1
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Zheng R, Zhao M, Du JS, Sudarshan TR, Zhou Y, Paravastu AK, De Yoreo JJ, Ferguson AL, Chen CL. Assembly of short amphiphilic peptoids into nanohelices with controllable supramolecular chirality. Nat Commun 2024; 15:3264. [PMID: 38627405 PMCID: PMC11021492 DOI: 10.1038/s41467-024-46839-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 03/12/2024] [Indexed: 04/19/2024] Open
Abstract
A long-standing challenge in bioinspired materials is to design and synthesize synthetic materials that mimic the sophisticated structures and functions of natural biomaterials, such as helical protein assemblies that are important in biological systems. Herein, we report the formation of a series of nanohelices from a type of well-developed protein-mimetics called peptoids. We demonstrate that nanohelix structures and supramolecular chirality can be well-controlled through the side-chain chemistry. Specifically, the ionic effects on peptoids from varying the polar side-chain groups result in the formation of either single helical fiber or hierarchically stacked helical bundles. We also demonstrate that the supramolecular chirality of assembled peptoid helices can be controlled by modifying assembling peptoids with a single chiral amino acid side chain. Computational simulations and theoretical modeling predict that minimizing exposure of hydrophobic domains within a twisted helical form presents the most thermodynamically favorable packing of these amphiphilic peptoids and suggests a key role for both polar and hydrophobic domains on nanohelix formation. Our findings establish a platform to design and synthesize chiral functional materials using sequence-defined synthetic polymers.
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Affiliation(s)
- Renyu Zheng
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Mingfei Zhao
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA
| | - Jingshan S Du
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Tarunya Rao Sudarshan
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Yicheng Zhou
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- Department of Materials Science, University of Washington, Seattle, WA, 98195, USA
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA
| | - Chun-Long Chen
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA.
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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2
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Verma G, Hostert J, Summerville AA, Robang AS, Garcia Carcamo R, Paravastu AK, Getman RB, Duval CE, Renner J. Investigation of Rare Earth Element Binding to a Surface-Bound Affinity Peptide Derived from EF-Hand Loop I of Lanmodulin. ACS Appl Mater Interfaces 2024; 16:16912-16926. [PMID: 38527460 PMCID: PMC10995902 DOI: 10.1021/acsami.3c17565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/17/2024] [Accepted: 02/27/2024] [Indexed: 03/27/2024]
Abstract
Bioinspired strategies have been given extensive attention for the recovery of rare earth elements (REEs) from waste streams because of their high selectivity, regeneration potential, and sustainability as well as low cost. Lanmodulin protein is an emerging biotechnology that is highly selective for REE binding. Mimicking lanmodulin with shorter peptides is advantageous because they are simpler and potentially easier to manipulate and optimize. Lanmodulin-derived peptides have been found to bind REEs, but their properties have not been explored when immobilized on solid substrates, which is required for many advanced separation technologies. Here, two peptides, LanM1 and scrambled LanM1, are designed from the EF-hand loop 1 of lanmodulin and investigated for their binding affinity toward different REEs when surface-bound. First, the ability of LanM1 to bind REEs was confirmed and characterized in solution using circular dichroism (CD), nuclear magnetic resonance (NMR), and molecular dynamics (MD) simulations for Ce(III) ions. Isothermal titration calorimetry (ITC) was used to further analyze the binding of the LanM1 to Ce(III), Nd(III), Eu(III), and Y(III) ions and in low-pH conditions. The performance of the immobilized peptides on a model gold surface was examined using a quartz crystal microbalance with dissipation (QCM-D). The studies show that the LanM1 peptide has a stronger REE binding affinity than that of scrambled LanM1 when in solution and when immobilized on a gold surface. QCM-D data were fit to the Langmuir adsorption model to estimate the surface-bound dissociation constant (Kd) of LanM1 with Ce(III) and Nd(III). The results indicate that LanM1 peptides maintain a high affinity for REEs when immobilized, and surface-bound LanM1 has no affinity for potential competitor calcium and copper ions. The utility of surface-bound LanM1 peptides was further demonstrated by immobilizing them to gold nanoparticles (GNPs) and capturing REEs from solution in experiments utilizing an Arsenazo III-based colorimetric dye displacement assay and ultraviolet-visible (UV-vis) spectrophotometry. The saturated adsorption capacity of GNPs was estimated to be around 3.5 μmol REE/g for Ce(III), Nd(III), Eu(III), and Y(III) ions, with no binding of non-REE Ca(II) ions observed.
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Affiliation(s)
- Geeta Verma
- Department
of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Jacob Hostert
- Department
of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Alex A. Summerville
- Department
of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Alicia S. Robang
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ricardo Garcia Carcamo
- Department
of Chemical and Biomolecular Engineering, Ohio State University, Columbus, Ohio 43210, United States
| | - Anant K. Paravastu
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, Georgia 30332, United States
| | - Rachel B. Getman
- Department
of Chemical and Biomolecular Engineering, Ohio State University, Columbus, Ohio 43210, United States
| | - Christine E. Duval
- Department
of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Julie Renner
- Department
of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, Ohio 44106, United States
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3
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Robang A, Roy A, Dodd-o JB, He D, Le JV, McShan AC, Hu Y, Kumar VA, Paravastu AK. Structural Consequences of Introducing Bioactive Domains to Designer β-Sheet Peptide Self-Assemblies. Biomacromolecules 2024; 25:1429-1438. [PMID: 38408372 PMCID: PMC10934295 DOI: 10.1021/acs.biomac.3c00962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
We applied solid- and solution-state nuclear magnetic resonance spectroscopy to examine the structure of multidomain peptides composed of self-assembling β-sheet domains linked to bioactive domains. Bioactive domains can be selected to stimulate specific biological responses (e.g., via receptor binding), while the β-sheets provide the desirable nanoscale properties. Although previous work has established the efficacy of multidomain peptides, molecular-level characterization is lacking. The bioactive domains are intended to remain solvent-accessible without being incorporated into the β-sheet structure. We tested for three possible anticipated molecular-level consequences of introducing bioactive domains to β-sheet-forming peptides: (1) the bioactive domain has no effect on the self-assembling peptide structure; (2) the bioactive domain is incorporated into the β-sheet nanofiber; and (3) the bioactive domain interferes with self-assembly such that nanofibers are not formed. The peptides involved in this study incorporated self-assembling domains based on the (SL)6 motif and bioactive domains including a VEGF-A mimic (QK), an IGF-mimic (IGF-1c), and a de novo SARS-CoV-2 binding peptide (SBP3). We observed all three of the anticipated outcomes from our examination of peptides, illustrating the unintended structural effects that could adversely affect the desired biofunctionality and biomaterial properties of the resulting peptide hydrogel. This work is the first attempt to evaluate the structural effects of incorporating bioactive domains into a set of peptides unified by a similar self-assembling peptide domain. These structural insights reveal unmet challenges in the design of highly tunable bioactive self-assembling peptide hydrogels.
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Affiliation(s)
- Alicia
S. Robang
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Abhishek Roy
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Joseph B. Dodd-o
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Dongjing He
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Justin V. Le
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Andrew C. McShan
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Yuhang Hu
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Vivek A. Kumar
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
- Department
of Chemicals and Materials Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
- Department
of Biology, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Anant K. Paravastu
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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4
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Dodd-O J, Roy A, Siddiqui Z, Jafari R, Coppola F, Ramasamy S, Kolloli A, Kumar D, Kaundal S, Zhao B, Kumar R, Robang AS, Li J, Azizogli AR, Pai V, Acevedo-Jake A, Heffernan C, Lucas A, McShan AC, Paravastu AK, Prasad BVV, Subbian S, Král P, Kumar V. Author Correction: Antiviral fibrils of self-assembled peptides with tunable compositions. Nat Commun 2024; 15:1505. [PMID: 38374216 PMCID: PMC10876924 DOI: 10.1038/s41467-024-46005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024] Open
Affiliation(s)
- Joseph Dodd-O
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Abhishek Roy
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Zain Siddiqui
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Roya Jafari
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Francesco Coppola
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Santhamani Ramasamy
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Afsal Kolloli
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Dilip Kumar
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Soni Kaundal
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Boyang Zhao
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ranjeet Kumar
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Alicia S Robang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Jeffrey Li
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Abdul-Rahman Azizogli
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Varun Pai
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Amanda Acevedo-Jake
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Corey Heffernan
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
- SAPHTx Inc, Newark, NJ, 07104, USA
| | - Alexandra Lucas
- Center for Personalized Diagnostics and Center for Immunotherapy Vaccines and Virotherapy, Biodesign Institute, Arizona State University, 727 E, Tempe, AZ, USA
| | - Andrew C McShan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - B V Venkataram Prasad
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Selvakumar Subbian
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Petr Král
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Physics, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL, 60607, USA.
| | - Vivek Kumar
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
- SAPHTx Inc, Newark, NJ, 07104, USA.
- Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
- Department of Endodontics, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA.
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5
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Dodd-O J, Roy A, Siddiqui Z, Jafari R, Coppola F, Ramasamy S, Kolloli A, Kumar D, Kaundal S, Zhao B, Kumar R, Robang AS, Li J, Azizogli AR, Pai V, Acevedo-Jake A, Heffernan C, Lucas A, McShan AC, Paravastu AK, Prasad BVV, Subbian S, Král P, Kumar V. Antiviral fibrils of self-assembled peptides with tunable compositions. Nat Commun 2024; 15:1142. [PMID: 38326301 PMCID: PMC10850501 DOI: 10.1038/s41467-024-45193-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Abstract
The lasting threat of viral pandemics necessitates the development of tailorable first-response antivirals with specific but adaptive architectures for treatment of novel viral infections. Here, such an antiviral platform has been developed based on a mixture of hetero-peptides self-assembled into functionalized β-sheets capable of specific multivalent binding to viral protein complexes. One domain of each hetero-peptide is designed to specifically bind to certain viral proteins, while another domain self-assembles into fibrils with epitope binding characteristics determined by the types of peptides and their molar fractions. The self-assembled fibrils maintain enhanced binding to viral protein complexes and retain high resilience to viral mutations. This method is experimentally and computationally tested using short peptides that specifically bind to Spike proteins of SARS-CoV-2. This platform is efficacious, inexpensive, and stable with excellent tolerability.
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Affiliation(s)
- Joseph Dodd-O
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Abhishek Roy
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Zain Siddiqui
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Roya Jafari
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Francesco Coppola
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Santhamani Ramasamy
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Afsal Kolloli
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Dilip Kumar
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Soni Kaundal
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Boyang Zhao
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ranjeet Kumar
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Alicia S Robang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Jeffrey Li
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Abdul-Rahman Azizogli
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Varun Pai
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Amanda Acevedo-Jake
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Corey Heffernan
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
- SAPHTx Inc, Newark, NJ, 07104, USA
| | - Alexandra Lucas
- Center for Personalized Diagnostics and Center for Immunotherapy Vaccines and Virotherapy, Biodesign Institute, Arizona State University, 727 E, Tempe, AZ, USA
| | - Andrew C McShan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - B V Venkataram Prasad
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Selvakumar Subbian
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Petr Král
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Physics, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL, 60607, USA.
| | - Vivek Kumar
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
- SAPHTx Inc, Newark, NJ, 07104, USA.
- Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
- Department of Endodontics, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA.
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6
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Roy A, Dodd-O JB, Robang AS, He D, West O, Siddiqui Z, Aguas ED, Goldberg H, Griffith A, Heffernan C, Hu Y, Paravastu AK, Kumar VA. Self-Assembling Peptides with Insulin-Like Growth Factor Mimicry. ACS Appl Mater Interfaces 2024; 16:364-375. [PMID: 38145951 DOI: 10.1021/acsami.3c15660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Growth factor (GF) mimicry involves recapitulating the signaling of larger molecules or cells. Although GF mimicry holds considerable promise in tissue engineering and drug design applications, difficulties in targeting the signaling molecule to the site of delivery and dissociation of mimicking peptides from their target receptors continue to limit its clinical application. To address these challenges, we utilized a self-assembling peptide (SAP) platform to generate synthetic insulin-like growth factor (IGF)-signaling, self-assembling GFs. Our peptide hydrogels are biocompatible and bind target IGF receptors in a dose-dependent fashion, activate proangiogenic signaling, and facilitate formation of angiogenic microtubules in vitro. Furthermore, infiltrated hydrogels are stable for weeks to months. We conclude that the enhanced targeting and long-term stability of our SAP/GF mimicry implants may improve the efficacy and safety of future GF mimic therapeutics.
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Affiliation(s)
- Abhishek Roy
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Joseph B Dodd-O
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Alicia S Robang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Dongjing He
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Owen West
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Zain Siddiqui
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Erika Davidoff Aguas
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey 08544, United States
| | - Hannah Goldberg
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Alexandra Griffith
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Corey Heffernan
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Yuhang Hu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Vivek A Kumar
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
- Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
- Department of Endodontics, Rutgers School of Dental Medicine, Newark, New Jersey 07103, United States
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7
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Liu R, Dong X, Seroski DT, Soto Morales B, Wong KM, Robang AS, Melgar L, Angelini TE, Paravastu AK, Hall CK, Hudalla GA. Side-Chain Chemistry Governs Hierarchical Order of Charge-Complementary β-sheet Peptide Coassemblies. Angew Chem Int Ed Engl 2023; 62:e202314531. [PMID: 37931093 PMCID: PMC10841972 DOI: 10.1002/anie.202314531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/08/2023]
Abstract
Self-assembly of proteinaceous biomolecules into functional materials with ordered structures that span length scales is common in nature yet remains a challenge with designer peptides under ambient conditions. This report demonstrates how charged side-chain chemistry affects the hierarchical co-assembly of a family of charge-complementary β-sheet-forming peptide pairs known as CATCH(X+/Y-) at physiologic pH and ionic strength in water. In a concentration-dependent manner, the CATCH(6K+) (Ac-KQKFKFKFKQK-Am) and CATCH(6D-) (Ac-DQDFDFDFDQD-Am) pair formed either β-sheet-rich microspheres or β-sheet-rich gels with a micron-scale plate-like morphology, which were not observed with other CATCH(X+/Y-) pairs. This hierarchical order was disrupted by replacing D with E, which increased fibril twisting. Replacing K with R, or mutating the N- and C-terminal amino acids in CATCH(6K+) and CATCH(6D-) to Qs, increased observed co-assembly kinetics, which also disrupted hierarchical order. Due to the ambient assembly conditions, active CATCH(6K+)-green fluorescent protein fusions could be incorporated into the β-sheet plates and microspheres formed by the CATCH(6K+/6D-) pair, demonstrating the potential to endow functionality.
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Affiliation(s)
- Renjie Liu
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL-32611, USA
| | - Xin Dong
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC-27695, USA
| | - Dillon T Seroski
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL-32611, USA
| | - Bethsymarie Soto Morales
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL-32611, USA
| | - Kong M Wong
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA-30332, USA
| | - Alicia S Robang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA-30332, USA
| | - Lucas Melgar
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL-32611, USA
| | - Thomas E Angelini
- Department of Mechanical and Aerospace Engineering, University of Florida, Gainesville, FL-32611, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA-30332, USA
| | - Carol K Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC-27695, USA
| | - Gregory A Hudalla
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL-32611, USA
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8
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Muhammedkutty FNK, Prasad R, Gao Y, Sudarshan TR, Robang AS, Watzlawik JO, Rosenberry TL, Paravastu AK, Zhou HX. A common pathway for detergent-assisted oligomerization of Aβ42. Commun Biol 2023; 6:1184. [PMID: 37989804 PMCID: PMC10663524 DOI: 10.1038/s42003-023-05556-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/08/2023] [Indexed: 11/23/2023] Open
Abstract
Amyloid beta (Aβ) aggregation is a slow process without seeding or assisted nucleation. Sodium dodecyl sulfate (SDS) micelles stabilize Aβ42 small oligomers (in the dimer to tetramer range); subsequent SDS removal leads to a 150-kD Aβ42 oligomer. Dodecylphosphorylcholine (DPC) micelles also stabilize an Aβ42 tetramer. Here we investigate the detergent-assisted oligomerization pathway by solid-state NMR spectroscopy and molecular dynamics simulations. SDS- and DPC-induced oligomers have the same structure, implying a common oligomerization pathway. An antiparallel β-sheet formed by the C-terminal region, the only stable structure in SDS and DPC micelles, is directly incorporated into the 150-kD oligomer. Three Gly residues (at positions 33, 37, and 38) create holes that are filled by the SDS and DPC hydrocarbon tails, thereby turning a potentially destabilizing feature into a stabilizing factor. These observations have implications for endogenous Aβ aggregation at cellular interfaces.
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Affiliation(s)
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Yuan Gao
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA, 30332, USA
| | - Tarunya Rao Sudarshan
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA, 30332, USA
| | - Alicia S Robang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA, 30332, USA
| | - Jens O Watzlawik
- Departments of Neuroscience and Pharmacology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Terrone L Rosenberry
- Departments of Neuroscience and Pharmacology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA, 30332, USA.
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA, 30332, USA.
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, 60607, USA.
- Department of Physics, University of Illinois Chicago, Chicago, IL, 60607, USA.
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9
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Lim S, Cordova DLM, Robang AS, Kuang Y, Ogura KS, Paravastu AK, Arguilla MQ, Ardoña HAM. Thermochromic Behavior of Polydiacetylene Nanomaterials Driven by Charged Peptide Amphiphiles. Biomacromolecules 2023; 24:4051-4063. [PMID: 37552220 PMCID: PMC10498447 DOI: 10.1021/acs.biomac.3c00422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/18/2023] [Indexed: 08/09/2023]
Abstract
The tunability of chromatic phases adapted by chromogenic polymers such as polydiacetylene (PDA) is key to their utility for robust sensing applications. Here, we investigated the influence of charged peptide interactions on the structure-dependent thermochromicity of amphiphilic PDAs. Solid-state NMR and circular dichroism analyses show that our oppositely charged peptide-PDA samples have distinct degrees of structural order, with the coassembled sample being in between the β-sheet-like positive peptide-PDA and the relatively disordered negative peptide-PDA. All solutions exhibit thermochromicity between 20 and 80 °C, whereby the hysteresis of the blue, planar phase is much larger than that of the red, twisted phase. Resonance Raman spectroscopy of films demonstrates that only coassemblies with electrostatic complementarity stabilize coexisting blue and red PDA phases. This work reveals the nature of the structural changes responsible for the thermally responsive chromatic transitions of biomolecule-functionalized polymeric materials and how this process can be directed by sequence-dictated electrostatic interactions.
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Affiliation(s)
- Sujeung Lim
- Department
of Chemical and Biomolecular Engineering, Samueli School of Engineering, University of California, Irvine, California 92697, United States
| | - Dmitri Leo M. Cordova
- Department
of Chemistry, School of Physical Sciences, University of California, Irvine, California 92697, United States
| | - Alicia S. Robang
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yuyao Kuang
- Department
of Chemical and Biomolecular Engineering, Samueli School of Engineering, University of California, Irvine, California 92697, United States
| | - Kaleolani S. Ogura
- Department
of Chemistry, School of Physical Sciences, University of California, Irvine, California 92697, United States
| | - Anant K. Paravastu
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Maxx Q. Arguilla
- Department
of Chemistry, School of Physical Sciences, University of California, Irvine, California 92697, United States
| | - Herdeline Ann M. Ardoña
- Department
of Chemical and Biomolecular Engineering, Samueli School of Engineering, University of California, Irvine, California 92697, United States
- Department
of Chemistry, School of Physical Sciences, University of California, Irvine, California 92697, United States
- Department
of Biomedical Engineering, Samueli School of Engineering, University of California, Irvine, California 92697, United States
- Sue
& Bill Gross Stem Cell Research Center, University of California, Irvine, California 92697, United States
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10
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Rosenberry TL, Zhou HX, Stagg SM, Paravastu AK. Oligomer Formation by Amyloid-β42 in a Membrane-Mimicking Environment in Alzheimer's Disease. Molecules 2022; 27:8804. [PMID: 36557940 PMCID: PMC9781152 DOI: 10.3390/molecules27248804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022] Open
Abstract
The brains of Alzheimer's disease (AD) patients contain numerous amyloid plaques that are diagnostic of the disease. The plaques are primarily composed of the amyloidogenic peptides proteins Aβ40 and Aβ42, which are derived by the processing of the amyloid pre-cursor protein (APP) by two proteases called β-secretase and γ-secretase. Aβ42 differs from Aβ40 in having two additional hydrophobic amino acids, ILE and ALA, at the C-terminus. A small percentage of AD is autosomal dominant (ADAD) and linked either to the genes for the presenilins, which are part of γ-secretase, or APP. Because ADAD shares most pathogenic features with widespread late-onset AD, Aβ peptides have become the focus of AD research. Fibrils formed by the aggregation of these peptides are the major component of plaques and were initially targeted in AD therapy. However, the fact that the abundance of plaques does not correlate well with cognitive decline in AD patients has led investigators to examine smaller Aβ aggregates called oligomers. The low levels and heterogeneity of Aβ oligomers have made the determination of their structures difficult, but recent structure determinations of oligomers either formed or initiated in detergents have been achieved. We report here on the structures of these oligomers and suggest how they may be involved in AD.
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Affiliation(s)
- Terrone L. Rosenberry
- The Departments of Neuroscience and Pharmacology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Huan-Xiang Zhou
- Departments of Chemistry and Physics, University of Illinois Chicago, Chicago, IL 60608, USA
| | - Scott M. Stagg
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Anant K. Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332, USA
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11
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Xiao X, Robang AS, Sarma S, Le JV, Helmicki ME, Lambert MJ, Guerrero-Ferreira R, Arboleda-Echavarria J, Paravastu AK, Hall CK. Sequence patterns and signatures: Computational and experimental discovery of amyloid-forming peptides. PNAS Nexus 2022; 1:pgac263. [PMID: 36712347 PMCID: PMC9802472 DOI: 10.1093/pnasnexus/pgac263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
Screening amino acid sequence space via experiments to discover peptides that self-assemble into amyloid fibrils is challenging. We have developed a computational peptide assembly design (PepAD) algorithm that enables the discovery of amyloid-forming peptides. Discontinuous molecular dynamics (DMD) simulation with the PRIME20 force field combined with the FoldAmyloid tool is used to examine the fibrilization kinetics of PepAD-generated peptides. PepAD screening of ∼10,000 7-mer peptides resulted in twelve top-scoring peptides with two distinct hydration properties. Our studies revealed that eight of the twelve in silico discovered peptides spontaneously form amyloid fibrils in the DMD simulations and that all eight have at least five residues that the FoldAmyloid tool classifies as being aggregation-prone. Based on these observations, we re-examined the PepAD-generated peptides in the sequence pool returned by PepAD and extracted five sequence patterns as well as associated sequence signatures for the 7-mer amyloid-forming peptides. Experimental results from Fourier transform infrared spectroscopy (FTIR), thioflavin T (ThT) fluorescence, circular dichroism (CD), and transmission electron microscopy (TEM) indicate that all the peptides predicted to assemble in silico assemble into antiparallel β-sheet nanofibers in a concentration-dependent manner. This is the first attempt to use a computational approach to search for amyloid-forming peptides based on customized settings. Our efforts facilitate the identification of β-sheet-based self-assembling peptides, and contribute insights towards answering a fundamental scientific question: "What does it take, sequence-wise, for a peptide to self-assemble?".
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Affiliation(s)
| | | | | | - Justin V Le
- Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Michael E Helmicki
- Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Matthew J Lambert
- Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ricardo Guerrero-Ferreira
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Johana Arboleda-Echavarria
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University School of Medicine, Atlanta, GA 30322, USA
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12
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Dhakal S, Robang AS, Bhatt N, Puangmalai N, Fung L, Kayed R, Paravastu AK, Rangachari V. Distinct neurotoxic TDP-43 fibril polymorphs are generated by heterotypic interactions with α-Synuclein. J Biol Chem 2022; 298:102498. [PMID: 36116552 PMCID: PMC9587012 DOI: 10.1016/j.jbc.2022.102498] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Amyloid aggregates of specific proteins constitute important pathological hallmarks in many neurodegenerative diseases, defining neuronal degeneration and disease onset. Recently, increasing numbers of patients show comorbidities and overlaps between multiple neurodegenerative diseases, presenting distinct phenotypes. Such overlaps are often accompanied by colocalizations of more than one amyloid protein, prompting the question of whether direct interactions between different amyloid proteins could generate heterotypic amyloids. To answer this question, we investigated the effect of α-synuclein (αS) on the DNA-binding protein TDP-43 aggregation inspired by their coexistence in pathologies such as Lewy body dementia and limbic predominant age-related TDP-43 encephalopathy. We previously showed αS and prion-like C-terminal domain (PrLD) of TDP-43 synergistically interact to generate toxic heterotypic aggregates. Here, we extend these studies to investigate whether αS induces structurally and functionally distinct polymorphs of PrLD aggregates. Using αS-PrLD heterotypic aggregates generated in two different stoichiometric proportions, we show αS can affect PrLD fibril forms. PrLD fibrils show distinctive residue level signatures determined by solid state NMR, dye-binding capability, proteinase K (PK) stability, and thermal stability toward SDS denaturation. Furthremore, by gold nanoparticle labeling and transmission electron microscopy, we show the presence of both αS and PrLD proteins within the same fibrils, confirming the existence of heterotypic amyloid fibrils. We also observe αS and PrLD colocalize in the cytosol of neuroblastoma cells and show that the heterotypic PrLD fibrils selectively induce synaptic dysfunction in primary neurons. These findings establish the existence of heterotypic amyloid and provide a molecular basis for the observed overlap between synucleinopathies and TDP-43 proteinopathies.
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Affiliation(s)
- Shailendra Dhakal
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, Mississippi, USA; Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, Mississippi, USA
| | - Alicia S Robang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nemil Bhatt
- Mitchell Center for Neurodegenerative Disorders, University of Texas Medical Branch, Galveston, Texas, USA
| | - Nicha Puangmalai
- Mitchell Center for Neurodegenerative Disorders, University of Texas Medical Branch, Galveston, Texas, USA
| | - Leiana Fung
- Mitchell Center for Neurodegenerative Disorders, University of Texas Medical Branch, Galveston, Texas, USA
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Disorders, University of Texas Medical Branch, Galveston, Texas, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA.
| | - Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, Mississippi, USA; Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, Mississippi, USA.
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13
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Wong KM, Robang AS, Lint AH, Wang Y, Dong X, Xiao X, Seroski DT, Liu R, Shao Q, Hudalla GA, Hall CK, Paravastu AK. Engineering β-Sheet Peptide Coassemblies for Biomaterial Applications. J Phys Chem B 2021; 125:13599-13609. [PMID: 34905370 DOI: 10.1021/acs.jpcb.1c04873] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Peptide coassembly, wherein at least two different peptides interact to form multicomponent nanostructures, is an attractive approach for generating functional biomaterials. Current efforts seek to design pairs of peptides, A and B, that form nanostructures (e.g., β-sheets with ABABA-type β-strand patterning) while resisting self-assembly (e.g., AAAAA-type or BBBBB-type β-sheets). To confer coassembly behavior, most existing designs have been based on highly charged variants of known self-assembling peptides; like-charge repulsion limits self-assembly while opposite-charge attraction promotes coassembly. Recent analyses using solid-state NMR and coarse-grained simulations reveal that preconceived notions of structure and molecular organization are not always correct. This perspective highlights recent advances and key challenges to understanding and controlling peptide coassembly.
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Affiliation(s)
- Kong M Wong
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Alicia S Robang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Annabelle H Lint
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Xin Dong
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Xingqing Xiao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Dillon T Seroski
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, 1275 Center Drive, Biomedical Sciences J293, P.O. BOX 116131, Gainesville, Florida 32611, United States
| | - Renjie Liu
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, 1275 Center Drive, Biomedical Sciences J293, P.O. BOX 116131, Gainesville, Florida 32611, United States
| | - Qing Shao
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Gregory A Hudalla
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, 1275 Center Drive, Biomedical Sciences J293, P.O. BOX 116131, Gainesville, Florida 32611, United States
| | - Carol K Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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14
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Xiao X, Wang Y, Seroski DT, Wong KM, Liu R, Paravastu AK, Hudalla GA, Hall CK. De novo design of peptides that coassemble into β sheet-based nanofibrils. Sci Adv 2021; 7:eabf7668. [PMID: 34516924 PMCID: PMC8442925 DOI: 10.1126/sciadv.abf7668] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Peptides’ hierarchical coassembly into nanostructures enables controllable fabrication of multicomponent biomaterials. In this work, we describe a computational and experimental approach to design pairs of charge-complementary peptides that selectively coassemble into β-sheet nanofibers when mixed together but remain unassembled when isolated separately. The key advance is a peptide coassembly design (PepCAD) algorithm that searches for pairs of coassembling peptides. Six peptide pairs are identified from a pool of ~106 candidates via the PepCAD algorithm and then subjected to DMD/PRIME20 simulations to examine their co-/self-association kinetics. The five pairs that spontaneously aggregate in kinetic simulations selectively coassemble in biophysical experiments, with four forming β-sheet nanofibers and one forming a stable nonfibrillar aggregate. Solid-state NMR, which is applied to characterize the coassembling pairs, suggests that the in silico peptides exhibit a higher degree of structural order than the previously reported CATCH(+/−) peptides.
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Affiliation(s)
- Xingqing Xiao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Dillon T. Seroski
- Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Kong M. Wong
- Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Renjie Liu
- Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Anant K. Paravastu
- Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gregory A. Hudalla
- Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Carol K. Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
- Corresponding author.
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15
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Wong KM, Shao Q, Wang Y, Seroski DT, Liu R, Lint AH, Hudalla GA, Hall CK, Paravastu AK. CATCH Peptides Coassemble into Structurally Heterogeneous β-Sheet Nanofibers with Little Preference to β-Strand Alignment. J Phys Chem B 2021; 125:4004-4015. [PMID: 33876641 DOI: 10.1021/acs.jpcb.0c11645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Coassembling peptides offer an additional degree of freedom in the design of nanostructured biomaterials when compared to analogous self-assembling peptides. Yet, our understanding of how amino acid sequences encodes coassembled nanofiber structure is limited. Prior work on a charge-complementary pair, CATCH+ and CATCH- peptides, detected like-peptide nearest neighbors (CATCH+:CATCH+ and CATCH-:CATCH-) within coassembled β-sheet nanofibers; these self-associated peptide pairs marked a departure from an "ideal" coassembled structure. In this work, we employ solid-state NMR, isotope-edited FTIR, and coarse-grained molecular dynamics simulations to evaluate the alignment of β-strands within CATCH peptide nanofibers. Both experimental and computational results suggest that CATCH molecules coassemble into structurally heterogeneous nanofibers, which is consistent with our observations in another coassembling system, the King-Webb peptides. Within β-sheet nanofibers, β-strands were found to have nearest neighbors aligned in-register parallel, in-register antiparallel, and out-of-register. In comparison to the King-Webb peptides, CATCH nanofibers exhibit a greater degree of structural heterogeneity. By comparing the amino acid sequences of CATCH and King-Webb peptides, we can begin to unravel sequence-to-structure relationships, which may encode more precise coassembled β-sheet nanostructures.
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Affiliation(s)
- Kong M Wong
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Qing Shao
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Dillon T Seroski
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, 1275 Center Drive, Biomedical Sciences J293, P.O. Box 116131, Gainesville, Florida 32611, United States
| | - Renjie Liu
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, 1275 Center Drive, Biomedical Sciences J293, P.O. Box 116131, Gainesville, Florida 32611, United States
| | - Annabelle H Lint
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Gregory A Hudalla
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, 1275 Center Drive, Biomedical Sciences J293, P.O. Box 116131, Gainesville, Florida 32611, United States
| | - Carol K Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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16
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Gao Y, Saccuzzo EG, Hill SE, Huard DJE, Robang AS, Lieberman RL, Paravastu AK. Structural Arrangement within a Peptide Fibril Derived from the Glaucoma-Associated Myocilin Olfactomedin Domain. J Phys Chem B 2021; 125:2886-2897. [PMID: 33683890 DOI: 10.1021/acs.jpcb.0c11460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Myocilin-associated glaucoma is a new addition to the list of diseases linked to protein misfolding and amyloid formation. Single point variants of the ∼257-residue myocilin olfactomedin domain (mOLF) lead to mutant myocilin aggregation. Here, we analyze the 12-residue peptide P1 (GAVVYSGSLYFQ), corresponding to residues 326-337 of mOLF, previously shown to form amyloid fibrils in vitro and in silico. We applied solid-state NMR structural measurements to test the hypothesis that P1 fibrils adopt one of three predicted structures. Our data are consistent with a U-shaped fibril arrangement for P1, one that is related to the U-shape predicted previously in silico. Our data are also consistent with an antiparallel fibril arrangement, likely driven by terminal electrostatics. Our proposed structural model is reminiscent of fibrils formed by the Aβ(1-40) Iowa mutant peptide, but with a different arrangement of molecular turn regions. Taken together, our results strengthen the connection between mOLF fibrils and the broader amylome and contribute to our understanding of the fundamental molecular interactions governing fibril architecture and stability.
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17
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Seroski DT, Dong X, Wong KM, Liu R, Shao Q, Paravastu AK, Hall CK, Hudalla GA. Charge guides pathway selection in β-sheet fibrillizing peptide co-assembly. Commun Chem 2020; 3:172. [PMID: 36703436 PMCID: PMC9814569 DOI: 10.1038/s42004-020-00414-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/15/2020] [Indexed: 01/29/2023] Open
Abstract
Peptide co-assembly is attractive for creating biomaterials with new forms and functions. Emergence of these properties depends on the peptide content of the final assembled structure, which is difficult to predict in multicomponent systems. Here using experiments and simulations we show that charge governs content by affecting propensity for self- and co-association in binary CATCH(+/-) peptide systems. Equimolar mixtures of CATCH(2+/2-), CATCH(4+/4-), and CATCH(6+/6-) formed two-component β-sheets. Solid-state NMR suggested the cationic peptide predominated in the final assemblies. The cationic-to-anionic peptide ratio decreased with increasing charge. CATCH(2+) formed β-sheets when alone, whereas the other peptides remained unassembled. Fibrillization rate increased with peptide charge. The zwitterionic CATCH parent peptide, "Q11", assembled slowly and only at decreased simulation temperature. These results demonstrate that increasing charge draws complementary peptides together faster, favoring co-assembly, while like-charged molecules repel. We foresee these insights enabling development of co-assembled peptide biomaterials with defined content and predictable properties.
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Affiliation(s)
- Dillon T Seroski
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Xin Dong
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA
| | - Kong M Wong
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Renjie Liu
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Qing Shao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Carol K Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA
| | - Gregory A Hudalla
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA.
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18
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Tsoras AN, Wong KM, Paravastu AK, Champion JA. Rational Design of Antigen Incorporation Into Subunit Vaccine Biomaterials Can Enhance Antigen-Specific Immune Responses. Front Immunol 2020; 11:1547. [PMID: 32849524 PMCID: PMC7396695 DOI: 10.3389/fimmu.2020.01547] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/11/2020] [Indexed: 12/29/2022] Open
Abstract
Peptide subunit vaccines increase safety by reducing the risk of off-target responses and improving the specificity of the induced adaptive immune response. The immunogenicity of most soluble peptides, however, is often insufficient to produce robust and lasting immunity. Many biomaterials and delivery vehicles have been developed for peptide antigens to improve immune response while maintaining specificity. Peptide nanoclusters (PNC) are a subunit peptide vaccine material that has shown potential to increase immunogenicity of peptide antigens. PNC are comprised only of crosslinked peptide antigen and have been synthesized from several peptide antigens as small as 8 amino acids in length. However, as with many peptide vaccine biomaterials, synthesis requires adding residues to the peptide and/or engaging amino acids within the antigen epitope covalently to form a stable material. The impact of antigen modifications made to enable biomaterial incorporation or formation is rarely investigated, since the goal of most studies is to compare the soluble antigen with biomaterial form of antigen. This study investigates PNC as a platform vaccine biomaterial to evaluate how peptide modification and biomaterial formation with different crosslinking chemistries affect epitope-specific immune cell presentation and activation. Several types of PNC were synthesized by desolvation from the model peptide epitope SIINFEKL, which is derived from the immunogenic protein ovalbumin. SIINFEKL was altered to include extra residues on each end, strategically chosen to enable multiple conjugation chemistry options for incorporation into PNC. Several crosslinking methods were used to control which functional groups were used to stabilize the PNC, as well as the reducibility of the crosslinking. These variations were evaluated for immune responses and biodistribution following in vivo immunization. All modified antigen formulations still induced comparable immune responses when incorporated into PNC compared to unmodified soluble antigen alone. However, some crosslinking methods led to a significant increase in desirable immune responses while others did not, suggesting that not all PNC were processed the same. These results help guide future peptide vaccine biomaterial design, including PNC and a wide variety of conjugated and self-assembled peptide antigen materials, to maximize and tune the desired immune response.
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Affiliation(s)
| | | | | | - Julie A. Champion
- School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
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19
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Gao Y, Guo C, Watzlawik JO, Randolph PS, Lee EJ, Huang D, Stagg SM, Zhou HX, Rosenberry TL, Paravastu AK. Out-of-Register Parallel β-Sheets and Antiparallel β-Sheets Coexist in 150-kDa Oligomers Formed by Amyloid-β(1-42). J Mol Biol 2020; 432:4388-4407. [PMID: 32470558 DOI: 10.1016/j.jmb.2020.05.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 12/15/2022]
Abstract
We present solid-state NMR measurements of β-strand secondary structure and inter-strand organization within a 150-kDa oligomeric aggregate of the 42-residue variant of the Alzheimer's amyloid-β peptide (Aβ(1-42)). We build upon our previous report of a β-strand spanned by residues 30-42, which arranges into an antiparallel β-sheet. New results presented here indicate that there is a second β-strand formed by residues 11-24. Contrary to expectations, NMR data indicate that this second β-strand is organized into a parallel β-sheet despite the co-existence of an antiparallel β-sheet in the same structure. In addition, the in-register parallel β-sheet commonly observed for amyloid fibril structure does not apply to residues 11-24 in the 150-kDa oligomer. Rather, we present evidence for an inter-strand registry shift of three residues that likely alternate in direction between adjacent molecules along the β-sheet. We corroborated this unexpected scheme for β-strand organization using multiple two-dimensional NMR and 13C-13C dipolar recoupling experiments. Our findings indicate a previously unknown assembly pathway and inspire a suggestion as to why this aggregate does not grow to larger sizes.
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Affiliation(s)
- Yuan Gao
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332, USA
| | - Cong Guo
- Department of Physics and International Centre for Quantum and Molecular Structures, Shanghai University, 99 Shangda Road, Shanghai, China
| | - Jens O Watzlawik
- Departments of Neuroscience and Pharmacology, Mayo Clinic College of Medicine, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Peter S Randolph
- Institute of Molecular Biophysics, Florida State University, Tallahasse, FL 32306, USA
| | - Elizabeth J Lee
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332, USA
| | - Danting Huang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332, USA
| | - Scott M Stagg
- Institute of Molecular Biophysics, Florida State University, Tallahasse, FL 32306, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Huan-Xiang Zhou
- Department of Chemistry and Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Terrone L Rosenberry
- Departments of Neuroscience and Pharmacology, Mayo Clinic College of Medicine, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332, USA.
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20
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Wong KM, Wang Y, Seroski DT, Larkin GE, Mehta AK, Hudalla GA, Hall CK, Paravastu AK. Molecular complementarity and structural heterogeneity within co-assembled peptide β-sheet nanofibers. Nanoscale 2020; 12:4506-4518. [PMID: 32039428 DOI: 10.1039/c9nr08725g] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Self-assembling peptides have garnered an increasing amount of interest as a functional biomaterial for medical and biotechnological applications. Recently, β-sheet peptide designs utilizing complementary pairs of peptides composed of charged amino acids positioned to impart co-assembly behavior have expanded the portfolio of peptide aggregate structures. Structural characterization of these charge-complementary peptide co-assemblies has been limited. Thus, it is not known how the complementary peptides organize on the molecular level. Through a combination of solid-state NMR measurements and discontinuous molecular dynamics simulations, we investigate the molecular organization of King-Webb peptide nanofibers. KW+ and KW- peptides co-assemble into near stoichiometric two-component β-sheet structures as observed by computational simulations and 13C-13C dipolar couplings. A majority of β-strands are aligned with antiparallel nearest neighbors within the β-sheet as previously suggested by Fourier transform infrared spectroscopy measurements. Surprisingly, however, a significant proportion of β-strand neighbors are parallel. While charge-complementary peptides were previously assumed to organize in an ideal (AB)n pattern, dipolar recoupling measurements on isotopically diluted nanofiber samples reveal a non-negligible amount of self-associated (AA and BB) pairs. Furthermore, computational simulations predict these different structures can coexist within the same nanofiber. Our results highlight structural disorder at the molecular level in a charge-complementary peptide system with implications on co-assembling peptide designs.
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Affiliation(s)
- Kong M Wong
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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21
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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: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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22
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Roberts EK, Wong KM, Lee EJ, Le MM, Patel DM, Paravastu AK. Post-assembly α-helix to β-sheet structural transformation within SAF-p1/p2a peptide nanofibers. Soft Matter 2018; 14:8986-8996. [PMID: 30375627 DOI: 10.1039/c8sm01754a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We report an unanticipated helix-to-sheet structural transformation within an assembly of SAF-p1 and SAF-p2a designer peptides. Solid-state NMR spectroscopic data support the assembled structure that was targeted by rational peptide design: an α-helical coiled-coil co-assembly of both peptides. Subsequent to assembly, however, the system converts to a β-sheet structure that continues to exhibit nearest-neighbor interactions between the two peptide components. The structural transition occurs at pH 7.4 and exhibits strongly temperature-dependent kinetics between room temperature (weeks) and 40 °C (minutes). We further observed evidence of reversibility on the timescale of months at 4 °C. The structural conversion from the anticipated structure to an unexpected structure highlights an important aspect to the challenge of designing peptide assemblies. Furthermore, the conformational switching mechanism mediated by a prerequisite α-helical nanostructure represents a previously unknown route for β-sheet designer peptide assembly.
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Affiliation(s)
- Evan K Roberts
- Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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23
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Wang Y, Gao Y, Hill SE, Huard DJE, Tomlin MO, Lieberman RL, Paravastu AK, Hall CK. Simulations and Experiments Delineate Amyloid Fibrilization by Peptides Derived from Glaucoma-Associated Myocilin. J Phys Chem B 2018; 122:5845-5850. [PMID: 29724098 DOI: 10.1021/acs.jpcb.8b03000] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mutant myocilin aggregation is associated with inherited open angle glaucoma, a prevalent optic neuropathy leading to blindness. Comprehension of mutant myocilin aggregation is of fundamental importance to glaucoma pathogenesis and ties glaucoma to amyloid diseases such as Alzheimer's. Here, we probe the aggregation properties of peptides derived from the myocilin olfactomedin domain. Peptides P1 (residues 326-337) and P3 (residues 426-442) were identified previously to form amyloids. Coarse-grained discontinuous molecular dynamics simulations using the PRIME20 force field (DMD/PRIME20) predict that P1 and P3 are aggregation-prone; P1 consistently forms fibrillar aggregates with parallel in-register β-sheets, whereas P3 forms β-sheet-containing aggregates without distinct order. Natural abundance 13C solid-state NMR spectra validate that aggregated P1 exhibits amyloid signatures and is more homogeneous than aggregated P3. DMD/PRIME20 simulations provide a viable method to predict peptide aggregation propensities and aggregate structure/order which cannot be accessed by bioinformatics or readily attained experimentally.
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Affiliation(s)
- Yiming Wang
- Department of Chemical and Biomolecular Engineering , North Carolina State University , Raleigh , North Carolina 27695-7905 , United States
| | | | | | | | | | | | | | - Carol K Hall
- Department of Chemical and Biomolecular Engineering , North Carolina State University , Raleigh , North Carolina 27695-7905 , United States
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24
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Hudson BC, Battigelli A, Connolly MD, Edison J, Spencer RK, Whitelam S, Zuckermann RN, Paravastu AK. Evidence for cis Amide Bonds in Peptoid Nanosheets. J Phys Chem Lett 2018; 9:2574-2578. [PMID: 29658722 DOI: 10.1021/acs.jpclett.8b01040] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Peptoid nanosheets are supramolecular protein-mimetic materials that form from amphiphilic polypeptoids with aromatic and ionic side chains. Nanosheets have been studied at the nanometer scale, but the molecular structure has been difficult to probe. We report the use of 13C-13C dipolar recoupling solid-state NMR measurements to reveal the configuration of backbone amide bonds selected by 13C isotopic labeling of adjacent α-carbons. Measurements on the same molecules in the amorphous state and in nanosheets revealed that amide bonds in the center of the amino block of peptoid (NaeNpe)7-(NceNpe)7 (B28) favor the trans configuration in the amorphous state and the cis configuration in the nanosheet. This unexpected result contrasts with previous NMR and theoretical studies of short solvated peptoids. Furthermore, examination of the amide bond at the junction of the two charged blocks within B28 revealed a mixture of both cis and trans configurational states, consistent with the previously predicted brickwork-like intermolecular organization.
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Affiliation(s)
- Benjamin C Hudson
- Department of Chemical and Biomolecular Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332-0100 , United States
| | - Alessia Battigelli
- Molecular Foundry , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Michael D Connolly
- Molecular Foundry , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - John Edison
- Molecular Foundry , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Ryan K Spencer
- Molecular Foundry , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Stephen Whitelam
- Molecular Foundry , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Ronald N Zuckermann
- Molecular Foundry , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Anant K Paravastu
- Department of Chemical and Biomolecular Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332-0100 , United States
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25
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Dudukovic NA, Hudson BC, Paravastu AK, Zukoski CF. Self-assembly pathways and polymorphism in peptide-based nanostructures. Nanoscale 2018; 10:1508-1516. [PMID: 29303206 DOI: 10.1039/c7nr06724k] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Dipeptide derivative molecules can self-assemble into space-filling nanofiber networks at low volume fractions (<1%), allowing the formation of molecular gels with tunable mechanical properties. The self-assembly of dipeptide-based molecules is reminiscent of pathological amyloid fibril formation by naturally occurring polypeptides. Fluorenylmethoxycarbonyl-diphenylalanine (Fmoc-FF) is the most widely studied such molecule, but the thermodynamic and kinetic phenomena giving rise to Fmoc-FF gel formation remain poorly understood. We have previously presented evidence that the gelation process is a first order phase transition characterized by low energy barriers to nucleation, short induction times, and rapid quasi-one-dimensional crystal growth, stemming from solvent-solute interactions and highly specific molecular packing. Here, we discuss the phase behavior of Fmoc-FF in different solvents. We find that Fmoc-FF gel formation can be induced in apolar solvents, in addition to previously established pathways in aqueous systems. We further show that in certain solvent systems anisotropic crystals (nanofibers) are an initial metastable state, after which macroscopic crystal aggregates with no preferred axis of growth are formed. The molecular conformation is sensitive to solvent composition during assembly, indicating that Fmoc-FF may be a simple model system to study complex thermodynamic and kinetic phenomena involved in peptide self-assembly.
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Affiliation(s)
- Nikola A Dudukovic
- Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, CA 94551, USA.
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26
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Huang D, Hudson BC, Gao Y, Roberts EK, Paravastu AK. Solid-State NMR Structural Characterization of Self-Assembled Peptides with Selective 13C and 15N Isotopic Labels. Methods Mol Biol 2018; 1777:23-68. [PMID: 29744827 PMCID: PMC7490753 DOI: 10.1007/978-1-4939-7811-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
For the structural characterization methods discussed here, information on molecular conformation and intermolecular organization within nanostructured peptide assemblies is discerned through analysis of solid-state NMR spectral features. This chapter reviews general NMR methodologies, requirements for sample preparation, and specific descriptions of key experiments. An attempt is made to explain choices of solid-state NMR experiments and interpretation of results in a way that is approachable to a nonspecialist. Measurements are designed to determine precise NMR peak positions and line widths, which are correlated with secondary structures, and probe nuclear spin-spin interactions that report on three-dimensional organization of atoms. The formulation of molecular structural models requires rationalization of data sets obtained from multiple NMR experiments on samples with carefully chosen 13C and 15N isotopic labels. The information content of solid-state NMR data has been illustrated mostly through the use of simulated data sets and references to recent structural work on amyloid fibril-forming peptides and designer self-assembling peptides.
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Affiliation(s)
- Danting Huang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Benjamin C Hudson
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Yuan Gao
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Evan K Roberts
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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27
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Longo LM, Gao Y, Tenorio CA, Wang G, Paravastu AK, Blaber M. Folding nucleus structure persists in thermally-aggregated FGF-1. Protein Sci 2017; 27:431-440. [PMID: 29076579 DOI: 10.1002/pro.3332] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/23/2017] [Accepted: 10/23/2017] [Indexed: 11/11/2022]
Abstract
An efficient protein-folding pathway leading to target structure, and the avoidance of aggregation, is essential to protein evolution and de novo design; however, design details to achieve efficient folding and avoid aggregation are poorly understood. We report characterization of the thermally-induced aggregate of fibroblast growth factor-1 (FGF-1), a small globular protein, by solid-state NMR. NMR spectra are consistent with residual structure in the aggregate and provide evidence of a structured region that corresponds to the region of the folding nucleus. NMR data on aggregated FGF-1 also indicate the presence of unstructured regions that exhibit hydration-dependent dynamics and suggest that unstructured regions of aggregated FGF-1 lie outside the folding nucleus. Since it is known that regions outside the folding nucleus fold late in the folding pathway, we postulate that these regions unfold early in the unfolding pathway and that the partially folded state is more prone to intermolecular aggregation. This interpretation is further supported by comparison with a designed protein that shares the same FGF-1 folding nucleus sequence, but has different 1° structure outside the folding nucleus, and does not thermally aggregate. The results suggest that design of an efficient folding nucleus, and the avoidance of aggregation in the folding pathway, are potentially separable design criteria - the latter of which could principally focus upon the physicochemical properties of 1° structure outside the folding nucleus.
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Affiliation(s)
- Liam M Longo
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL, 32306-4300, USA.,Program in Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA
| | - Yuan Gao
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332-0100, USA
| | - Connie A Tenorio
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL, 32306-4300, USA
| | - Gan Wang
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332-0100, USA
| | - Anant K Paravastu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332-0100, USA
| | - Michael Blaber
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL, 32306-4300, USA.,Program in Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA
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28
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Huang D, Zimmerman MI, Martin PK, Nix AJ, Rosenberry TL, Paravastu AK. Antiparallel β-Sheet Structure within the C-Terminal Region of 42-Residue Alzheimer's Amyloid-β Peptides When They Form 150-kDa Oligomers. J Mol Biol 2015; 427:2319-28. [PMID: 25889972 DOI: 10.1016/j.jmb.2015.04.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/25/2015] [Accepted: 04/09/2015] [Indexed: 11/28/2022]
Abstract
Understanding the molecular structures of amyloid-β (Aβ) oligomers and underlying assembly pathways will advance our understanding of Alzheimer's disease (AD) at the molecular level. This understanding could contribute to disease prevention, diagnosis, and treatment strategies, as oligomers play a central role in AD pathology. We have recently presented a procedure for production of 150-kDa oligomeric samples of Aβ(1-42) (the 42-residue variant of the Aβ peptide) that are compatible with solid-state nuclear magnetic resonance (NMR) analysis, and we have shown that these oligomers and amyloid fibrils differ in intermolecular arrangement of β-strands. Here we report new solid-state NMR constraints that indicate antiparallel intermolecular alignment of β-strands within the oligomers. Specifically, 150-kDa Aβ(1-42) oligomers with uniform (13)C and (15)N isotopic labels at I32, M35, G37, and V40 exhibit β-strand secondary chemical shifts in 2-dimensional (2D) finite-pulse radiofrequency-driven recoupling NMR spectra, spatial proximities between I32 and V40 as well as between M35 and G37 in 2D dipolar-assisted rotational resonance spectra, and close proximity between M35 H(α) and G37 H(α) in 2D CHHC spectra. Furthermore, 2D dipolar-assisted rotational resonance analysis of an oligomer sample prepared with 30% labeled peptide indicates that the I32-V40 and M35-G37 contacts are between residues on different molecules. We employ molecular modeling to compare the newly derived experimental constraints with previously proposed geometries for arrangement of Aβ molecules into oligomers.
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Affiliation(s)
- Danting Huang
- Department of Chemical and Biomedical Engineering, Florida Agricultural & Mechanical University-Florida State University College of Engineering, 2525 Pottsdamer Street, Tallahassee, FL 32310-6046, USA; National High Magnetic Field Laboratory, 1800 E. Paul Dirac Drive, Tallahassee, FL 32310, USA
| | - Maxwell I Zimmerman
- Department of Chemical and Biomedical Engineering, Florida Agricultural & Mechanical University-Florida State University College of Engineering, 2525 Pottsdamer Street, Tallahassee, FL 32310-6046, USA; National High Magnetic Field Laboratory, 1800 E. Paul Dirac Drive, Tallahassee, FL 32310, USA
| | - Patricia K Martin
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - A Jeremy Nix
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Terrone L Rosenberry
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Anant K Paravastu
- Department of Chemical and Biomedical Engineering, Florida Agricultural & Mechanical University-Florida State University College of Engineering, 2525 Pottsdamer Street, Tallahassee, FL 32310-6046, USA; National High Magnetic Field Laboratory, 1800 E. Paul Dirac Drive, Tallahassee, FL 32310, USA.
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29
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Agyare EK, Jaruszewski KM, Curran GL, Rosenberg JT, Grant SC, Lowe VJ, Ramakrishnan S, Paravastu AK, Poduslo JF, Kandimalla KK. Engineering theranostic nanovehicles capable of targeting cerebrovascular amyloid deposits. J Control Release 2014; 185:121-9. [PMID: 24735640 DOI: 10.1016/j.jconrel.2014.04.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/21/2014] [Accepted: 04/04/2014] [Indexed: 11/26/2022]
Abstract
Cerebral amyloid angiopathy (CAA) is characterized by the deposition of amyloid beta (Aβ) proteins within the walls of the cerebral vasculature with subsequent aggressive vascular inflammation leading to recurrent hemorrhagic strokes. The objective of the study was to develop theranostic nanovehicles (TNVs) capable of a) targeting cerebrovascular amyloid; b) providing magnetic resonance imaging (MRI) contrast for the early detection of CAA; and c) treating cerebrovascular inflammation resulting from CAA. The TNVs comprised of a polymeric nanocore made from Magnevist (MRI contrast agent) conjugated chitosan. The nanocore was also loaded with cyclophosphamide (CYC), an immunosuppressant shown to reduce the cerebrovascular inflammation in CAA. Putrescine modified F(ab')2 fragment of anti-amyloid antibody, IgG4.1 (pF(ab')24.1) was conjugated to the surface of the nanocore to target cerebrovascular amyloid. The average size of the control chitosan nanoparticles (conjugated with albumin and are devoid of Magnevist, CYC, and pF(ab')24.1) was 164±1.2 nm and that of the TNVs was 239±4.1 nm. The zeta potential values of the CCNs and TNVs were 21.6±1.7 mV and 11.9±0.5 mV, respectively. The leakage of Magnevist from the TNVs was a modest 0.2% over 4 days, and the CYC release from the TNVs followed Higuchi's model that describes sustained drug release from polymeric matrices. The studies conducted in polarized human microvascular endothelial cell monolayers (hCMEC/D3) in vitro as well as in mice in vivo have demonstrated the ability of TNVs to target cerebrovascular amyloid. In addition, the TNVs provided contrast for imaging cerebrovascular amyloid using MRI and single photon emission computed tomography. Moreover, the TNVs were shown to reduce pro-inflammatory cytokine production by the Aβ challenged blood brain barrier (BBB) endothelium more effectively than the cyclophosphamide alone.
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Affiliation(s)
- Edward K Agyare
- Division of Basic Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, 1520 S. MLK BLVD, Tallahassee 32307, USA
| | - Kristen M Jaruszewski
- Department of Pharmaceutics and Brain Barriers Research Center, University of Minnesota, 308 Harvard St. SE, Room 9-149A WDH, Minneapolis 55455, USA; Molecular Neurobiology Laboratory, Departments of Neurology, Neuroscience, and Biochemistry/Molecular Biology, Mayo Clinic College of Medicine, 200 1st Street SW, Rochester 55905, USA
| | - Geoffry L Curran
- Molecular Neurobiology Laboratory, Departments of Neurology, Neuroscience, and Biochemistry/Molecular Biology, Mayo Clinic College of Medicine, 200 1st Street SW, Rochester 55905, USA
| | - Jens T Rosenberg
- The Florida State University and National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee 32310, USA
| | - Samuel C Grant
- The Florida State University and National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee 32310, USA; Department of Chemical and Biomedical Engineering, Florida A&M University-Florida State University College of Engineering, 2525 Pottsdamer Street, Tallahassee 32310, USA
| | - Val J Lowe
- Nuclear Medicine, Department of Radiology, Mayo Clinic, 200 1st Street SW, Rochester 55905, USA
| | - Subramanian Ramakrishnan
- Department of Chemical and Biomedical Engineering, Florida A&M University-Florida State University College of Engineering, 2525 Pottsdamer Street, Tallahassee 32310, USA
| | - Anant K Paravastu
- The Florida State University and National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee 32310, USA; Department of Chemical and Biomedical Engineering, Florida A&M University-Florida State University College of Engineering, 2525 Pottsdamer Street, Tallahassee 32310, USA
| | - Joseph F Poduslo
- Molecular Neurobiology Laboratory, Departments of Neurology, Neuroscience, and Biochemistry/Molecular Biology, Mayo Clinic College of Medicine, 200 1st Street SW, Rochester 55905, USA
| | - Karunya K Kandimalla
- Department of Pharmaceutics and Brain Barriers Research Center, University of Minnesota, 308 Harvard St. SE, Room 9-149A WDH, Minneapolis 55455, USA; Molecular Neurobiology Laboratory, Departments of Neurology, Neuroscience, and Biochemistry/Molecular Biology, Mayo Clinic College of Medicine, 200 1st Street SW, Rochester 55905, USA.
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Abstract
The designer self-assembling peptide RADA16-I forms nanofiber matrices which have shown great promise for regenerative medicine and three-dimensional cell culture. The RADA16-I amino acid sequence has a β-strand-promoting alternating hydrophobic/charged motif, but arrangement of β-strands into the nanofiber structure has not been previously determined. Here we present a structural model of RADA16-I nanofibers, based on solid-state NMR measurements on samples with different schemes for (13)C isotopic labeling. NMR peak positions and line widths indicate an ordered structure composed of β-strands. The NMR data show that the nanofibers are composed of two stacked β-sheets stabilized by a hydrophobic core formed by alanine side chains, consistent with previous proposals. However, the previously proposed antiparallel β-sheet structure is ruled out by measured (13)C-(13)C dipolar couplings. Instead, neighboring β-strands within β-sheets are parallel, with a registry shift that allows cross-strand staggering of oppositely charged arginine and aspartate side chains. The resulting structural model is compared to nanofiber dimensions observed via images taken by transmission electron microscopy and atomic force microscopy. Multiple NMR peaks for each alanine side chain were observed and could be attributed to multiple configurations of side chain packing within a single scheme for intermolecular packing.
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Affiliation(s)
- Ashley R. Cormier
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, 2525 Pottsdamer Street, Tallahassee, FL 32310-6046
- National High Magnetic Field Laboratory, 1800 E. Paul Dirac Drive, Tallahassee, FL 32310
| | - Xiaodong Pang
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
| | - Maxwell I. Zimmerman
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, 2525 Pottsdamer Street, Tallahassee, FL 32310-6046
- National High Magnetic Field Laboratory, 1800 E. Paul Dirac Drive, Tallahassee, FL 32310
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
| | - Anant K. Paravastu
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, 2525 Pottsdamer Street, Tallahassee, FL 32310-6046
- National High Magnetic Field Laboratory, 1800 E. Paul Dirac Drive, Tallahassee, FL 32310
- Address correspondence to
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32
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Tay WM, Huang D, Rosenberry TL, Paravastu AK. The Alzheimer's amyloid-β(1-42) peptide forms off-pathway oligomers and fibrils that are distinguished structurally by intermolecular organization. J Mol Biol 2013; 425:2494-508. [PMID: 23583777 PMCID: PMC7490758 DOI: 10.1016/j.jmb.2013.04.003] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/14/2013] [Accepted: 04/02/2013] [Indexed: 12/20/2022]
Abstract
Increasing evidence suggests that soluble aggregates of amyloid-β (Aβ) initiate the neurotoxicity that eventually leads to dementia in Alzheimer's disease. Knowledge on soluble aggregate structures will enhance our understanding of the relationship between structures and toxicities. Our group has reported a stable and homogeneous preparation of Aβ(1-42) oligomers that has been characterized by various biophysical techniques. Here, we have further analyzed this species by solid state nuclear magnetic resonance (NMR) spectroscopy and compared NMR results to similar observations on amyloid fibrils. NMR experiments on Aβ(1-42) oligomers reveal chemical shifts of labeled residues that are indicative of β-strand secondary structure. Results from two-dimensional dipolar-assisted rotational resonance experiments indicate proximities between I31 aliphatic and F19 aromatic carbons. An isotope dilution experiment further indicates that these contacts between F19 and I31 are intermolecular, contrary to models of Aβ oligomers proposed previously by others. For Aβ(1-42) fibrils, we observed similar NMR lineshapes and inter-side-chain contacts, indicating similar secondary and quaternary structures. The most prominent structural differences between Aβ(1-42) oligomers and fibrils were observed through measurements of intermolecular (13)C-(13)C dipolar couplings observed in PITHIRDS-CT experiments. PITHIRDS-CT data indicate that, unlike fibrils, oligomers are not characterized by in-register parallel β-sheets. Structural similarities and differences between Aβ(1-42) oligomers and fibrils suggest that folded β-strand peptide conformations form early in the course of self-assembly and that oligomers and fibrils differ primarily in schemes of intermolecular organization. Distinct intermolecular arrangements between Aβ(1-42) oligomers and fibrils may explain why this oligomeric state appears off-pathway for monomer self-assembly to fibrils.
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Affiliation(s)
- William M. Tay
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd., Jacksonville, FL 32224
| | - Danting Huang
- Department of Chemical and Biomedical Engineering, Florida State University, 2525 Pottsdamer St., Tallahassee, FL 32310
- National High Magnetic Field Laboratory, 1800 E. Paul Dirac Drive, Tallahassee, FL 32310
| | | | - Anant K. Paravastu
- Department of Chemical and Biomedical Engineering, Florida State University, 2525 Pottsdamer St., Tallahassee, FL 32310
- National High Magnetic Field Laboratory, 1800 E. Paul Dirac Drive, Tallahassee, FL 32310
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33
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Cormier AR, Lopez-Majada JM, Alamo RG, Paravastu AK. Distinct solid and solution state self-assembly pathways of RADA16-I designer peptide. J Pept Sci 2013; 19:477-84. [DOI: 10.1002/psc.2524] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 04/22/2013] [Accepted: 05/03/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Ashley R. Cormier
- FAMU-FSU College of Engineering; Department of Chemical and Biomedical Engineering; 2525 Pottsdamer Street Tallahassee FL 32310-6046 USA
- National High Magnetic Field Laboratory; 1800 E. Paul Dirac Drive Tallahassee FL 32310 USA
| | - Juan M. Lopez-Majada
- FAMU-FSU College of Engineering; Department of Chemical and Biomedical Engineering; 2525 Pottsdamer Street Tallahassee FL 32310-6046 USA
- National High Magnetic Field Laboratory; 1800 E. Paul Dirac Drive Tallahassee FL 32310 USA
| | - Rufina G. Alamo
- FAMU-FSU College of Engineering; Department of Chemical and Biomedical Engineering; 2525 Pottsdamer Street Tallahassee FL 32310-6046 USA
- National High Magnetic Field Laboratory; 1800 E. Paul Dirac Drive Tallahassee FL 32310 USA
| | - Anant K. Paravastu
- FAMU-FSU College of Engineering; Department of Chemical and Biomedical Engineering; 2525 Pottsdamer Street Tallahassee FL 32310-6046 USA
- National High Magnetic Field Laboratory; 1800 E. Paul Dirac Drive Tallahassee FL 32310 USA
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Desai PR, Cormier AR, Shah PP, Patlolla RR, Paravastu AK, Singh M. (31)P solid-state NMR based monitoring of permeation of cell penetrating peptides into skin. Eur J Pharm Biopharm 2013; 86:190-9. [PMID: 23702274 DOI: 10.1016/j.ejpb.2013.05.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Revised: 03/19/2013] [Accepted: 05/06/2013] [Indexed: 11/18/2022]
Abstract
The main objective of the current study was to investigate penetration of cell penetrating peptides (CPPs: TAT, R8, R11, and YKA) through skin intercellular lipids using (31)P magic angle spinning (MAS) solid-state NMR. In vitro skin permeation studies were performed on rat skin, and sections (0-60, 61-120, and 121-180μm) were collected and analyzed for (31)P NMR signal. The concentration-dependent shift of 0, 25, 50, 100, and 200mg/ml of TAT on skin layers, diffusion of TAT, R8, R11, and YKA in the skin and time dependent permeation of R11 was measured on various skin sections using (31)P solid-state NMR. Further, CPPs and CPP-tagged fluorescent dye encapsulate liposomes (FLip) in skin layers were tagged using confocal microscopy. The change in (31)P NMR chemical shift was found to depend monotonically on the amount of CPP applied on skin, with saturation behavior above 100mg/ml CPP concentration. R11 and TAT caused more shift in solid-state NMR peaks compared to other peptides. Furthermore, NMR spectra showed R11 penetration up to 180μm within 30min. The results of the solid-state NMR study were in agreement with confocal microscopy studies. Thus, (31)P solid-state NMR can be used to track CPP penetration into different skin layers.
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Affiliation(s)
- Pinaki R Desai
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, USA
| | - Ashley R Cormier
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, USA; National High Magnetic Field Laboratory, Tallahassee, USA
| | - Punit P Shah
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, USA
| | - Ram R Patlolla
- Dr. Reddys Laboratories, Integrated Product Development, Hyderabad, India
| | - Anant K Paravastu
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, USA; National High Magnetic Field Laboratory, Tallahassee, USA.
| | - Mandip Singh
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, USA.
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35
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Agyare EK, Leonard SR, Curran GL, Yu CC, Lowe VJ, Paravastu AK, Poduslo JF, Kandimalla KK. Traffic jam at the blood-brain barrier promotes greater accumulation of Alzheimer's disease amyloid-β proteins in the cerebral vasculature. Mol Pharm 2013; 10:1557-65. [PMID: 23249146 DOI: 10.1021/mp300352c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloid-β (Aβ) deposition in the brain vasculature results in cerebral amyloid angiopathy (CAA), which occurs in about 80% of Alzheimer's disease (AD) patients. While Aβ42 predominates parenchymal amyloid plaques in AD brain, Aβ40 is prevalent in the cerebrovascular amyloid. Dutch mutation of Aβ40 (E22Q) promotes aggressive cerebrovascular accumulation and leads to severe CAA in the mutation carriers; knowledge of how DutchAβ40 drives this process more efficiently than Aβ40 could reveal various pathophysiological events that promote CAA. In this study we have demonstrated that DutchAβ40 shows preferential accumulation in the blood-brain-barrier (BBB) endothelial cells due to its inefficient blood-to-brain transcytosis. Consequently, DutchAβ40 establishes a permeation barrier in the BBB endothelium, prevents its own clearance from the brain, and promotes the formation of amyloid deposits in the cerebral microvessels. The BBB endothelial accumulation of native Aβ40 is not robust enough to exercise such a significant impact on its brain clearance. Hence, the cerebrovascular accumulation of Aβ40 is slow and may require other copathologies to precipitate into CAA. In conclusion, the magnitude of Aβ accumulation in the BBB endothelial cells is a critical factor that promotes CAA; hence, clearing vascular endothelium of Aβ proteins may halt or even reverse CAA.
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Affiliation(s)
- Edward K Agyare
- Basic Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, Florida, United States
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Affiliation(s)
- Ashley R. Cormier
- Department of Chemical and Biomedical Engineering,
FAMU-FSU College of Engineering, Florida State University, 2525 Pottsdamer Street, Tallahassee, Florida 32310-6046, United
States
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee,
Florida 32310, United
States
| | - Carolina Ruiz-Orta
- Department of Chemical and Biomedical Engineering,
FAMU-FSU College of Engineering, Florida State University, 2525 Pottsdamer Street, Tallahassee, Florida 32310-6046, United
States
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee,
Florida 32310, United
States
| | - Rufina G. Alamo
- Department of Chemical and Biomedical Engineering,
FAMU-FSU College of Engineering, Florida State University, 2525 Pottsdamer Street, Tallahassee, Florida 32310-6046, United
States
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee,
Florida 32310, United
States
| | - Anant K. Paravastu
- Department of Chemical and Biomedical Engineering,
FAMU-FSU College of Engineering, Florida State University, 2525 Pottsdamer Street, Tallahassee, Florida 32310-6046, United
States
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee,
Florida 32310, United
States
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Eby DM, Artyushkova K, Paravastu AK, Johnson GR. Probing the molecular structure of antimicrobial peptide-mediated silica condensation using X-ray photoelectron spectroscopy. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm30837a] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Lovingood DD, Achey R, Paravastu AK, Strouse GF. Size- and Site-Dependent Reconstruction in CdSe QDs Evidenced by 77Se{1H} CP-MAS NMR Spectroscopy. J Am Chem Soc 2010; 132:3344-54. [DOI: 10.1021/ja907511r] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Derek D. Lovingood
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390 and Department of Chemical and Biological Engineering, FAMU-FSU College of Engineering, Tallahassee, Florida 32310-6046
| | - Randall Achey
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390 and Department of Chemical and Biological Engineering, FAMU-FSU College of Engineering, Tallahassee, Florida 32310-6046
| | - Anant K. Paravastu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390 and Department of Chemical and Biological Engineering, FAMU-FSU College of Engineering, Tallahassee, Florida 32310-6046
| | - Geoffrey F. Strouse
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390 and Department of Chemical and Biological Engineering, FAMU-FSU College of Engineering, Tallahassee, Florida 32310-6046
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Abstract
We introduce a new approach to frequency-selective homonuclear dipolar recoupling in solid state nuclear magnetic resonance (NMR) with magic-angle spinning (MAS). This approach, to which we give the acronym SEASHORE, employs alternating periods of double-quantum recoupling and chemical shift evolution to produce phase modulations of the recoupled dipole-dipole interactions that average out undesired couplings, leaving only dipole-dipole couplings between nuclear spins with a selected pair of NMR frequencies. In principle, SEASHORE is applicable to systems with arbitrary coupling strengths and arbitrary sets of NMR frequencies. Arbitrary MAS frequencies are also possible, subject only to restrictions imposed by the pulse sequence chosen for double-quantum recoupling. We demonstrate the efficacy of SEASHORE in experimental (13)C NMR measurements of frequency-selective polarization transfer in uniformly (15)N, (13)C-labeled L-valine powder and frequency-selective intermolecular polarization transfer in amyloid fibrils formed by a synthetic decapeptide containing uniformly (15)N, (13)C-labeled residues.
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Affiliation(s)
- Anant K. Paravastu
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520
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40
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Abstract
We report investigations of the morphology and molecular structure of amyloid fibrils comprised of residues 10-40 of the Alzheimer's beta-amyloid peptide (Abeta(10-40)), prepared under various solution conditions and degrees of agitation. Omission of residues 1-9 from the full-length Alzheimer's beta-amyloid peptide (Abeta(1-40)) did not prevent the peptide from forming amyloid fibrils or eliminate fibril polymorphism. These results are consistent with residues 1-9 being disordered in Abeta(1-40) fibrils, and show that fibril polymorphism is not a consequence of disorder in residues 1-9. Fibril morphology was analyzed by atomic force and electron microscopy, and secondary structure and inter-side-chain proximity were probed using solid-state NMR. Abeta(1-40) fibrils were found to be structurally compatible with Abeta(10-40): Abeta(1-40) fibril fragments were used to seed the growth of Abeta(10-40) fibrils, with propagation of fibril morphology and molecular structure. In addition, comparison of lyophilized and hydrated fibril samples revealed no effect of hydration on molecular structure, indicating that Abeta(10-40) fibrils are unlikely to contain bulk water.
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Affiliation(s)
- Anant K Paravastu
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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41
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Lou J, Paravastu AK, Laibinis PE, Hatton TA. Effect of Temperature on the Dielectric Relaxation in Solvent Mixtures at Microwave Frequencies. J Phys Chem A 1997. [DOI: 10.1021/jp972785+] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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