1
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Mohanta I, Sahu N, Guchhait C, Kaur L, Mandal D, Adhikari B. Ag +-Induced Supramolecular Polymers of Folic Acid: Reinforced by External Kosmotropic Anions Exhibiting Salting Out. Biomacromolecules 2024; 25:6203-6215. [PMID: 39153217 DOI: 10.1021/acs.biomac.4c01063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2024]
Abstract
Introducing kosmotropic salts enhances protein stability and reduces solubility by withdrawing water from the protein surface, leading to 'salting out', a phenomenon we have mimicked in supramolecular polymers (SPs). Under the guidance of Ag+, folic acid (FA) self-assembled in water through slipped-stacking and hydrophobic interactions into elongated, robust one-dimensional SPs, resulting in thermo-stable supergels. The SPs exhibited temperature and dilution tolerance, attributed to the stability of the FA-Ag+ complex and its hydrophobic stacking. Importantly, FA-Ag+ SP's stability has been augmented by the kosmotropic anions, such as SO42-, strengthening hydrophobic interactions in the SP, evident from the enhanced J-band, causing improvement of gel's mechanical property. Interestingly, higher kosmotrope concentrations caused a significant decrease in SP's solubility, leading to precipitation of the reinforced SPs─a 'salting out' effect. Conversely, chaotropes like ClO4- slightly destabilized hydrophobic stacking and promoted an extended conformation of individual SP chain with enhanced solubility, resembling a 'salting in' effect.
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Affiliation(s)
- Indrajit Mohanta
- Department of Chemistry, National Institute of Technology Rourkela, Rourkela, Odisha 769008, India
| | - Nihar Sahu
- Department of Chemistry, National Institute of Technology Rourkela, Rourkela, Odisha 769008, India
| | - Chandrakanta Guchhait
- Department of Chemistry, National Institute of Technology Rourkela, Rourkela, Odisha 769008, India
| | - Lovleen Kaur
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala, Punjab 147004, India
| | - Debasish Mandal
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala, Punjab 147004, India
| | - Bimalendu Adhikari
- Department of Chemistry, National Institute of Technology Rourkela, Rourkela, Odisha 769008, India
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2
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Teng T, Bernal‐Chanchavac J, Stephanopoulos N, Castro CE. Construction of Reconfigurable and Polymorphic DNA Origami Assemblies with Coiled-Coil Patches and Patterns. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307257. [PMID: 38459678 PMCID: PMC11132032 DOI: 10.1002/advs.202307257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/22/2023] [Indexed: 03/10/2024]
Abstract
DNA origami nanodevices achieve programmable structure and tunable mechanical and dynamic properties by leveraging the sequence-specific interactions of nucleic acids. Previous advances have also established DNA origami as a useful building block to make well-defined micron-scale structures through hierarchical self-assembly, but these efforts have largely leveraged the structural features of DNA origami. The tunable dynamic and mechanical properties also provide an opportunity to make assemblies with adaptive structures and properties. Here the integration of DNA origami hinge nanodevices and coiled-coil peptides are reported into hybrid reconfigurable assemblies. With the same dynamic device and peptide interaction, it is made multiple higher-order assemblies (i.e., polymorphic assembly) by organizing clusters of peptides into patches or arranging single peptides into patterns on the surfaces of DNA origami to control the relative orientation of devices. The coiled-coil interactions are used to construct circular and linear assemblies whose structure and mechanical properties can be modulated with DNA-based reconfiguration. Reconfiguration of linear assemblies leads to micron scale motions and ≈2.5-10-fold increase in bending stiffness. The results provide a foundation for stimulus-responsive hybrid assemblies that can adapt their structure and properties in response to nucleic acid, peptide, protein, or other triggers.
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Affiliation(s)
- Teng Teng
- Department of Mechanical and Aerospace EngineeringThe Ohio State UniversityColumbusOH43210USA
| | - Julio Bernal‐Chanchavac
- School of Molecular SciencesArizona State UniversityTempeAZ85287USA
- Center for Molecular Design and BiomimeticsThe Biodesign Institute, Arizona State UniversityTempeAZ85287USA
| | - Nicholas Stephanopoulos
- School of Molecular SciencesArizona State UniversityTempeAZ85287USA
- Center for Molecular Design and BiomimeticsThe Biodesign Institute, Arizona State UniversityTempeAZ85287USA
| | - Carlos E. Castro
- Department of Mechanical and Aerospace EngineeringThe Ohio State UniversityColumbusOH43210USA
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3
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Roy S, Chaturvedi A, Dey S, Puneeth Kumar DRGKR, Pahan S, Panda Mahapatra S, Mandal P, Gopi HN. Anion Tuned Structural Modulation and Nonlinear Optical Effects of Metal-Ion Directed 3 10 -Helix Networks. Chemistry 2023; 29:e202303135. [PMID: 37867145 DOI: 10.1002/chem.202303135] [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: 09/26/2023] [Revised: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 10/24/2023]
Abstract
Metals play an important role in the structure and functions of various proteins. The combination of metal ions and peptides have been emerging as an attractive field to create advanced structures and biomaterials. Here, we are reporting the anion-influenced, silver ion coordinated diverse networks of designed short tripeptide 310 -helices with terminal pyridyl groups. The short peptides adopted classical right-handed, left-handed and 310 EL -helical conformations in the presence of different silver salts. The peptides have displayed conformational flexibility to accommodate different sizes and interactions of anions to yield a variety of metal-coordinated networks. The complexes of metal ions and peptides have shown different porous networks, right- and left-handed helical polymers, transformation of helix into superhelix and 2 : 2 metal-peptide macrocycles. Further, the metal-peptide crystals with inherent dipoles of helical peptides gave striking second harmonic generation response. The optical energy upconversion from NIR to red and green light is demonstrated. Overall, we have shown the utilization of short 310 -helices for the construction of diverse metal-coordinated helical networks and notable non-linear optical effects.
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Affiliation(s)
- Souvik Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - Aman Chaturvedi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - Sanjit Dey
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - DRGKoppalu R Puneeth Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - Saikat Pahan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - Souvik Panda Mahapatra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - Pankaj Mandal
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - Hosahudya N Gopi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
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4
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Teng T, Bernal-Chanchavac J, Stephanopoulos N, Castro CE. Construction and reconfiguration of dynamic DNA origami assemblies with coiled-coil patches and patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.23.559112. [PMID: 37790447 PMCID: PMC10542533 DOI: 10.1101/2023.09.23.559112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
DNA origami nanodevices achieve programmable structure and tunable mechanical and dynamic properties by leveraging the sequence specific interactions of nucleic acids. Previous advances have also established DNA origami as a useful building block to make well-defined micron-scale structures through hierarchical self-assembly, but these efforts have largely leveraged the structural features of DNA origami. The tunable dynamic and mechanical properties also provide an opportunity to make assemblies with adaptive structure and properties. Here we report the integration of DNA origami hinge nanodevices and coiled-coil peptides into hybrid reconfigurable assemblies. With the same dynamic device and peptide interaction, we make multiple higher order assemblies by organizing clusters of peptides (i.e. patches) or arranging single peptides (i.e. patterns) on the surfaces of DNA origami to control the relative orientation of devices. We use coiled-coil interactions to construct circular and linear assemblies whose structure and mechanical properties can be modulated with DNA-based actuation. Actuation of linear assemblies leads to micron scale motions and ~2.5-10-fold increase in bending stiffness. Our results provide a foundation for stimulus responsive hybrid assemblies that can adapt their structure and properties in response to nucleic acid, peptide, protein, or other triggers.
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Affiliation(s)
- T Teng
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, United States
| | - J Bernal-Chanchavac
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - N Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - C E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, United States
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5
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Guo P, Wang D, Zhang S, Cheng D, Wu S, Zuo X, Jiang YB, Jiang T. Reassembly of Peptide Nanofibrils on Live Cell Surfaces Promotes Cell-Cell Interactions. NANO LETTERS 2023. [PMID: 37399537 DOI: 10.1021/acs.nanolett.3c01100] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Nature regulates cellular interactions through the cell-surface molecules and plasma membranes. Despite advances in cell-surface engineering with diverse ligands and reactive groups, modulating cell-cell interactions through scaffolds of the cell-binding cues remains a challenging endeavor. Here, we assembled peptide nanofibrils on live cell surfaces to present the ligands that bind to the target cells. Surprisingly, with the same ligands, reducing the thermal stability of the nanofibrils promoted cellular interactions. Characterizations of the system revealed a thermally induced fibril disassembly and reassembly pathway that facilitated the complexation of the fibrils with the cells. Using the nanofibrils of varied stabilities, the cell-cell interaction was promoted to different extents with free-to-bound cell conversion ratios achieved at low (31%), medium (54%), and high (93%) levels. This study expands the toolbox to generate desired cell behaviors for applications in many areas and highlights the merits of thermally less stable nanoassemblies in designing functional materials.
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Affiliation(s)
- Pan Guo
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China
| | - Di Wang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China
| | - Shumin Zhang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China
| | - Dan Cheng
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China
| | - Siyu Wu
- X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Yun-Bao Jiang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Tao Jiang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
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6
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Patkar SS, Tang Y, Bisram AM, Zhang T, Saven JG, Pochan DJ, Kiick KL. Genetic Fusion of Thermoresponsive Polypeptides with UCST-type Behavior Mediates 1D Assembly of Coiled-Coil Bundlemers. Angew Chem Int Ed Engl 2023; 62:e202301331. [PMID: 36988077 DOI: 10.1002/anie.202301331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/25/2023] [Accepted: 03/28/2023] [Indexed: 03/30/2023]
Abstract
Thermoresponsive resilin-like polypeptides (RLPs) of various lengths were genetically fused to two different computationally designed coiled coil-forming peptides with distinct thermal stability, to develop new strategies to assemble coiled coil peptides via temperature-triggered phase separation of the RLP units. Their successful production in bacterial expression hosts was verified via gel electrophoresis, mass spectrometry, and amino acid analysis. Circular dichroism (CD) spectroscopy, ultraviolet-visible (UV/Vis) turbidimetry, and dynamic light scattering (DLS) measurements confirmed the stability of the coiled coils and showed that the thermosensitive phase behavior of the RLPs was preserved in the genetically fused hybrid polypeptides. Cryogenic-transmission electron microscopy and coarse-grained modeling revealed that functionalizing the coiled coils with thermoresponsive RLPs leads to their thermally triggered noncovalent assembly into nanofibrillar assemblies.
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Affiliation(s)
- Sai S Patkar
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA
| | - Yao Tang
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA
| | - Arriana M Bisram
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA
| | - Tianren Zhang
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA
| | - Kristi L Kiick
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA
- Department of Biomedical Engineering, University of Delaware, Newark, DE 19716, USA
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7
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Crone NSA, van Hilten N, van der Ham A, Risselada HJ, Kros A, Boyle AL. Azobenzene-Based Amino Acids for the Photocontrol of Coiled-Coil Peptides. Bioconjug Chem 2023; 34:345-357. [PMID: 36705971 PMCID: PMC9936496 DOI: 10.1021/acs.bioconjchem.2c00534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Coiled-coil peptides are high-affinity, selective, self-assembling binding motifs, making them attractive components for the preparation of functional biomaterials. Photocontrol of coiled-coil self-assembly allows for the precise localization of their activity. To rationally explore photoactivity in a model coiled coil, three azobenzene-containing amino acids were prepared and substituted into the hydrophobic core of the E3/K3 coiled-coil heterodimer. Two of the non-natural amino acids, APhe1 and APhe2, are based on phenylalanine and differ in the presence of a carboxylic acid group. These have previously been demonstrated to modulate protein activity. When incorporated into peptide K3, coiled-coil binding strength was affected upon isomerization, with the two variants differing in their most folded state. The third azobenzene-containing amino acid, APgly, is based on phenylglycine and was prepared to investigate the effect of amino acid size on photoisomerization. When APgly is incorporated into the coiled coil, a 4.7-fold decrease in folding constant is observed upon trans-to-cis isomerization─the largest difference for all three amino acids. Omitting the methylene group between azobenzene and α-carbon was theorized to both position the diazene of APgly closer to the hydrophobic amino acids and reduce the possible rotations of the amino acid, with molecular dynamics simulations supporting these hypotheses. These results demonstrate the ability of photoswitchable amino acids to control coiled-coil assembly through disruption of the hydrophobic interface, a strategy that should be widely applicable.
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Affiliation(s)
- Niek S A Crone
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| | - Niek van Hilten
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| | - Alex van der Ham
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| | - Herre Jelger Risselada
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| | - Alexander Kros
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| | - Aimee L Boyle
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
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8
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Bajpayee N, Vijayakanth T, Rencus-Lazar S, Dasgupta S, Desai AV, Jain R, Gazit E, Misra R. Exploring Helical Peptides and Foldamers for the Design of Metal Helix Frameworks: Current Trends and Future Perspectives. Angew Chem Int Ed Engl 2023; 62:e202214583. [PMID: 36434750 DOI: 10.1002/anie.202214583] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 11/27/2022]
Abstract
Flexible and biocompatible metal peptide frameworks (MPFs) derived from short and ultra-short peptides have been explored for the storage of greenhouse gases, molecular recognition, and chiral transformations. In addition to short flexible peptides, peptides with specifically folded conformations have recently been utilized to fabricate a variety of metal helix frameworks (MHFs). The secondary structures of the peptides govern the structure-assembly relationship and thereby control the formation of three-dimensional (3D)-MHFs. Particularly, the hierarchical structural organization of peptide-based MHFs has not yet been discussed in detail. Here, we describe the recent progress of metal-driven folded peptide assembly to construct 3D porous structures for use in future energy storage, chiral recognition, and biomedical applications, which could be envisioned as an alternative to the conventional metal-organic frameworks (MOFs).
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Affiliation(s)
- Nikhil Bajpayee
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Mohali, S.A.S. Nagar, Mohali, 160062, India.,Department of Materials Science and Engineering, Tel-Aviv University, 6997801, Tel-Aviv, Israel
| | - Thangavel Vijayakanth
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 6997801, Tel-Aviv, Israel
| | - Sigal Rencus-Lazar
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 6997801, Tel-Aviv, Israel
| | - Sneha Dasgupta
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Mohali, S.A.S. Nagar, Mohali, 160062, India.,Department of Materials Science and Engineering, Tel-Aviv University, 6997801, Tel-Aviv, Israel
| | - Aamod V Desai
- School of Chemistry, University of St Andrews North Haugh, St Andrews, KY16 9ST, UK
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Mohali, S.A.S. Nagar, Mohali, 160062, India.,Department of Materials Science and Engineering, Tel-Aviv University, 6997801, Tel-Aviv, Israel
| | - Ehud Gazit
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 6997801, Tel-Aviv, Israel
| | - Rajkumar Misra
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Mohali, S.A.S. Nagar, Mohali, 160062, India.,Department of Materials Science and Engineering, Tel-Aviv University, 6997801, Tel-Aviv, Israel
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9
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Jorgensen MD, Chmielewski J. Recent advances in coiled-coil peptide materials and their biomedical applications. Chem Commun (Camb) 2022; 58:11625-11636. [PMID: 36172799 DOI: 10.1039/d2cc04434j] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extensive research has gone into deciphering the sequence requirements for peptides to fold into coiled-coils of varying oligomeric states. More recently, additional signals have been introduced within coiled-coils to promote higher order assembly into biomaterials with a rich distribution of morphologies. Herein we describe these strategies for association of coiled-coil building blocks and biomedical applications. With many of the systems described herein having proven use in protein storage, cargo binding and delivery, three dimensional cell culturing and vaccine development, the future potential of coiled-coil materials to have significant biomedical impact is highly promising.
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Affiliation(s)
- Michael D Jorgensen
- Purdue University, Department of Chemistry, 560 Oval Drive, West Lafayette, Indiana, USA.
| | - Jean Chmielewski
- Purdue University, Department of Chemistry, 560 Oval Drive, West Lafayette, Indiana, USA.
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10
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Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022; 122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.
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Affiliation(s)
- Rui Qing
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shilei Hao
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Eva Smorodina
- Department
of Immunology, University of Oslo and Oslo
University Hospital, Oslo 0424, Norway
| | - David Jin
- Avalon GloboCare
Corp., Freehold, New Jersey 07728, United States
| | - Arthur Zalevsky
- Laboratory
of Bioinformatics Approaches in Combinatorial Chemistry and Biology, Shemyakin−Ovchinnikov Institute of Bioorganic
Chemistry RAS, Moscow 117997, Russia
| | - Shuguang Zhang
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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11
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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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12
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Duan H, Yin L, Chen T, Qi D, Zhang D. A “metal ions-induced poisoning behavior of biomolecules” inspired polymeric probe for Cu2+ selective detection on basis of coil to helix conformation transition. Eur Polym J 2022. [DOI: 10.1016/j.eurpolymj.2022.111070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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13
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Shi L, Kuang D, Ma X, Jalalah M, Alsareii SA, Gao T, Harraz FA, Yang J, Li G. Peptide Assembled in a Nano-confined Space as a Molecular Rectifier for the Availability of Ionic Current Modulation. NANO LETTERS 2022; 22:1083-1090. [PMID: 35049303 DOI: 10.1021/acs.nanolett.1c04154] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Bioinspired nanochannels have emerged as a powerful tool for bioengineering and biomedical research due to their robust mechanical and controllable chemical properties. Inspired by inward-rectifier potassium (K+) channels, herein, the charged peptide assembly has been introduced into a nano-confined space for the modulation of ion current rectification (ICR). Peptide-responsive reaction-triggered sequence changes can contribute to polarity conversion of the surface charge; therefore, ICR reversal (ICRR) is generated. Compared with other responsive elements, natural charged peptides show the merit of controllable charge polarity. By electrochemically monitoring the ICRR as an output signal, one can utilize the peptide assembly-mediated ICRR to construct an ionic sensory platform. In addition, a logic gate has been established to demonstrate the availability of an ionic sensory platform for inhibitor screening. As peptide nanoassemblies may also have various structures and functions due to their diverse properties, the ionic modulation system can provide alternatives for the assay of peptide-associated biotargets with biomedical applications.
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Affiliation(s)
- Liu Shi
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Deqi Kuang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Xuemei Ma
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Mohammed Jalalah
- Promising Centre for Sensors and Electronic Devices (PCSED), Advanced Materials and Nano-Research Centre, Najran University, Najran 11001, Saudi Arabia
- Department of Electrical Engineering, Faculty of Engineering, Najran University, Najran 11001, Saudi Arabia
| | - Saeed A Alsareii
- Promising Centre for Sensors and Electronic Devices (PCSED), Advanced Materials and Nano-Research Centre, Najran University, Najran 11001, Saudi Arabia
- Department of Surgery, College of Medicine, Najran University, Najran 11001, Saudi Arabia
| | - Tao Gao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Farid A Harraz
- Promising Centre for Sensors and Electronic Devices (PCSED), Advanced Materials and Nano-Research Centre, Najran University, Najran 11001, Saudi Arabia
- Nanomaterials and Nanotechnology Department, Central Metallurgical Research and Development Institute (CMRDI), Cairo 11421, Egypt
| | - Jie Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Genxi Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
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14
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Ma X, Zhao Y, He C, Zhou X, Qi H, Wang Y, Chen C, Wang D, Li J, Ke Y, Wang J, Xu H. Ordered Packing of β-Sheet Nanofibrils into Nanotubes: Multi-hierarchical Assembly of Designed Short Peptides. NANO LETTERS 2021; 21:10199-10207. [PMID: 34870987 DOI: 10.1021/acs.nanolett.1c02944] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Although it is well-known proteins and their complexes are hierarchically organized and highly ordered structures, it remains a major challenge to replicate their hierarchical self-assembly process and to fabricate multihierarchical architectures with well-defined shapes and monodisperse characteristic sizes via peptide self-assembly. Here we describe an amphiphilic short peptide Ac-I3GGHK-NH2 that first preassembles into thin, left-handed β-sheet nanofibrils, followed by their ordered packing into right-handed nanotubes. The key intermediate morphology and structures featuring the hierarchical process are simultaneously demonstrated. Further mechanistic exploration with the variants Ac-I3GGGK-NH2, Ac-I3GGFK-NH2, and Ac-I3GGDHDK-NH2 reveals the vital role of multiple His-His side chain interactions between nanofibrils in mediating higher-order assembly and architectures. Altogether, our findings not only advance current understanding of hierarchical assembly of peptides and proteins but also afford a paradigm of how to take advantage of side chain interactions to construct higher-order assemblies with enhanced complexities.
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Affiliation(s)
- Xiaoyue Ma
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Yurong Zhao
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Chunyong He
- Spallation Neutron Source Science Center, Dalang, Dongguan 523803, China
- Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Xing Zhou
- Qingdao West Coast New Area Marine Development Bureau, 59 Shuilingshan Road, Qingdao 266400, China
| | - Hao Qi
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Yan Wang
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Cuixia Chen
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Dong Wang
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Jie Li
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Yubin Ke
- Spallation Neutron Source Science Center, Dalang, Dongguan 523803, China
- Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Jiqian Wang
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
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15
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Sinha NJ, Langenstein MG, Pochan DJ, Kloxin CJ, Saven JG. Peptide Design and Self-assembly into Targeted Nanostructure and Functional Materials. Chem Rev 2021; 121:13915-13935. [PMID: 34709798 DOI: 10.1021/acs.chemrev.1c00712] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptides have been extensively utilized to construct nanomaterials that display targeted structure through hierarchical assembly. The self-assembly of both rationally designed peptides derived from naturally occurring domains in proteins as well as intuitively or computationally designed peptides that form β-sheets and helical secondary structures have been widely successful in constructing nanoscale morphologies with well-defined 1-d, 2-d, and 3-d architectures. In this review, we discuss these successes of peptide self-assembly, especially in the context of designing hierarchical materials. In particular, we emphasize the differences in the level of peptide design as an indicator of complexity within the targeted self-assembled materials and highlight future avenues for scientific and technological advances in this field.
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Affiliation(s)
- Nairiti J Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Matthew G Langenstein
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Christopher J Kloxin
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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16
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Zhang HN, Yu WB, Lin YJ, Jin GX. Stimuli-Responsive Topological Transformation of a Molecular Borromean Ring via Controlled Oxidation of Thioether Moieties. Angew Chem Int Ed Engl 2021; 60:15466-15471. [PMID: 33871131 DOI: 10.1002/anie.202103264] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Indexed: 01/31/2023]
Abstract
A Cp*-Rh based D-shaped binuclear metallacycle and a template-free molecular Borromean ring (BR) were obtained in high yield using the semi-rigid thioether dipyridyl ligand 1,4-bis[(pyridin-4-ylthio)methyl]benzene (Bptmb). The topological transformation from a binuclear metallacycle and a BR to tetranuclear metallacycles was realized via the controlled oxidation of thioethers. The strategy used in this work can be regarded as a new form of stimuli-responsive post-synthesis modification (PSM).
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Affiliation(s)
- Hai-Ning Zhang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of, Polymers, Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | - Wei-Bin Yu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of, Polymers, Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | - Yue-Jian Lin
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of, Polymers, Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | - Guo-Xin Jin
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of, Polymers, Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
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17
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Zhang H, Yu W, Lin Y, Jin G. Stimuli‐Responsive Topological Transformation of a Molecular Borromean Ring via Controlled Oxidation of Thioether Moieties. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Hai‐Ning Zhang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials State Key Laboratory of Molecular Engineering of, Polymers Department of Chemistry Fudan University Shanghai 200433 P. R. China
| | - Wei‐Bin Yu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials State Key Laboratory of Molecular Engineering of, Polymers Department of Chemistry Fudan University Shanghai 200433 P. R. China
| | - Yue‐Jian Lin
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials State Key Laboratory of Molecular Engineering of, Polymers Department of Chemistry Fudan University Shanghai 200433 P. R. China
| | - Guo‐Xin Jin
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials State Key Laboratory of Molecular Engineering of, Polymers Department of Chemistry Fudan University Shanghai 200433 P. R. China
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18
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Dey S, Misra R, Saseendran A, Pahan S, Gopi HN. Metal‐Coordinated Supramolecular Polymers from the Minimalistic Hybrid Peptide Foldamers. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015838] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sanjit Dey
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
| | - Rajkumar Misra
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
| | - Abhijith Saseendran
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
| | - Saikat Pahan
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
| | - Hosahudya N. Gopi
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
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19
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Dey S, Misra R, Saseendran A, Pahan S, Gopi HN. Metal‐Coordinated Supramolecular Polymers from the Minimalistic Hybrid Peptide Foldamers. Angew Chem Int Ed Engl 2021; 60:9863-9868. [DOI: 10.1002/anie.202015838] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/19/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Sanjit Dey
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
| | - Rajkumar Misra
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
| | - Abhijith Saseendran
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
| | - Saikat Pahan
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
| | - Hosahudya N. Gopi
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
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20
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Structural resolution of switchable states of a de novo peptide assembly. Nat Commun 2021; 12:1530. [PMID: 33750792 PMCID: PMC7943578 DOI: 10.1038/s41467-021-21851-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/12/2021] [Indexed: 12/18/2022] Open
Abstract
De novo protein design is advancing rapidly. However, most designs are for single states. Here we report a de novo designed peptide that forms multiple α-helical-bundle states that are accessible and interconvertible under the same conditions. Usually in such designs amphipathic α helices associate to form compact structures with consolidated hydrophobic cores. However, recent rational and computational designs have delivered open α-helical barrels with functionalisable cavities. By placing glycine judiciously in the helical interfaces of an α-helical barrel, we obtain both open and compact states in a single protein crystal. Molecular dynamics simulations indicate a free-energy landscape with multiple and interconverting states. Together, these findings suggest a frustrated system in which steric interactions that maintain the open barrel and the hydrophobic effect that drives complete collapse are traded-off. Indeed, addition of a hydrophobic co-solvent that can bind within the barrel affects the switch between the states both in silico and experimentally. So far most of the de novo designed proteins are for single states only. Here, the authors present the de novo design and crystal structure determination of a coiled-coil peptide that assembles into multiple, distinct conformational states under the same conditions and further characterise its properties with biophysical experiments, NMR and MD simulations.
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21
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Li XY, Zhou XD, Hu JM. A straightforward and reliable evaluation of Ag(I) binding affinity mediated by a peptide ligand for constructing an efficient sensing platform. Talanta 2021; 226:122089. [PMID: 33676647 DOI: 10.1016/j.talanta.2021.122089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/29/2020] [Accepted: 01/03/2021] [Indexed: 10/22/2022]
Abstract
The reliable determination of the Ag(I) affinity for biomolecules is an essential issue in the fields of structural analysis and sensor design. However, the urgent problem confronting researchers is lack of a direct and accurate Ag(I) affinity evaluation as a reference standard for ligand analysis. We communicated here a straightforward and high-efficiency method of measuring Ag(I) affinity exactly on the basis of the unique calculation algorithm and the design of a special peptide RFPRDD (P) as Ag(I) binding motif. According to UV-vis competition between the corresponding complexes (AgP) and biomolecules (peptides, amino acids and ssDNA), the decrease of the signature at 300 nm characteristic of AgP was obtained for quantitative analysis. The primary advantages of this strategy were the widespread application, high accuracy and reference significance, which were corroborated by theoretical calculations. To identify its potential in biosensing, two kinds of testing models for Ag(I) were proposed by AgBP2-decorated and Ag4-decorated gold nanoparticles, the detection limits of which were 2 nM and 75 nM respectively. By contrast of the sensing property of the functional peptides (AgBP2, Ag4), we afforded evidence that this conception could be regarded as an evaluation criterion for the selection and performance optimization of sensitive elements, thereby holding a dominant position in the biosensors.
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Affiliation(s)
- Xin-Yi Li
- The Centre of Analysis and Measurement of Wuhan University, Wuhan University, Wuhan, 430072, PR China
| | - Xiao-Dong Zhou
- The Centre of Analysis and Measurement of Wuhan University, Wuhan University, Wuhan, 430072, PR China.
| | - Ji-Ming Hu
- The Centre of Analysis and Measurement of Wuhan University, Wuhan University, Wuhan, 430072, PR China.
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22
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Li J, Zhao Y, Zhou P, Hu X, Wang D, King SM, Rogers SE, Wang J, Lu JR, Xu H. Ordered Nanofibers Fabricated from Hierarchical Self-Assembling Processes of Designed α-Helical Peptides. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2003945. [PMID: 33015967 DOI: 10.1002/smll.202003945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/15/2020] [Indexed: 06/11/2023]
Abstract
Peptide self-assembly is fast evolving into a powerful method for the development of bio-inspired nanomaterials with great potential for many applications, but it remains challenging to control the self-assembling processes and nanostrucutres because of the intricate interplay of various non-covalent interactions. A group of 28-residue α-helical peptides is designed including NN, NK, and HH that display distinct hierarchical events. The key of the design lies in the incorporation of two asparagine (Asn) or histidine (His) residues at the a positions of the second and fourth heptads, which allow one sequence to pack into homodimers with sticky ends through specific interhelical Asn-Asn or metal complexation interactions, followed by their longitudinal association into ordered nanofibers. This is in contrast to classical self-assembling helical peptide systems consisting of two complementary peptides. The collaborative roles played by the four main non-covalent interactions, including hydrogen-bonding, hydrophobic interactions, electrostatic interactions, and metal ion coordination, are well demonstrated during the hierarchical self-assembling processes of these peptides. Different nanostructures, for example, long and short nanofibers, thin and thick fibers, uniform metal ion-entrapped nanofibers, and polydisperse globular stacks, can be prepared by harnessing these interactions at different levels of hierarchy.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Yurong Zhao
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Peng Zhou
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Xuzhi Hu
- Biological Physics Group, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
| | - Dong Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Stephen M King
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Didcot, Oxon, OX11 0QX, UK
| | - Sarah E Rogers
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Didcot, Oxon, OX11 0QX, UK
| | - Jiqian Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Jian R Lu
- Biological Physics Group, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
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23
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Surfactant-like peptides: From molecular design to controllable self-assembly with applications. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213418] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Curtis RW, Chmielewski J. A comparison of the collagen triple helix and
coiled‐coil
peptide building blocks on metal
ion‐mediated
supramolecular assembly. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Ryan W. Curtis
- Department of Chemistry Purdue University West Lafayette Indiana USA
| | - Jean Chmielewski
- Department of Chemistry Purdue University West Lafayette Indiana USA
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25
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Nagarkar RP, Fichman G, Schneider JP. Engineering and characterization of apH‐sensitive homodimeric antiparallel coiled coil. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Radhika P. Nagarkar
- Department of Chemistry and Biochemistry University of Delaware Newark Delaware USA
| | - Galit Fichman
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Frederick Maryland USA
| | - Joel P. Schneider
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Frederick Maryland USA
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26
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Yan LL, Yao LY, Yam VWW. Concentration- and Solvation-Induced Reversible Structural Transformation and Assembly of Polynuclear Gold(I) Sulfido Complexes. J Am Chem Soc 2020; 142:11560-11568. [DOI: 10.1021/jacs.0c04677] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Liang-Liang Yan
- Institute of Molecular Functional Materials and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Liao-Yuan Yao
- Institute of Molecular Functional Materials and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Vivian Wing-Wah Yam
- Institute of Molecular Functional Materials and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
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27
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Bhattacharyya S, Maity M, Chowdhury A, Saha ML, Panja SK, Stang PJ, Mukherjee PS. Coordination-Assisted Reversible Photoswitching of Spiropyran-Based Platinum Macrocycles. Inorg Chem 2020; 59:2083-2091. [PMID: 31971781 PMCID: PMC10615217 DOI: 10.1021/acs.inorgchem.9b03572] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Control over the stimuli-responsive behavior of smart molecular systems can influence their capability to execute complex functionalities. Herein, we report the development of a suite of spiropyran-based multi-stimuli-responsive self-assembled platinum(II) macrocycles (5-7), rendering coordination-assisted enhanced photochromism relative to the corresponding ligands. 5 showed shrinking and swelling during photoreversal, while 6 and 7 are fast and fatigue-free supramolecular photoswitches. 6 turns out to be a better fatigue-resistant photoswitch and can retain an intact photoswitching ability of up to 20 reversible cycles. The switching behavior of the macrocycles can also be precisely controlled by tuning the pH of the medium. Our present strategy for the construction of rapid stimuli-responsive supramolecular architectures via coordination-driven self-assembly represents an efficient route for the development of smart molecular switches.
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Affiliation(s)
- Soumalya Bhattacharyya
- Department of Inorganic and Physical Chemistry , Indian Institute of Science , Bangalore , Karnataka 560012 India
| | - Manoranjan Maity
- Department of Inorganic and Physical Chemistry , Indian Institute of Science , Bangalore , Karnataka 560012 India
| | - Aniket Chowdhury
- Department of Inorganic and Physical Chemistry , Indian Institute of Science , Bangalore , Karnataka 560012 India
- Department of Industrial Chemistry , Mizoram University , Aizawl , Mizoram 796004 , India
| | - Manik Lal Saha
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Sumit Kumar Panja
- Department of Inorganic and Physical Chemistry , Indian Institute of Science , Bangalore , Karnataka 560012 India
| | - Peter J Stang
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Partha Sarathi Mukherjee
- Department of Inorganic and Physical Chemistry , Indian Institute of Science , Bangalore , Karnataka 560012 India
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28
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Mittal N, Paul I, Pramanik S, Schmittel M. Remote control of the reversible assembly/disassembly of supramolecular aggregates. Supramol Chem 2020. [DOI: 10.1080/10610278.2020.1711907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Nikita Mittal
- Center of Micro and Nanochemistry and Engineering, Organische Chemie I, Universität Siegen, Siegen, Germany
| | - Indrajit Paul
- Center of Micro and Nanochemistry and Engineering, Organische Chemie I, Universität Siegen, Siegen, Germany
| | - Susnata Pramanik
- Center of Micro and Nanochemistry and Engineering, Organische Chemie I, Universität Siegen, Siegen, Germany
| | - Michael Schmittel
- Center of Micro and Nanochemistry and Engineering, Organische Chemie I, Universität Siegen, Siegen, Germany
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29
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Nambiar M, Nepal M, Chmielewski J. Self-Assembling Coiled-Coil Peptide Nanotubes with Biomolecular Cargo Encapsulation. ACS Biomater Sci Eng 2019; 5:5082-5087. [PMID: 33455255 DOI: 10.1021/acsbiomaterials.9b01304] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Monessha Nambiar
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Manish Nepal
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Jean Chmielewski
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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30
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Boyle AL, Rabe M, Crone NSA, Rhys GG, Soler N, Voskamp P, Pannu NS, Kros A. Selective coordination of three transition metal ions within a coiled-coil peptide scaffold. Chem Sci 2019; 10:7456-7465. [PMID: 31489168 PMCID: PMC6713864 DOI: 10.1039/c9sc01165j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/19/2019] [Indexed: 12/13/2022] Open
Abstract
Designing peptides that fold and assemble in response to metal ions tests our understanding of how peptide folding and metal binding influence one another. Here, histidine residues are introduced into the hydrophobic core of a coiled-coil trimer, generating a peptide that self-assembles upon the addition of metal ions. HisAD, the resulting peptide, is unstructured in the absence of metal and folds selectively to form an α-helical construct upon complexation with Cu(ii) and Ni(ii) but not Co(ii) or Zn(ii). The structure, and metal-binding ability, of HisAD is probed using a combination of circular dichroism (CD) spectroscopy, analytical ultracentrifugation (AUC), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. These show the peptide is trimeric and binds to both Cu(ii) and Ni(ii) in a 1 : 1 ratio with the histidine residues involved in the metal coordination, as designed. The X-ray crystal structure of the HisAD-Cu(ii) complex reveals the trimeric HisAD peptide coordinates three Cu(ii) ions; this is the first example of such a structure. Additionally, HisAD demonstrates an unprecedented discrimination between transition metal ions, the basis of which is likely to be related to the stability of the peptide-metal complexes formed.
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Affiliation(s)
- Aimee L Boyle
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Martin Rabe
- Max-Planck-Institut für Eisenforschung GmbH , Max-Planck-Straße 1 , 40237 Düsseldorf , Germany
| | - Niek S A Crone
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Guto G Rhys
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK
| | - Nicolas Soler
- Structural Biology Unit , Institute of Molecular Biology of Barcelona (IBMB-CSIC) , Baldiri Reixac 15 , 08028 Barcelona , Spain
| | - Patrick Voskamp
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Navraj S Pannu
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Alexander Kros
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
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31
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Lou S, Wang X, Yu Z, Shi L. Peptide Tectonics: Encoded Structural Complementarity Dictates Programmable Self-Assembly. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1802043. [PMID: 31380179 PMCID: PMC6662064 DOI: 10.1002/advs.201802043] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 03/20/2019] [Indexed: 05/23/2023]
Abstract
Programmable self-assembly of peptides into well-defined nanostructures represents one promising approach for bioinspired and biomimetic synthesis of artificial complex systems and functional materials. Despite the progress made over the past two decades in the development of strategies for precise manipulation of the self-assembly of peptides, there is a remarkable gap between current peptide assemblies and biological systems in terms of structural complexity and functions. Here, the concept of peptide tectonics for the creation of well-defined nanostructures predominately driven by the complementary association at the interacting interfaces of tectons is introduced. Peptide tectons are defined as peptide building blocks exhibiting structural complementarity at the interacting interfaces of commensurate domains and undergoing programmable self-assembly into defined supramolecular structures promoted by complementary interactions. Peptide tectons are categorized based on their conformational entropy and the underlying mechanism for the programmable self-assembly of peptide tectons is highlighted focusing on the approaches for incorporating the structural complementarity within tectons. Peptide tectonics not only provides an alternative perspective to understand the self-assembly of peptides, but also allows for precise manipulation of peptide interactions, thus leading to artificial systems with advanced complexity and functions and paves the way toward peptide-related functional materials resembling natural systems.
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Affiliation(s)
- Shaofeng Lou
- Key Laboratory of Functional Polymer Materials, Ministryof EducationState Key Laboratory of Medicinal Chemical BiologyInstitute of Polymer ChemistryCollege of ChemistryNankai UniversityWeijin Road 94Tianjin300071China
| | - Xinmou Wang
- Key Laboratory of Functional Polymer Materials, Ministryof EducationState Key Laboratory of Medicinal Chemical BiologyInstitute of Polymer ChemistryCollege of ChemistryNankai UniversityWeijin Road 94Tianjin300071China
| | - Zhilin Yu
- Key Laboratory of Functional Polymer Materials, Ministryof EducationState Key Laboratory of Medicinal Chemical BiologyInstitute of Polymer ChemistryCollege of ChemistryNankai UniversityWeijin Road 94Tianjin300071China
| | - Linqi Shi
- Key Laboratory of Functional Polymer Materials, Ministryof EducationState Key Laboratory of Medicinal Chemical BiologyInstitute of Polymer ChemistryCollege of ChemistryNankai UniversityWeijin Road 94Tianjin300071China
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32
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Ansammlungen gefalteter Proteine im Kontext von Evolution, Krankheiten und Proteinentwicklung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201806092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
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33
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Assembly of Folded Proteins in Evolution, Disease, and Engineering. Angew Chem Int Ed Engl 2019; 58:5514-5531. [PMID: 30133878 PMCID: PMC6471489 DOI: 10.1002/anie.201806092] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/06/2018] [Indexed: 12/14/2022]
Abstract
Mutations and changes in a protein's environment are well known for their potential to induce misfolding and aggregation, including amyloid formation. Alternatively, such perturbations can trigger new interactions that lead to the polymerization of folded proteins. In contrast to aggregation, this process does not require misfolding and, to highlight this difference, we refer to it as agglomeration. This term encompasses the amorphous assembly of folded proteins as well as the polymerization in one, two, or three dimensions. We stress the remarkable potential of symmetric homo-oligomers to agglomerate even by single surface point mutations, and we review the double-edged nature of this potential: how aberrant assemblies resulting from agglomeration can lead to disease, but also how agglomeration can serve in cellular adaptation and be exploited for the rational design of novel biomaterials.
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Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
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34
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Scheib KA, Tavenor NA, Lawless MJ, Saxena S, Horne WS. Understanding and controlling the metal-directed assembly of terpyridine-functionalized coiled-coil peptides. Chem Commun (Camb) 2019; 55:7752-7755. [DOI: 10.1039/c9cc03496j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Spectroscopic elucidation of the interaction between terpyridine-functionalized coiled-coil peptides and Cu(ii) enables the construction of rationally designed supramolecular lattices.
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Affiliation(s)
| | | | | | - Sunil Saxena
- Department of Chemistry
- University of Pittsburgh
- Pittsburgh
- USA
| | - W. Seth Horne
- Department of Chemistry
- University of Pittsburgh
- Pittsburgh
- USA
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35
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Zheng W, Wang W, Jiang ST, Yang G, Li Z, Wang XQ, Yin GQ, Zhang Y, Tan H, Li X, Ding H, Chen G, Yang HB. Supramolecular Transformation of Metallacycle-linked Star Polymers Driven by Simple Phosphine Ligand-Exchange Reaction. J Am Chem Soc 2018; 141:583-591. [DOI: 10.1021/jacs.8b11642] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Wei Zheng
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, P. R. China
| | - Wei Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, P. R. China
| | - Shu-Ting Jiang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, P. R. China
| | - Guang Yang
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, P. R. China
| | - Zhen Li
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, P. R. China
| | - Xu-Qing Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, P. R. China
| | - Guang-Qiang Yin
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, P. R. China
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Ying Zhang
- Department of Chemistry, Beijing Normal University, Beijing 100050, P. R. China
| | - Hongwei Tan
- Department of Chemistry, Beijing Normal University, Beijing 100050, P. R. China
| | - Xiaopeng Li
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Hongming Ding
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, P. R. China
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, P. R. China
| | - Hai-Bo Yang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, P. R. China
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36
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Li Y, Zou Q, Yuan C, Li S, Xing R, Yan X. Amino Acid Coordination Driven Self‐Assembly for Enhancing both the Biological Stability and Tumor Accumulation of Curcumin. Angew Chem Int Ed Engl 2018; 57:17084-17088. [DOI: 10.1002/anie.201810087] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Yongxin Li
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences 100190 Beijing China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Qianli Zou
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences 100190 Beijing China
| | - Chengqian Yuan
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences 100190 Beijing China
| | - Shukun Li
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences 100190 Beijing China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Ruirui Xing
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences 100190 Beijing China
| | - Xuehai Yan
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences 100190 Beijing China
- Center for Mesoscience Institute of Process Engineering Chinese Academy of Sciences 100190 Beijing China
- University of Chinese Academy of Sciences 100049 Beijing China
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37
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Li Y, Zou Q, Yuan C, Li S, Xing R, Yan X. Amino Acid Coordination Driven Self‐Assembly for Enhancing both the Biological Stability and Tumor Accumulation of Curcumin. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810087] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Yongxin Li
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences 100190 Beijing China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Qianli Zou
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences 100190 Beijing China
| | - Chengqian Yuan
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences 100190 Beijing China
| | - Shukun Li
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences 100190 Beijing China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Ruirui Xing
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences 100190 Beijing China
| | - Xuehai Yan
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences 100190 Beijing China
- Center for Mesoscience Institute of Process Engineering Chinese Academy of Sciences 100190 Beijing China
- University of Chinese Academy of Sciences 100049 Beijing China
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38
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Tian Y, Polzer FB, Zhang HV, Kiick KL, Saven JG, Pochan DJ. Nanotubes, Plates, and Needles: Pathway-Dependent Self-Assembly of Computationally Designed Peptides. Biomacromolecules 2018; 19:4286-4298. [DOI: 10.1021/acs.biomac.8b01163] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yu Tian
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
| | - Frank B. Polzer
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
| | - Huixi Violet Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Kristi L. Kiick
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffery G. Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Darrin J. Pochan
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
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39
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Nambiar M, Wang LS, Rotello V, Chmielewski J. Reversible Hierarchical Assembly of Trimeric Coiled-Coil Peptides into Banded Nano- and Microstructures. J Am Chem Soc 2018; 140:13028-13033. [DOI: 10.1021/jacs.8b08163] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Monessha Nambiar
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Li-Sheng Wang
- Department of Chemistry, University of Massachusetts−Amherst, 710 N. Pleasant Street, Amherst, Massachusetts 01002, United States
| | - Vincent Rotello
- Department of Chemistry, University of Massachusetts−Amherst, 710 N. Pleasant Street, Amherst, Massachusetts 01002, United States
| | - Jean Chmielewski
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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40
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Haider MJ, Zhang HV, Sinha N, Fagan JA, Kiick KL, Saven JG, Pochan DJ. Self-assembly and soluble aggregate behavior of computationally designed coiled-coil peptide bundles. SOFT MATTER 2018; 14:5488-5496. [PMID: 29923575 PMCID: PMC6355460 DOI: 10.1039/c8sm00435h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Coiled-coil peptides have proven useful in a range of materials applications ranging from the formation of well-defined fibrils to responsive hydrogels. The ability to design from first principles their oligomerization and subsequent higher order assembly offers their expanded use in producing new materials. Toward these ends, homo-tetrameric, antiparallel, coiled-coil, peptide bundles have been designed computationally, synthesized via solid-phase methods, and their solution behavior characterized. Two different bundle-forming peptides were designed and examined. Within the targeted coiled coil structure, both bundles contained the same hydrophobic core residues. However, different exterior residues on the two different designs yielded sequences with different distributions of charged residues and two different expected isoelectric points of pI 4.4 and pI 10.5. Both coiled-coil bundles were extremely stable with respect to temperature (Tm > 80 C) and remained soluble in solution even at high (millimolar) peptide concentrations. The coiled-coil tetramer was confirmed to be the dominant species in solution by analytical sedimentation studies and by small-angle neutron scattering, where the scattering form factor is well represented by a cylinder model with the dimensions of the targeted coiled coil. At high concentrations (5-15 mM), evidence of interbundle structure was observed via neutron scattering. At these concentrations, the synthetic bundles form soluble aggregates, and interbundle distances can be determined via a structure factor fit to scattering data. The data support the successful design of robust coiled-coil bundles. Despite their different sequences, each sequence forms loosely associated but soluble aggregates of the bundles, suggesting similar dissociated states for each. The behavior of the dispersed bundles is similar to that observed for natural proteins.
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Affiliation(s)
- Michael J. Haider
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA. ,
| | - Huixi Violet Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Nairiti Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA. ,
| | - Jeffrey A. Fagan
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.
| | - Kristi L. Kiick
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA. ,
| | - Jeffery G. Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Darrin J. Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA. ,
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41
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Nagarkar RP, Miller SE, Zhong S, Pochan DJ, Schneider JP. Dynamic protein folding at the surface of stimuli-responsive peptide fibrils. Protein Sci 2018; 27:1243-1251. [PMID: 29493033 PMCID: PMC6032354 DOI: 10.1002/pro.3394] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/26/2018] [Accepted: 02/26/2018] [Indexed: 01/01/2023]
Abstract
The repetitive self-assembled structure of amyloid can serve as inspiration to design functional materials. Herein, we describe the design of α/β6, a peptide that contains distinct α-helical and β-structure forming domains. The folding and association state of each domain can be controlled by temperature. At low temperatures, the α-domain favors a coiled-coil state while the β-domain is unstructured. Irreversible fibril formation via self-assembly of the β-domain is triggered at high temperatures where the α-domain is unfolded. Resultant fibrils serve as templates upon which reversible coiled coil formation of the α-domain can be thermally controlled. At concentrations of α/β6 ≥ 2.5 wt%, the peptide forms a mechanically defined hydrogel highlighting the possibility of designing materials whose function can be actively modulated by controlling the folded state of proteins displayed from the surface of fibrils that constitute the gel.
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Affiliation(s)
- Radhika P. Nagarkar
- Department of Chemistry and BiochemistryUniversity of DelawareNewarkDelaware19716
| | - Stephen E. Miller
- Chemical Biology LaboratoryNational Cancer Institute, National Institutes of HealthFrederickMaryland21702
| | - Sheng Zhong
- Department of Materials Science and EngineeringUniversity of DelawareNewarkDelaware19716
| | - Darrin J. Pochan
- Department of Materials Science and EngineeringUniversity of DelawareNewarkDelaware19716
| | - Joel P. Schneider
- Chemical Biology LaboratoryNational Cancer Institute, National Institutes of HealthFrederickMaryland21702
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42
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Singh R, Kumar Mishra N, Kumar V, Vinayak V, Ballabh Joshi K. Transition Metal Ion-Mediated Tyrosine-Based Short-Peptide Amphiphile Nanostructures Inhibit Bacterial Growth. Chembiochem 2018; 19:1630-1637. [PMID: 29771457 DOI: 10.1002/cbic.201800220] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Indexed: 12/29/2022]
Abstract
We report the design and synthesis of a biocompatible small-peptide-based compound for the controlled and targeted delivery of encapsulated bioactive metal ions through transformation of the internal nanostructures of its complexes. A tyrosine-based short-peptide amphiphile (sPA) was synthesized and observed to self-assemble into β-sheet-like secondary structures. The self-assembly of the designed sPA was modulated by application of different bioactive transition-metal ions, as was confirmed by spectroscopic and microscopic techniques. These bioactive metal-ion-conjugated sPA hybrid structures were further used to develop antibacterial materials. As a result of the excellent antibacterial activity of zinc ions the growth of clinically relevant bacteria such as Escherichia coli was inhibited in the presence of zinc⋅sPA conjugate. Bacterial testing demonstrated that, due to high biocompatibility with bacterial cells, the designed sPA acted as a metal ion delivery agent and might therefore show great potential in locally addressing bacterial infections.
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Affiliation(s)
- Ramesh Singh
- Department of Chemistry, School of Chemical Science and Technology, Dr. Harisingh Gour Central University, Sagar, MP, 470003, India
| | - Narendra Kumar Mishra
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
| | - Vikas Kumar
- Department of Chemistry, School of Chemical Science and Technology, Dr. Harisingh Gour Central University, Sagar, MP, 470003, India
| | - Vandana Vinayak
- Diatom Nanoengineering and Metabolism Lab (DNM), School of Applied Sciences, Dr. Harisingh Gour Central University, Sagar, MP, 470003, India
| | - Khashti Ballabh Joshi
- Department of Chemistry, School of Chemical Science and Technology, Dr. Harisingh Gour Central University, Sagar, MP, 470003, India
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43
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Ganta S, Chand DK. Molecular Recombination Phenomena in Palladium(II)-Based Self-Assembled Complexes. Inorg Chem 2018; 57:5145-5158. [DOI: 10.1021/acs.inorgchem.8b00213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Sudhakar Ganta
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | - Dillip K. Chand
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
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44
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Shimizu T. Self-Assembly of Discrete Organic Nanotubes. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20170424] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Toshimi Shimizu
- AIST Fellow, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
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45
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Yu H, Wang J, Guo X, Zhang R, He C, Duan C. Diversity of metal-organic macrocycles assembled from carbazole based ligands with different lengths. Dalton Trans 2018; 47:4040-4044. [PMID: 29473087 DOI: 10.1039/c8dt00252e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A series of carbazole based ligands with different lengths were assembled with nickel ions to construct metal-organic macrocycles. High-resolution mass spectrometry and ion mobility-mass spectrometry have been used to analyse the resulting MnLn assembly coexisting in solution. Combining with the structural analysis of their solid confirmation, it was revealed that the diversity of the metal-organic macrocycles was increased with the flexibility of the ligands.
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Affiliation(s)
- Hao Yu
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116012, China.
| | - Jing Wang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116012, China.
| | - Xiangyang Guo
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116012, China.
| | - Rong Zhang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116012, China.
| | - Cheng He
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116012, China.
| | - Chunying Duan
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116012, China.
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46
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Eibling MJ, MacDermaid CM, Qian Z, Lanci CJ, Park SJ, Saven JG. Controlling Association and Separation of Gold Nanoparticles with Computationally Designed Zinc-Coordinating Proteins. J Am Chem Soc 2017; 139:17811-17823. [DOI: 10.1021/jacs.7b04786] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Matthew J. Eibling
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Christopher M. MacDermaid
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zhaoxia Qian
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Christopher J. Lanci
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - So-Jung Park
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department
of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, South Korea
| | - Jeffery G. Saven
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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47
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Abstract
The development of biomaterials designed for specific applications is an important objective in personalized medicine. While the breadth and prominence of biomaterials have increased exponentially over the past decades, critical challenges remain to be addressed, particularly in the development of biomaterials that exhibit highly specific functions. These functional properties are often encoded within the molecular structure of the component molecules. Proteins, as a consequence of their structural specificity, represent useful substrates for the construction of functional biomaterials through rational design. This chapter provides an in-depth survey of biomaterials constructed from coiled-coils, one of the best-understood protein structural motifs. We discuss the utility of this structurally diverse and functionally tunable class of proteins for the creation of novel biomaterials. This discussion illustrates the progress that has been made in the development of coiled-coil biomaterials by showcasing studies that bridge the gap between the academic science and potential technological impact.
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Affiliation(s)
- David A.D. Parry
- Institute of Fundamental Sciences and Riddet Institute, Massey University, Palmerston North, New Zealand
| | - John M. Squire
- Muscle Contraction Group, School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
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48
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Tavenor NA, Murnin MJ, Horne WS. Supramolecular Metal-Coordination Polymers, Nets, and Frameworks from Synthetic Coiled-Coil Peptides. J Am Chem Soc 2017; 139:2212-2215. [DOI: 10.1021/jacs.7b00651] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Nathan A. Tavenor
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Matthew J. Murnin
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - W. Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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49
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Li Z, Xing H, Shi B. Two novel supramolecular metallogels constructed by platinum(ii) coordination and pillar[5]arene-based host–guest interactions. Polym Chem 2017. [DOI: 10.1039/c7py00280g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Two multi-responsive supramolecular metallogels were constructed by coordination-driven self-assembly, host–guest interaction and supramolecular polymerization.
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Affiliation(s)
- Zhengtao Li
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Hao Xing
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Bingbing Shi
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- P. R. China
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50
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Ekiz MS, Cinar G, Khalily MA, Guler MO. Self-assembled peptide nanostructures for functional materials. NANOTECHNOLOGY 2016; 27:402002. [PMID: 27578525 DOI: 10.1088/0957-4484/27/40/402002] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Nature is an important inspirational source for scientists, and presents complex and elegant examples of adaptive and intelligent systems created by self-assembly. Significant effort has been devoted to understanding these sophisticated systems. The self-assembly process enables us to create supramolecular nanostructures with high order and complexity, and peptide-based self-assembling building blocks can serve as suitable platforms to construct nanostructures showing diverse features and applications. In this review, peptide-based supramolecular assemblies will be discussed in terms of their synthesis, design, characterization and application. Peptide nanostructures are categorized based on their chemical and physical properties and will be examined by rationalizing the influence of peptide design on the resulting morphology and the methods employed to characterize these high order complex systems. Moreover, the application of self-assembled peptide nanomaterials as functional materials in information technologies and environmental sciences will be reviewed by providing examples from recently published high-impact studies.
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Affiliation(s)
- Melis Sardan Ekiz
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, 06800 Turkey
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