1
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Robang A, Wong KM, Leisen J, Liu R, Radford WL, Rao Sudarshan T, Hudalla GA, Paravastu AK. Parallel β-Sheet Structure and Structural Heterogeneity Detected within Q11 Self-Assembling Peptide Nanofibers. J Phys Chem B 2024; 128:5387-5396. [PMID: 38787393 PMCID: PMC11163420 DOI: 10.1021/acs.jpcb.4c00825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/26/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Q11 peptide nanofibers are used as a biomaterial for applications such as antigen presentation and tissue engineering, yet detailed knowledge of molecular-level structure has not been reported. The Q11 peptide sequence was designed using heuristics-based patterning of hydrophobic and polar amino acids with oppositely charged amino acids placed at opposite ends of the sequence to promote antiparallel β-sheet formation. In this work, we employed solid-state nuclear magnetic resonance spectroscopy (NMR) to evaluate whether the molecular organization within Q11 self-assembled peptide nanofibers is consistent with the expectations of the peptide designers. We discovered that Q11 forms a distribution of molecular structures. NMR data from two-dimensional (2D) 13C-13C dipolar-assisted rotational resonance indicate that the K3 and E9 residues between Q11 β-strands are spatially proximate (within ∼0.6 nm). Frequency-selective rotational echo double resonance (fsREDOR) on K3 Nζ and E9 Cδ-labeled sites showed that approximately 9% of the sites are close enough for salt bridge formation to occur. Surprisingly, dipolar recoupling measurements revealed that Q11 peptides do not assemble into antiparallel β-sheets as expected, and structural analysis using Fourier-transform infrared spectroscopy and 2D NMR alone can be misleading. 13C PITHIRDS-CT dipolar recoupling measurements showed that the most abundant structure consists of parallel β-sheets, in contrast to the expected antiparallel β-sheet structure. Structural heterogeneity was detected from 15N{13C} REDOR measurements, with approximately 22% of β-strands having antiparallel nearest neighbors. We cannot propose a complete structural model of Q11 nanofibers because of the complexity involved when examining structurally heterogeneous samples using NMR. Altogether, our results show that while heuristics-based patterning is effective in promoting β-sheet formation, designing a peptide sequence to form a targeted β-strand arrangement remains challenging.
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Affiliation(s)
- Alicia
S. Robang
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Kong M. Wong
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Johannes Leisen
- School
of Chemistry & Biochemistry, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Renjie Liu
- J. Crayton
Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida 32611, United States
| | - Walker L. Radford
- School
of Chemistry & Biochemistry, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Tarunya Rao Sudarshan
- 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, Gainesville, Florida 32611, 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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2
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Liu W, Zhang C, Zhang H, Ma S, Deng J, Wang D, Chang Z, Yang J. Molecular basis for curvature formation in SepF polymerization. Proc Natl Acad Sci U S A 2024; 121:e2316922121. [PMID: 38381790 PMCID: PMC10907229 DOI: 10.1073/pnas.2316922121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 11/20/2023] [Indexed: 02/23/2024] Open
Abstract
The self-assembly of proteins into curved structures plays an important role in many cellular processes. One good example of this phenomenon is observed in the septum-forming protein (SepF), which forms polymerized structures with uniform curvatures. SepF is essential for regulating the thickness of the septum during bacteria cell division. In Bacillus subtilis, SepF polymerization involves two distinct interfaces, the β-β and α-α interfaces, which define the assembly unit and contact interfaces, respectively. However, the mechanism of curvature formation in this step is not yet fully understood. In this study, we employed solid-state NMR (SSNMR) to compare the structures of cyclic wild-type SepF assemblies with linear assemblies resulting from a mutation of G137 on the β-β interface. Our results demonstrate that while the sequence differences arise from the internal assembly unit, the dramatic changes in the shape of the assemblies depend on the α-α interface between the units. We further provide atomic-level insights into how the angular variation of the α2 helix on the α-α interface affects the curvature of the assemblies, using a combination of SSNMR, cryo-electron microscopy, and simulation methods. Our findings shed light on the shape control of protein assemblies and emphasize the importance of interhelical contacts in retaining curvature.
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Affiliation(s)
- Wenjing Liu
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan430071, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Chang Zhang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan430071, People’s Republic of China
| | - Huawei Zhang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, People’s Republic of China
- Southern University of Science and Technology, Shenzhen518055, People’s Republic of China
| | - Shaojie Ma
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan430071, People’s Republic of China
| | - Jing Deng
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan430071, People’s Republic of China
| | - Daping Wang
- Southern University of Science and Technology, Shenzhen518055, People’s Republic of China
- Department of Orthopedics, Shenzhen Intelligent Orthopaedics and Biomedical Innovation Platform, Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen518000, People’s Republic of China
| | - Ziwei Chang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan430071, People’s Republic of China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan430071, People’s Republic of China
- Interdisciplinary Institute of NMR and Molecular Sciences, School of Chemistry and Chemical Engineering, The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan430081, People’s Republic of China
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3
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Jones SJ, Perez A. Molecular Modeling of Self-Assembling Peptides. ACS APPLIED BIO MATERIALS 2024; 7:543-552. [PMID: 36795608 DOI: 10.1021/acsabm.2c00921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Peptide epitopes mediate as many as 40% of protein-protein interactions and fulfill signaling, inhibition, and activation roles within the cell. Beyond protein recognition, some peptides can self- or coassemble into stable hydrogels, making them a readily available source of biomaterials. While these 3D assemblies are routinely characterized at the fiber level, there are missing atomistic details about the assembly scaffold. Such atomistic detail can be useful in the rational design of more stable scaffold structures and with improved accessibility to functional motifs. Computational approaches can in principle reduce the experimental cost of such an endeavor by predicting the assembly scaffold and identifying novel sequences that adopt said structure. Yet, inaccuracies in physical models and inefficient sampling have limited atomistic studies to short (two or three amino acid) peptides. Given recent developments in machine learning and advances in sampling strategies, we revisit the suitability of physical models for this task. We use the MELD (Modeling Employing Limited Data) approach to drive self-assembly in combination with generic data in cases where conventional MD is unsuccessful. Finally, despite recent developments in machine learning algorithms for protein structure and sequence predictions, we find the algorithms are not yet suited for studying the assembly of short peptides.
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Affiliation(s)
- Stephen J Jones
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
| | - Alberto Perez
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
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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 APPLIED MATERIALS & 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] [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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5
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Hidalgo-Alvarez V, Madl CM. Leveraging Biomaterial Platforms to Study Aging-Related Neural and Muscular Degeneration. Biomolecules 2024; 14:69. [PMID: 38254669 PMCID: PMC10813704 DOI: 10.3390/biom14010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/28/2023] [Accepted: 12/30/2023] [Indexed: 01/24/2024] Open
Abstract
Aging is a complex multifactorial process that results in tissue function impairment across the whole organism. One of the common consequences of this process is the loss of muscle mass and the associated decline in muscle function, known as sarcopenia. Aging also presents with an increased risk of developing other pathological conditions such as neurodegeneration. Muscular and neuronal degeneration cause mobility issues and cognitive impairment, hence having a major impact on the quality of life of the older population. The development of novel therapies that can ameliorate the effects of aging is currently hindered by our limited knowledge of the underlying mechanisms and the use of models that fail to recapitulate the structure and composition of the cell microenvironment. The emergence of bioengineering techniques based on the use of biomimetic materials and biofabrication methods has opened the possibility of generating 3D models of muscular and nervous tissues that better mimic the native extracellular matrix. These platforms are particularly advantageous for drug testing and mechanistic studies. In this review, we discuss the developments made in the creation of 3D models of aging-related neuronal and muscular degeneration and we provide a perspective on the future directions for the field.
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Affiliation(s)
| | - Christopher M. Madl
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA;
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6
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Bellavita R, Braccia S, Falanga A, Galdiero S. An Overview of Supramolecular Platforms Boosting Drug Delivery. Bioinorg Chem Appl 2023; 2023:8608428. [PMID: 38028018 PMCID: PMC10661875 DOI: 10.1155/2023/8608428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/03/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Numerous supramolecular platforms inspired by natural self-assembly are exploited as drug delivery systems. The spontaneous arrangement of single building blocks into inorganic and organic structures is determined and controlled by noncovalent forces such as electrostatic interactions, π-π interactions, hydrogen bonds, and van der Waals interactions. This review describes the main structures and characteristics of several building blocks used to obtain stable, self-assembling nanostructures tailored for numerous biological applications. Owing to their versatility, biocompatibility, and controllability, these nanostructures find application in diverse fields ranging from drug/gene delivery, theranostics, tissue engineering, and nanoelectronics. Herein, we described the different approaches used to design and functionalize these nanomaterials to obtain selective drug delivery in a specific disease. In particular, the review highlights the efficiency of these supramolecular structures in applications related to infectious diseases and cancer.
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Affiliation(s)
- Rosa Bellavita
- Department of Pharmacy, University of Naples ‘Federico II', Naples 80131, Italy
| | - Simone Braccia
- Department of Pharmacy, University of Naples ‘Federico II', Naples 80131, Italy
| | - Annarita Falanga
- Department of Agricultural Sciences, University of Naples ‘Federico II', Portici 80055, Italy
| | - Stefania Galdiero
- Department of Pharmacy, University of Naples ‘Federico II', Naples 80131, Italy
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7
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Zhao P, Yang P, Zhou W, Liu H, Jin X, Zhu X. Injectable Sealants Based on Silk Fibroin for Fast Hemostasis and Wound Repairing. Adv Healthc Mater 2023; 12:e2301310. [PMID: 37531236 DOI: 10.1002/adhm.202301310] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/17/2023] [Indexed: 08/04/2023]
Abstract
Uncontrollable blood loss poses fatality risks and most recently developed sealants still share common limitations on controversial components, degradability, mechanical strength or gelation time. Herein, series of injectable sealants based on silk fibroin (SF) is developed. Random coil/β-sheet conformation transition in SF is achieved by forming dendritic intermediates under induction of the structurally compatible and chemically complementary assembly peptide (Ac-KAEA-KAEA-KAEA-KAEA-NH2 , KA16 ). A ratio of 1:5 (KA-SF-15) shown an accelerating gelation process (≈12 s) and enhanced mechanical strength at physiological conditions. The interweaved nanofibers effectively impeded the bleeding within 30 s and no obvious adverse effects are observed. The supramolecular interactions and in vivo degradation benefit the inflammatory host cells infiltration and cytokines diffusion. Without any exogenous factors, the increased expression of VEGF and PDGF led to a positive feedback regulation on fibroblasts and vascular endothelial cell growth/proliferation and promoted the wound healing. These findings indicated the few assembly-peptide can accelerate fibroin gelation transition at a limited physiological condition, and the injectable amino acid-based sealants show obvious advantages on biocompatibility, degradability, rapid gelation and matched strength, with strong potential to act as next generation of biomedical materials.
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Affiliation(s)
- Peng Zhao
- State Key Laboratory of Metal Matrix Composites, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
- School of Physical Science and Technology, Shanghai Tech University, Shanghai, 201210, P. R. China
| | - Peilang Yang
- Department of Burn, Ruijin Hospital Affliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Wei Zhou
- School of Physical Science and Technology, Shanghai Tech University, Shanghai, 201210, P. R. China
| | - Haoyang Liu
- Shanghai World Foreign Language Academy, 400 Baihua Street, Shanghai, 200233, P. R. China
| | - Xin Jin
- State Key Laboratory of Metal Matrix Composites, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Xinyuan Zhu
- State Key Laboratory of Metal Matrix Composites, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
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Yao X, Hu Y, Lin M, Peng K, Wang P, Gao Y, Gao X, Guo T, Zhang X, Zhou H. Self-assembling peptide RADA16: a promising scaffold for tissue engineering and regenerative medicine. Nanomedicine (Lond) 2023. [PMID: 37750388 DOI: 10.2217/nnm-2023-0161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023] Open
Abstract
RADA16 is a peptide-based biomaterial whose acidic aqueous solution spontaneously forms an extracellular matrix-like 3D structure within seconds upon contact with physiological pH body fluids. Meanwhile, its good biocompatibility, low immunogenicity, nontoxic degradation products and ease of modification make it an ideal scaffold for tissue engineering. RADA16 is a good delivery vehicle for cells, drugs and factors. Its shear thinning and thixotropic properties allow it to fill tissue voids by injection and not to swell. However, the weaker mechanical properties and poor hydrophilicity are troubling limitations of RADA16. To compensate for this limitation, various functional groups and polymers have been designed to modify RADA16, thus contributing to its scope and progress in the field of tissue engineering.
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Affiliation(s)
- Xin Yao
- Department of Orthopaedics, Lanzhou University Second Hospital, Lanzhou 730030, Gansu, China
- Key Laboratory of Bone & Joint Disease Research of Gansu Provincial, Lanzhou 730030, Gansu, China
| | - Yicun Hu
- Department of Orthopaedics, Lanzhou University Second Hospital, Lanzhou 730030, Gansu, China
- Key Laboratory of Bone & Joint Disease Research of Gansu Provincial, Lanzhou 730030, Gansu, China
| | - Maoqiang Lin
- Department of Orthopaedics, Lanzhou University Second Hospital, Lanzhou 730030, Gansu, China
- Key Laboratory of Bone & Joint Disease Research of Gansu Provincial, Lanzhou 730030, Gansu, China
| | - Kaichen Peng
- Department of Orthopaedics, Lanzhou University Second Hospital, Lanzhou 730030, Gansu, China
- Key Laboratory of Bone & Joint Disease Research of Gansu Provincial, Lanzhou 730030, Gansu, China
| | - Peng Wang
- Department of Orthopaedics, Lanzhou University Second Hospital, Lanzhou 730030, Gansu, China
- Key Laboratory of Bone & Joint Disease Research of Gansu Provincial, Lanzhou 730030, Gansu, China
| | - Yanbing Gao
- Department of Orthopaedics, Lanzhou University Second Hospital, Lanzhou 730030, Gansu, China
- Key Laboratory of Bone & Joint Disease Research of Gansu Provincial, Lanzhou 730030, Gansu, China
| | - Xidan Gao
- Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an 710000, Shaanxi, China
| | - Taowen Guo
- Department of Orthopaedics, Lanzhou University Second Hospital, Lanzhou 730030, Gansu, China
- Key Laboratory of Bone & Joint Disease Research of Gansu Provincial, Lanzhou 730030, Gansu, China
| | - Xiaobo Zhang
- Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an 710000, Shaanxi, China
| | - Haiyu Zhou
- Department of Orthopaedics, Lanzhou University Second Hospital, Lanzhou 730030, Gansu, China
- Key Laboratory of Bone & Joint Disease Research of Gansu Provincial, Lanzhou 730030, Gansu, China
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Yang Z, Chen L, Liu J, Zhuang H, Lin W, Li C, Zhao X. Short Peptide Nanofiber Biomaterials Ameliorate Local Hemostatic Capacity of Surgical Materials and Intraoperative Hemostatic Applications in Clinics. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2301849. [PMID: 36942893 DOI: 10.1002/adma.202301849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/12/2023] [Indexed: 06/18/2023]
Abstract
Short designer self-assembling peptide (dSAP) biomaterials are a new addition to the hemostat group. It may provide a diverse and robust toolbox for surgeons to integrate wound microenvironment with much safer and stronger hemostatic capacity than conventional materials and hemostatic agents. Especially in noncompressible torso hemorrhage (NCTH), diffuse mucosal surface bleeding, and internal medical bleeding (IMB), with respect to the optimal hemostatic formulation, dSAP biomaterials are the ingenious nanofiber alternatives to make bioactive neural scaffold, nasal packing, large mucosal surface coverage in gastrointestinal surgery (esophagus, gastric lesion, duodenum, and lower digestive tract), epicardiac cell-delivery carrier, transparent matrix barrier, and so on. Herein, in multiple surgical specialties, dSAP-biomaterial-based nano-hemostats achieve safe, effective, and immediate hemostasis, facile wound healing, and potentially reduce the risks in delayed bleeding, rebleeding, post-operative bleeding, or related complications. The biosafety in vivo, bleeding indications, tissue-sealing quality, surgical feasibility, and local usability are addressed comprehensively and sequentially and pursued to develop useful surgical techniques with better hemostatic performance. Here, the state of the art and all-round advancements of nano-hemostatic approaches in surgery are provided. Relevant critical insights will inspire exciting investigations on peptide nanotechnology, next-generation biomaterials, and better promising prospects in clinics.
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Affiliation(s)
- Zehong Yang
- Department of Biochemistry and Molecular Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, China
- Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital of Sichuan University, Chengdu, Sichuan, 610041, China
| | - Lihong Chen
- Department of Biochemistry and Molecular Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ji Liu
- Department of Biochemistry and Molecular Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Hua Zhuang
- Department of Ultrasonography, West China Hospital of Sichuan University, No. 37 Guoxue Road, Wuhou District, Chengdu, Sichuan, 610041, China
| | - Wei Lin
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Women and Children Diseases of the Ministry of Education, Sichuan University, No. 17 People's South Road, Chengdu, Sichuan, 610041, China
| | - Changlong Li
- Department of Biochemistry and Molecular Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiaojun Zhao
- Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital of Sichuan University, Chengdu, Sichuan, 610041, China
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10
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Koss KM, Sereda TJ, Kumirov VK, Wertheim JA. A class of peptides designed to replicate and enhance the Receptor for Hyaluronic Acid Mediated Motility binding domain. Acta Biomater 2023:S1742-7061(23)00251-9. [PMID: 37178990 DOI: 10.1016/j.actbio.2023.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023]
Abstract
The extra-cellular matrix (ECM) is a complex and rich microenvironment that is exposed and over-expressed across several injury or disease pathologies. Biomaterial therapeutics are often enriched with peptide binders to target the ECM with greater specificity. Hyaluronic acid (HA) is a major component of the ECM, yet to date, few HA adherent peptides have been discovered. A class of HA binding peptides was designed using B(X7)B hyaluronic acid binding domains inspired from the helical face of the Receptor for Hyaluronic Acid Mediated Motility (RHAMM). These peptides were bioengineered using a custom alpha helical net method, allowing for the enrichment of multiple B(X7)B domains and the optimisation of contiguous and non-contiguous domain orientations. Unexpectedly, the molecules also exhibited the behaviour of nanofiber forming self-assembling peptides and were investigated for this characteristic. Ten 23-27 amino acid residue peptides were assessed. Simple molecular modelling was used to depict helical secondary structures. Binding assays were performed with varying concentrations (1-10 mg/mL) and extra-cellular matrices (HA, collagens I-IV, elastin, and Geltrex). Concentration mediated secondary structures were assessed using circular dichroism (CD), and higher order nanostructures were visualized using transmission electron microscopy (TEM). All peptides formed the initial apparent 310/alpha-helices, yet peptides 17x-3, 4, BHP3 and BHP4 were HA specific and potent (i.e., a significant effect) binders at increasing concentrations. These peptides shifted from apparent 310/alpha-helical structures at low concentration to beta-sheets at increasing concentration and also formed nanofibers which are noted as self-assembling structures. Several of the HA binding peptides outperformed our positive control (mPEP35) at 3-4 times higher concentrations, and were enhanced by self-assembly as each of these groups had observable nanofibers. STATEMENT OF SIGNIFICANCE: Specific biomolecules or peptides have played a crucial role in developing materials or systems to deliver key drugs and therapeutics to a broad spectrum of diseases and disorders. In these diseased tissues, cells build protein/sugar networks, which are uniquely exposed and great targets to deliver drugs to. Hyaluronic acid (HA) is involved in every stage of injury and is abundant in cancer. To date, only two HA specific peptides have been discovered. In our work, we have designed a way to model and trace binding regions as they appear on the face of a helical peptide. Using this method we have created a family of peptides enriched with HA binding domains that stick with 3-4 higher affinity than those previously discovered.
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Affiliation(s)
- Kyle M Koss
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL; Department of Surgery, University of Arizona College of Medicine, Tucson, AZ
| | | | - Vlad K Kumirov
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ
| | - Jason A Wertheim
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL; Department of Surgery, University of Arizona College of Medicine, Tucson, AZ
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Dzierżyńska M, Sawicka J, Deptuła M, Sosnowski P, Sass P, Peplińska B, Pietralik-Molińska Z, Fularczyk M, Kasprzykowski F, Zieliński J, Kozak M, Sachadyn P, Pikuła M, Rodziewicz-Motowidło S. Release systems based on self-assembling RADA16-I hydrogels with a signal sequence which improves wound healing processes. Sci Rep 2023; 13:6273. [PMID: 37072464 PMCID: PMC10113214 DOI: 10.1038/s41598-023-33464-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023] Open
Abstract
Self-assembling peptides can be used for the regeneration of severely damaged skin. They can act as scaffolds for skin cells and as a reservoir of active compounds, to accelerate scarless wound healing. To overcome repeated administration of peptides which accelerate healing, we report development of three new peptide biomaterials based on the RADA16-I hydrogel functionalized with a sequence (AAPV) cleaved by human neutrophil elastase and short biologically active peptide motifs, namely GHK, KGHK and RDKVYR. The peptide hybrids were investigated for their structural aspects using circular dichroism, thioflavin T assay, transmission electron microscopy, and atomic force microscopy, as well as their rheological properties and stability in different fluids such as water or plasma, and their susceptibility to digestion by enzymes present in the wound environment. In addition, the morphology of the RADA-peptide hydrogels was examined with a unique technique called scanning electron cryomicroscopy. These experiments enabled us to verify if the designed peptides increased the bioactivity of the gel without disturbing its gelling processes. We demonstrate that the physicochemical properties of the designed hybrids were similar to those of the original RADA16-I. The materials behaved as expected, leaving the active motif free when treated with elastase. XTT and LDH tests on fibroblasts and keratinocytes were performed to assess the cytotoxicity of the RADA16-I hybrids, while the viability of cells treated with RADA16-I hybrids was evaluated in a model of human dermal fibroblasts. The hybrid peptides revealed no cytotoxicity; the cells grew and proliferated better than after treatment with RADA16-I alone. Improved wound healing following topical delivery of RADA-GHK and RADA-KGHK was demonstrated using a model of dorsal skin injury in mice and histological analyses. The presented results indicate further research is warranted into the engineered peptides as scaffolds for wound healing and tissue engineering.
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Affiliation(s)
- Maria Dzierżyńska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Justyna Sawicka
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Milena Deptuła
- Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Medical University of Gdańsk, Gdańsk, Poland
| | - Paweł Sosnowski
- Laboratory for Regenerative Biotechnology, Faculty of Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Piotr Sass
- Laboratory for Regenerative Biotechnology, Faculty of Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | | | | | - Martyna Fularczyk
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | | | - Jacek Zieliński
- Department of Surgical Oncology, Medical University of Gdańsk, Gdańsk, Poland
| | - Maciej Kozak
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Poznań, Poland
| | - Paweł Sachadyn
- Laboratory for Regenerative Biotechnology, Faculty of Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Michał Pikuła
- Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Medical University of Gdańsk, Gdańsk, Poland
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Rehman AU, Khurshid B, Ali Y, Rasheed S, Wadood A, Ng HL, Chen HF, Wei Z, Luo R, Zhang J. Computational approaches for the design of modulators targeting protein-protein interactions. Expert Opin Drug Discov 2023; 18:315-333. [PMID: 36715303 PMCID: PMC10149343 DOI: 10.1080/17460441.2023.2171396] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/18/2023] [Indexed: 01/31/2023]
Abstract
BACKGROUND Protein-protein interactions (PPIs) are intriguing targets for designing novel small-molecule inhibitors. The role of PPIs in various infectious and neurodegenerative disorders makes them potential therapeutic targets . Despite being portrayed as undruggable targets, due to their flat surfaces, disorderedness, and lack of grooves. Recent progresses in computational biology have led researchers to reconsider PPIs in drug discovery. AREAS COVERED In this review, we introduce in-silico methods used to identify PPI interfaces and present an in-depth overview of various computational methodologies that are successfully applied to annotate the PPIs. We also discuss several successful case studies that use computational tools to understand PPIs modulation and their key roles in various physiological processes. EXPERT OPINION Computational methods face challenges due to the inherent flexibility of proteins, which makes them expensive, and result in the use of rigid models. This problem becomes more significant in PPIs due to their flexible and flat interfaces. Computational methods like molecular dynamics (MD) simulation and machine learning can integrate the chemical structure data into biochemical and can be used for target identification and modulation. These computational methodologies have been crucial in understanding the structure of PPIs, designing PPI modulators, discovering new drug targets, and predicting treatment outcomes.
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Affiliation(s)
- Ashfaq Ur Rehman
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California Irvine, Irvine, California, USA
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, Zhejiang, China
| | - Beenish Khurshid
- Department of Biochemistry, Abdul Wali Khan University Mardan, Pakistan
| | - Yasir Ali
- National Center for Bioinformatics, Quaid-e-Azam University, Islamabad, Pakistan
| | - Salman Rasheed
- National Center for Bioinformatics, Quaid-e-Azam University, Islamabad, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Pakistan
| | - Ho-Leung Ng
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, Zhejiang, China
| | - Zhiqiang Wei
- Medicinal Chemistry and Bioinformatics Center, Ocean University of China, Qingdao, Shandong, China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California Irvine, Irvine, California, USA
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, Zhejiang, China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
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13
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Chen L, Wei L, Su X, Qin L, Xu Z, Huang X, Chen H, Hu N. Preparation and Characterization of Biomimetic Functional Scaffold with Gradient Structure for Osteochondral Defect Repair. Bioengineering (Basel) 2023; 10:bioengineering10020213. [PMID: 36829707 PMCID: PMC9952804 DOI: 10.3390/bioengineering10020213] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 02/08/2023] Open
Abstract
Osteochondral (OC) defects cannot adequately repair themselves due to their sophisticated layered structure and lack of blood supply in cartilage. Although therapeutic interventions are reaching an advanced stage, current clinical therapies to repair defects are in their infancy. Among the possible therapies, OC tissue engineering has shown considerable promise, and multiple approaches utilizing scaffolds, cells, and bioactive factors have been pursued. The most recent trend in OC tissue engineering has been to design gradient scaffolds using different materials and construction strategies (such as bi-layered, multi-layered, and continuous gradient structures) to mimic the physiological and mechanical properties of OC tissues while further enabling OC repair. This review focuses specifically on design and construction strategies for gradient scaffolds and their role in the successful engineering of OC tissues. The current dilemmas in the field of OC defect repair and the efforts of tissue engineering to address these challenges were reviewed. In addition, the advantages and limitations of the typical fabrication techniques for gradient scaffolds were discussed, with examples of recent studies summarizing the future prospects for integrated gradient scaffold construction. This updated and enlightening review could provide insights into our current understanding of gradient scaffolds in OC tissue engineering.
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Affiliation(s)
| | | | | | | | | | - Xiao Huang
- Correspondence: (X.H.); (H.C.); (N.H.); Tel.: +86-023-89011202 (X.H. & H.C. & N.H.)
| | - Hong Chen
- Correspondence: (X.H.); (H.C.); (N.H.); Tel.: +86-023-89011202 (X.H. & H.C. & N.H.)
| | - Ning Hu
- Correspondence: (X.H.); (H.C.); (N.H.); Tel.: +86-023-89011202 (X.H. & H.C. & N.H.)
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14
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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] [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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15
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Rizzo MG, Palermo N, D’Amora U, Oddo S, Guglielmino SPP, Conoci S, Szychlinska MA, Calabrese G. Multipotential Role of Growth Factor Mimetic Peptides for Osteochondral Tissue Engineering. Int J Mol Sci 2022; 23:ijms23137388. [PMID: 35806393 PMCID: PMC9266819 DOI: 10.3390/ijms23137388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 12/25/2022] Open
Abstract
Articular cartilage is characterized by a poor self-healing capacity due to its aneural and avascular nature. Once injured, it undergoes a series of catabolic processes which lead to its progressive degeneration and the onset of a severe chronic disease called osteoarthritis (OA). In OA, important alterations of the morpho-functional organization occur in the cartilage extracellular matrix, involving all the nearby tissues, including the subchondral bone. Osteochondral engineering, based on a perfect combination of cells, biomaterials and biomolecules, is becoming increasingly successful for the regeneration of injured cartilage and underlying subchondral bone tissue. To this end, recently, several peptides have been explored as active molecules and enrichment motifs for the functionalization of biomaterials due to their ability to be easily chemically synthesized, as well as their tunable physico-chemical features, low immunogenicity issues and functional group modeling properties. In addition, they have shown a good aptitude to penetrate into the tissue due to their small size and stability at room temperature. In particular, growth-factor-derived peptides can play multiple functions in bone and cartilage repair, exhibiting chondrogenic/osteogenic differentiation properties. Among the most studied peptides, great attention has been paid to transforming growth factor-β and bone morphogenetic protein mimetic peptides, cell-penetrating peptides, cell-binding peptides, self-assembling peptides and extracellular matrix-derived peptides. Moreover, recently, phage display technology is emerging as a powerful selection technique for obtaining functional peptides on a large scale and at a low cost. In particular, these peptides have demonstrated advantages such as high biocompatibility; the ability to be immobilized directly on chondro- and osteoinductive nanomaterials; and improving the cell attachment, differentiation, development and regeneration of osteochondral tissue. In this context, the aim of the present review was to go through the recent literature underlining the importance of studying novel functional motifs related to growth factor mimetic peptides that could be a useful tool in osteochondral repair strategies. Moreover, the review summarizes the current knowledge of the use of phage display peptides in osteochondral tissue regeneration.
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Affiliation(s)
- Maria Giovanna Rizzo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres, 31, 98168 Messina, Italy; (M.G.R.); (N.P.); (S.O.); (S.P.P.G.)
| | - Nicoletta Palermo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres, 31, 98168 Messina, Italy; (M.G.R.); (N.P.); (S.O.); (S.P.P.G.)
| | - Ugo D’Amora
- Institute of Polymers, Composites and Biomaterials—National Research Council, Viale J. F. Kennedy 54, Mostra d’Oltremare, Pad. 20, 80125 Naples, Italy;
| | - Salvatore Oddo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres, 31, 98168 Messina, Italy; (M.G.R.); (N.P.); (S.O.); (S.P.P.G.)
| | - Salvatore Pietro Paolo Guglielmino
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres, 31, 98168 Messina, Italy; (M.G.R.); (N.P.); (S.O.); (S.P.P.G.)
| | - Sabrina Conoci
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres, 31, 98168 Messina, Italy; (M.G.R.); (N.P.); (S.O.); (S.P.P.G.)
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
- Correspondence: (S.C.); (G.C.)
| | - Marta Anna Szychlinska
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), University of Palermo, Via del Vespro, 129, 90127 Palermo, Italy;
| | - Giovanna Calabrese
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres, 31, 98168 Messina, Italy; (M.G.R.); (N.P.); (S.O.); (S.P.P.G.)
- Correspondence: (S.C.); (G.C.)
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16
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Xu F, Xu B, Chen H, Ju X, Gonzalez de Mejia E. Enhancement of DPP-IV inhibitory activity and the capacity for enabling GLP-1 secretion through RADA16-assisted molecular designed rapeseed peptide nanogels. Food Funct 2022; 13:5215-5228. [PMID: 35438092 DOI: 10.1039/d1fo04367f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The potential of pentapeptide IPQVS (RAP1) and octapeptide ELHQEEPL (RAP2) derived from rapeseed napin as natural dipeptidyl-peptidase IV (DPP-IV) inhibitors is promising. The objective was to develop a nanogel strategy to resist the hydrolysis of digestive and intestinal enzymes to enhance the DPP-IV inhibitory activity of RAP1 and RAP2, and stimulate glucagon-like peptide 1 (GLP-1) secretion of RAP2 by a RADA16-assisted molecular design. The linker of double Gly was used in the connection of RADA16 and the functional oligopeptide region (RAP1 and RAP2). Compared to the original oligopeptides, DPP-IV IC50 of the nanogels RADA16-RAP1 and RADA16-RAP2 decreased by 26.43% and 17.46% in Caco-2 cell monolayers, respectively. The results showed that the two nanogel peptides with no toxicity to cells had higher contents of stable β-sheet structures (increased by 5.6-fold and 5.2-fold, respectively) than the original oligopeptides, and a self-assembled fibrous morphology. Rheological results suggested that the nanogels RADA16-RAP1 and RADA16-RAP2 exhibit good rheological properties for potential injectable applications; the storage modulus (G') was 10 times higher than the low modulus (G''). Furthermore, the RAP2 and its RADA16-assisted nanogel peptide at the concentration of 250 μM significantly (P < 0.05) increased the release of GLP-1 by 35.46% through the calcium-sensing receptor pathway in the enteroendocrine STC-1 cells. Hence, the innovative and harmless nanogels with the sequence of RADA16-GG-Xn have the potential for use by oral and injection administration for treating or relieving type 2 diabetes.
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Affiliation(s)
- Feiran Xu
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, People's Republic of China.,Department of Food Science and Human Nutrition, Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, 228 Edward R. Madigan Laboratory (ERML), 1201 West Gregory Drive, Urbana, Illinois 61801, USA.
| | - Baocai Xu
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, People's Republic of China
| | - Hong Chen
- Department of Food Science and Human Nutrition, Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, 228 Edward R. Madigan Laboratory (ERML), 1201 West Gregory Drive, Urbana, Illinois 61801, USA.
| | - Xingrong Ju
- National Engineering Laboratory for Cereal Fermentation Technology, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Elvira Gonzalez de Mejia
- Department of Food Science and Human Nutrition, Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, 228 Edward R. Madigan Laboratory (ERML), 1201 West Gregory Drive, Urbana, Illinois 61801, USA.
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17
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Miller JG, Hughes SA, Modlin C, Conticello VP. Structures of synthetic helical filaments and tubes based on peptide and peptido-mimetic polymers. Q Rev Biophys 2022; 55:1-103. [PMID: 35307042 DOI: 10.1017/s0033583522000014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractSynthetic peptide and peptido-mimetic filaments and tubes represent a diverse class of nanomaterials with a broad range of potential applications, such as drug delivery, vaccine development, synthetic catalyst design, encapsulation, and energy transduction. The structures of these filaments comprise supramolecular polymers based on helical arrangements of subunits that can be derived from self-assembly of monomers based on diverse structural motifs. In recent years, structural analyses of these materials at near-atomic resolution (NAR) have yielded critical insights into the relationship between sequence, local conformation, and higher-order structure and morphology. This structural information offers the opportunity for development of new tools to facilitate the predictable and reproduciblede novodesign of synthetic helical filaments. However, these studies have also revealed several significant impediments to the latter process – most notably, the common occurrence of structural polymorphism due to the lability of helical symmetry in structural space. This article summarizes the current state of knowledge on the structures of designed peptide and peptido-mimetic filamentous assemblies, with a focus on structures that have been solved to NAR for which reliable atomic models are available.
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Affiliation(s)
- Jessalyn G Miller
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
| | - Spencer A Hughes
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
| | - Charles Modlin
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
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18
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Bioinspired Sandcastle Worm-Derived Peptide-Based Hybrid Hydrogel for Promoting the Formation of Liver Spheroids. Gels 2022; 8:gels8030149. [PMID: 35323262 PMCID: PMC8950079 DOI: 10.3390/gels8030149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 12/10/2022] Open
Abstract
The generation of hepatic spheroids is beneficial for a variety of potential applications, including drug development, disease modeling, transplantation, and regenerative medicine. Natural hydrogels are obtained from tissues and have been widely used to promote the growth, differentiation, and retention of specific functionalities of hepatocytes. However, relying on natural hydrogels for the generation of hepatic spheroids, which have batch to batch variations, may in turn limit the previously mentioned potential applications. For this reason, we researched a way to establish a three-dimensional (3D) culture system that more closely mimics the interaction between hepatocytes and their surrounding microenvironments, thereby potentially offering a more promising and suitable system for drug development, disease modeling, transplantation, and regenerative medicine. Here, we developed self-assembling and bioactive hybrid hydrogels to support the generation and growth of hepatic spheroids. Our hybrid hydrogels (PC4/Cultrex) inspired by the sandcastle worm, an Arg-Gly-Asp (RGD) cell adhesion sequence, and bioactive molecules derived from Cultrex BME (Basement Membrane Extract). By performing optimizations to the design, the PC4/Cultrex hybrid hydrogels can enhance HepG2 cells to form spheroids and express their molecular signatures (e.g., Cyp3A4, Cyp7a1, A1at, Afp, Ck7, Ck1, and E-cad). Our study demonstrated that this hybrid hydrogel system offers potential advantages for hepatocytes in proliferating, differentiating, and self-organizing to form hepatic spheroids in a more controllable and reproducible manner. In addition, it is a versatile and cost-effective method for 3D tissue cultures in mass quantities. Importantly, we demonstrate that it is feasible to adapt a bioinspired approach to design biomaterials for 3D culture systems, which accelerates the design of novel peptide structures and broadens our research choices on peptide-based hydrogels.
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Kim NH, Choi H, Shahzad ZM, Ki H, Lee J, Chae H, Kim YH. Supramolecular assembly of protein building blocks: from folding to function. NANO CONVERGENCE 2022; 9:4. [PMID: 35024976 PMCID: PMC8755899 DOI: 10.1186/s40580-021-00294-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Several phenomena occurring throughout the life of living things start and end with proteins. Various proteins form one complex structure to control detailed reactions. In contrast, one protein forms various structures and implements other biological phenomena depending on the situation. The basic principle that forms these hierarchical structures is protein self-assembly. A single building block is sufficient to create homogeneous structures with complex shapes, such as rings, filaments, or containers. These assemblies are widely used in biology as they enable multivalent binding, ultra-sensitive regulation, and compartmentalization. Moreover, with advances in the computational design of protein folding and protein-protein interfaces, considerable progress has recently been made in the de novo design of protein assemblies. Our review presents a description of the components of supramolecular protein assembly and their application in understanding biological phenomena to therapeutics.
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Affiliation(s)
- Nam Hyeong Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hojae Choi
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Zafar Muhammad Shahzad
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
- School of Chemical Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Heesoo Ki
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jaekyoung Lee
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Heeyeop Chae
- School of Chemical Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Yong Ho Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- Center for Neuroscience Imaging Research, Institute for Basic Science (IBS), Suwon, 16419, Republic of Korea.
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20
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Kalelkar PP, Riddick M, García AJ. Biomaterial-based delivery of antimicrobial therapies for the treatment of bacterial infections. NATURE REVIEWS. MATERIALS 2022; 7:39-54. [PMID: 35330939 PMCID: PMC8938918 DOI: 10.1038/s41578-021-00362-4] [Citation(s) in RCA: 129] [Impact Index Per Article: 64.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
UNLABELLED The rise in antibiotic-resistant bacteria, including strains that are resistant to last-resort antibiotics, and the limited ability of antibiotics to eradicate biofilms, have necessitated the development of alternative antibacterial therapeutics. Antibacterial biomaterials, such as polycationic polymers, and biomaterial-assisted delivery of non-antibiotic therapeutics, such as bacteriophages, antimicrobial peptides and antimicrobial enzymes, have improved our ability to treat antibiotic-resistant and recurring infections. Biomaterials not only allow targeted delivery of multiple agents, but also sustained release at the infection site, thereby reducing potential systemic adverse effects. In this Review, we discuss biomaterial-based non-antibiotic antibacterial therapies for the treatment of community- and hospital-acquired infectious diseases, with a focus in in vivo results. We highlight the translational potential of different biomaterial-based strategies, and provide a perspective on the challenges associated with their clinical translation. Finally, we discuss the future scope of biomaterial-assisted antibacterial therapies. WEB SUMMARY The development of antibiotic tolerance and resistance has demanded the search for alternative antibacterial therapies. This Review discusses antibacterial biomaterials and biomaterial-assisted delivery of non-antibiotic therapeutics for the treatment of bacterial infectious diseases, with a focus on clinical translation.
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Affiliation(s)
- Pranav P. Kalelkar
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Milan Riddick
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Andrés J. García
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
- author to whom correspondence should be addressed:
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21
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Pitz ME, Nukovic AM, Elpers MA, Alexander-Bryant AA. Factors Affecting Secondary and Supramolecular Structures of Self-Assembling Peptide Nanocarriers. Macromol Biosci 2021; 22:e2100347. [PMID: 34800001 DOI: 10.1002/mabi.202100347] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/19/2021] [Indexed: 01/12/2023]
Abstract
Self-assembling peptides are a popular vector for therapeutic cargo delivery due to their versatility, tunability, and biocompatibility. Accurately predicting secondary and supramolecular structures of self-assembling peptides is essential for de novo peptide design. However, computational modeling of such assemblies is not yet able to accurately predict structure formation for many peptide sequences. This review identifies patterns in literature between secondary and supramolecular structures, primary sequences, and applications to provide a guide for informed peptide design. An overview of peptide structures, their applications as nanocarriers, and analytical methods for characterizing secondary and supramolecular structure is examined. A top-down approach is then used to identify trends between peptide sequence and assembly structure from the current literature, including an analysis of the drivers at work, such as local and nonlocal sequence effects and solution conditions.
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Affiliation(s)
- Megan E Pitz
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
| | - Alexandra M Nukovic
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
| | - Margaret A Elpers
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
| | - Angela A Alexander-Bryant
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
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22
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Yaguchi A, Oshikawa M, Watanabe G, Hiramatsu H, Uchida N, Hara C, Kaneko N, Sawamoto K, Muraoka T, Ajioka I. Efficient protein incorporation and release by a jigsaw-shaped self-assembling peptide hydrogel for injured brain regeneration. Nat Commun 2021; 12:6623. [PMID: 34799548 PMCID: PMC8604910 DOI: 10.1038/s41467-021-26896-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
During injured tissue regeneration, the extracellular matrix plays a key role in controlling and coordinating various cellular events by binding and releasing secreted proteins in addition to promoting cell adhesion. Herein, we develop a cell-adhesive fiber-forming peptide that mimics the jigsaw-shaped hydrophobic surface in the dovetail-packing motif of glycophorin A as an artificial extracellular matrix for regenerative therapy. We show that the jigsaw-shaped self-assembling peptide forms several-micrometer-long supramolecular nanofibers through a helix-to-strand transition to afford a hydrogel under physiological conditions and disperses homogeneously in the hydrogel. The molecular- and macro-scale supramolecular properties of the jigsaw-shaped self-assembling peptide hydrogel allow efficient incorporation and sustained release of vascular endothelial growth factor, and demonstrate cell transplantation-free regenerative therapeutic effects in a subacute-chronic phase mouse stroke model. This research highlights a therapeutic strategy for injured tissue regeneration using the jigsaw-shaped self-assembling peptide supramolecular hydrogel. The extracellular matrix contributes to tissue regeneration by binding and releasing growth factors. Here the authors present the jigsaw-shaped self-assembling peptide JigSAP as an artificial ECM and show that VEGF-JigSAP has therapeutic effects on the subacute-chronic phase of brain stroke.
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Affiliation(s)
- Atsuya Yaguchi
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, 184-8588, Japan
| | - Mio Oshikawa
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan.,Kanagawa Institute of Industrial Science and Technology (KISTEC), Kanagawa, 243-0435, Japan
| | - Go Watanabe
- Kanagawa Institute of Industrial Science and Technology (KISTEC), Kanagawa, 243-0435, Japan.,Department of Physics, School of Science, Kitasato University, Kanagawa, 252-0373, Japan
| | - Hirotsugu Hiramatsu
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan.,Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan
| | - Noriyuki Uchida
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, 184-8588, Japan
| | - Chikako Hara
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan.,Kanagawa Institute of Industrial Science and Technology (KISTEC), Kanagawa, 243-0435, Japan
| | - Naoko Kaneko
- Department of Developmental and Regenerative Neurobiology, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Aichi, 467-8601, Japan
| | - Kazunobu Sawamoto
- Department of Developmental and Regenerative Neurobiology, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Aichi, 467-8601, Japan.,Division of Neural Development and Regeneration, National Institute for Physiological Sciences, Aichi, 444-8585, Japan
| | - Takahiro Muraoka
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, 184-8588, Japan. .,Kanagawa Institute of Industrial Science and Technology (KISTEC), Kanagawa, 243-0435, Japan.
| | - Itsuki Ajioka
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan. .,Kanagawa Institute of Industrial Science and Technology (KISTEC), Kanagawa, 243-0435, Japan.
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23
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Mirzaei S, Kulkarni K, Zhou K, Crack PJ, Aguilar MI, Finkelstein DI, Forsythe JS. Biomaterial Strategies for Restorative Therapies in Parkinson's Disease. ACS Chem Neurosci 2021; 12:4224-4235. [PMID: 34634903 DOI: 10.1021/acschemneuro.1c00484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Parkinson's disease (PD) is a progressive neurological disorder, in which dopaminergic midbrain neurons degenerate, leading to dopamine depletion that is associated with neuronal death. In this Review, we initially describe the pathogenesis of PD and established therapies that unfortunately only delay progression of the disease. With a rapidly escalating incidence in PD, there is an urgent need to develop new therapies that not only halt progression but even reverse degeneration. Biomaterials are playing critical roles in these new therapies which include controlled and site-specific delivery of neurotrophins, increased engraftment of implanted neural stem cells, and redirection of endogenous stem cell populations away from their niche to encourage reparative mechanisms. This Review will therefore cover important design features of biomaterials used in regenerative medicine and tissue engineering strategies targeted at PD.
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Affiliation(s)
- Samaneh Mirzaei
- Department of Materials Science and Engineering, Monash Institute of Medical Engineering, Monash University, Clayton, Victoria 3800, Australia
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ketav Kulkarni
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Kun Zhou
- Department of Materials Science and Engineering, Monash Institute of Medical Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Peter J. Crack
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - David I. Finkelstein
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - John S. Forsythe
- Department of Materials Science and Engineering, Monash Institute of Medical Engineering, Monash University, Clayton, Victoria 3800, Australia
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24
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Li F, Gao L, Zhang X, Wang P, Liu Y, Feng J, Zhang C, Zhao C, Zhang S. "PP-type" self-assembling peptides with superior rheological properties. NANOSCALE ADVANCES 2021; 3:6056-6062. [PMID: 36133953 PMCID: PMC9417066 DOI: 10.1039/d1na00534k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/01/2021] [Indexed: 06/16/2023]
Abstract
The ionic-complementary self-assembling peptides discovered by Zhang Shuguang have solution-to-gel (sol-gel) transition capacity and one such peptide RADA16 has been commercialized into hemostatic agents. However, their sol-gel transition ability was not obvious because the peptide aqueous solution with a concentration greater than 1% w/v appeared to be thick and viscous. The current report describes PP-type self-assembling peptides. In addition to the ionic-complementary sequence, they have prolines at both ends of the sequence. This feature has led to better solubility, lower viscosity of the peptide solution, and simplified synthesis and purification processes while maintaining the great gelling performance of the ionic-complementary peptides. The PP-type peptides self-assembled into a well-organized nanofiber scaffold as shown by TEM. Among the PP-type peptides, the PRVDP9 sequence peptide was tested as a hemostatic agent and a mucosal elevating agent. The results were comparable to the classic RADA16. The PP-type self-assembling peptides have superior sol-gel transition ability. Therefore, it is predicted that they will be more suitable to be transported through catheters or endoscopes and have higher commercialization potential as compared with the classic self-assembling peptide sequences.
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Affiliation(s)
- Fangmin Li
- Success Bio-Tech Co., Ltd. 2222 Kaituo Road Jinan 250101 China
- Biomedical Material Engineering Laboratory of Shandong Province 2222 Kaituo Road Jinan 250101 China
| | - Lichang Gao
- Success Bio-Tech Co., Ltd. 2222 Kaituo Road Jinan 250101 China
- Biomedical Material Engineering Laboratory of Shandong Province 2222 Kaituo Road Jinan 250101 China
| | - Xudong Zhang
- Success Bio-Tech Co., Ltd. 2222 Kaituo Road Jinan 250101 China
- Biomedical Material Engineering Laboratory of Shandong Province 2222 Kaituo Road Jinan 250101 China
| | - Pin Wang
- Success Bio-Tech Co., Ltd. 2222 Kaituo Road Jinan 250101 China
- Biomedical Material Engineering Laboratory of Shandong Province 2222 Kaituo Road Jinan 250101 China
| | - Yuanxue Liu
- Success Bio-Tech Co., Ltd. 2222 Kaituo Road Jinan 250101 China
- Biomedical Material Engineering Laboratory of Shandong Province 2222 Kaituo Road Jinan 250101 China
| | - Jinhui Feng
- Success Bio-Tech Co., Ltd. 2222 Kaituo Road Jinan 250101 China
- Biomedical Material Engineering Laboratory of Shandong Province 2222 Kaituo Road Jinan 250101 China
| | - Chunxia Zhang
- Success Bio-Tech Co., Ltd. 2222 Kaituo Road Jinan 250101 China
- Biomedical Material Engineering Laboratory of Shandong Province 2222 Kaituo Road Jinan 250101 China
| | - Chengru Zhao
- Success Bio-Tech Co., Ltd. 2222 Kaituo Road Jinan 250101 China
- Biomedical Material Engineering Laboratory of Shandong Province 2222 Kaituo Road Jinan 250101 China
| | - Shang Zhang
- Success Bio-Tech Co., Ltd. 2222 Kaituo Road Jinan 250101 China
- Biomedical Material Engineering Laboratory of Shandong Province 2222 Kaituo Road Jinan 250101 China
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25
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Wang F, Gnewou O, Wang S, Osinski T, Zuo X, Egelman EH, Conticello VP. Deterministic chaos in the self-assembly of β sheet nanotubes from an amphipathic oligopeptide. MATTER 2021; 4:3217-3231. [PMID: 34632372 PMCID: PMC8494133 DOI: 10.1016/j.matt.2021.06.037] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The self-assembly of designed peptides into filaments and other higher-order structures has been the focus of intense interest because of the potential for creating new biomaterials and biomedical devices. These peptide assemblies have also been used as models for understanding biological processes, such as the pathological formation of amyloid. We investigate the assembly of an octapeptide sequence, Ac-FKFEFKFE-NH2, motivated by prior studies that demonstrated that this amphipathic β strand peptide self-assembled into fibrils and biocompatible hydrogels. Using high-resolution cryoelectron microscopy (cryo-EM), we are able to determine the atomic structure for two different coexisting forms of the fibrils, containing four and five β sandwich protofilaments, respectively. Surprisingly, the inner walls in both forms are parallel β sheets, while the outer walls are antiparallel β sheets. Our results demonstrate the chaotic nature of peptide self-assembly and illustrate the importance of cryo-EM structural analysis to understand the complex phase behavior of these materials at near-atomic resolution.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Ordy Gnewou
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Shengyuan Wang
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Tomasz Osinski
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Edward H. Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence: (E.H.E.), (V.P.C.)
| | - Vincent P. Conticello
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
- The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), Emory University, Atlanta, GA 30322, USA
- Lead contact
- Correspondence: (E.H.E.), (V.P.C.)
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26
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Lopez-Silva TL, Schneider JP. From structure to application: Progress and opportunities in peptide materials development. Curr Opin Chem Biol 2021; 64:131-144. [PMID: 34329941 PMCID: PMC8585687 DOI: 10.1016/j.cbpa.2021.06.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/10/2021] [Accepted: 06/20/2021] [Indexed: 01/12/2023]
Abstract
For over 20 years, peptide materials in their hydrogel or soluble fibril form have been used for biomedical applications such as drug delivery, cell culture, vaccines, and tissue regeneration. To facilitate the translation of these materials, key areas of research still need to be addressed. Their structural characterization lags compared to amyloid proteins. Many of the structural features designed to guide materials formation are primarily being characterized by their observation in atomic resolution structures of amyloid assemblies. Herein, these motifs are examined in relation to peptide designs identifying common interactions that drive assembly and provide structural specificity. Current efforts to design complex structures, as reviewed here, highlight the need to extend the structural revolution of amyloid proteins to peptide assemblies to validate design principles. With respect to clinical applications, the fundamental interactions and responses of proteins, cells, and the immune system to peptide materials are still not well understood. Only a few trends are just now emerging for peptide materials interactions with biological systems. Understanding how peptide material properties influence these interactions will enable the translation of materials towards current and emerging applications.
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Affiliation(s)
- Tania L Lopez-Silva
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, United States
| | - Joel P Schneider
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, United States.
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27
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Li Z, Cai B, Yang W, Chen CL. Hierarchical Nanomaterials Assembled from Peptoids and Other Sequence-Defined Synthetic Polymers. Chem Rev 2021; 121:14031-14087. [PMID: 34342989 DOI: 10.1021/acs.chemrev.1c00024] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In nature, the self-assembly of sequence-specific biopolymers into hierarchical structures plays an essential role in the construction of functional biomaterials. To develop synthetic materials that can mimic and surpass the function of these natural counterparts, various sequence-defined bio- and biomimetic polymers have been developed and exploited as building blocks for hierarchical self-assembly. This review summarizes the recent advances in the molecular self-assembly of hierarchical nanomaterials based on peptoids (or poly-N-substituted glycines) and other sequence-defined synthetic polymers. Modern techniques to monitor the assembly mechanisms and characterize the physicochemical properties of these self-assembly systems are highlighted. In addition, discussions about their potential applications in biomedical sciences and renewable energy are also included. This review aims to highlight essential features of sequence-defined synthetic polymers (e.g., high stability and protein-like high-information content) and how these unique features enable the construction of robust biomimetic functional materials with high programmability and predictability, with an emphasis on peptoids and their self-assembled nanomaterials.
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Affiliation(s)
- Zhiliang Li
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Institute of Molecular Science and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, China
| | - Bin Cai
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,School of Chemistry and Chemical Engineering, Shandong University, Shandong 250100, China
| | - Wenchao Yang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, China
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
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28
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Perez JJ, Perez RA, Perez A. Computational Modeling as a Tool to Investigate PPI: From Drug Design to Tissue Engineering. Front Mol Biosci 2021; 8:681617. [PMID: 34095231 PMCID: PMC8173110 DOI: 10.3389/fmolb.2021.681617] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/05/2021] [Indexed: 12/13/2022] Open
Abstract
Protein-protein interactions (PPIs) mediate a large number of important regulatory pathways. Their modulation represents an important strategy for discovering novel therapeutic agents. However, the features of PPI binding surfaces make the use of structure-based drug discovery methods very challenging. Among the diverse approaches used in the literature to tackle the problem, linear peptides have demonstrated to be a suitable methodology to discover PPI disruptors. Unfortunately, the poor pharmacokinetic properties of linear peptides prevent their direct use as drugs. However, they can be used as models to design enzyme resistant analogs including, cyclic peptides, peptide surrogates or peptidomimetics. Small molecules have a narrower set of targets they can bind to, but the screening technology based on virtual docking is robust and well tested, adding to the computational tools used to disrupt PPI. We review computational approaches used to understand and modulate PPI and highlight applications in a few case studies involved in physiological processes such as cell growth, apoptosis and intercellular communication.
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Affiliation(s)
- Juan J Perez
- Department of Chemical Engineering, Universitat Politecnica de Catalunya, Barcelona, Spain
| | - Roman A Perez
- Bioengineering Institute of Technology, Universitat Internacional de Catalunya, Sant Cugat, Spain
| | - Alberto Perez
- The Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, FL, United States
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29
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Xing Z, Chen Y, Qiu F. Alternative Causal Link between Peptide Fibrillization and β-Strand Conformation. ACS OMEGA 2021; 6:12904-12912. [PMID: 34056442 PMCID: PMC8154227 DOI: 10.1021/acsomega.1c01423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/23/2021] [Indexed: 02/08/2023]
Abstract
In the prevailing phenomenon of peptide fibrillization, β-strand conformation has long been believed to be an important structural basis for peptide assembly. According to a widely accepted theory, in most peptide fibrillization processes, peptide monomers need to intrinsically take or transform to β-strand conformation before they can undergo ordered packing to form nanofibers. In this study, we reported our findings on an alternative peptide fibrillization pathway starting from a disordered secondary structure, which could then transform to β-strand after fibrillization. By using circular dichroism, thioflavin-T binding test, and transmission electron microscopy, we studied the secondary structure and assembly behavior of Ac-RADARADARADARADA-NH2 (RADA16-I) in a low concentration range. The effects of peptide concentration, solvent polarity, pH, and temperature were investigated in detail. Our results showed that at very low concentrations, even though the peptide was in a disordered secondary structure, it could still form nanofibers through intermolecular assembly, and under higher peptide concentrations, the transformation from the disordered structure to β-strand could happen with the growth of nanofibers. Our results indicated that even without ordered β-strand conformation, driving forces such as hydrophobic interaction and electrostatic interaction could still play a determinative role in the self-assembly of peptides. At least in some cases, the formation of β-strand might be the consequence rather than the cause of peptide fibrillization.
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Affiliation(s)
- Zhihua Xing
- Laboratory
of Anesthesia and Critical Care Medicine, Translational Neuroscience
Center and National Clinical Research Center for Geriatrics, West
China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory
of Ethnopharmacology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yongzhu Chen
- Laboratory
of Anesthesia and Critical Care Medicine, Translational Neuroscience
Center and National Clinical Research Center for Geriatrics, West
China Hospital, Sichuan University, Chengdu 610041, China
- Periodical
Press of West China Hospital, Sichuan University, Chengdu 610041, China
| | - Feng Qiu
- Laboratory
of Anesthesia and Critical Care Medicine, Translational Neuroscience
Center and National Clinical Research Center for Geriatrics, West
China Hospital, Sichuan University, Chengdu 610041, China
- National-Local
Joint Engineering Research Center of Translational Medicine of Anesthesiology,
West China Hospital, Sichuan University, Chengdu 610041, China
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30
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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] [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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31
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Kajtez J, Nilsson F, Fiorenzano A, Parmar M, Emnéus J. 3D biomaterial models of human brain disease. Neurochem Int 2021; 147:105043. [PMID: 33887378 DOI: 10.1016/j.neuint.2021.105043] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/21/2021] [Accepted: 04/06/2021] [Indexed: 01/25/2023]
Abstract
Inherent limitations of the traditional approaches to study brain function and disease, such as rodent models and 2D cell culture platforms, have led to the development of 3D in vitro cell culture systems. These systems, products of multidisciplinary efforts encompassing stem cell biology, materials engineering, and biofabrication, have quickly shown great potential to mimic biochemical composition, structural properties, and cellular morphology and diversity found in the native brain tissue. Crucial to these developments have been the advancements in stem cell technology and cell reprogramming protocols that allow reproducible generation of human subtype-specific neurons and glia in laboratory conditions. At the same time, biomaterials have been designed to provide cells in 3D with a microenvironment that mimics functional and structural aspects of the native extracellular matrix with increasing fidelity. In this article, we review the use of biomaterials in 3D in vitro models of neurological disorders with focus on hydrogel technology and with biochemical composition and physical properties of the in vivo environment as reference.
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Affiliation(s)
- Janko Kajtez
- Department of Experimental Medical Sciences, Wallenberg Neuroscience Center, Division of Neurobiology and Lund Stem Cell Center, BMC A11, Lund University, Lund, S-22184, Sweden.
| | - Fredrik Nilsson
- Department of Experimental Medical Sciences, Wallenberg Neuroscience Center, Division of Neurobiology and Lund Stem Cell Center, BMC A11, Lund University, Lund, S-22184, Sweden
| | - Alessandro Fiorenzano
- Department of Experimental Medical Sciences, Wallenberg Neuroscience Center, Division of Neurobiology and Lund Stem Cell Center, BMC A11, Lund University, Lund, S-22184, Sweden
| | - Malin Parmar
- Department of Experimental Medical Sciences, Wallenberg Neuroscience Center, Division of Neurobiology and Lund Stem Cell Center, BMC A11, Lund University, Lund, S-22184, Sweden
| | - Jenny Emnéus
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Kongens Lyngby, Denmark
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32
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Wang F, Gnewou O, Modlin C, Beltran LC, Xu C, Su Z, Juneja P, Grigoryan G, Egelman EH, Conticello VP. Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials. Nat Commun 2021; 12:407. [PMID: 33462223 PMCID: PMC7814010 DOI: 10.1038/s41467-020-20689-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/02/2020] [Indexed: 12/12/2022] Open
Abstract
The exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-α supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within the cross-α nanotubes. The structure of the resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to flagella and pili.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Ordy Gnewou
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Charles Modlin
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Leticia C Beltran
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Chunfu Xu
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Zhangli Su
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Puneet Juneja
- The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), Emory University, Atlanta, GA, 30322, USA
| | - Gevorg Grigoryan
- Department of Computer Science, Dartmouth College, Hanover, NH, 03755, USA.,Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Vincent P Conticello
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA. .,The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), Emory University, Atlanta, GA, 30322, USA.
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Chen CH, Hsu EL, Stupp SI. Supramolecular self-assembling peptides to deliver bone morphogenetic proteins for skeletal regeneration. Bone 2020; 141:115565. [PMID: 32745692 PMCID: PMC7680412 DOI: 10.1016/j.bone.2020.115565] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 12/15/2022]
Abstract
Recombinant human bone morphogenetic proteins (BMPs) have shown clinical success in promoting bone healing, but they are also associated with unwanted side effects. The development of improved BMP carriers that can retain BMP at the defect site and maximize its efficacy would decrease the therapeutic BMP dose and thus improve its safety profile. In this review, we discuss the advantages of using self-assembling peptides, a class of synthetic supramolecular biomaterials, to deliver recombinant BMPs. Peptide amphiphiles (PAs) are a broad class of self-assembling peptides, and the use of PAs for BMP delivery and bone regeneration has been explored extensively over the past decade. Like many self-assembling peptide systems, PAs can be designed to form nanofibrous supramolecular biomaterials in which molecules are held together by non-covalent bonds. Chemical and biological functionality can be added to PA nanofibers, through conjugation of chemical moieties or biological epitopes to PA molecules. For example, PA nanofibers have been designed to bind heparan sulfate, a natural polysaccharide that is known to bind BMPs and potentiate their signal. Alternatively, PA nanofibers have been designed to synthetically mimic the structure and function of heparan sulfate, or to directly bind BMP specifically. In small animal models, these bio-inspired PA materials have shown the capacity to promote bone regeneration using BMP at doses 10-100 times lower than established therapeutic doses. These promising results have motivated further evaluation of PAs in large animal models, where their safety and efficacy must be established before clinical translation. We conclude with a discussion on the possiblity of combining PAs with other materials used in orthopaedic surgery to maximize their utility for clinical translation.
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Affiliation(s)
- Charlotte H Chen
- Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Chicago, IL 60611, USA; Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, IL 60208, USA
| | - Erin L Hsu
- Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Chicago, IL 60611, USA; Department of Orthopaedic Surgery, Northwestern University, 676 North St. Clair Street, Chicago, IL 60611, USA
| | - Samuel I Stupp
- Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Chicago, IL 60611, USA; Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, IL 60208, USA; Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA; Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA; Department of Medicine, Northwestern University, 676 North St. Clair Street, Chicago, IL 60611, USA.
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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] [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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Abudula T, Bhatt K, Eggermont LJ, O'Hare N, Memic A, Bencherif SA. Supramolecular Self-Assembled Peptide-Based Vaccines: Current State and Future Perspectives. Front Chem 2020; 8:598160. [PMID: 33195107 PMCID: PMC7662149 DOI: 10.3389/fchem.2020.598160] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/05/2020] [Indexed: 02/01/2023] Open
Abstract
Despite the undeniable success of vaccination programs in preventing diseases, effective vaccines against several life-threatening infectious pathogens such as human immunodeficiency virus are still unavailable. Vaccines are designed to boost the body's natural ability to protect itself against foreign pathogens. To enhance vaccine-based immunotherapies to combat infections, cancer, and other conditions, biomaterials have been harnessed to improve vaccine safety and efficacy. Recently, peptides engineered to self-assemble into specific nanoarchitectures have shown great potential as advanced biomaterials for vaccine development. These supramolecular nanostructures (i.e., composed of many peptides) can be programmed to organize into various forms, including nanofibers, nanotubes, nanoribbons, and hydrogels. Additionally, they have been designed to be responsive upon exposure to various external stimuli, providing new innovations in the development of smart materials for vaccine delivery and immunostimulation. Specifically, self-assembled peptides can provide cell adhesion sites, epitope recognition, and antigen presentation, depending on their biochemical and structural characteristics. Furthermore, they have been tailored to form exquisite nanostructures that provide improved enzymatic stability and biocompatibility, in addition to the controlled release and targeted delivery of immunomodulatory factors (e.g., adjuvants). In this mini review, we first describe the different types of self-assembled peptides and resulting nanostructures that have recently been investigated. Then, we discuss the recent progress and development trends of self-assembled peptide-based vaccines, their challenges, and clinical translatability, as well as their future perspectives.
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Affiliation(s)
| | - Khushbu Bhatt
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, United States
| | - Loek J Eggermont
- Department of Chemical Engineering, Northeastern University, Boston, MA, United States
| | - Nick O'Hare
- Department of Chemical Engineering, Northeastern University, Boston, MA, United States
| | - Adnan Memic
- Center of Nanotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sidi A Bencherif
- Department of Chemical Engineering, Northeastern University, Boston, MA, United States.,Department of Bioengineering, Northeastern University, Boston, MA, United States.,Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, United States.,Sorbonne University, UTC CNRS UMR 7338, Biomechanics and Bioengineering (BMBI), University of Technology of Compiègne, Compiègne, France
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Ao DS, Gao LY, Gu JH, Qiao JH, Wang H, Liu YF, Song H. Study on Adenovirus Infection in vitro with Nanoself-Assembling Peptide as Scaffolds for 3D Culture. Int J Nanomedicine 2020; 15:6327-6338. [PMID: 32922004 PMCID: PMC7457861 DOI: 10.2147/ijn.s239395] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/30/2020] [Indexed: 01/04/2023] Open
Abstract
Purpose To construct a three-dimensional (3D) culture model of adenovirus in vitro using the nanoself-assembling peptide RADA16-I as a 3D cell culture scaffold combined with virology experimental technology to provide a novel research method for virus isolation and culture, pathogenesis research, antiviral drug screening and vaccine preparation. Methods The nanoself-assembling peptide RADA16-I was used as a 3D scaffold material for 293T cell culture, and adenovirus was cultured in the cells. The growth, morphological characteristics and pathological effects of 3D-cultured 293T cells after adenovirus infection were observed with an inverted microscope and MTS. The proliferation of adenovirus in 293T cells was observed by TEM and detected by qPCR. The levels of TNF-α and IL-8 secreted by adenovirus-infected 293T cells in the RADA16-I 3D culture system were detected by ELISA. Results The 293T cells grew well in the RADA16-I 3D culture system for a prolonged period of time. The adenovirus infection persisted for a long time with multiple proliferation peaks, which closely resembled those of in vivo infections. The adenovirus virions amplified in the 3D system remained infectious. There were multiple secretion peaks of TNF-α and IL-8 secretion levels in adenovirus-infected 293T cells cultured in 3D culture systems. Conclusion The nanoself-assembling peptide RADA16-I can be used as a 3D scaffold for adenovirus isolation, culture and research. The 3D culture system shows more realistic in vivo effects than two-dimensional (2D) culture.
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Affiliation(s)
- Di-Shu Ao
- Department of Microbiology, School of Basic Medical Sciences, Zunyi Medical University, Zunyi 563000, People's Republic of China
| | - Lu-Yao Gao
- Department of Microbiology, School of Basic Medical Sciences, Zunyi Medical University, Zunyi 563000, People's Republic of China
| | - Jing-Han Gu
- Department of Microbiology, School of Basic Medical Sciences, Zunyi Medical University, Zunyi 563000, People's Republic of China
| | - Jun-Hua Qiao
- Department of Microbiology, School of Basic Medical Sciences, Zunyi Medical University, Zunyi 563000, People's Republic of China
| | - Huan Wang
- Department of Microbiology, School of Basic Medical Sciences, Zunyi Medical University, Zunyi 563000, People's Republic of China
| | - Yan-Fei Liu
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, People's Republic of China
| | - Hong Song
- Department of Microbiology, School of Basic Medical Sciences, Zunyi Medical University, Zunyi 563000, People's Republic of China
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Wei W, Liu Y, Xiong N, Yu L, Zhang T, Song H, Tang F. A Peptide-Based Method for the Fabrication of 1D Rail-Like Nanoparticle Chains and 2D Nanoparticle Membranes: Higher-Order Self-Assembly. Chempluschem 2020; 84:374-381. [PMID: 31939204 DOI: 10.1002/cplu.201900040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/13/2019] [Indexed: 12/22/2022]
Abstract
Functionalized histidine-rich peptide sequences were designed for the site-directed assembly of nanoparticles. TEM and AFM images shown that the peptides self-assembled into well-ordered nanofibrils at pH 7.2. The nanofibrils could lie parallel to one another and form membranes when the solution was acidic (pH 3.8) resulting from the hierarchical assembly of the nanofibrils in the direction of the peptide backbone. These peptide structures served as a template for nucleation and growth of Au nanocrystals. Further characterization showed that the Au nanocrystals grew on both sides of the nanofibrils, and a 1D system with a rail-like structure and a 2D membrane were synthesized after reduction with hydrazine hydrate at neutral and acidic pH values, respectively. The size and packing density of the Au nanocrystals were positively correlated with the incubation time of the Au ions. This approach can be extended further to the controlled synthesis of 1D and 2D architectures formed from metals, metal sulfides, and metal oxides in a low-cost and simple manner. Finally, the nanostructures could catalyze the reduction of p-nitrophenol with rate constants of 0.83±0.14 and 0.69±0.09 min-1 for the 1D and 2D structures, respectively.
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Affiliation(s)
- Wei Wei
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - Yanfei Liu
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - Na Xiong
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - Limei Yu
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - Tao Zhang
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - Hong Song
- Department of Microbiology, Zunyi Medical University, Zunyi, 563000, China
| | - Fushan Tang
- Key Laboratory of Clinical Pharmacy in Zunyi City Department of Clinical Pharmacy School of Pharmacy, Zunyi Medical University, Zunyi, 563000, China
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Song H, Cai GH, Liang J, Ao DS, Wang H, Yang ZH. Three-dimensional culture and clinical drug responses of a highly metastatic human ovarian cancer HO-8910PM cells in nanofibrous microenvironments of three hydrogel biomaterials. J Nanobiotechnology 2020; 18:90. [PMID: 32527266 PMCID: PMC7291456 DOI: 10.1186/s12951-020-00646-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/01/2020] [Indexed: 01/18/2023] Open
Abstract
Background Ovarian cancer is a highly aggressive malignant disease in gynecologic cancer. It is an urgent task to develop three-dimensional (3D) cell models in vitro and dissect the cell progression-related drug resistance mechanisms in vivo. In the present study, RADA16-I peptide has the reticulated nanofiber scaffold networks in hydrogel, which is utilized to develop robust 3D cell culture of a high metastatic human ovarian cancer HO-8910PM cell line accompanied with the counterparts of Matrigel and collagen I. Results Consequently, HO-8910PM cells were successfully cultivated in three types of hydrogel biomaterials, such as RADA16-I hydrogel, Matrigel, and collagen I, according to 3D cell culture protocols. Designer RADA16-I peptide had well-defined nanofiber networks architecture in hydrogel, which provided nanofiber cell microenvironments analogous to Matrigel and collagen I. 3D-cultured HO-8910PM cells in RADA16-I hydrogel, Matrigel, and collagen I showed viable cell proliferation, proper cell growth, and diverse cell shapes in morphology at the desired time points. For a long 3D cell culture period, HO-8910PM cells showed distinct cell aggregate growth patterns in RADA16-I hydrogel, Matrigel, and collagen I, such as cell aggregates, cell colonies, cell clusters, cell strips, and multicellular tumor spheroids (MCTS). The cell distribution and alignment were described vigorously. Moreover, the molecular expression of integrin β1, E-cadherin and N-cadherin were quantitatively analyzed in 3D-cultured MCTS of HO-8910PM cells by immunohistochemistry and western blotting assays. The chemosensitivity assay for clinical drug responses in 3D context indicated that HO-8910PM cells in three types of hydrogels showed significantly higher chemoresistance to cisplatin and paclitaxel compared to 2D flat cell culture, including IC50 values and inhibition rates. Conclusion Based on these results, RADA16-I hydrogel is a highly competent, high-profile, and proactive nanofiber scaffold to maintain viable cell proliferation and high cell vitality in 3D cell models, which may be particularly utilized to develop useful clinical drug screening platform in vitro.
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Affiliation(s)
- Hong Song
- College of Basic Medicine, Zunyi Medical University, No.201 Dalian Road, Huichuan District, Zunyi, Guizhou, 563003, China
| | - Guo-Hui Cai
- College of Basic Medicine, Zunyi Medical University, No.201 Dalian Road, Huichuan District, Zunyi, Guizhou, 563003, China
| | - Jian Liang
- School of Resources and Environment, ABA Normal University, Shuimo Town, Wenchuan County, Aba Prefecture, Sichuan, 623002, China
| | - Di-Shu Ao
- College of Basic Medicine, Zunyi Medical University, No.201 Dalian Road, Huichuan District, Zunyi, Guizhou, 563003, China
| | - Huan Wang
- College of Basic Medicine, Zunyi Medical University, No.201 Dalian Road, Huichuan District, Zunyi, Guizhou, 563003, China
| | - Ze-Hong Yang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No.17 People's South Road, Chengdu, Sichuan, 610041, China.
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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] [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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Zottig X, Côté-Cyr M, Arpin D, Archambault D, Bourgault S. Protein Supramolecular Structures: From Self-Assembly to Nanovaccine Design. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E1008. [PMID: 32466176 PMCID: PMC7281494 DOI: 10.3390/nano10051008] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 12/19/2022]
Abstract
Life-inspired protein supramolecular assemblies have recently attracted considerable attention for the development of next-generation vaccines to fight against infectious diseases, as well as autoimmune diseases and cancer. Protein self-assembly enables atomic scale precision over the final architecture, with a remarkable diversity of structures and functionalities. Self-assembling protein nanovaccines are associated with numerous advantages, including biocompatibility, stability, molecular specificity and multivalency. Owing to their nanoscale size, proteinaceous nature, symmetrical organization and repetitive antigen display, protein assemblies closely mimic most invading pathogens, serving as danger signals for the immune system. Elucidating how the structural and physicochemical properties of the assemblies modulate the potency and the polarization of the immune responses is critical for bottom-up design of vaccines. In this context, this review briefly covers the fundamentals of supramolecular interactions involved in protein self-assembly and presents the strategies to design and functionalize these assemblies. Examples of advanced nanovaccines are presented, and properties of protein supramolecular structures enabling modulation of the immune responses are discussed. Combining the understanding of the self-assembly process at the molecular level with knowledge regarding the activation of the innate and adaptive immune responses will support the design of safe and effective nanovaccines.
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Affiliation(s)
- Ximena Zottig
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC H2L 2C4, Canada; (X.Z.); (M.C.-C.); (D.A.)
- The Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Quebec, QC G1V 0A6, Canada
- The Swine and Poultry Infectious Diseases Research Centre, CRIPA, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Mélanie Côté-Cyr
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC H2L 2C4, Canada; (X.Z.); (M.C.-C.); (D.A.)
- The Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Quebec, QC G1V 0A6, Canada
- The Swine and Poultry Infectious Diseases Research Centre, CRIPA, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Dominic Arpin
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC H2L 2C4, Canada; (X.Z.); (M.C.-C.); (D.A.)
- The Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Quebec, QC G1V 0A6, Canada
- The Swine and Poultry Infectious Diseases Research Centre, CRIPA, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Denis Archambault
- The Swine and Poultry Infectious Diseases Research Centre, CRIPA, Saint-Hyacinthe, QC J2S 2M2, Canada
- Department of Biological Sciences, Université du Québec à Montréal, Montreal, QC H2L 2C4, Canada
| | - Steve Bourgault
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC H2L 2C4, Canada; (X.Z.); (M.C.-C.); (D.A.)
- The Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Quebec, QC G1V 0A6, Canada
- The Swine and Poultry Infectious Diseases Research Centre, CRIPA, Saint-Hyacinthe, QC J2S 2M2, Canada
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Weber R, McCullagh M. The Role of Hydrophobicity in the Stability and pH-Switchability of (RXDX) 4 and Coumarin-(RXDX) 4 Conjugate β-Sheets. J Phys Chem B 2020; 124:1723-1732. [PMID: 32045245 DOI: 10.1021/acs.jpcb.0c00048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
pH-Switchable, self-assembling materials are of interest in biological imaging and sensing applications. Here we propose that combining the pH-switchability of RXDX (X = Ala, Val, Leu, Ile, Phe) peptides and the optical properties of coumarin creates an ideal candidate for these materials. This suggestion is tested with a thorough set of all-atom molecular dynamics simulations. We first investigate the dependence of pH-switchabiliy on the identity of the hydrophobic residue, X, in the bare (RXDX)4 systems. Increasing the hydrophobicity stabilizes the fiber which, in turn, reduces the pH-switchabilty of the system. This behavior is found to be somewhat transferable to systems in which a single hydrophobic residue is replaced with a coumarin containing amino acid. In this case, conjugates with X = Ala are found to be unstable at both pHs, while conjugates with X = Val, Leu, Ile, and Phe are found to form stable β-sheets at least at neutral pH. The coumarin-(RFDF)4 conjugate is found to have the largest relative entropy value of 0.884 ± 0.001 between neutral and acidic coumarin ordering distributions. Thus, we posit that coumarin-(RFDF)4 containing peptide sequences are ideal candidates for pH-sensing bioelectronic materials.
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Affiliation(s)
- Ryan Weber
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74074, United States
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42
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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] [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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43
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Jakubowski J, Orr AA, Le DA, Tamamis P. Interactions between Curcumin Derivatives and Amyloid-β Fibrils: Insights from Molecular Dynamics Simulations. J Chem Inf Model 2020; 60:289-305. [PMID: 31809572 PMCID: PMC7732148 DOI: 10.1021/acs.jcim.9b00561] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Indexed: 12/24/2022]
Abstract
The aggregation of amyloid-β (Aβ) peptides into senile plaques is a hallmark of Alzheimer's disease (AD) and is hypothesized to be the primary cause of AD related neurodegeneration. Previous studies have shown the ability of curcumin to both inhibit the aggregation of Aβ peptides into oligomers or fibrils and reduce amyloids in vivo. Despite the promise of curcumin and its derivatives to serve as diagnostic, preventative, and potentially therapeutic AD molecules, the mechanism by which curcumin and its derivatives bind to and inhibit Aβ fibrils' formation remains elusive. Here, we investigated curcumin and a set of curcumin derivatives in complex with a hexamer peptide model of the Aβ1-42 fibril using nearly exhaustive docking, followed by multi-ns molecular dynamics simulations, to provide atomistic-detail insights into the molecules' binding and inhibitory properties. In the vast majority of the simulations, curcumin and its derivatives remain firmly bound in complex with the fibril through primarily three different principle binding modes, in which the molecules interact with residue domain 17LVFFA21, in line with previous experiments. In a small subset of these simulations, the molecules partly dissociate the outermost peptide of the Aβ1-42 fibril by disrupting β-sheets within the residue domain 12VHHQKLVFF20. A comparison between binding modes leading or not leading to partial dissociation of the outermost peptide suggests that the latter is attributed to a few subtle key structural and energetic interaction-based differences. Interestingly, partial dissociation appears to be either an outcome of high affinity interactions or a cause leading to high affinity interactions between the molecules and the fibril, which could partly serve as a compensation for the energy loss in the fibril due to partial dissociation. In conjunction with this, we suggest a potential inhibition mechanism of Αβ1-42 aggregation by the molecules, where the partially dissociated 16KLVFF20 domain of the outermost peptide could either remain unstructured or wrap around to form intramolecular interactions with the same peptide's 29GAIIG33 domain, while the molecules could additionally act as a patch against the external edge of the second outermost peptide's 16KLVFF20 domain. Thereby, individually or concurrently, these could prohibit fibril elongation.
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Affiliation(s)
| | | | - Doan A. Le
- Artie McFerrin Department
of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Phanourios Tamamis
- Artie McFerrin Department
of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
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44
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The use of bioactive matrices in regenerative therapies for traumatic brain injury. Acta Biomater 2020; 102:1-12. [PMID: 31751809 DOI: 10.1016/j.actbio.2019.11.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/22/2019] [Accepted: 11/13/2019] [Indexed: 01/01/2023]
Abstract
Functional deficits due to neuronal loss are a common theme across multiple neuropathologies, including traumatic brain injury (TBI). Apart from mitigating cell death, another approach to treating brain injuries involves re-establishing the neural circuitry at the lesion site by utilizing exogeneous and/or endogenous stem cells to achieve functional recovery. While there has been limited success, the emergence of new bioactive matrices that promote neural repair introduces new perspectives on the development of regenerative therapies for TBI. This review briefly discusses current development on cell-based therapies and the use of bioactive matrices, hydrogels in particular, when incorporated in regenerative therapies. Desirable characteristics of bioactive matrices that have been shown to augment neural repair in TBI models were identified and further discussed. Understanding the relative outcomes of newly developed biomaterials implanted in vivo can better guide the development of biomaterials as a therapeutic strategy, for biomaterial-based cellular therapies are still in their nascent stages. Nonetheless, the value of bioactive matrices as a treatment for acute brain injuries should be appreciated and further developed. STATEMENT OF SIGNIFICANCE: Cell-based therapies have received attention as an alternative therapeutic strategy to improve clinical outcome post-traumatic brain injury but have achieved limited success. Whilst the incorporation of newly developed biomaterials in regenerative therapies has shown promise in augmenting neural repair, studies have revealed new hurdles which must be overcome to improve their therapeutic efficacy. This review discusses the recent development of cell-based therapies with a specific focus on the use of bioactive matrices in the form of hydrogels, to complement cell transplantation within the injured brain. Moreover, this review consolidates in vivo animal studies that demonstrate relative functional outcome upon the implantation of different biomaterials to highlight their desirable traits to guide their development for regenerative therapies in traumatic brain injury.
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45
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Lord J, Britton H, Spain SG, Lewis AL. Advancements in the development on new liquid embolic agents for use in therapeutic embolisation. J Mater Chem B 2020; 8:8207-8218. [DOI: 10.1039/d0tb01576h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This review covers the current state-of-the-art in the development of liquid embolics for therapeutic embolisation.
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Affiliation(s)
- Jasmine Lord
- Department of Chemistry
- University of Sheffield
- Sheffield
- UK
| | - Hugh Britton
- Biocompatibles UK Ltd (a BTG International group company)
- Lakeview
- Camberley
- UK
| | | | - Andrew L. Lewis
- Biocompatibles UK Ltd (a BTG International group company)
- Lakeview
- Camberley
- UK
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46
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Crowet JM, Sinnaeve D, Fehér K, Laurin Y, Deleu M, Martins JC, Lins L. Molecular Model for the Self-Assembly of the Cyclic Lipodepsipeptide Pseudodesmin A. J Phys Chem B 2019; 123:8916-8922. [PMID: 31558021 DOI: 10.1021/acs.jpcb.9b08035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Self-assembly of peptides into supramolecular structures represents an active field of research with potential applications ranging from material science to medicine. Their study typically involves the application of a large toolbox of spectroscopic and imaging techniques. However, quite often, the structural aspects remain underexposed. Besides, molecular modeling of the self-assembly process is usually difficult to handle, since a vast conformational space has to be sampled. Here, we have used an approach that combines short molecular dynamics simulations for peptide dimerization and NMR restraints to build a model of the supramolecular structure from the dimeric units. Experimental NMR data notably provide crucial information about the conformation of the monomeric units, the supramolecular assembly dimensions, and the orientation of the individual peptides within the assembly. This in silico/in vitro mixed approach enables us to define accurate atomistic models of supramolecular structures of the bacterial cyclic lipodepsipeptide pseudodesmin A.
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Affiliation(s)
- Jean-Marc Crowet
- Laboratory of Molecular Biophysics at Interfaces, TERRA Research Center, Gembloux Agro-Bio Tech , University of Liège , Passage des déportés 2 , B-5030 Gembloux , Belgium
| | - Davy Sinnaeve
- CNRS-Unité de Glycobiologie structurale et fonctionnelle (UGSF) UMR 8576 , 50, Avenue de Halley, Campus CNRS de la Haute Borne , 59658 Villeneuve d'Ascq , France
| | - Krisztina Fehér
- Heidelberg Institute for Theoretical Studies , Schloss-Wolfsbrunnenweg 35 , 69118 Heidelberg , Germany
| | - Yoann Laurin
- Laboratory of Molecular Biophysics at Interfaces, TERRA Research Center, Gembloux Agro-Bio Tech , University of Liège , Passage des déportés 2 , B-5030 Gembloux , Belgium
| | - Magali Deleu
- Laboratory of Molecular Biophysics at Interfaces, TERRA Research Center, Gembloux Agro-Bio Tech , University of Liège , Passage des déportés 2 , B-5030 Gembloux , Belgium
| | - José C Martins
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry , Ghent University , Krijgslaan 281 S4 , B-9000 Gent , Belgium
| | - Laurence Lins
- Laboratory of Molecular Biophysics at Interfaces, TERRA Research Center, Gembloux Agro-Bio Tech , University of Liège , Passage des déportés 2 , B-5030 Gembloux , Belgium
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47
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Sis MJ, Webber MJ. Drug Delivery with Designed Peptide Assemblies. Trends Pharmacol Sci 2019; 40:747-762. [DOI: 10.1016/j.tips.2019.08.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/07/2019] [Accepted: 08/08/2019] [Indexed: 12/18/2022]
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48
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Chen W, Yang S, Li S, Lang JC, Mao C, Kroll P, Tang L, Dong H. Self-Assembled Peptide Nanofibers Display Natural Antimicrobial Peptides to Selectively Kill Bacteria without Compromising Cytocompatibility. ACS APPLIED MATERIALS & INTERFACES 2019; 11:28681-28689. [PMID: 31328913 DOI: 10.1021/acsami.9b09583] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
One of the major hurdles in the development of antimicrobial peptide (AMP)-based materials is their poor capacity in selectively killing bacteria without harming nearby mammalian cells. Namely, they are antimicrobial but cytotoxic. Current methods of nanoparticle-encapsulated AMPs to target bacteria selectively still have not yet overcome this hurdle. Here, we demonstrate a simple yet effective method to address this daunting challenge by associating a natural AMP with a β-sheet-forming synthetic peptide. The integrated peptides self-assembled to form a supramolecular nanofiber, resulting in the presentation of the AMP at the nanofiber-solvent interface in a precisely controlled manner. Using melittin as a model natural AMP, we found that the conformation of melittin changed dramatically when presented on the nanofiber surface, which, in turn, modulated the induced membrane permeability of the bacterial and mammalian cell membranes. Specifically, the presentation of melittin on the nanofiber restricted its hydrophobic residues, leading to a reduction of the hydrophobic interaction with lipids in the cell membranes. Compellingly, the reduced hydrophobic interaction led to a considerable decrease of melittin's induced permeability of the mammalian cell membrane than that of the bacterial cell membrane. As a result, the AMP-displaying nanofiber preferentially permeabilized and disrupted the membrane of the bacteria without compromising the mammalian cells. Such improved membrane selectivity and cytocompatibility were confirmed in a cell-based membrane localization and live-dead assay. Our new strategy holds great promise for fabricating cytocompatible antimicrobial assemblies that offer safer and more effective administration of therapeutic AMPs. These assemblies, with intrinsic antimicrobial activity and cytocompatibility, can also serve as building blocks for the construction of higher-ordered scaffolds for other biomedical applications such as tissue engineering and regenerative medicine.
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Affiliation(s)
| | | | | | | | - Chuanbin Mao
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center , University of Oklahoma , Norman , Oklahoma 73019 , United States
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49
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Hughes SA, Wang F, Wang S, Kreutzberger MAB, Osinski T, Orlova A, Wall JS, Zuo X, Egelman EH, Conticello VP. Ambidextrous helical nanotubes from self-assembly of designed helical hairpin motifs. Proc Natl Acad Sci U S A 2019; 116:14456-14464. [PMID: 31262809 PMCID: PMC6642399 DOI: 10.1073/pnas.1903910116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tandem repeat proteins exhibit native designability and represent potentially useful scaffolds for the construction of synthetic biomimetic assemblies. We have designed 2 synthetic peptides, HEAT_R1 and LRV_M3Δ1, based on the consensus sequences of single repeats of thermophilic HEAT (PBS_HEAT) and Leucine-Rich Variant (LRV) structural motifs, respectively. Self-assembly of the peptides afforded high-aspect ratio helical nanotubes. Cryo-electron microscopy with direct electron detection was employed to analyze the structures of the solvated filaments. The 3D reconstructions from the cryo-EM maps led to atomic models for the HEAT_R1 and LRV_M3Δ1 filaments at resolutions of 6.0 and 4.4 Å, respectively. Surprisingly, despite sequence similarity at the lateral packing interface, HEAT_R1 and LRV_M3Δ1 filaments adopt the opposite helical hand and differ significantly in helical geometry, while retaining a local conformation similar to previously characterized repeat proteins of the same class. The differences in the 2 filaments could be rationalized on the basis of differences in cohesive interactions at the lateral and axial interfaces. These structural data reinforce previous observations regarding the structural plasticity of helical protein assemblies and the need for high-resolution structural analysis. Despite these observations, the native designability of tandem repeat proteins offers the opportunity to engineer novel helical nanotubes. Moreover, the resultant nanotubes have independently addressable and chemically distinguishable interior and exterior surfaces that would facilitate applications in selective recognition, transport, and release.
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Affiliation(s)
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Shengyuan Wang
- Department of Chemistry, Emory University, Atlanta, GA 30322
| | - Mark A B Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Tomasz Osinski
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Albina Orlova
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Joseph S Wall
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973
| | - Xiaobing Zuo
- X-Ray Science Division, Argonne National Laboratory, Argonne, IL 60439
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
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50
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Sato K. Self-assembling Peptides and Their Applications in Regenerative Medicine. J SYN ORG CHEM JPN 2019. [DOI: 10.5059/yukigoseikyokaishi.77.716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kohei Sato
- Department of Life Science and Technology, Tokyo Institute of Technology
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