in cell viability. By contrast, unmodified terthiophene and the respective S,S-dioxide cause no harm to the cells and lead to the formation and secretion of fluorescent and electroactive protein-fluorophore coassembled microfibers with a large aspect ratio, a micrometer-sized length and width, and a nanometer-sized thickness, as monitored in real-time by laser scanning confocal microscopy (LSCM). With respect to the microfibers formed by unmodified terthiophene, those formed by the S,S-dioxide display markedly red-shifted fluorescence and an increased n-type character of the material, as shown by macroscopic Kelvin probe in agreement with cyclovoltammetry data. Electrophoretic analyses and Q-TOF mass spectrometry of the isolated microfibers indicate that in all cases the prevalent proteins present are vimentin and histone H4, thus revealing the capability of these fluorophores to selectively coassemble with these proteins. Finally, DFT calculations help to illuminate the fluorophore-fluorophore intermolecular interactions contributing to the formation of the microfibers.
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Affiliation(s)
- Ilaria Elena Palamà
- Nanotechnology Institute (CNR-NANOTEC) and Department of
Mathematics and Physics, University of Salento, Monteroni Street, 73100 Lecce, Italy
| | - Gabriele Maiorano
- Nanotechnology Institute (CNR-NANOTEC) and Department of
Mathematics and Physics, University of Salento, Monteroni Street, 73100 Lecce, Italy
| | - Francesca Di Maria
- CNR-ISOF
and Mediteknology srl Area Ricerca CNR, Piero Gobetti Street 101, 40129 Bologna, Italy
| | - Mattia Zangoli
- CNR-ISOF
and Mediteknology srl Area Ricerca CNR, Piero Gobetti Street 101, 40129 Bologna, Italy
| | - Andrea Candini
- CNR-ISOF
and Mediteknology srl Area Ricerca CNR, Piero Gobetti Street 101, 40129 Bologna, Italy
| | - Alberto Zanelli
- CNR-ISOF
and Mediteknology srl Area Ricerca CNR, Piero Gobetti Street 101, 40129 Bologna, Italy
| | - Stefania D’Amone
- Nanotechnology Institute (CNR-NANOTEC) and Department of
Mathematics and Physics, University of Salento, Monteroni Street, 73100 Lecce, Italy
| | - Eduardo Fabiano
- Institute
for Microelectronics and Microsystems (CNR-IMM), Monteroni Street, 73100 Lecce, Italy
- Center
for Biomolecular Nanotechnologies, UNILE
Istituto Italiano di Tecnologia, Barsanti Street, 73010 Arnesano, Italy
| | - Giuseppe Gigli
- Nanotechnology Institute (CNR-NANOTEC) and Department of
Mathematics and Physics, University of Salento, Monteroni Street, 73100 Lecce, Italy
| | - Giovanna Barbarella
- CNR-ISOF
and Mediteknology srl Area Ricerca CNR, Piero Gobetti Street 101, 40129 Bologna, Italy
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16
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Guo R, Sinha NJ, Misra R, Tang Y, Langenstein M, Kim K, Fagan JA, Kloxin CJ, Jensen G, Pochan DJ, Saven JG. Computational Design of Homotetrameric Peptide Bundle Variants Spanning a Wide Range of Charge States. Biomacromolecules 2022; 23:1652-1661. [PMID: 35312288 DOI: 10.1021/acs.biomac.1c01539] [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
With the ability to design their sequences and structures, peptides can be engineered to realize a wide variety of functionalities and structures. Herein, computational design was used to identify a set of 17 peptides having a wide range of putative charge states but the same tetrameric coiled-coil bundle structure. Calculations were performed to identify suitable locations for ionizable residues (D, E, K, and R) at the bundle's exterior sites, while interior hydrophobic interactions were retained. The designed bundle structures spanned putative charge states of -32 to +32 in units of electron charge. The peptides were experimentally investigated using spectroscopic and scattering techniques. Thermal stabilities of the bundles were investigated using circular dichroism. Molecular dynamics simulations assessed structural fluctuations within the bundles. The cylindrical peptide bundles, 4 nm long by 2 nm in diameter, were covalently linked to form rigid, micron-scale polymers and characterized using transmission electron microscopy. The designed suite of sequences provides a set of readily realized nanometer-scale structures of tunable charge that can also be polymerized to yield rigid-rod polyelectrolytes.
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Affiliation(s)
- Rui Guo
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Nairiti J Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.,NIST Center for Neutron Research (NCNR), National Institute of Standards & Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Rajkumar Misra
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Yao Tang
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Matthew Langenstein
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Kyunghee Kim
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffrey A Fagan
- Materials Science and Engineering Division, National Institute of Standards & Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Christopher J Kloxin
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Grethe Jensen
- NIST Center for Neutron Research (NCNR), National Institute of Standards & Technology (NIST), Gaithersburg, Maryland 20899, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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17
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Chu S, Wang AL, Bhattacharya A, Montclare JK. Protein Based Biomaterials for Therapeutic and Diagnostic Applications. PROGRESS IN BIOMEDICAL ENGINEERING (BRISTOL, ENGLAND) 2022; 4:012003. [PMID: 34950852 PMCID: PMC8691744 DOI: 10.1088/2516-1091/ac2841] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Proteins are some of the most versatile and studied macromolecules with extensive biomedical applications. The natural and biological origin of proteins offer such materials several advantages over their synthetic counterparts, such as innate bioactivity, recognition by cells and reduced immunogenic potential. Furthermore, proteins can be easily functionalized by altering their primary amino acid sequence and can often be further self-assembled into higher order structures either spontaneously or under specific environmental conditions. This review will feature the recent advances in protein-based biomaterials in the delivery of therapeutic cargo such as small molecules, genetic material, proteins, and cells. First, we will discuss the ways in which secondary structural motifs, the building blocks of more complex proteins, have unique properties that enable them to be useful for therapeutic delivery. Next, supramolecular assemblies, such as fibers, nanoparticles, and hydrogels, made from these building blocks that are engineered to behave in a cohesive manner, are discussed. Finally, we will cover additional modifications to protein materials that impart environmental responsiveness to materials. This includes the emerging field of protein molecular robots, and relatedly, protein-based theranostic materials that combine therapeutic potential with modern imaging modalities, including near-infrared fluorescence spectroscopy (NIRF), single-photo emission computed tomography/computed tomography (SPECT/CT), positron emission tomography (PET), magnetic resonance imaging (MRI), and ultrasound/photoacoustic imaging (US/PAI).
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Affiliation(s)
- Stanley Chu
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
| | - Andrew L Wang
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
- Department of Biomedical Engineering, State University of New York Downstate Medical Center, Brooklyn, NY, USA
- College of Medicine, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - Aparajita Bhattacharya
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
- Department of Molecular and Cellular Biology, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
- Department of Chemistry, NYU, New York, NY, USA
- Department of Biomaterials, NYU College of Dentistry, New York, NY, USA
- Department of Radiology, NYU Langone Health, New York, NY, USA
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18
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Meleties M, Katyal P, Lin B, Britton D, Montclare JK. Self-assembly of stimuli-responsive coiled-coil fibrous hydrogels. SOFT MATTER 2021; 17:6470-6476. [PMID: 34137426 DOI: 10.1039/d1sm00780g] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Owing to their tunable properties, hydrogels comprised of stimuli-sensitive polymers are one of the most appealing scaffolds with applications in tissue engineering, drug delivery and other biomedical fields. We previously reported a thermoresponsive hydrogel formed using a coiled-coil protein, Q. Here, we expand our studies to identify the gelation of Q protein at distinct pH conditions, creating a protein hydrogel system that is sensitive to temperature and pH. Through secondary structure analysis, transmission electron microscopy, and rheology, we observed that Q self-assembles and forms fiber-based hydrogels exhibiting upper critical solution temperature behavior with increased elastic properties at pH 7.4 and pH 10. At pH 6, however, Q forms polydisperse nanoparticles, which do not further self-assemble and undergo gelation. The high net positive charge of Q at pH 6 creates significant electrostatic repulsion, preventing its gelation. This study will potentially guide the development of novel scaffolds and functional biomaterials that are sensitive towards biologically relevant stimuli.
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Affiliation(s)
- Michael Meleties
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, USA.
| | - Priya Katyal
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, USA.
| | - Bonnie Lin
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, USA.
| | - Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, USA.
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, USA. and Department of Radiology, New York University Langone Health, New York, New York 10016, USA and Department of Biomaterials, New York University College of Dentistry, New York, New York 10010, USA and Department of Chemistry, New York University, New York, New York 10003, USA
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19
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Dawson WM, Martin FJO, Rhys GG, Shelley KL, Brady RL, Woolfson DN. Coiled coils 9-to-5: rational de novo design of α-helical barrels with tunable oligomeric states. Chem Sci 2021; 12:6923-6928. [PMID: 34745518 PMCID: PMC8503928 DOI: 10.1039/d1sc00460c] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/13/2021] [Indexed: 01/10/2023] Open
Abstract
The rational design of linear peptides that assemble controllably and predictably in water is challenging. Short sequences must encode unique target structures and avoid alternative states. However, the non-covalent forces that stabilize and discriminate between states are weak. Nonetheless, for α-helical coiled-coil assemblies considerable progress has been made in rational de novo design. In these, sequence repeats of nominally hydrophobic (h) and polar (p) residues, hpphppp, direct the assembly of amphipathic helices into dimeric to tetrameric bundles. Expanding this pattern to hpphhph can produce larger α-helical barrels. Here, we show that pentameric to nonameric barrels are accessed by varying the residue at one of the h sites. In peptides with four L/I-K-E-I-A-x-Z repeats, decreasing the size of Z from threonine to serine to alanine to glycine gives progressively larger oligomers. X-ray crystal structures of the resulting α-helical barrels rationalize this: side chains at Z point directly into the helical interfaces, and smaller residues allow closer helix contacts and larger assemblies.
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Affiliation(s)
- William M Dawson
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Freddie J O Martin
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Guto G Rhys
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Department of Chemistry, University of Bayreuth, Universitätsstraße 30 95447 Bayreuth Germany
| | - Kathryn L Shelley
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- School of Biochemistry, University of Bristol Biomedical Sciences Building, University Walk Bristol BS8 1TD UK
| | - R Leo Brady
- School of Biochemistry, University of Bristol Biomedical Sciences Building, University Walk Bristol BS8 1TD UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- School of Biochemistry, University of Bristol Biomedical Sciences Building, University Walk Bristol BS8 1TD UK
- Bristol BioDesign Institute, University of Bristol Life Sciences Building, Tyndall Avenue Bristol BS8 1TQ UK
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20
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Wang Y, Wang X, Montclare JK. Effect of Divalent Metal Cations on the Conformation, Elastic Behavior, and Controlled Release of a Photocrosslinked Protein Engineered Hydrogel. ACS APPLIED BIO MATERIALS 2021; 4:3587-3597. [PMID: 35014444 DOI: 10.1021/acsabm.1c00091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We investigate the effect of Zn2+, Cu2+, and Ni2+ coordination on the conformation, mechanical properties, contraction, and small-molecule drug encapsulation and release of a photocrosslinked protein-engineered hydrogel, CEC-D. The treatment of the CEC-D hydrogel with divalent metal (M2+) results in significant conformational changes where a loss in structure is observed with Zn2+, while both Cu2+ and Ni2+ induce a blueshift. The relationship of M2+ to mechanical properties illustrates a trend, while the CEC-D hydrogel in the presence of 2 mM Cu2+ reveals the highest increase in G' to 14.4 ± 0.7 kPa followed by 9.7 ± 0.9 kPa by addition of 2 mM Zn2+, and a decrease to 1.1 ± 0.2 kPa is demonstrated in the presence of 2 mM Ni2+. A similar observation in M2+ responsiveness emerges where CEC-D hydrogels contract into a condensed state of 2.6-fold for Cu2+, 2.4-fold for Zn2+, and 1.6-fold for Ni2+. Furthermore, CEC-D hydrogels coordinated with M2+ demonstrate control over the encapsulation and release of the small molecule curcumin. The trend of release is opposite of the mechanical and contraction properties with a 70.0 ± 5.3% release with Ni2+, 64.2 ± 1.2% release with Zn2+, and 42.3 ± 11.3 release with Cu2+. Taken together, these results indicate that the CEC-D hydrogel tuned by M2+ is a promising drug delivery platform with tunable physicochemical properties.
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Affiliation(s)
- Yao Wang
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Xiaole Wang
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States.,Department of Chemistry, New York University, New York, New York 10003, United States.,Department of Biomaterials, New York University College of Dentistry, New York, New York 10010, United States.,Department of Radiology, New York University Langone Health, New York, New York 10016, United States
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21
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Wang Y, Wang X, Montclare JK. Free-Standing Photocrosslinked Protein Polymer Hydrogels for Sustained Drug Release. Biomacromolecules 2021; 22:1509-1522. [PMID: 33685120 DOI: 10.1021/acs.biomac.0c01721] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The fabrication of protein hydrogels consisting of different properties and functional motifs is critical in the development of protein-based materials for biomedical applications. Here, we report the design and characterization of a triblock protein polymer, CEC, composed of two different self-assembling domains derived from elastin protein (E) and coiled-coil protein (C), photopolymerized with a NHS-diazirine (D) crosslinker into a CEC-D hydrogel. The optimal photocrosslinker concentration and exposure time is determined to fabricate a free-standing hydrogel. Upon increasing the concentration of the CEC-D monomer and environmental temperature, the CEC-D hydrogel's conformation decreases in helical content from 58.0% to 44.8% and increases in β-content from 25.9% to 38.1%. These gels experience 55 ± 6% protein erosion from the free-standing gel in 13 days as the gel films gradually decrease in size. The swelling ratio of 12 ± 1% denotes that the gel has a swelling ability comparable to other protein hydrogels. These photocrosslinked CEC-D hydrogels can be employed for drug delivery with high encapsulation and 14 ± 2% release of curcumin into the supernatant in a week long study. Overall, the photocrosslinked CEC-D hydrogels exhibit stability, swelling ability, and sustained release of drug.
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Affiliation(s)
- Yao Wang
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Xiaole Wang
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States.,Department of Chemistry, New York University, New York, New York 10003, United States.,Department of Biomaterials, New York University College of Dentistry, New York, New York 10010, United States.,Department of Radiology, New York University Langone Health, New York, New York 10016, United States
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22
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Utterström J, Naeimipour S, Selegård R, Aili D. Coiled coil-based therapeutics and drug delivery systems. Adv Drug Deliv Rev 2021; 170:26-43. [PMID: 33378707 DOI: 10.1016/j.addr.2020.12.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/18/2020] [Accepted: 12/20/2020] [Indexed: 12/20/2022]
Abstract
Coiled coils are characterized by an arrangement of two or more α-helices into a superhelix and one of few protein motifs where the sequence-to-structure relationship to a large extent have been decoded and understood. The abundance of both natural and de novo designed coil coils provides a rich molecular toolbox for self-assembly of elaborate bespoke molecular architectures, nanostructures, and materials. Leveraging on the numerous possibilities to tune both affinities and preferences for polypeptide oligomerization, coiled coils offer unique possibilities to design modular and dynamic assemblies that can respond in a predictable manner to biomolecular interactions and subtle physicochemical cues. In this review, strategies to use coiled coils in design of novel therapeutics and advanced drug delivery systems are discussed. The applications of coiled coils for generating drug carriers and vaccines, and various aspects of using coiled coils for controlling and triggering drug release, and for improving drug targeting and drug uptake are described. The plethora of innovative coiled coil-based molecular systems provide new knowledge and techniques for improving efficacy of existing drugs and can facilitate development of novel therapeutic strategies.
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23
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Wang Y, Delgado-Fukushima E, Fu RX, Doerk GS, Monclare JK. Controlling Drug Absorption, Release, and Erosion of Photopatterned Protein Engineered Hydrogels. Biomacromolecules 2020; 21:3608-3619. [DOI: 10.1021/acs.biomac.0c00616] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yao Wang
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Erika Delgado-Fukushima
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Richard X. Fu
- Sensors and Electron Devices Directorate, Advanced Concepts and Modeling Branch, US Army Research Lab, Adelphi, Maryland 20783, United States
| | - Gregory S. Doerk
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Jin Kim Monclare
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York 11201, United States
- Department of Chemistry, New York University, New York, New York 10003, United States
- Department of Biomaterials, NYU College of Dentistry, New York, New York 10010, United States
- Department of Radiology, NYU Langone Health, New York, New York 10016, United States
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24
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Katyal P, Mahmoudinobar F, Montclare JK. Recent trends in peptide and protein-based hydrogels. Curr Opin Struct Biol 2020; 63:97-105. [PMID: 32512499 DOI: 10.1016/j.sbi.2020.04.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/22/2022]
Abstract
Hydrogels are classic examples of biomaterials that have found its niche in biomedical and allied fields. Here, we describe examples of peptide-based and protein-based hydrogels with a focus on smart gels that respond to various stimuli including temperature, pH, light, and ionic strength. With the recent advancements in computational modeling, it has been possible to predict as well as design peptide and protein sequences that can assemble into hydrogels with unique and improved properties. We briefly discuss coarse grained and atomistic simulations in designing peptides that can form hydrogels. In addition, we highlight the trends that will influence the future design and applications of hydrogels, with emphasis on bioadhesion, exosomes delivery, tissue and organoids engineering, and even intracellular production of gels.
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Affiliation(s)
- Priya Katyal
- Department of Chemical and Biomolecular Engineering, New York University, Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Farbod Mahmoudinobar
- Department of Chemical and Biomolecular Engineering, New York University, Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University, Tandon School of Engineering, Brooklyn, NY 11201, USA; Department of Radiology, New York University Langone Health, New York, NY, 10016, USA; Department of Biomaterials, New York University College of Dentistry, New York, NY, 10010, USA; Department of Chemistry, New York University, New York, NY 10003, USA.
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25
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Moros M, Di Maria F, Dardano P, Tommasini G, Castillo-Michel H, Kovtun A, Zangoli M, Blasio M, De Stefano L, Tino A, Barbarella G, Tortiglione C. In Vivo Bioengineering of Fluorescent Conductive Protein-Dye Microfibers. iScience 2020; 23:101022. [PMID: 32283525 PMCID: PMC7155203 DOI: 10.1016/j.isci.2020.101022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/17/2020] [Accepted: 03/25/2020] [Indexed: 01/01/2023] Open
Abstract
Engineering protein-based biomaterials is extremely challenging in bioelectronics, medicine, and materials science, as mechanical, electrical, and optical properties need to be merged to biocompatibility and resistance to biodegradation. An effective strategy is the engineering of physiological processes in situ, by addition of new properties to endogenous components. Here we show that a green fluorescent semiconducting thiophene dye, DTTO, promotes, in vivo, the biogenesis of fluorescent conductive protein microfibers via metabolic pathways. By challenging the simple freshwater polyp Hydra vulgaris with DTTO, we demonstrate the stable incorporation of the dye into supramolecular protein-dye co-assembled microfibers without signs of toxicity. An integrated multilevel analysis including morphological, optical, spectroscopical, and electrical characterization shows electrical conductivity of biofibers, opening the door to new opportunities for augmenting electronic functionalities within living tissue, which may be exploited for the regulation of cell and animal physiology, or in pathological contexts to enhance bioelectrical signaling. The oligothiophene DTTO promotes the synthesis of microfibers in Hydra vulgaris DTTO co-assembles with proteins giving rise to fluorescent and conductive microfibers The biofiber synthesis is an active process, based on protein synthesis In situ produced hybrid microfibers have great potential in biolectronics and biomedicine
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Affiliation(s)
- Maria Moros
- Istituto di Scienze Applicate e Sistemi Intelligenti "E.Caianiello", Consiglio Nazionale delle Ricerche, Via Campi Flegrei, 34, 80078 Pozzuoli, Italy
| | - Francesca Di Maria
- Istituto per la Sintesi Organica e Fotoreattività, Consiglio Nazionale delle Ricerche, Via Piero Gobetti, 101, 40129 Bologna, Italy; Istituto di Nanotecnologia, Consiglio Nazionale delle Ricerche, c/o Campus Ecotekne - Università del Salento, via Monteroni, 73100 Lecce, Italy
| | - Principia Dardano
- Istituto per la Microelettronica e Microsistemi, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Giuseppina Tommasini
- Istituto di Scienze Applicate e Sistemi Intelligenti "E.Caianiello", Consiglio Nazionale delle Ricerche, Via Campi Flegrei, 34, 80078 Pozzuoli, Italy
| | | | - Alessandro Kovtun
- Istituto per la Sintesi Organica e Fotoreattività, Consiglio Nazionale delle Ricerche, Via Piero Gobetti, 101, 40129 Bologna, Italy
| | - Mattia Zangoli
- Istituto per la Sintesi Organica e Fotoreattività, Consiglio Nazionale delle Ricerche, Via Piero Gobetti, 101, 40129 Bologna, Italy
| | - Martina Blasio
- Istituto di Scienze Applicate e Sistemi Intelligenti "E.Caianiello", Consiglio Nazionale delle Ricerche, Via Campi Flegrei, 34, 80078 Pozzuoli, Italy
| | - Luca De Stefano
- Istituto per la Microelettronica e Microsistemi, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Angela Tino
- Istituto di Scienze Applicate e Sistemi Intelligenti "E.Caianiello", Consiglio Nazionale delle Ricerche, Via Campi Flegrei, 34, 80078 Pozzuoli, Italy
| | - Giovanna Barbarella
- Istituto per la Sintesi Organica e Fotoreattività, Consiglio Nazionale delle Ricerche, Via Piero Gobetti, 101, 40129 Bologna, Italy
| | - Claudia Tortiglione
- Istituto di Scienze Applicate e Sistemi Intelligenti "E.Caianiello", Consiglio Nazionale delle Ricerche, Via Campi Flegrei, 34, 80078 Pozzuoli, Italy.
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26
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Wu D, Sinha N, Lee J, Sutherland BP, Halaszynski NI, Tian Y, Caplan J, Zhang HV, Saven JG, Kloxin CJ, Pochan DJ. Polymers with controlled assembly and rigidity made with click-functional peptide bundles. Nature 2019; 574:658-662. [PMID: 31666724 DOI: 10.1038/s41586-019-1683-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/14/2019] [Indexed: 01/20/2023]
Abstract
The engineering of biological molecules is a key concept in the design of highly functional, sophisticated soft materials. Biomolecules exhibit a wide range of functions and structures, including chemical recognition (of enzyme substrates or adhesive ligands1, for instance), exquisite nanostructures (composed of peptides2, proteins3 or nucleic acids4), and unusual mechanical properties (such as silk-like strength3, stiffness5, viscoelasticity6 and resiliency7). Here we combine the computational design of physical (noncovalent) interactions with pathway-dependent, hierarchical 'click' covalent assembly to produce hybrid synthetic peptide-based polymers. The nanometre-scale monomeric units of these polymers are homotetrameric, α-helical bundles of low-molecular-weight peptides. These bundled monomers, or 'bundlemers', can be designed to provide complete control of the stability, size and spatial display of chemical functionalities. The protein-like structure of the bundle allows precise positioning of covalent linkages between the ends of distinct bundlemers, resulting in polymers with interesting and controllable physical characteristics, such as rigid rods, semiflexible or kinked chains, and thermally responsive hydrogel networks. Chain stiffness can be controlled by varying only the linkage. Furthermore, by controlling the amino acid sequence along the bundlemer periphery, we use specific amino acid side chains, including non-natural 'click' chemistry functionalities, to conjugate moieties into a desired pattern, enabling the creation of a wide variety of hybrid nanomaterials.
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Affiliation(s)
- Dongdong Wu
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA
| | - Nairiti Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA
| | - Jeeyoung Lee
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA
| | - Bryan P Sutherland
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA
| | - Nicole I Halaszynski
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA
| | - Yu Tian
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA
| | - Jeffrey Caplan
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Huixi Violet Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.
| | - Christopher J Kloxin
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA. .,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA.
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27
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Katyal P, Meleties M, Montclare JK. Self-Assembled Protein- and Peptide-Based Nanomaterials. ACS Biomater Sci Eng 2019; 5:4132-4147. [PMID: 33417774 DOI: 10.1021/acsbiomaterials.9b00408] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Considerable effort has been devoted to generating novel protein- and peptide-based nanomaterials with their applications in a wide range of fields. Specifically, the unique property of proteins to self-assemble has been utilized to create a variety of nanoassemblies, which offer significant possibilities for next-generation biomaterials. In this minireview, we describe self-assembled protein- and peptide-based nanomaterials with focus on nanofibers and nanoparticles. Their applications in delivering therapeutic drugs and genes are discussed.
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Affiliation(s)
- Priya Katyal
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, Brooklyn, New York 11201, United States
| | - Michael Meleties
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, Brooklyn, New York 11201, United States
| | - Jin K Montclare
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, Brooklyn, New York 11201, United States.,Department of Radiology, New York University Langone Health, New York, New York 10016, United States.,Department of Biomaterials, College of Dentistry, New York University, New York, New York 10010, United States.,Department of Chemistry, New York University, New York, New York 10003, United States
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28
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Hill LK, Meleties M, Katyal P, Xie X, Delgado-Fukushima E, Jihad T, Liu CF, O’Neill S, Tu RS, Renfrew PD, Bonneau R, Wadghiri YZ, Montclare JK. Thermoresponsive Protein-Engineered Coiled-Coil Hydrogel for Sustained Small Molecule Release. Biomacromolecules 2019; 20:3340-3351. [DOI: 10.1021/acs.biomac.9b00107] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Lindsay K. Hill
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Department of Biomedical Engineering, SUNY Downstate Medical Center, Brooklyn, New York 11203, United States
| | - Michael Meleties
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Priya Katyal
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Xuan Xie
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Erika Delgado-Fukushima
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Teeba Jihad
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Che-Fu Liu
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Sean O’Neill
- Chemical Engineering Department, The City College of New York, 160 Convent Avenue, New York, New York 10031, United States
| | - Raymond S. Tu
- Chemical Engineering Department, The City College of New York, 160 Convent Avenue, New York, New York 10031, United States
| | - P. Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York 10010, United States
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York 10010, United States
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, United States
- Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, New York 10009, United States
| | | | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Department of Chemistry, New York University, New York, New York 10012, United States
- Department of Biomaterials, New York University College of Dentistry, New York, New York 10010, United States
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29
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Wang Y, Katyal P, Montclare JK. Protein-Engineered Functional Materials. Adv Healthc Mater 2019; 8:e1801374. [PMID: 30938924 PMCID: PMC6703858 DOI: 10.1002/adhm.201801374] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 02/25/2019] [Indexed: 12/13/2022]
Abstract
Proteins are versatile macromolecules that can perform a variety of functions. In the past three decades, they have been commonly used as building blocks to generate a range of biomaterials. Owing to their flexibility, proteins can either be used alone or in combination with other functional molecules. Advances in synthetic and chemical biology have enabled new protein fusions as well as the integration of new functional groups leading to biomaterials with emergent properties. This review discusses protein-engineered materials from the perspectives of domain-based designs as well as physical and chemical approaches for crosslinked materials, with special emphasis on the creation of hydrogels. Engineered proteins that organize or template metal ions, bear noncanonical amino acids (NCAAs), and their potential applications, are also reviewed.
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Affiliation(s)
- Yao Wang
- Department of Chemical and Biomolecular Engineering, New
York University, Tandon School of Engineering, Brooklyn, NY 11201, United
States
| | - Priya Katyal
- Department of Chemical and Biomolecular Engineering, New
York University, Tandon School of Engineering, Brooklyn, NY 11201, United
States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New
York University, Tandon School of Engineering, Brooklyn, NY 11201, United
States
- Department of Chemistry, New York University, New York, NY
10003, United States
- Department of Biomaterials, New York University College of
Dentistry, New York, NY 10010, United States
- Department of Radiology, New York University School of
Medicine, New York, New York, 10016, United States
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30
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Ansammlungen gefalteter Proteine im Kontext von Evolution, Krankheiten und Proteinentwicklung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201806092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
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31
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Assembly of Folded Proteins in Evolution, Disease, and Engineering. Angew Chem Int Ed Engl 2019; 58:5514-5531. [PMID: 30133878 PMCID: PMC6471489 DOI: 10.1002/anie.201806092] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/06/2018] [Indexed: 12/14/2022]
Abstract
Mutations and changes in a protein's environment are well known for their potential to induce misfolding and aggregation, including amyloid formation. Alternatively, such perturbations can trigger new interactions that lead to the polymerization of folded proteins. In contrast to aggregation, this process does not require misfolding and, to highlight this difference, we refer to it as agglomeration. This term encompasses the amorphous assembly of folded proteins as well as the polymerization in one, two, or three dimensions. We stress the remarkable potential of symmetric homo-oligomers to agglomerate even by single surface point mutations, and we review the double-edged nature of this potential: how aberrant assemblies resulting from agglomeration can lead to disease, but also how agglomeration can serve in cellular adaptation and be exploited for the rational design of novel biomaterials.
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Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
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32
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Hill LK, Frezzo JA, Katyal P, Hoang DM, Gironda ZBY, Xu C, Xie X, Delgado-Fukushima E, Wadghiri YZ, Montclare JK. Protein-Engineered Nanoscale Micelles for Dynamic 19F Magnetic Resonance and Therapeutic Drug Delivery. ACS NANO 2019; 13:2969-2985. [PMID: 30758189 PMCID: PMC6945506 DOI: 10.1021/acsnano.8b07481] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Engineered proteins provide an interesting template for designing fluorine-19 (19F) magnetic resonance imaging (MRI) contrast agents, yet progress has been hindered by the unpredictable relaxation properties of fluorine. Herein, we present the biosynthesis of a protein block copolymer, termed "fluorinated thermoresponsive assembled protein" (F-TRAP), which assembles into a monodisperse nanoscale micelle with interesting 19F NMR properties and the ability to encapsulate and release small therapeutic molecules, imparting potential as a diagnostic and therapeutic (theranostic) agent. The assembly of the F-TRAP micelle, composed of a coiled-coil pentamer corona and a hydrophobic, thermoresponsive elastin-like polypeptide core, results in a drastic depression in spin-spin relaxation ( T2) times and unaffected spin-lattice relaxation ( T1) times. The nearly unchanging T1 relaxation rates and linearly dependent T2 relaxation rates have allowed for detection via zero echo time 19F MRI, and the in vivo MR potential has been preliminarily explored using 19F magnetic resonance spectroscopy (MRS). This fluorinated micelle has also demonstrated the ability to encapsulate the small-molecule chemotherapeutic doxorubicin and release its cargo in a thermoresponsive manner owing to its inherent stimuli-responsive properties, presenting an interesting avenue for the development of thermoresponsive 19F MRI/MRS-traceable theranostic agents.
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Affiliation(s)
- Lindsay K. Hill
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Center for Advanced Imaging Innovation and Research (CAIR), New York University School of Medicine, New York, New York 10016, United States
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
- Department of Biomedical Engineering, SUNY Downstate Medical Center, Brooklyn, New York 11203, United States
| | - Joseph A. Frezzo
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Priya Katyal
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Dung Minh Hoang
- Center for Advanced Imaging Innovation and Research (CAIR), New York University School of Medicine, New York, New York 10016, United States
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
| | - Zakia Ben Youss Gironda
- Center for Advanced Imaging Innovation and Research (CAIR), New York University School of Medicine, New York, New York 10016, United States
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
| | - Cynthia Xu
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Xuan Xie
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Erika Delgado-Fukushima
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Youssef Z. Wadghiri
- Center for Advanced Imaging Innovation and Research (CAIR), New York University School of Medicine, New York, New York 10016, United States
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
- Department of Chemistry, New York University, New York, New York 10012, United States
- Department of Biomaterials, New York University College of Dentistry, New York, New York 10010, United States
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33
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Gong C, Sun S, Zhang Y, Sun L, Su Z, Wu A, Wei G. Hierarchical nanomaterials via biomolecular self-assembly and bioinspiration for energy and environmental applications. NANOSCALE 2019; 11:4147-4182. [PMID: 30806426 DOI: 10.1039/c9nr00218a] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bioinspired synthesis offers potential green strategies to build highly complex nanomaterials by utilizing the unique nanostructures, functions, and properties of biomolecules, in which the biomolecular recognition and self-assembly processes play important roles in tailoring the structures and functions of bioinspired materials. Further understanding of biomolecular self-assembly for inspiring the formation and assembly of nanoparticles would promote the design and fabrication of functional nanomaterials for various applications. In this review, we focus on recent advances in bioinspired synthesis and applications of hierarchical nanomaterials based on biomolecular self-assembly. We first discuss biomolecular self-assembly towards biological nanomaterials, in which the mechanisms and ways of biomolecular self-assembly as well as various self-assembled biomolecular nanostructures are demonstrated. Secondly, the bioinspired synthesis strategies including molecule-molecule interaction, molecule-material recognition, molecule-mediated nucleation and growth, and molecule-mediated reduction/oxidation are introduced and discussed. Meanwhile, typical examples and discussions on how biomolecular self-assembly inspires the formation of hierarchical hybrid nanomaterials are presented. Finally, the applications of bioinspired nanomaterials in biofuel cells, light-harvesting systems, batteries, supercapacitors, catalysis, water/air purification, and environmental monitoring are presented and discussed. We believe that this review will be very helpful for readers to understand the self-assembly of biomolecules and the biomimetic/bioinspired strategies for synthesizing hierarchical nanomaterials on the one hand, and on the other hand to design novel materials for extended applications in nanotechnology, materials science, analytical science, and biomedical engineering.
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Affiliation(s)
- Coucong Gong
- Faculty of Production Engineering and Center for Environmental Research and Sustainable technology (UFT), University of Bremen, D-28359 Bremen, Germany.
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34
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Wilson CJ, Bommarius AS, Champion JA, Chernoff YO, Lynn DG, Paravastu AK, Liang C, Hsieh MC, Heemstra JM. Biomolecular Assemblies: Moving from Observation to Predictive Design. Chem Rev 2018; 118:11519-11574. [PMID: 30281290 PMCID: PMC6650774 DOI: 10.1021/acs.chemrev.8b00038] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Biomolecular assembly is a key driving force in nearly all life processes, providing structure, information storage, and communication within cells and at the whole organism level. These assembly processes rely on precise interactions between functional groups on nucleic acids, proteins, carbohydrates, and small molecules, and can be fine-tuned to span a range of time, length, and complexity scales. Recognizing the power of these motifs, researchers have sought to emulate and engineer biomolecular assemblies in the laboratory, with goals ranging from modulating cellular function to the creation of new polymeric materials. In most cases, engineering efforts are inspired or informed by understanding the structure and properties of naturally occurring assemblies, which has in turn fueled the development of predictive models that enable computational design of novel assemblies. This Review will focus on selected examples of protein assemblies, highlighting the story arc from initial discovery of an assembly, through initial engineering attempts, toward the ultimate goal of predictive design. The aim of this Review is to highlight areas where significant progress has been made, as well as to outline remaining challenges, as solving these challenges will be the key that unlocks the full power of biomolecules for advances in technology and medicine.
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Affiliation(s)
- Corey J. Wilson
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Andreas S. Bommarius
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Julie A. Champion
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yury O. Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Laboratory of Amyloid Biology & Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
| | - David G. Lynn
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Anant K. Paravastu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Chen Liang
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Ming-Chien Hsieh
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jennifer M. Heemstra
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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Maintaining and breaking symmetry in homomeric coiled-coil assemblies. Nat Commun 2018; 9:4132. [PMID: 30297707 PMCID: PMC6175849 DOI: 10.1038/s41467-018-06391-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/22/2018] [Indexed: 11/24/2022] Open
Abstract
In coiled-coil (CC) protein structures α-helices wrap around one another to form rope-like assemblies. Most natural and designed CCs have two–four helices and cyclic (Cn) or dihedral (Dn) symmetry. Increasingly, CCs with five or more helices are being reported. A subset of these higher-order CCs is of interest as they have accessible central channels that can be functionalised; they are α-helical barrels. These extended cavities are surprising given the drive to maximise buried hydrophobic surfaces during protein folding and assembly in water. Here, we show that α-helical barrels can be maintained by the strategic placement of β-branched aliphatic residues lining the lumen. Otherwise, the structures collapse or adjust to give more-complex multi-helix assemblies without Cn or Dn symmetry. Nonetheless, the structural hallmark of CCs—namely, knobs-into-holes packing of side chains between helices—is maintained leading to classes of CCs hitherto unobserved in nature or accessed by design. Higher order coiled coils with five or more helices can form α-helical barrels. Here the authors show that placing β-branched aliphatic residues along the lumen yields stable and open α-helical barrels, which is of interest for the rational design of functional proteins; whereas, the absence of β-branched side chains leads to unusual low-symmetry α-helical bundles.
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Nambiar M, Wang LS, Rotello V, Chmielewski J. Reversible Hierarchical Assembly of Trimeric Coiled-Coil Peptides into Banded Nano- and Microstructures. J Am Chem Soc 2018; 140:13028-13033. [DOI: 10.1021/jacs.8b08163] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Monessha Nambiar
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Li-Sheng Wang
- Department of Chemistry, University of Massachusetts−Amherst, 710 N. Pleasant Street, Amherst, Massachusetts 01002, United States
| | - Vincent Rotello
- Department of Chemistry, University of Massachusetts−Amherst, 710 N. Pleasant Street, Amherst, Massachusetts 01002, United States
| | - Jean Chmielewski
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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Thomas F, Dawson WM, Lang EJM, Burton AJ, Bartlett GJ, Rhys GG, Mulholland AJ, Woolfson DN. De Novo-Designed α-Helical Barrels as Receptors for Small Molecules. ACS Synth Biol 2018; 7:1808-1816. [PMID: 29944338 DOI: 10.1021/acssynbio.8b00225] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We describe de novo-designed α-helical barrels (αHBs) that bind and discriminate between lipophilic biologically active molecules. αHBs have five or more α-helices arranged around central hydrophobic channels the diameters of which scale with oligomer state. We show that pentameric, hexameric, and heptameric αHBs bind the environmentally sensitive dye 1,6-diphenylhexatriene (DPH) in the micromolar range and fluoresce. Displacement of the dye is used to report the binding of nonfluorescent molecules: palmitic acid and retinol bind to all three αHBs with submicromolar inhibitor constants; farnesol binds the hexamer and heptamer; but β-carotene binds only the heptamer. A co-crystal structure of the hexamer with farnesol reveals oriented binding in the center of the hydrophobic channel. Charged side chains engineered into the lumen of the heptamer facilitate binding of polar ligands: a glutamate variant binds a cationic variant of DPH, and introducing lysine allows binding of the biosynthetically important farnesol diphosphate.
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Affiliation(s)
- Franziska Thomas
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany
| | - William M. Dawson
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Eric J. M. Lang
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Antony J. Burton
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- Frick Chemistry Laboratory, Princeton, New Jersey 084544, United States
| | - Gail J. Bartlett
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Guto G. Rhys
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Adrian J. Mulholland
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, U.K
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Yin L, Agustinus AS, Yuvienco C, Minashima T, Schnabel NL, Kirsch T, Montclare JK. Engineered Coiled-Coil Protein for Delivery of Inverse Agonist for Osteoarthritis. Biomacromolecules 2018; 19:1614-1624. [PMID: 29601728 DOI: 10.1021/acs.biomac.8b00158] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Osteoarthritis (OA) results from degenerative and abnormal function of joints, with localized biochemistry playing a critical role in its onset and progression. As high levels of all- trans retinoic acid (ATRA) in synovial fluid have been identified as a contributive factor to OA, the synthesis of de novo antagonists for retinoic acid receptors (RARs) has been exploited to interrupt the mechanism of ATRA action. BMS493, a pan-RAR inverse agonist, has been reported as an effective inhibitor of ATRA signaling pathway; however, it is unstable and rapidly degrades under physiological conditions. We employed an engineered cartilage oligomeric matrix protein coiled-coil (CccS) protein for the encapsulation, protection, and delivery of BMS493. In this study, we determine the binding affinity of CccS to BMS493 and the stimulator, ATRA, via competitive binding assay, in which ATRA exhibits approximately 5-fold superior association with CccS than BMS493. Interrogation of the structure of CccS indicates that ATRA causes about 10% loss in helicity, while BMS493 did not impact the structure. Furthermore, CccS self-assembles into nanofibers when bound to BMS493 or ATRA as expected, displaying 11-15 nm in diameter. Treatment of human articular chondrocytes in vitro reveals that CccS·BMS493 demonstrates a marked improvement in efficacy in reducing the mRNA levels of matrix metalloproteinase-13 (MMP-13), one of the main proteases responsible for the degradation of the extracellular cartilage matrix compared to BMS493 alone in the presence of ATRA, interleukin-1 beta (IL-1β), or IL-1 β together with ATRA. These results support the feasibility of utilizing coiled-coil proteins as drug delivery vehicles for compounds of relatively limited bioavailability for the potential treatment of OA.
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Affiliation(s)
- Liming Yin
- Department of Chemical and Biomolecular Engineering , NYU Tandon School of Engineering , Brooklyn , New York 11201 , United States
| | - Albert S Agustinus
- Department of Chemical and Biomolecular Engineering , NYU Tandon School of Engineering , Brooklyn , New York 11201 , United States
| | - Carlo Yuvienco
- Department of Chemical and Biomolecular Engineering , NYU Tandon School of Engineering , Brooklyn , New York 11201 , United States
| | | | - Nicole L Schnabel
- Department of Chemical and Biomolecular Engineering , NYU Tandon School of Engineering , Brooklyn , New York 11201 , United States
| | | | - Jin K Montclare
- Department of Chemical and Biomolecular Engineering , NYU Tandon School of Engineering , Brooklyn , New York 11201 , United States.,Department of Chemistry , New York University , New York , New York 10003 , United States.,Department of Biomaterials , NYU College of Dentistry , New York , New York 10010 , United States.,Department of Biochemistry , SUNY Downstate Medical Center , Brooklyn , New York 11203 , United States
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39
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Yagi S, Akanuma S, Yamagishi A. Creation of artificial protein-protein interactions using α-helices as interfaces. Biophys Rev 2018; 10:411-420. [PMID: 29214605 PMCID: PMC5899712 DOI: 10.1007/s12551-017-0352-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/15/2017] [Indexed: 12/31/2022] Open
Abstract
Designing novel protein-protein interactions (PPIs) with high affinity is a challenging task. Directed evolution, a combination of randomization of the gene for the protein of interest and selection using a display technique, is one of the most powerful tools for producing a protein binder. However, the selected proteins often bind to the target protein at an undesired surface. More problematically, some selected proteins bind to their targets even though they are unfolded. Current state-of-the-art computational design methods have successfully created novel protein binders. These computational methods have optimized the non-covalent interactions at interfaces and thus produced artificial protein complexes. However, to date there are only a limited number of successful examples of computationally designed de novo PPIs. De novo design of coiled-coil proteins has been extensively performed and, therefore, a large amount of knowledge of the sequence-structure relationship of coiled-coil proteins has been accumulated. Taking advantage of this knowledge, de novo design of inter-helical interactions has been used to produce artificial PPIs. Here, we review recent progress in the in silico design and rational design of de novo PPIs and the use of α-helices as interfaces.
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Affiliation(s)
- Sota Yagi
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Satoshi Akanuma
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama, 359-1192, Japan
| | - Akihiko Yamagishi
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan.
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40
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Fujita S, Matsuura K. Self-assembled artificial viral capsids bearing coiled-coils at the surface. Org Biomol Chem 2018; 15:5070-5077. [PMID: 28574073 DOI: 10.1039/c7ob00998d] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In order to construct artificial viral capsids bearing complementary dimeric coiled-coils on the surface, a β-annulus peptide bearing a coiled-coil forming sequence at the C-terminus (β-annulus-coiled-coil-B) was synthesized by a native chemical ligation of a β-annulus-SBn peptide with a Cys-containing coiled-coil-B peptide. Dynamic light scattering (DLS) measurements and transmission electron microscopy (TEM) images revealed that the β-annulus-coiled-coil-B peptide self-assembled into spherical structures of about 50 nm in 10 mM Tris-HCl buffer. Circular dichroism (CD) spectra indicated the formation of the complementary coiled-coil structure on the spherical assemblies. Addition of 0.25 equivalent of the complementary coiled-coil-A peptide to the β-annulus-coiled-coil-B peptide showed the formation of spherical assemblies of 46 ± 14 nm with grains of 5 nm at the surface, whereas addition of 1 equivalent of the complementary coiled-coil-A peptide generated fibrous assemblies.
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Affiliation(s)
- Seiya Fujita
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, 680-8552, Japan.
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41
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Sanchez-deAlcazar D, Mejias SH, Erazo K, Sot B, Cortajarena AL. Self-assembly of repeat proteins: Concepts and design of new interfaces. J Struct Biol 2018; 201:118-129. [DOI: 10.1016/j.jsb.2017.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/09/2017] [Accepted: 09/02/2017] [Indexed: 11/25/2022]
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42
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Araújo A, Olsen BD, Machado AV. Engineering Elastin-Like Polypeptide-Poly(ethylene glycol) Multiblock Physical Networks. Biomacromolecules 2018; 19:329-339. [PMID: 29253332 DOI: 10.1021/acs.biomac.7b01424] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hybrids of protein biopolymers and synthetic polymers are a promising new class of soft materials, as the advantages of each component can be complementary. A recombinant elastin-like polypeptide (ELP) was conjugated to poly(ethylene glycol) (PEG) by macromolecular coupling in solution to form multiblock ELP-PEG copolymers. The hydrated copolymer preserved the thermoresponsive properties from the ELP block and formed hydrogels with different transition temperatures depending on salt concentration. Small angle scattering indicates that the copolymer hydrogels form sphere-like aggregates with a "fuzzy" interface, while the films form a fractal network of nanoscale aggregates. The use of solutions with different salt concentrations to prepare the hydrogels was found to influence the transition temperature, the mechanical properties, and the size of the nanoscale structure of the hydrogel without changing the secondary structure of the ELP. The salt variation and the addition of a plasticizer also affected the nanoscale structure and the mechanical characteristics of the films.
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Affiliation(s)
- Andreia Araújo
- Institute for Polymers and Composites/I3N, University of Minho , Campus de Azurém, 4800-058 Guimarães, Portugal
| | - Bradley D Olsen
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Ana Vera Machado
- Institute for Polymers and Composites/I3N, University of Minho , Campus de Azurém, 4800-058 Guimarães, Portugal
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43
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Katyal P, Montclare JK. Design and Characterization of Fibers and Bionanocomposites Using the Coiled-Coil Domain of Cartilage Oligomeric Matrix Protein. Methods Mol Biol 2018; 1798:239-263. [PMID: 29868965 DOI: 10.1007/978-1-4939-7893-9_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tremendous effort has been dedicated to the design and assembly of bioinspired protein-based architectures with potential applications in drug delivery, tissue engineering, biosensing, and bioimaging. Here, we describe our strategy to generate fibers and bionanocomposites using the coiled-coil domain of cartilage oligomeric matrix protein (COMPcc). Our construct, Q, engineered by swapping particular regions of COMPcc to optimize surface charge, self-assembles to form nanofibers. The Q protein nanofibers can efficiently bind curcumin to form robust mesofibers that can be potentially used for drug delivery and biomedical applications. In addition, using the same Q protein, we describe the biotemplation of gold nanoparticles (AuNP) in the presence and absence of the hexahistidine tag (His-tag). The Q bearing His-tag·AuNP (Q·AuNP) readily deposits on electrode surfaces, while Q without His-tag·AuNP (Qx·AuNP) stabilizes the soluble protein·gold bionanocomposites for several days without aggregating.
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Affiliation(s)
- Priya Katyal
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, Brooklyn, NY, USA
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, Brooklyn, NY, USA.
- Department of Biochemistry, SUNY Downstate Medical Center, Brooklyn, NY, USA.
- Department of Biomaterials, New York University College of Dentistry, New York, NY, USA.
- Department of Chemistry, New York University, New York, NY, USA.
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44
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Lin Y, Koga N, Vorobiev SM, Baker D. Cyclic oligomer design with de novo αβ-proteins. Protein Sci 2017; 26:2187-2194. [PMID: 28801928 PMCID: PMC5654858 DOI: 10.1002/pro.3270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/28/2017] [Accepted: 08/10/2017] [Indexed: 12/11/2022]
Abstract
We have previously shown that monomeric globular αβ-proteins can be designed de novo with considerable control over topology, size, and shape. In this paper, we investigate the design of cyclic homo-oligomers from these starting points. We experimented with both keeping the original monomer backbones fixed during the cyclic docking and design process, and allowing the backbone of the monomer to conform to that of adjacent subunits in the homo-oligomer. The latter flexible backbone protocol generated designs with shape complementarity approaching that of native homo-oligomers, but experimental characterization showed that the fixed backbone designs were more stable and less aggregation prone. Designed C2 oligomers with β-strand backbone interactions were structurally confirmed through x-ray crystallography and small-angle X-ray scattering (SAXS). In contrast, C3-C5 designed homo-oligomers with primarily nonpolar residues at interfaces all formed a range of oligomeric states. Taken together, our results suggest that for homo-oligomers formed from globular building blocks, improved structural specificity will be better achieved using monomers with increased shape complementarity and with more polar interfaces.
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Affiliation(s)
- Yu‐Ru Lin
- Department of BiochemistryUniversity of Washington, and Howard Hughes Medical InstituteSeattleWashington 98195
| | - Nobuyasu Koga
- Research Center of Integrative Molecular SystemsInstitute for Molecular Science, National Institute of Natural Sciences (NINS)Okazaki 444‐8585Japan
- JST, PRESTOKawaguchiSaitama 332‐0012Japan
| | - Sergey M. Vorobiev
- Department of Biological ScienceNortheast Structural Genomics Consortium, Columbia UniversityNew YorkNew York
| | - David Baker
- Department of BiochemistryUniversity of Washington, and Howard Hughes Medical InstituteSeattleWashington 98195
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45
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Liu CF, Chen R, Frezzo JA, Katyal P, Hill LK, Yin L, Srivastava N, More HT, Renfrew PD, Bonneau R, Montclare JK. Efficient Dual siRNA and Drug Delivery Using Engineered Lipoproteoplexes. Biomacromolecules 2017; 18:2688-2698. [PMID: 28686014 DOI: 10.1021/acs.biomac.7b00203] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An engineered supercharged coiled-coil protein (CSP) and the cationic transfection reagent Lipofectamine 2000 are combined to form a lipoproteoplex for the purpose of dual delivery of siRNA and doxorubicin. CSP, bearing an external positive charge and axial hydrophobic pore, demonstrates the ability to condense siRNA and encapsulate the small-molecule chemotherapeutic, doxorubicin. The lipoproteoplex demonstrates improved doxorubicin loading relative to Lipofectamine 2000. Furthermore, it induces effective transfection of GAPDH (60% knockdown) in MCF-7 breast cancer cells with efficiencies comparing favorably to Lipofectamine 2000. When the lipoproteoplex is loaded with doxorubicin, the improved doxorubicin loading (∼40 μg Dox/mg CSP) results in a substantial decrease in MCF-7 cell viability.
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Affiliation(s)
- Che Fu Liu
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering , Brooklyn, New York 11201, United States
| | - Raymond Chen
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering , Brooklyn, New York 11201, United States
| | - Joseph A Frezzo
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering , Brooklyn, New York 11201, United States
| | - Priya Katyal
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering , Brooklyn, New York 11201, United States
| | - Lindsay K Hill
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering , Brooklyn, New York 11201, United States.,Department of Biomedical Engineering, State University of New York Downstate Medical Center , Brooklyn, New York 11203, United States.,Department of Radiology, New York University School of Medicine , New York, New York 10016, United States
| | - Liming Yin
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering , Brooklyn, New York 11201, United States
| | - Nikita Srivastava
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering , Brooklyn, New York 11201, United States
| | - Haresh T More
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering , Brooklyn, New York 11201, United States
| | - P Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, Simons Foundation , 162 Fifth Avenue, New York, New York 10010, United States
| | - Richard Bonneau
- Center for Genomics and Systems Biology, New York University , New York, New York 10003, United States.,Courant Institute of Mathematical Sciences, Computer Science Department, New York University , New York, New York 10009, United States.,Center for Computational Biology, Flatiron Institute, Simons Foundation , 162 Fifth Avenue, New York, New York 10010, United States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering , Brooklyn, New York 11201, United States.,Department of Chemistry, New York University , New York, New York 10003, United States.,Department of Biochemistry, SUNY Downstate Medical Center , Brooklyn, New York 11203, United States
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46
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Abstract
The development of biomaterials designed for specific applications is an important objective in personalized medicine. While the breadth and prominence of biomaterials have increased exponentially over the past decades, critical challenges remain to be addressed, particularly in the development of biomaterials that exhibit highly specific functions. These functional properties are often encoded within the molecular structure of the component molecules. Proteins, as a consequence of their structural specificity, represent useful substrates for the construction of functional biomaterials through rational design. This chapter provides an in-depth survey of biomaterials constructed from coiled-coils, one of the best-understood protein structural motifs. We discuss the utility of this structurally diverse and functionally tunable class of proteins for the creation of novel biomaterials. This discussion illustrates the progress that has been made in the development of coiled-coil biomaterials by showcasing studies that bridge the gap between the academic science and potential technological impact.
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Affiliation(s)
- David A.D. Parry
- Institute of Fundamental Sciences and Riddet Institute, Massey University, Palmerston North, New Zealand
| | - John M. Squire
- Muscle Contraction Group, School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
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47
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Towards designing new nano-scale protein architectures. Essays Biochem 2017; 60:315-324. [PMID: 27903819 DOI: 10.1042/ebc20160018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 08/11/2016] [Accepted: 08/18/2016] [Indexed: 11/17/2022]
Abstract
The complexity of designed bionano-scale architectures is rapidly increasing mainly due to the expanding field of DNA-origami technology and accurate protein design approaches. The major advantage offered by polypeptide nanostructures compared with most other polymers resides in their highly programmable complexity. Proteins allow in vivo formation of well-defined structures with a precise spatial arrangement of functional groups, providing extremely versatile nano-scale scaffolds. Extending beyond existing proteins that perform a wide range of functions in biological systems, it became possible in the last few decades to engineer and predict properties of completely novel protein folds, opening the field of protein nanostructure design. This review offers an overview on rational and computational design approaches focusing on the main achievements of novel protein nanostructure design.
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48
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Yin L, Yuvienco C, Montclare JK. Protein based therapeutic delivery agents: Contemporary developments and challenges. Biomaterials 2017; 134:91-116. [PMID: 28458031 DOI: 10.1016/j.biomaterials.2017.04.036] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/18/2017] [Accepted: 04/21/2017] [Indexed: 12/15/2022]
Abstract
As unique biopolymers, proteins can be employed for therapeutic delivery. They bear important features such as bioavailability, biocompatibility, and biodegradability with low toxicity serving as a platform for delivery of various small molecule therapeutics, gene therapies, protein biologics and cells. Depending on size and characteristic of the therapeutic, a variety of natural and engineered proteins or peptides have been developed. This, coupled to recent advances in synthetic and chemical biology, has led to the creation of tailor-made protein materials for delivery. This review highlights strategies employing proteins to facilitate the delivery of therapeutic matter, addressing the challenges for small molecule, gene, protein and cell transport.
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Affiliation(s)
- Liming Yin
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, United States
| | - Carlo Yuvienco
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, United States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, United States; Department of Chemistry, New York University, New York, NY 10003, United States; Department of Biomaterials, NYU College of Dentistry, New York, NY 10010, United States; Department of Biochemistry, SUNY Downstate Medical Center, Brooklyn, NY 11203, United States.
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49
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Abstract
α-Helical coiled coils are ubiquitous protein-folding and protein-interaction domains in which two or more α-helical chains come together to form bundles. Through a combination of bioinformatics analysis of many thousands of natural coiled-coil sequences and structures, plus empirical protein engineering and design studies, there is now a deep understanding of the sequence-to-structure relationships for this class of protein architecture. This has led to considerable success in rational design and what might be termed in biro de novo design of simple coiled coils, which include homo- and hetero-meric parallel dimers, trimers and tetramers. In turn, these provide a toolkit for directing the assembly of both natural proteins and more complex designs in protein engineering, materials science and synthetic biology. Moving on, the increased and improved use of computational design is allowing access to coiled-coil structures that are rare or even not observed in nature, for example α-helical barrels, which comprise five or more α-helices and have central channels into which different functions may be ported. This chapter reviews all of these advances, outlining improvements in our knowledge of the fundamentals of coiled-coil folding and assembly, and highlighting new coiled coil-based materials and applications that this new understanding is opening up. Despite considerable progress, however, challenges remain in coiled-coil design, and the next decade promises to be as productive and exciting as the last.
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Affiliation(s)
- Derek N Woolfson
- School of Chemistry, University of Bristol, BS8 1TS, Bristol, UK.
- School of Biochemistry, University of Bristol, BS8 1TD, Bristol, UK.
- BrisSynBio, Life Sciences Building, University of Bristol, BS8 1TQ, Bristol, UK.
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Wu Y, Collier JH. α-Helical coiled-coil peptide materials for biomedical applications. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2016; 9. [PMID: 27597649 DOI: 10.1002/wnan.1424] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/07/2016] [Accepted: 07/17/2016] [Indexed: 12/31/2022]
Abstract
Self-assembling coiled coils, which occur commonly in native proteins, have received significant interest for the design of new biomaterials-based medical therapies. Considerable effort over recent years has led to a detailed understanding of the self-assembly process of coiled coils, and a diverse collection of strategies have been developed for designing functional materials using this motif. The ability to engineer the interface between coiled coils allows one to achieve variously connected components, leading to precisely defined structures such as nanofibers, nanotubes, nanoparticles, networks, gels, and combinations of these. Currently these materials are being developed for a range of biotechnological and medical applications, including drug delivery systems for controlled release, targeted nanomaterials, 'drug-free' therapeutics, vaccine delivery systems, and others. WIREs Nanomed Nanobiotechnol 2017, 9:e1424. doi: 10.1002/wnan.1424 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Yaoying Wu
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Joel H Collier
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
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