1
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Hilditch AT, Romanyuk A, Hodgson LR, Mantell J, Neal CR, Verkade P, Obexer R, Serpell LC, McManus JJ, Woolfson DN. Maturation and Conformational Switching of a De Novo Designed Phase-Separating Polypeptide. J Am Chem Soc 2024; 146:10240-10245. [PMID: 38578222 PMCID: PMC11027135 DOI: 10.1021/jacs.4c00256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/06/2024]
Abstract
Cellular compartments formed by biomolecular condensation are widespread features of cell biology. These organelle-like assemblies compartmentalize macromolecules dynamically within the crowded intracellular environment. However, the intermolecular interactions that produce condensed droplets may also create arrested states and potentially pathological assemblies such as fibers, aggregates, and gels through droplet maturation. Protein liquid-liquid phase separation is a metastable process, so maturation may be an intrinsic property of phase-separating proteins, where nucleation of different phases or states arises in supersaturated condensates. Here, we describe the formation of both phase-separated droplets and proteinaceous fibers driven by a de novo designed polypeptide. We characterize the formation of supramolecular fibers in vitro and in bacterial cells. We show that client proteins can be targeted to the fibers in cells using a droplet-forming construct. Finally, we explore the interplay between phase separation and fiber formation of the de novo polypeptide, showing that the droplets mature with a post-translational switch to largely β conformations, analogous to models of pathological phase separation.
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Affiliation(s)
- Alexander T. Hilditch
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
- Max
Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Andrey Romanyuk
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
- Max
Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Lorna R. Hodgson
- Wolfson
Bioimaging Facility, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K.
| | - Judith Mantell
- Wolfson
Bioimaging Facility, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K.
| | - Christopher R. Neal
- Wolfson
Bioimaging Facility, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K.
| | - Paul Verkade
- School
of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K.
- Bristol
BioDesign Institute, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Richard Obexer
- Department
of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, U.K.
| | - Louise C. Serpell
- School
of Life Sciences, University of Sussex, Falmer, Brighton, JMS 3B17, U.K.
| | - Jennifer J. McManus
- Bristol
BioDesign Institute, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
- HH Wills
Physics Laboratory, School of Physics, University
of Bristol, Tyndall Avenue, Bristol BS8 1TL, U.K.
| | - Derek N. Woolfson
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
- Max
Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
- School
of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K.
- Bristol
BioDesign Institute, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
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2
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Christians LF, Halingstad EV, Kram E, Okolovitch EM, Pak AJ. Formalizing Coarse-Grained Representations of Anisotropic Interactions at Multimeric Protein Interfaces Using Virtual Sites. J Phys Chem B 2024; 128:1394-1406. [PMID: 38316012 DOI: 10.1021/acs.jpcb.3c07023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Molecular simulations of biomacromolecules that assemble into multimeric complexes remain a challenge due to computationally inaccessible length and time scales. Low-resolution and implicit-solvent coarse-grained modeling approaches using traditional nonbonded interactions (both pairwise and spherically isotropic) have been able to partially address this gap. However, these models may fail to capture the complex anisotropic interactions present at macromolecular interfaces unless higher-order interaction potentials are incorporated at the expense of the computational cost. In this work, we introduce an alternate and systematic approach to represent directional interactions at protein-protein interfaces by using virtual sites restricted to pairwise interactions. We show that virtual site interaction parameters can be optimized within a relative entropy minimization framework by using only information from known statistics between coarse-grained sites. We compare our virtual site models to traditional coarse-grained models using two case studies of multimeric protein assemblies and find that the virtual site models predict pairwise correlations with higher fidelity and, more importantly, assembly behavior that is morphologically consistent with experiments. Our study underscores the importance of anisotropic interaction representations and paves the way for more accurate yet computationally efficient coarse-grained simulations of macromolecular assembly in future research.
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Affiliation(s)
- Luc F Christians
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Ethan V Halingstad
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Emiel Kram
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Evan M Okolovitch
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Alexander J Pak
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
- Quantitative Biosciences and Engineering Program, Colorado School of Mines, Golden, Colorado 80401, United States
- Materials Science Program, Colorado School of Mines, Golden, Colorado 80401, United States
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3
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Nakagawa S, Kurokawa M, Kambara O, Takei T, Daidoji K, Naito A, Takita M, Kawamoto A, Hirose M, Tamura A. Structural Analyses of Designed α-Helix and β-Sheet Peptide Nanofibers Using Solid-State Nuclear Magnetic Resonance and Cryo-Electron Microscopy and Introduction of Structure-Based Metal-Responsive Properties. Int J Mol Sci 2024; 25:1111. [PMID: 38256184 PMCID: PMC10816960 DOI: 10.3390/ijms25021111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/11/2024] [Accepted: 01/14/2024] [Indexed: 01/24/2024] Open
Abstract
The 21-residue peptide α3, which is artificially designed and consists of three repeats of 7 residues, is known to rapidly assemble into the α-helix nanofiber. However, its molecular structure within the fiber has not yet been fully elucidated. Thus, we conducted a thorough investigation of the fiber's molecular structure using solid-state NMR and other techniques. The molecules were found to be primarily composed of the α-helix structure, with some regions near the C- and N-terminal adopting a 310-helix structure. Furthermore, it was discovered that β-sheet hydrogen bonds were formed between the molecules at both ends. These intermolecular interactions caused the molecules to assemble parallelly in the same direction, forming helical fibers. In contrast, we designed two molecules, CaRP2 and βKE, that can form β-sheet intermolecular hydrogen bonds using the entire molecule instead of just the ends. Cryo-EM and other measurements confirmed that the nanofibers formed in a cross β structure, albeit at a slow rate, with the formation times ranging from 1 to 42 days. To create peptide nanofibers that instantaneously respond to changes in the external environment, we designed several molecules (HDM1-3) based on α3 by introducing metal-binding sites. One of these molecules was found to be highly responsive to the addition of metal ions, inducing α-helix formation and simultaneously assembling into nanofibers. The nanofibers lost their structure upon removal of the metal ion. The change occurred promptly and was reversible, demonstrating that the intended level of responsiveness was attained.
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Affiliation(s)
- Shota Nakagawa
- Graduate School of Science, Department of Chemistry, Kobe University, Kobe 657-8501, Japan; (S.N.); (M.K.)
| | - Minami Kurokawa
- Graduate School of Science, Department of Chemistry, Kobe University, Kobe 657-8501, Japan; (S.N.); (M.K.)
| | - Ohki Kambara
- Graduate School of Science, Department of Chemistry, Kobe University, Kobe 657-8501, Japan; (S.N.); (M.K.)
| | - Toshiaki Takei
- Graduate School of Science, Department of Chemistry, Kobe University, Kobe 657-8501, Japan; (S.N.); (M.K.)
| | - Kengo Daidoji
- Graduate School of Engineering, Yokohama National University, Yokohama 240-8501, Japan (A.N.)
| | - Akira Naito
- Graduate School of Engineering, Yokohama National University, Yokohama 240-8501, Japan (A.N.)
| | - Mao Takita
- Graduate School of Science, Department of Chemistry, Kobe University, Kobe 657-8501, Japan; (S.N.); (M.K.)
| | - Akihiro Kawamoto
- Institute for Protein Research, Osaka University, Suita 565-0871, Japan; (A.K.); (M.H.)
| | - Mika Hirose
- Institute for Protein Research, Osaka University, Suita 565-0871, Japan; (A.K.); (M.H.)
| | - Atsuo Tamura
- Graduate School of Science, Department of Chemistry, Kobe University, Kobe 657-8501, Japan; (S.N.); (M.K.)
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4
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Bhowmik S, Ghosh T, Sanghvi YS, Das AK. Synthesis and Structural Studies of Nucleobase Functionalized Hydrogels for Controlled Release of Vitamins. ACS APPLIED BIO MATERIALS 2023; 6:5301-5309. [PMID: 37971725 DOI: 10.1021/acsabm.3c00582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The development of biomolecule-derived biocompatible scaffolds for drug delivery applications is an emerging research area. Herein, we have synthesized a series of nucleobase guanine (G) functionalized amino acid conjugates having different chain lengths to study their molecular self-assembly in the hydrogel state. The gelation properties have been induced by the correct choice of chain lengths of fatty acids present in nucleobase functionalized molecules. The effect of alkali metal cations, pH, and the concentration of nucleobase functionalized amino acid conjugates in the molecular self-assembly process has been explored. The presence of Hoogsteen hydrogen bonding interaction drives the formation of a G-quadruplex functionalized hydrogel. The DOSY nuclear magnetic resonance is also performed to evaluate the self-assembling behavior of the newly formed nucleobase functionalized hydrogel. The nanofibrillar morphology is responsible for the formation of a hydrogel, which has been confirmed by various microscopic experiments. The mechanical behaviors of the hydrogel were evaluated by rheological experiments. The in vitro biostability of the synthesized nucleobase amino acid conjugate is also investigated in the presence of hydrolytic enzymes proteinase K and chymotrypsin. Finally, the nucleobase functionalized hydrogel has been used as a drug delivery platform for the control and sustained pH-responsive release of vitamins B2 and B12. This synthesized nucleobase functionalized hydrogel also exhibits noncytotoxic behavior, which has been evaluated by their in vitro cell viability experiment using HEK 293 and MCF-7 cell lines.
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Affiliation(s)
- Sourav Bhowmik
- Department of Chemistry, Indian Institute of Technology Indore, Indore 453552, India
| | - Tapas Ghosh
- Department of Chemistry, Indian Institute of Technology Indore, Indore 453552, India
| | - Yogesh S Sanghvi
- Rasayan Inc., 2802 Crystal Ridge Road, Encinitas, California 92024-6615, United States
| | - Apurba K Das
- Department of Chemistry, Indian Institute of Technology Indore, Indore 453552, India
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5
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Agrahari A, Lipton M, Chmielewski J. Metal-Promoted Higher-Order Assembly of Disulfide-Stapled Helical Barrels. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2645. [PMID: 37836285 PMCID: PMC10574645 DOI: 10.3390/nano13192645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023]
Abstract
Peptide-based helical barrels are a noteworthy building block for hierarchical assembly, with a hydrophobic cavity that can serve as a host for cargo. In this study, disulfide-stapled helical barrels were synthesized containing ligands for metal ions on the hydrophilic face of each amphiphilic peptide helix. The major product of the disulfide-stapling reaction was found to be composed of five amphiphilic peptides, thereby going from a 16-amino-acid peptide to a stapled 80-residue protein in one step. The structure of this pentamer, 5HB1, was optimized in silico, indicating a significant hydrophobic cavity of ~6 Å within a helical barrel. Metal-ion-promoted assembly of the helical barrel building blocks generated higher order assemblies with a three-dimensional (3D) matrix morphology. The matrix was decorated with hydrophobic dyes and His-tagged proteins both before and after assembly, taking advantage of the hydrophobic pocket within the helical barrels and coordination sites within the metal ion-peptide framework. As such, this peptide-based biomaterial has potential for a number of biotechnology applications, including supplying small molecule and protein growth factors during cell and tissue growth within the matrix.
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Affiliation(s)
| | - Mark Lipton
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA;
| | - Jean Chmielewski
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA;
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6
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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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7
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Yu T, Luo X, Prendergast D, Butterfoss GL, Rad B, Balsara NP, Zuckermann RN, Jiang X. Structural Elucidation of a Polypeptoid Chain in a Crystalline Lattice Reveals Key Morphology-Directing Role of the N-Terminus. ACS NANO 2023; 17:4958-4970. [PMID: 36821346 PMCID: PMC10018772 DOI: 10.1021/acsnano.2c12503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/13/2023] [Indexed: 06/12/2023]
Abstract
The ability to engineer synthetic polymers with the same structural precision as biomacromolecules is crucial to enable the de novo design of robust nanomaterials with biomimetic function. Peptoids, poly(N-substituted) glycines, are a highly controllable bio-inspired polymer family that can assemble into a variety of functional, crystalline nanostructures over a wide range of sequences. Extensive investigation on the molecular packing in these lattices has been reported; however, many key atomic-level details of the molecular structure remain underexplored. Here, we use cryo-TEM 3D reconstruction to directly visualize the conformation of an individual polymer chain within a peptoid nanofiber lattice in real space at 3.6 Å resolution. The backbone in the N-decylglycine hydrophobic core is shown to clearly adopt an extended, all-cis-sigma strand conformation, as previously suggested in many peptoid lattice models. We also show that packing interactions (covalent and noncovalent) at the solvent-exposed N-termini have a dominant impact on the local chain ordering and hence the ability of the chains to pack into well-ordered lattices. Peptoids in pure water form fibers with limited growth in the a direction (<14 molecules in width), whereas in the presence of formamide, they grow to over microns in length in the a direction. This dependence points to the significant role of the chain terminus in determining the long-range order in the packing of peptoid lattices and provides an opportunity to modulate lattice stability and nanoscale morphology by the addition of exogenous small molecules. These findings help resolve a major challenge in the de novo structure-based design of sequence-defined biomimetic nanostructures based on crystalline domains and should accelerate the design of functional nanostructures.
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Affiliation(s)
- Tianyi Yu
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Xubo Luo
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - David Prendergast
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Glenn L. Butterfoss
- Center
for Genomics and Systems Biology, New York
University, Abu Dhabi, United Arab Emirates
| | - Behzad Rad
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Nitash P. Balsara
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Ronald N. Zuckermann
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Xi Jiang
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
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8
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Woolfson DN. Understanding a protein fold: the physics, chemistry, and biology of α-helical coiled coils. J Biol Chem 2023; 299:104579. [PMID: 36871758 PMCID: PMC10124910 DOI: 10.1016/j.jbc.2023.104579] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/07/2023] Open
Abstract
Protein science is being transformed by powerful computational methods for structure prediction and design: AlphaFold2 can predict many natural protein structures from sequence, and other AI methods are enabling the de novo design of new structures. This raises a question: how much do we understand the underlying sequence-to-structure/function relationships being captured by these methods? This perspective presents our current understanding of one class of protein assembly, the α-helical coiled coils. At first sight, these are straightforward: sequence repeats of hydrophobic (h) and polar (p) residues, (hpphppp)n, direct the folding and assembly of amphipathic α helices into bundles. However, many different bundles are possible: they can have two or more helices (different oligomers); the helices can have parallel, antiparallel or mixed arrangements (different topologies); and the helical sequences can be the same (homomers) or different (heteromers). Thus, sequence-to-structure relationships must be present within the hpphppp repeats to distinguish these states. I discuss the current understanding of this problem at three levels: First, physics gives a parametric framework to generate the many possible coiled-coil backbone structures. Second, chemistry provides a means to explore and deliver sequence-to-structure relationships. Third, biology shows how coiled coils are adapted and functionalized in nature, inspiring applications of coiled coils in synthetic biology. I argue that the chemistry is largely understood; the physics is partly solved, though the considerable challenge of predicting even relative stabilities of different coiled-coil states remains; but there is much more to explore in the biology and synthetic biology of coiled coils.
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Affiliation(s)
- Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, United Kingdom; School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, United Kingdom; BrisEngBio, School of Chemistry, University of Bristol, Bristol, United Kingdom; Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, United Kingdom.
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9
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Supramolecular assembly of a trivalent peptide hydrogel vaccine for cancer immunotherapy. Acta Biomater 2023; 158:535-546. [PMID: 36632876 DOI: 10.1016/j.actbio.2022.12.070] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/10/2022] [Accepted: 12/30/2022] [Indexed: 01/11/2023]
Abstract
Vaccination shows great promise in cancer immunotherapy. However, the induction of robust and broad therapeutic CD8 T cell immunity against tumors is challenging due to the essential heterogenicity of tumor antigen expression. Recently, bioinspired materials have reshaped the field of cancer nanomedicine. Herein, a bioinspired nanofibrous trivalent peptide hydrogel vaccine was constructed using the spontaneous supramolecular co-assembly of three antigenic epitope-conjugated peptides, which could mimic the fibrillar structure and biological function of the extracellular matrix and naturally occurring protein assembly. The hydrogel vaccine could be accurately and flexibly adjusted to load each antigenic peptide at a defined ratio, which facilitated the antigen presentation of dendritic cells and significantly improved the initiation of CD8 T cell response and the secretion of interferon-γ (IFN-γ). C57BL/6 mice were immunized with the trivalent peptide hydrogel vaccine, where it elicited a high broad-spectrum antitumor CD8 T cell response that significantly inhibited the growth of B16 tumors in the absence of additional immunoadjuvants or delivery systems. In summary, the supramolecular assembly of triple antigenic epitope-conjugated peptides offers a simple, customizable, and versatile approach for the development of cancer vaccines with remarkable therapeutic efficacy, thereby providing a highly versatile platform for the application of personalized multivalent tumor vaccines. STATEMENT OF SIGNIFICANCE: (1) We report a feasible, versatile and bioinspired approach to manufacture a multivalent peptide-based hydrogel cancer vaccine in the absence of additional adjuvants, which closely mimics immune niches, co-delivers antigen epitopes, greatly promotes antigen presentation to DCs and their subsequent homing to dLNs and elicits a broad-spectrum antitumor CD8 T cell response, resulting in significant inhibition of B16 tumor growth. (2) This feasible and efficient co-assembly strategy provides an attractive platform for engineering a range of multivalent vaccines at defined ratios to further enhance antigen-specific T cell responses. This approach may also be used for personalized immunotherapy with neo-epitopes.
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10
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Differential sensing with arrays of de novo designed peptide assemblies. Nat Commun 2023; 14:383. [PMID: 36693847 PMCID: PMC9873944 DOI: 10.1038/s41467-023-36024-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/11/2023] [Indexed: 01/25/2023] Open
Abstract
Differential sensing attempts to mimic the mammalian senses of smell and taste to identify analytes and complex mixtures. In place of hundreds of complex, membrane-bound G-protein coupled receptors, differential sensors employ arrays of small molecules. Here we show that arrays of computationally designed de novo peptides provide alternative synthetic receptors for differential sensing. We use self-assembling α-helical barrels (αHBs) with central channels that can be altered predictably to vary their sizes, shapes and chemistries. The channels accommodate environment-sensitive dyes that fluoresce upon binding. Challenging arrays of dye-loaded barrels with analytes causes differential fluorophore displacement. The resulting fluorimetric fingerprints are used to train machine-learning models that relate the patterns to the analytes. We show that this system discriminates between a range of biomolecules, drink, and diagnostically relevant biological samples. As αHBs are robust and chemically diverse, the system has potential to sense many analytes in various settings.
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11
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Rosa E, de Mello L, Castelletto V, Dallas ML, Accardo A, Seitsonen J, Hamley IW. Cell Adhesion Motif-Functionalized Lipopeptides: Nanostructure and Selective Myoblast Cytocompatibility. Biomacromolecules 2023; 24:213-224. [PMID: 36520063 PMCID: PMC9832505 DOI: 10.1021/acs.biomac.2c01068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The conformation and self-assembly of four lipopeptides, peptide amphiphiles comprising peptides conjugated to lipid chains, in aqueous solution have been examined. The peptide sequence in all four lipopeptides contains the integrin cell adhesion RGDS motif, and the cytocompatibility of the lipopeptides is also analyzed. Lipopeptides have either tetradecyl (C14, myristyl) or hexadecyl (C16, palmitoyl) lipid chains and peptide sequence WGGRGDS or GGGRGDS, that is, with either a tryptophan-containing WGG or triglycine GGG tripeptide spacer between the bioactive peptide motif and the alkyl chain. All four lipopeptides self-assemble above a critical aggregation concentration (CAC), determined through several comparative methods using circular dichroism (CD) and fluorescence. Spectroscopic methods [CD and Fourier transform infrared (FTIR) spectroscopy] show the presence of β-sheet structures, consistent with the extended nanotape, helical ribbon, and nanotube structures observed by cryogenic transmission electron microscopy (cryo-TEM). The high-quality cryo-TEM images clearly show the coexistence of helically twisted ribbon and nanotube structures for C14-WGGRGDS, which highlight the mechanism of nanotube formation by the closure of the ribbons. Small-angle X-ray scattering shows that the nanotapes comprise highly interdigitated peptide bilayers, which are also present in the walls of the nanotubes. Hydrogel formation was observed at sufficiently high concentrations or could be induced by a heat/cool protocol at lower concentrations. Birefringence due to nematic phase formation was observed for several of the lipopeptides, along with spontaneous flow alignment of the lyotropic liquid crystal structure in capillaries. Cell viability assays were performed using both L929 fibroblasts and C2C12 myoblasts to examine the potential uses of the lipopeptides in tissue engineering, with a specific focus on application to cultured (lab-grown) meat, based on myoblast cytocompatibility. Indeed, significantly higher cytocompatibility of myoblasts was observed for all four lipopeptides compared to that for fibroblasts, in particular at a lipopeptide concentration below the CAC. Cytocompatibility could also be improved using hydrogels as cell supports for fibroblasts or myoblasts. Our work highlights that precision control of peptide sequences using bulky aromatic residues within "linker sequences" along with alkyl chain selection can be used to tune the self-assembled nanostructure. In addition, the RGDS-based lipopeptides show promise as materials for tissue engineering, especially those of muscle precursor cells.
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Affiliation(s)
- Elisabetta Rosa
- School
of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights,
Reading, Berkshire RG6 6AD, U.K.,Department
of Pharmacy and Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Via Domenico Montesano 49, Naples 80131, Italy
| | - Lucas de Mello
- School
of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights,
Reading, Berkshire RG6 6AD, U.K.,Departamento
de Biofísica, Universidade Federal
de São Paulo, São
Paulo 04023-062, Brazil
| | - Valeria Castelletto
- School
of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights,
Reading, Berkshire RG6 6AD, U.K.
| | - Mark L. Dallas
- School
of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights,
Reading, Berkshire RG6 6AD, U.K.
| | - Antonella Accardo
- Department
of Pharmacy and Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Via Domenico Montesano 49, Naples 80131, Italy
| | - Jani Seitsonen
- Nanomicroscopy
Center, Aalto University, Puumiehenkuja 2, Espoo FIN-02150, Finland
| | - Ian W. Hamley
- School
of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights,
Reading, Berkshire RG6 6AD, U.K.,
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12
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Hao L, Wang A, Fu J, Sen Liang, Han Q, Jing Y, Li J, Li Q, Bai S, Seeberger PH, Yin J. Biomineralized Dipeptide Self-Assembled Hydrogel with Ultrahigh Mechanical Strength and Osteoinductivity for Bone Regeneration. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.130622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Jorgensen MD, Chmielewski J. Recent advances in coiled-coil peptide materials and their biomedical applications. Chem Commun (Camb) 2022; 58:11625-11636. [PMID: 36172799 DOI: 10.1039/d2cc04434j] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extensive research has gone into deciphering the sequence requirements for peptides to fold into coiled-coils of varying oligomeric states. More recently, additional signals have been introduced within coiled-coils to promote higher order assembly into biomaterials with a rich distribution of morphologies. Herein we describe these strategies for association of coiled-coil building blocks and biomedical applications. With many of the systems described herein having proven use in protein storage, cargo binding and delivery, three dimensional cell culturing and vaccine development, the future potential of coiled-coil materials to have significant biomedical impact is highly promising.
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Affiliation(s)
- Michael D Jorgensen
- Purdue University, Department of Chemistry, 560 Oval Drive, West Lafayette, Indiana, USA.
| | - Jean Chmielewski
- Purdue University, Department of Chemistry, 560 Oval Drive, West Lafayette, Indiana, USA.
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14
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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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15
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Jiang L, Zuo X, Li J, Traaseth NJ, Kirshenbaum K. Programmed Supramolecular Assemblies Using Orthogonal Pairs of Heterodimeric Coiled Coil Peptides. Angew Chem Int Ed Engl 2022; 61:e202201895. [PMID: 35415953 PMCID: PMC10361782 DOI: 10.1002/anie.202201895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Indexed: 11/05/2022]
Abstract
Despite recent progress, it remains challenging to program biomacromolecules to assemble into discrete nanostructures with pre-determined sizes and topologies. We report here a novel strategy to address this challenge. By using two orthogonal pairs of heterodimeric coiled coils as the building blocks, we constructed six discrete supramolecular assemblies, each composed of a prescribed number of coiled coil components. Within these assemblies, different coiled coils were connected via end-to-side covalent linkages strategically pre-installed between the non-complementary pairs. The overall topological features of two highly complex assemblies, a "barbell" and a "quadrilateral" form, were characterized experimentally and were in good agreement to the designs. This work expands the design paradigms for peptide-based discrete supramolecular assemblies and will provide a route for de novo fabrication of functional protein materials.
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Affiliation(s)
- Linhai Jiang
- Chemistry Department, New York University, 100 Washington Square E, New York, NY 10003, USA
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Jianping Li
- Chemistry Department, New York University, 100 Washington Square E, New York, NY 10003, USA
| | - Nathaniel J Traaseth
- Chemistry Department, New York University, 100 Washington Square E, New York, NY 10003, USA
| | - Kent Kirshenbaum
- Chemistry Department, New York University, 100 Washington Square E, New York, NY 10003, USA
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16
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Lam NT, McCluskey JB, Glover DJ. Harnessing the Structural and Functional Diversity of Protein Filaments as Biomaterial Scaffolds. ACS APPLIED BIO MATERIALS 2022; 5:4668-4686. [PMID: 35766918 DOI: 10.1021/acsabm.2c00275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The natural ability of many proteins to polymerize into highly structured filaments has been harnessed as scaffolds to align functional molecules in a diverse range of biomaterials. Protein-engineering methodologies also enable the structural and physical properties of filaments to be tailored for specific biomaterial applications through genetic engineering or filaments built from the ground up using advances in the computational prediction of protein folding and assembly. Using these approaches, protein filament-based biomaterials have been engineered to accelerate enzymatic catalysis, provide routes for the biomineralization of inorganic materials, facilitate energy production and transfer, and provide support for mammalian cells for tissue engineering. In this review, we describe how the unique structural and functional diversity in natural and computationally designed protein filaments can be harnessed in biomaterials. In addition, we detail applications of these protein assemblies as material scaffolds with a particular emphasis on applications that exploit unique properties of specific filaments. Through the diversity of protein filaments, the biomaterial engineer's toolbox contains many modular protein filaments that will likely be incorporated as the main structural component of future biomaterials.
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Affiliation(s)
- Nga T Lam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Joshua B McCluskey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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17
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Jorgensen M, Chmielewski J. Co-assembled Coiled-Coil Peptide Nanotubes with Enhanced Stability and Metal-Dependent Cargo Loading. ACS OMEGA 2022; 7:20945-20951. [PMID: 35755377 PMCID: PMC9219066 DOI: 10.1021/acsomega.2c01669] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/30/2022] [Indexed: 05/07/2023]
Abstract
Peptide nanotube biomaterials are attractive for their range of applications. Herein, we disclose the co-assembly of coiled-coil peptides, one with ligands for metal ions that demonstrate hierarchical assembly into nanotubes, with spatial control of the metal-binding ligands. Enhanced stability of the nanotubes to phosphate-buffered saline was successfully accomplished in a metal-dependent fashion, depending on the levels and placement of the ligand-containing coiled-coil peptide. This spatial control also allowed for site-specific labeling of the nanotubes with His-tagged fluorophores through the length of the tubes or at the termini, in a metal-dependent manner.
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18
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Liu Z, Shi X, Shu W, Qi S, Wang X, He X. The effect of hydration and dehydration on the conformation, assembling behavior and photoluminescence of PBLG. SOFT MATTER 2022; 18:4396-4401. [PMID: 35635105 DOI: 10.1039/d2sm00344a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Hydration and dehydration play crucial roles in hydrophobic effects (HEs) and are yet to be understood. Poly(γ-benzyl-L-glutamate) (PBLG) homopolymers in THF/water with various water contents were investigated. We discovered that PBLG was hydrated at low water contents and adopted a helical conformation. The chain became dehydrated with increasing water content, which converted the PBLG100 helix to a PPII-helix. The variation in the conformation resulted in an alteration of the self-assembled morphologies from fibers to particles. For PBLG12 with a shorter chain, the chain underwent an α-to-β transition in the conformation due to dehydration as the water content increased, and correspondingly the morphologies varied from tapes to helical ribbons, and eventually to toroids at a higher water content. We also observed that this α-to-β transition is accompanied by an increase in intensity of the fluorescence, which is attributed to the through-space-conjugation of tightly packed phenyl groups within the β-sheet. The discovered effect of hydration and dehydration on the PBLG chain conformation, self-assembling behavior and optical function is essential for the innovation of polypeptide materials and understanding of water-mediated biological systems.
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Affiliation(s)
- Zhen Liu
- School of Chemistry and Molecular Engineering, East China Normal University, No. 500 Dongchuan Road, shanghai 200241, China.
| | - Xinjie Shi
- School of Chemistry and Molecular Engineering, East China Normal University, No. 500 Dongchuan Road, shanghai 200241, China.
| | - Wenchao Shu
- School of Chemistry and Molecular Engineering, East China Normal University, No. 500 Dongchuan Road, shanghai 200241, China.
| | - Shuo Qi
- School of Chemistry and Molecular Engineering, East China Normal University, No. 500 Dongchuan Road, shanghai 200241, China.
| | - Xiaosong Wang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N21 3G1, Canada.
| | - Xiaohua He
- School of Chemistry and Molecular Engineering, East China Normal University, No. 500 Dongchuan Road, shanghai 200241, China.
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19
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Curtis RW, Scrudders KL, Ulcickas JRW, Simpson GJ, Low-Nam ST, Chmielewski J. Supramolecular Assembly of His-Tagged Fluorescent Protein Guests within Coiled-Coil Peptide Crystal Hosts: Three-Dimensional Ordering and Protein Thermal Stability. ACS Biomater Sci Eng 2022; 8:1860-1866. [PMID: 35377599 PMCID: PMC9840175 DOI: 10.1021/acsbiomaterials.2c00155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The use of biomaterials for the inclusion and stabilization of biopolymers is an ongoing challenge. Herein, we disclose three-dimensional (3D) coiled-coil peptide crystals with metal ions that include and overgrow His-tagged fluorescent proteins within the crystal. The protein guests are found within two symmetry-related growth sectors of the crystalline host that are associated with faces of the growing crystal that display ligands for metal ions. The fluorescent proteins are included within this "hourglass" region of the crystals at a notably high level, display order within the crystal hosts, and demonstrate sufficiently tight packing to enable energy transfer between a donor-acceptor pair. His-tagged fluorescent proteins display remarkable thermal stability to denaturation over extended periods of time (days) at high temperatures when within the crystals. Ultimately, this strategy may prove useful for the prolonged storage of thermally sensitive biopolymer guests within a 3D crystalline matrix.
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Affiliation(s)
- Ryan W. Curtis
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Kevin L. Scrudders
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - James R. W. Ulcickas
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Garth J. Simpson
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Shalini T. Low-Nam
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Jean Chmielewski
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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20
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Jiang L, Zuo X, Li J, Traaseth NJ, Kirshenbaum K. Programmed Supramolecular Assemblies Using Orthogonal Pairs of Heterodimeric Coiled Coil Peptides. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Linhai Jiang
- Chemistry Department New York University 100 Washington Square E New York NY 10003 USA
| | - Xiaobing Zuo
- X-ray Science Division Argonne National Laboratory Lemont IL 60439 USA
| | - Jianping Li
- Chemistry Department New York University 100 Washington Square E New York NY 10003 USA
| | - Nathaniel J. Traaseth
- Chemistry Department New York University 100 Washington Square E New York NY 10003 USA
| | - Kent Kirshenbaum
- Chemistry Department New York University 100 Washington Square E New York NY 10003 USA
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21
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Chatterjee A, Reja A, Pal S, Das D. Systems chemistry of peptide-assemblies for biochemical transformations. Chem Soc Rev 2022; 51:3047-3070. [PMID: 35316323 DOI: 10.1039/d1cs01178b] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
During the billions of years of the evolutionary journey, primitive polymers, involved in proto metabolic pathways with low catalytic activity, played critical roles in the emergence of modern enzymes with remarkable substrate specificity. The precise positioning of amino acid residues and the complex orchestrated interplay in the binding pockets of evolved enzymes promote covalent and non-covalent interactions to foster a diverse set of complex catalytic transformations. Recent efforts to emulate the structural and functional information of extant enzymes by minimal peptide based assemblies have attempted to provide a holistic approach that could help in discerning the prebiotic origins of catalytically active binding pockets of advanced proteins. In addition to the impressive sets of advanced biochemical transformations, catalytic promiscuity and cascade catalysis by such small molecule based dynamic systems can foreshadow the ancestral catalytic processes required for the onset of protometabolism. Looking beyond minimal systems that work close to equilibrium, catalytic systems and compartments under non-equilibrium conditions utilizing simple prebiotically relevant precursors have attempted to shed light on how bioenergetics played an essential role in chemical emergence of complex behaviour. Herein, we map out these recent works and progress where diverse sets of complex enzymatic transformations were demonstrated by utilizing minimal peptide based self-assembled systems. Further, we have attempted to cover the examples of peptide assemblies that could feature promiscuous activity and promote complex multistep cascade reaction networks. The review also covers a few recent examples of minimal transient catalytic assemblies under non-equilibrium conditions. This review attempts to provide a broad perspective for potentially programming functionality via rational selection of amino acid sequences leading towards minimal catalytic systems that resemble the traits of contemporary enzymes.
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Affiliation(s)
- Ayan Chatterjee
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Antara Reja
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Sumit Pal
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
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22
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Guo R, Sinha NJ, Misra R, Tang Y, Langenstein M, Kim K, Fagan JA, Kloxin CJ, Jensen G, Pochan DJ, Saven JG. Computational Design of Homotetrameric Peptide Bundle Variants Spanning a Wide Range of Charge States. Biomacromolecules 2022; 23:1652-1661. [PMID: 35312288 DOI: 10.1021/acs.biomac.1c01539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the ability to design their sequences and structures, peptides can be engineered to realize a wide variety of functionalities and structures. Herein, computational design was used to identify a set of 17 peptides having a wide range of putative charge states but the same tetrameric coiled-coil bundle structure. Calculations were performed to identify suitable locations for ionizable residues (D, E, K, and R) at the bundle's exterior sites, while interior hydrophobic interactions were retained. The designed bundle structures spanned putative charge states of -32 to +32 in units of electron charge. The peptides were experimentally investigated using spectroscopic and scattering techniques. Thermal stabilities of the bundles were investigated using circular dichroism. Molecular dynamics simulations assessed structural fluctuations within the bundles. The cylindrical peptide bundles, 4 nm long by 2 nm in diameter, were covalently linked to form rigid, micron-scale polymers and characterized using transmission electron microscopy. The designed suite of sequences provides a set of readily realized nanometer-scale structures of tunable charge that can also be polymerized to yield rigid-rod polyelectrolytes.
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Affiliation(s)
- Rui Guo
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Nairiti J Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.,NIST Center for Neutron Research (NCNR), National Institute of Standards & Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Rajkumar Misra
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Yao Tang
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Matthew Langenstein
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Kyunghee Kim
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffrey A Fagan
- Materials Science and Engineering Division, National Institute of Standards & Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Christopher J Kloxin
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Grethe Jensen
- NIST Center for Neutron Research (NCNR), National Institute of Standards & Technology (NIST), Gaithersburg, Maryland 20899, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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23
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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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24
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Sasselli IR, Syrgiannis Z, Sather NA, Palmer LC, Stupp SI. Modeling Interactions within and between Peptide Amphiphile Supramolecular Filaments. J Phys Chem B 2022; 126:650-659. [PMID: 35029997 DOI: 10.1021/acs.jpcb.1c09258] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many peptides are able to self-assemble into one-dimensional (1D) nanostructures, such as cylindrical fibers or ribbons of variable widths, but the relationship between the morphology of 1D objects and their molecular structure is not well understood. Here, we use coarse-grained molecular dynamics (CG-MD) simulations to study the nanostructures formed by self-assembly of different peptide amphiphiles (PAs). The results show that ribbons are hierarchical superstructures formed by laterally assembled cylindrical fibers. Simulations starting from bilayer structures demonstrate the formation of filaments, whereas other simulations starting from filaments indicate varying degrees of interaction among them depending on chemical structure. These interactions are verified by observations using atomic force microscopy of the various systems. The interfilament interactions are predicted to be strongest in supramolecular assemblies that display hydrophilic groups on their surfaces, while those with hydrophobic ones are predicted to interact more weakly as confirmed by viscosity measurements. The simulations also suggest that peptide amphiphiles with hydrophobic termini bend to reduce their interfacial energy with water, which may explain why these systems do not collapse into superstructures of bundled filaments. The simulations suggest that future experiments will need to address mechanistic questions about the self-assembly of these systems into hierarchical structures, namely, the preformation of interactive filaments vs equilibration of large assemblies into superstructures.
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Affiliation(s)
- Ivan R Sasselli
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Zois Syrgiannis
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Nicholas A Sather
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States
| | - Liam C Palmer
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Samuel I Stupp
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States.,Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States.,Department of Medicine, Northwestern University, 676 N St. Clair, Chicago, Illinois 60611, United States.,Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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25
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Kim NH, Choi H, Shahzad ZM, Ki H, Lee J, Chae H, Kim YH. Supramolecular assembly of protein building blocks: from folding to function. NANO CONVERGENCE 2022; 9:4. [PMID: 35024976 PMCID: PMC8755899 DOI: 10.1186/s40580-021-00294-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Several phenomena occurring throughout the life of living things start and end with proteins. Various proteins form one complex structure to control detailed reactions. In contrast, one protein forms various structures and implements other biological phenomena depending on the situation. The basic principle that forms these hierarchical structures is protein self-assembly. A single building block is sufficient to create homogeneous structures with complex shapes, such as rings, filaments, or containers. These assemblies are widely used in biology as they enable multivalent binding, ultra-sensitive regulation, and compartmentalization. Moreover, with advances in the computational design of protein folding and protein-protein interfaces, considerable progress has recently been made in the de novo design of protein assemblies. Our review presents a description of the components of supramolecular protein assembly and their application in understanding biological phenomena to therapeutics.
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Affiliation(s)
- Nam Hyeong Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hojae Choi
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Zafar Muhammad Shahzad
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
- School of Chemical Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Heesoo Ki
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jaekyoung Lee
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Heeyeop Chae
- School of Chemical Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Yong Ho Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- Center for Neuroscience Imaging Research, Institute for Basic Science (IBS), Suwon, 16419, Republic of Korea.
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26
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Dong Q, Wang M, Wang A, Yu C, Bai S, Yin J, You Q. Self-assembly of Fmoc-amino acids in capillary confined space forming parallel ordered fiber network for application of vascularization. Biomater Sci 2022; 10:1470-1475. [DOI: 10.1039/d2bm00041e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Matrix formed by self-assembly of amino acids and their derivatives are suitable for cell spreading, migration and proliferation, and widely used in tissue engineering and organ regeneration, due to the...
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27
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Guo K, Liu W, Wang Y, Wei H, Li B, Li Y, Yang Y. Handedness inversion of the self-assemblies of lipotetrapeptides regulated by the shift of the methyl group. NEW J CHEM 2022. [DOI: 10.1039/d2nj00465h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four lipotetrapeptides containing three glycines and one l-alanine self-assembled into twisted nanoribbons. Handedness inversion was observed with the movement of l-alanine.
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Affiliation(s)
- Kexiao Guo
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Key Laboratory of Polymeric Materials Design and Synthesis for Biomedical Function, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Wei Liu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Key Laboratory of Polymeric Materials Design and Synthesis for Biomedical Function, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Yong Wang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Key Laboratory of Polymeric Materials Design and Synthesis for Biomedical Function, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - He Wei
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Key Laboratory of Polymeric Materials Design and Synthesis for Biomedical Function, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Baozong Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Key Laboratory of Polymeric Materials Design and Synthesis for Biomedical Function, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Yi Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Key Laboratory of Polymeric Materials Design and Synthesis for Biomedical Function, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Yonggang Yang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Key Laboratory of Polymeric Materials Design and Synthesis for Biomedical Function, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
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28
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Priegue JM, Louzao I, Gallego I, Montenegro J, Granja JR. 1D alignment of proteins and other nanoparticles by using reversible covalent bonds on cyclic peptide nanotubes. Org Chem Front 2022. [DOI: 10.1039/d1qo01349a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide nanotubes deposit on mica surface can be used for the alignment of proteins thank to the use of dynamic covalent bonds that allow the incorporation of appropriate ligands on nanotube surface.
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Affiliation(s)
- Juan M. Priegue
- Singular Research Centre in Chemical Biology and Molecular Materials, (CIQUS), Organic Chemistry Department, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
| | - Iria Louzao
- Singular Research Centre in Chemical Biology and Molecular Materials, (CIQUS), Organic Chemistry Department, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
| | - Iván Gallego
- Singular Research Centre in Chemical Biology and Molecular Materials, (CIQUS), Organic Chemistry Department, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
| | - Javier Montenegro
- Singular Research Centre in Chemical Biology and Molecular Materials, (CIQUS), Organic Chemistry Department, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
| | - Juan R. Granja
- Singular Research Centre in Chemical Biology and Molecular Materials, (CIQUS), Organic Chemistry Department, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
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29
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Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
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Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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30
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Coiled coil exposure and histidine tags drive function of an intracellular protein drug carrier. J Control Release 2021; 339:248-258. [PMID: 34563592 DOI: 10.1016/j.jconrel.2021.09.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 09/09/2021] [Accepted: 09/20/2021] [Indexed: 01/05/2023]
Abstract
In recent years, protein engineering efforts have yielded a diverse set of binding proteins that hold promise for various therapeutic applications. Despite this, their inability to reach intracellular targets limits their applications to cell surface or soluble targets. To address this challenge, we previously reported a protein carrier that binds antibodies and delivers them to therapeutic targets inside cancer cells. This carrier, known as the Hex carrier, is comprised of a self-assembling coiled coil hexamer at the core, with each alpha helix fused to a linker, an antibody binding domain, and a six Histidine-tag (His-tag). In this work, we designed different versions of the carrier to determine the role of each building block in cytosolic protein delivery. We found that increasing exposure of the Hex coiled coil on the carriers, through molecular design or removing antibodies, increased internalization, pointing to a role of the coiled coil in promoting endocytosis. We observed a clear increase in endosomal disruption events when His-tags were present on the carrier relative to when they were removed, due to an endosomal buffering effect. Finally, we found that the antibody binding domains of the Hex carrier could be replaced with monomeric ultra-stable GFP for intracellular delivery and endosomal escape. Our results demonstrate that the Hex coiled coil, in conjunction with His-tags, could be a generalizable vehicle for delivering small and large proteins to intracellular targets. This work also highlights new biological applications for oligomeric coiled coils and shows the direct and quantifiable impact of histidine residues on endosomal disruption. These findings could inform the design of future drug delivery vehicles in applications beyond intracellular protein delivery.
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31
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Wang Y, Wan K, Pan F, Zhu X, Jiang Y, Wang H, Chen Y, Shi X, Liu M. Bamboo-like π-Nanotubes with Tunable Helicity and Circularly Polarized Luminescence. Angew Chem Int Ed Engl 2021; 60:16615-16621. [PMID: 33960094 DOI: 10.1002/anie.202104843] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Indexed: 01/02/2023]
Abstract
We report the fabrication of an exotic bamboo-like π-nanotube via the hierarchical self-assembly of a dipeptide-substituted naphthalenediimide gelator with tunable helicity and circularly polarized luminescence (CPL). It was found that in the presence of trifluoroacetic acid (TFA) the gelator molecules self-assembled into a bamboo-like π-nanotube, which is composed of truncated nanocones and CPL active. When defining the diameter ratio of the lower to upper edge of each nanocone as a parameter to express the helicity of different nanotubes, it was found that both the helicity and CPL of these nanotubes can be adjusted by the amount of TFA. Moreover, the helicity of the nanotube can be conveyed to the achiral quantum dots (QDs) and produce a hybrid nanotube/QDs CPL active materials with adjustable dissymmetry factor. This work finds a new type self-assembled bamboo-like π-nanotube and unveils their helicity and CPL control.
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Affiliation(s)
- Yuan Wang
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kaiwei Wan
- University of Chinese Academy of Sciences, Beijing, 100049, China.,Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, P. R. China
| | - Fei Pan
- Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, P. R. China.,Institute of Solid Mechanics, Beihang University, Beijing, 100191, China
| | - Xuefeng Zhu
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yuqian Jiang
- Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, P. R. China
| | - Hui Wang
- Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, P. R. China
| | - Yuli Chen
- Institute of Solid Mechanics, Beihang University, Beijing, 100191, China
| | - Xinghua Shi
- University of Chinese Academy of Sciences, Beijing, 100049, China.,Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, P. R. China
| | - Minghua Liu
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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32
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Wang Y, Wan K, Pan F, Zhu X, Jiang Y, Wang H, Chen Y, Shi X, Liu M. Bamboo‐like π‐Nanotubes with Tunable Helicity and Circularly Polarized Luminescence. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104843] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Yuan Wang
- Beijing National Laboratory for Molecular Science CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Kaiwei Wan
- University of Chinese Academy of Sciences Beijing 100049 China
- Laboratory of Theoretical and Computational Nanoscience CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology (NCNST) Beijing 100190 P. R. China
| | - Fei Pan
- Laboratory of Theoretical and Computational Nanoscience CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology (NCNST) Beijing 100190 P. R. China
- Institute of Solid Mechanics Beihang University Beijing 100191 China
| | - Xuefeng Zhu
- Beijing National Laboratory for Molecular Science CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Yuqian Jiang
- Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology (NCNST) Beijing 100190 P. R. China
| | - Hui Wang
- Laboratory of Theoretical and Computational Nanoscience CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology (NCNST) Beijing 100190 P. R. China
| | - Yuli Chen
- Institute of Solid Mechanics Beihang University Beijing 100191 China
| | - Xinghua Shi
- University of Chinese Academy of Sciences Beijing 100049 China
- Laboratory of Theoretical and Computational Nanoscience CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology (NCNST) Beijing 100190 P. R. China
| | - Minghua Liu
- Beijing National Laboratory for Molecular Science CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 China
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33
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Babi J, Zhu L, Lin A, Uva A, El‐Haddad H, Peloewetse A, Tran H. Self‐assembled free‐floating
nanomaterials from
sequence‐defined
polymers. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jon Babi
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Linglan Zhu
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Angela Lin
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Azalea Uva
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Hana El‐Haddad
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Atang Peloewetse
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Helen Tran
- Department of Chemistry University of Toronto Toronto Ontario Canada
- Department of Chemical Engineering University of Toronto Toronto Ontario Canada
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34
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Dawson WM, Martin FJO, Rhys GG, Shelley KL, Brady RL, Woolfson DN. Coiled coils 9-to-5: rational de novo design of α-helical barrels with tunable oligomeric states. Chem Sci 2021; 12:6923-6928. [PMID: 34745518 PMCID: PMC8503928 DOI: 10.1039/d1sc00460c] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/13/2021] [Indexed: 01/10/2023] Open
Abstract
The rational design of linear peptides that assemble controllably and predictably in water is challenging. Short sequences must encode unique target structures and avoid alternative states. However, the non-covalent forces that stabilize and discriminate between states are weak. Nonetheless, for α-helical coiled-coil assemblies considerable progress has been made in rational de novo design. In these, sequence repeats of nominally hydrophobic (h) and polar (p) residues, hpphppp, direct the assembly of amphipathic helices into dimeric to tetrameric bundles. Expanding this pattern to hpphhph can produce larger α-helical barrels. Here, we show that pentameric to nonameric barrels are accessed by varying the residue at one of the h sites. In peptides with four L/I-K-E-I-A-x-Z repeats, decreasing the size of Z from threonine to serine to alanine to glycine gives progressively larger oligomers. X-ray crystal structures of the resulting α-helical barrels rationalize this: side chains at Z point directly into the helical interfaces, and smaller residues allow closer helix contacts and larger assemblies.
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Affiliation(s)
- William M Dawson
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Freddie J O Martin
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Guto G Rhys
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Department of Chemistry, University of Bayreuth, Universitätsstraße 30 95447 Bayreuth Germany
| | - Kathryn L Shelley
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- School of Biochemistry, University of Bristol Biomedical Sciences Building, University Walk Bristol BS8 1TD UK
| | - R Leo Brady
- School of Biochemistry, University of Bristol Biomedical Sciences Building, University Walk Bristol BS8 1TD UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- School of Biochemistry, University of Bristol Biomedical Sciences Building, University Walk Bristol BS8 1TD UK
- Bristol BioDesign Institute, University of Bristol Life Sciences Building, Tyndall Avenue Bristol BS8 1TQ UK
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35
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A nanobody toolbox targeting dimeric coiled-coil modules for functionalization of designed protein origami structures. Proc Natl Acad Sci U S A 2021; 118:2021899118. [PMID: 33893235 PMCID: PMC8092592 DOI: 10.1073/pnas.2021899118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Coiled-coil (CC) dimers are widely used in protein design because of their modularity and well-understood sequence-structure relationship. In CC protein origami design, a polypeptide chain is assembled from a defined sequence of CC building segments that determine the self-assembly of protein cages into polyhedral shapes, such as the tetrahedron, triangular prism, or four-sided pyramid. However, a targeted functionalization of the CC modules could significantly expand the versatility of protein origami scaffolds. Here, we describe a panel of single-chain camelid antibodies (nanobodies) directed against different CC modules of a de novo designed protein origami tetrahedron. We show that these nanobodies are able to recognize the same CC modules in different polyhedral contexts, such as isolated CC dimers, tetrahedra, triangular prisms, or trigonal bipyramids, thereby extending the ability to functionalize polyhedra with nanobodies in a desired stoichiometry. Crystal structures of five nanobody-CC complexes in combination with small-angle X-ray scattering show binding interactions between nanobodies and CC dimers forming the edges of a tetrahedron with the nanobody entering the tetrahedral cavity. Furthermore, we identified a pair of allosteric nanobodies in which the binding to the distant epitopes on the antiparallel homodimeric APH CC is coupled via a strong positive cooperativity. A toolbox of well-characterized nanobodies specific for CC modules provides a unique tool to target defined sites in the designed protein structures, thus opening numerous opportunities for the functionalization of CC protein origami polyhedra or CC-based bionanomaterials.
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36
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Saha PC, Bera T, Chatterjee T, Samanta J, Sengupta A, Bhattacharyya M, Guha S. Supramolecular Dipeptide-Based Near-Infrared Fluorescent Nanotubes for Cellular Mitochondria Targeted Imaging and Early Apoptosis. Bioconjug Chem 2021; 32:833-841. [PMID: 33826302 DOI: 10.1021/acs.bioconjchem.1c00106] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Herein, we have designed and synthesized unsymmetrical visible Cy-3 and near-infrared (NIR) Cy-5 chromophores anchoring mitochondria targeting functional group conjugated with a Phe-Phe dipeptide by a microwave-assisted Fmoc solid phase peptide synthesis method on Wang resin. These dipeptide-based Cy-3-TPP/FF as well as Cy-5-TPP/FF molecules self-assemble to form fluorescent nanotubes in solution, and it has been confirmed by TEM, SEM, and AFM. The Cy-3-TPP/FF and Cy-5-TPP/FF molecules in solution exhibit narrow excitation as well as emission bands in the visible and NIR region, respectively. These lipophilic cationic fluorescent peptide molecules spontaneously and selectively accumulate inside the mitochondria of human carcinoma cells that have been experimentally validated by live cell confocal laser scanning microscopy and display a high Pearson's correlation coefficient in a colocalization assay. Live cell multicolor confocal imaging using the NIR Cy-5-TPP/FF in combination with other organelle specific dye is also accomplished. Moreover, these lipophilic dipeptide-based cationic molecules reach the critical aggregation concentration inside the mitochondria because of the extremely negative inner mitochondrial membrane potential [(ΔΨm)cancer ≈ -220 mV] and form supramolecular nanotubes which are accountable for malignant mitochondria targeted early apoptosis. The early apoptosis is arrested using Cy-5-TPP/FF and confirmed by annexin V-FITC/PI apoptosis detection assay.
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Affiliation(s)
- Pranab Chandra Saha
- Department of Chemistry, Organic Chemistry Section, Jadavpur University, Kolkata 700032, India
| | - Tapas Bera
- Department of Chemistry, Organic Chemistry Section, Jadavpur University, Kolkata 700032, India
| | - Tanima Chatterjee
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, India
| | - Jayeeta Samanta
- Department of Life Sciences and Biotechnology, Jadavpur University, Kolkata 700032, India
| | - Arunima Sengupta
- Department of Life Sciences and Biotechnology, Jadavpur University, Kolkata 700032, India
| | - Maitree Bhattacharyya
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, India
| | - Samit Guha
- Department of Chemistry, Organic Chemistry Section, Jadavpur University, Kolkata 700032, India
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37
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Castelletto V, Seitsonen J, Ruokolainen J, Hamley IW. Alpha helical surfactant-like peptides self-assemble into pH-dependent nanostructures. SOFT MATTER 2021; 17:3096-3104. [PMID: 33598669 DOI: 10.1039/d0sm02095h] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A designed surfactant-like peptide is shown, using a combination of cryogenic-transmission electron microscopy and small-angle X-ray scattering, to have remarkable pH-dependent self-assembly properties. Peptide Arg3-Leu12 (R3L12) forms a network of peptide nanotubes at pH 9 and below. These are associated with α-helical conformation in a "cross-α" nanotube structure, in which peptide dimers lie perpendicular to the nanotube axis, with arginine coated inner and outer nanotube walls. In contrast, this peptide forms decorated vesicular aggregates at higher pH values, close to the pKa of the arginine residues. These structures are associated with a loss of α-helical order as detected through X-ray scattering, circular dichroism and FTIR spectroscopy, the latter technique also revealing a loss of ordering of leucine side chains. This suggests a proposed model for the decorated or patchy vesicular structures that comprises disordered peptide as the matrix of the membrane, with small domains of ordered peptide dimers forming the minority domains. We ascribe this to a lipid-raft like phase separation process, due to conformational disordering of the leucine hydrophobic chains. The observation of the self-assembly of a simple surfactant-like peptide into these types of nanostructure is remarkable, and peptide R3L12 shows unique pH-dependent morphological and conformational behaviour, with the potential for a range of future applications.
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38
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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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39
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Chen Y, Zhou Y, Yin H. Recent advances in biosensor for histone acetyltransferase detection. Biosens Bioelectron 2021; 175:112880. [DOI: 10.1016/j.bios.2020.112880] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/26/2020] [Accepted: 12/01/2020] [Indexed: 12/15/2022]
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40
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Wang F, Gnewou O, Modlin C, Beltran LC, Xu C, Su Z, Juneja P, Grigoryan G, Egelman EH, Conticello VP. Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials. Nat Commun 2021; 12:407. [PMID: 33462223 PMCID: PMC7814010 DOI: 10.1038/s41467-020-20689-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/02/2020] [Indexed: 12/12/2022] Open
Abstract
The exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-α supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within the cross-α nanotubes. The structure of the resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to flagella and pili.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Ordy Gnewou
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Charles Modlin
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Leticia C Beltran
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Chunfu Xu
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Zhangli Su
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Puneet Juneja
- The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), Emory University, Atlanta, GA, 30322, USA
| | - Gevorg Grigoryan
- Department of Computer Science, Dartmouth College, Hanover, NH, 03755, USA.,Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Vincent P Conticello
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA. .,The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), Emory University, Atlanta, GA, 30322, USA.
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41
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Jiang Y, Zhang W, Yang F, Wan C, Cai X, Liu J, Zhang Q, Li Z, Han W. Molecular design of stapled pentapeptides as building blocks of self-assembled coiled coil-like fibers. SCIENCE ADVANCES 2021; 7:eabd0492. [PMID: 33523941 PMCID: PMC10662664 DOI: 10.1126/sciadv.abd0492] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Peptide self-assembly inspired by natural superhelical coiled coils has been actively pursued but remains challenging due to limited helicity of short peptides. Side chain stapling can strengthen short helices but is unexplored in design of self-assembled helical nanofibers as it is unknown how staples could be adapted to coiled coil architecture. Here, we demonstrate the feasibility of this design for pentapeptides using a computational method capable of predicting helicity and fiber-forming tendency of stapled peptides containing noncoded amino acids. Experiments showed that the best candidates, which carried an aromatically substituted staple and phenylalanine analogs, displayed exceptional helicity and assembled into nanofibers via specific head-to-tail hydrogen bonding and packing between staple and noncoded side chains. The fibers exhibited sheet-of-helix structures resembling the recently found collapsed coiled coils whose formation was sensitive to side chain flexibility. This study expands the chemical space of coiled coil assemblies and provides guidance for their design.
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Affiliation(s)
- Yixiang Jiang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518055, China
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen Key Laboratory of Functional Polymer, Shenzhen 518055, China
| | - Wan Zhang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
| | - Fadeng Yang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Chuan Wan
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xiang Cai
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
| | - Jianbo Liu
- Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Qianling Zhang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen Key Laboratory of Functional Polymer, Shenzhen 518055, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China.
- Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Wei Han
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China.
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42
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Choudhury CK, Kuksenok O. Native-Based Dissipative Particle Dynamics Approach for α-Helical Folding. J Phys Chem B 2020; 124:11379-11386. [PMID: 33270459 DOI: 10.1021/acs.jpcb.0c08603] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We developed a dissipative particle dynamics (DPD) approach that captures polyalanine folding into a stable helical conformation. Within the proposed native-based approach, the DPD parameters are derived based on the contact map constructed from the molecular dynamics (MD) simulations. We show that the proposed approach reproduces the folding of polypeptides of various lengths, including bundle formation for sufficiently long polypeptides. The proposed approach also allows one to capture the folding of the helical segments of the lysozyme. With further development of computationally efficient native-based DPD approaches for folding, modeling of a range of biomaterials incorporating α-helical segments could be extended to time and length scales far beyond those accessible in molecular dynamics simulations.
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Affiliation(s)
- Chandan Kumar Choudhury
- Department of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Olga Kuksenok
- Department of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
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43
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Structures and Properties of the Self-Assembling Diphenylalanine Peptide Nanotubes Containing Water Molecules: Modeling and Data Analysis. NANOMATERIALS 2020; 10:nano10101999. [PMID: 33050446 PMCID: PMC7600064 DOI: 10.3390/nano10101999] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 12/31/2022]
Abstract
The structures and properties of the diphenylalanine (FF) peptide nanotubes (PNTs), both L-chiral and D-chiral (L-FF and D-FF) and empty and filled with water/ice clusters, are presented and analyzed. DFT (VASP) and semi-empirical calculations (HyperChem) to study these structural and physical properties of PNTs (including ferroelectric) were used. The results obtained show that after optimization the dipole moment and polarization of both chiral type L-FF and D-FF PNT and embedded water/ice cluster are enhanced; the water/ice cluster acquire the helix-like structure similar as L-FF and D-FF PNT. Ferroelectric properties of tubular water/ice helix-like cluster, obtained after optimization inside L-FF and D-FF PNT, as well of the total L-FF and D-FF PNT with embedded water/ice cluster, are discussed.
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44
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Lynch C, Rao S, Sansom MSP. Water in Nanopores and Biological Channels: A Molecular Simulation Perspective. Chem Rev 2020; 120:10298-10335. [PMID: 32841020 PMCID: PMC7517714 DOI: 10.1021/acs.chemrev.9b00830] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Indexed: 12/18/2022]
Abstract
This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.
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Affiliation(s)
- Charlotte
I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
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45
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Castelletto V, Seitsonen J, Ruokolainen J, Piras C, Cramer R, Edwards-Gayle CJC, Hamley IW. Peptide nanotubes self-assembled from leucine-rich alpha helical surfactant-like peptides. Chem Commun (Camb) 2020; 56:11977-11980. [PMID: 33033814 DOI: 10.1039/d0cc04299d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The designed arginine-rich surfactant-like peptide R3L12 (arginine3-leucine12) is shown to form a remarkable diversity of self-assembled nanostructures in aqueous solution, depending on pH, including nanotubes, mesh-like tubular networks in three-dimensions and square planar arrays in two-dimensions. These structures are built from α-helical antiparallel coiled-coil peptide dimers arranged perpendicular to the nanotube axis, in a "cross-α" nanotube structure. The aggregation behavior is rationalized based on the effects of dimensionality, and the balance of hydrophobic and electrostatic interactions. The nanotube and nanomesh structures display arginine at high density on their surfaces, which may be valuable for future applications.
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Affiliation(s)
- Valeria Castelletto
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK.
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46
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Park WM. Coiled-Coils: the Molecular Zippers that Self-Assemble Protein Nanostructures. Int J Mol Sci 2020; 21:E3584. [PMID: 32438665 PMCID: PMC7278914 DOI: 10.3390/ijms21103584] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023] Open
Abstract
Coiled-coils, the bundles of intertwined helical protein motifs, have drawn much attention as versatile molecular toolkits. Because of programmable interaction specificity and affinity as well as well-established sequence-to-structure relationships, coiled-coils have been used as subunits that self-assemble various molecular complexes in a range of fields. In this review, I describe recent advances in the field of protein nanotechnology, with a focus on programming assembly of protein nanostructures using coiled-coil modules. Modular design approaches to converting the helical motifs into self-assembling building blocks are described, followed by a discussion on the molecular basis and principles underlying the modular designs. This review also provides a summary of recently developed nanostructures with a variety of structural features, which are in categories of unbounded nanostructures, discrete nanoparticles, and well-defined origami nanostructures. Challenges existing in current design strategies, as well as desired improvements for controls over material properties and functionalities for applications, are also provided.
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Affiliation(s)
- Won Min Park
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, KS 66506, USA
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47
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Edgell CL, Savery NJ, Woolfson DN. Robust De Novo-Designed Homotetrameric Coiled Coils. Biochemistry 2020; 59:1087-1092. [DOI: 10.1021/acs.biochem.0c00082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Caitlin L. Edgell
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Nigel J. Savery
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
- BrisSynBio, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, United Kingdom
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
- BrisSynBio, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, United Kingdom
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48
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Weber R, McCullagh M. The Role of Hydrophobicity in the Stability and pH-Switchability of (RXDX) 4 and Coumarin-(RXDX) 4 Conjugate β-Sheets. J Phys Chem B 2020; 124:1723-1732. [PMID: 32045245 DOI: 10.1021/acs.jpcb.0c00048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
pH-Switchable, self-assembling materials are of interest in biological imaging and sensing applications. Here we propose that combining the pH-switchability of RXDX (X = Ala, Val, Leu, Ile, Phe) peptides and the optical properties of coumarin creates an ideal candidate for these materials. This suggestion is tested with a thorough set of all-atom molecular dynamics simulations. We first investigate the dependence of pH-switchabiliy on the identity of the hydrophobic residue, X, in the bare (RXDX)4 systems. Increasing the hydrophobicity stabilizes the fiber which, in turn, reduces the pH-switchabilty of the system. This behavior is found to be somewhat transferable to systems in which a single hydrophobic residue is replaced with a coumarin containing amino acid. In this case, conjugates with X = Ala are found to be unstable at both pHs, while conjugates with X = Val, Leu, Ile, and Phe are found to form stable β-sheets at least at neutral pH. The coumarin-(RFDF)4 conjugate is found to have the largest relative entropy value of 0.884 ± 0.001 between neutral and acidic coumarin ordering distributions. Thus, we posit that coumarin-(RFDF)4 containing peptide sequences are ideal candidates for pH-sensing bioelectronic materials.
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Affiliation(s)
- Ryan Weber
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74074, United States
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Abstract
Proteins are molecular machines whose function depends on their ability to achieve complex folds with precisely defined structural and dynamic properties. The rational design of proteins from first-principles, or de novo, was once considered to be impossible, but today proteins with a variety of folds and functions have been realized. We review the evolution of the field from its earliest days, placing particular emphasis on how this endeavor has illuminated our understanding of the principles underlying the folding and function of natural proteins, and is informing the design of macromolecules with unprecedented structures and properties. An initial set of milestones in de novo protein design focused on the construction of sequences that folded in water and membranes to adopt folded conformations. The first proteins were designed from first-principles using very simple physical models. As computers became more powerful, the use of the rotamer approximation allowed one to discover amino acid sequences that stabilize the desired fold. As the crystallographic database of protein structures expanded in subsequent years, it became possible to construct proteins by assembling short backbone fragments that frequently recur in Nature. The second set of milestones in de novo design involves the discovery of complex functions. Proteins have been designed to bind a variety of metals, porphyrins, and other cofactors. The design of proteins that catalyze hydrolysis and oxygen-dependent reactions has progressed significantly. However, de novo design of catalysts for energetically demanding reactions, or even proteins that bind with high affinity and specificity to highly functionalized complex polar molecules remains an importnant challenge that is now being achieved. Finally, the protein design contributed significantly to our understanding of membrane protein folding and transport of ions across membranes. The area of membrane protein design, or more generally of biomimetic polymers that function in mixed or non-aqueous environments, is now becoming increasingly possible.
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50
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Qian Y, Zhou X, He J, Zhou C. Polycaprolactone-Based Mimetic Antimicrobial Peptide Copolymers Vesicles as an Effective Drug-Carrier for Cancer Therapy. Polymers (Basel) 2019; 11:E1783. [PMID: 31683611 PMCID: PMC6918241 DOI: 10.3390/polym11111783] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/25/2019] [Accepted: 10/25/2019] [Indexed: 12/24/2022] Open
Abstract
A novel series of amphiphilic mimicking antimicrobial peptide copolymers PCL16-b-Kn can assemble in water to form uniform vesicles. Transmission electron microscopy was used to observe the vesicular structure of the nanoparticles, and dynamic light scattering revealed their uniform size and narrow dispersion. Critical vesiculation concentrations were also tested, revealing that these vesicles can exist at low concentrations. Furthermore, in vitro and intracellular drug release of doxorubicin(DOX)-vesicles were conducted. These vesicles could encapsulate DOX and achieve efficient intracellular drug release. Overall, these copolymer vesicles exhibit potential application value as multifunctional drug-carrier systems with antibacterial capability in cancer therapy.
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Affiliation(s)
- Yusheng Qian
- School of Materials Science and Engineering, Tongji University, 4800 Caoan Road, Shanghai 201804, China.
| | - Xinyu Zhou
- School of Materials Science and Engineering, Tongji University, 4800 Caoan Road, Shanghai 201804, China.
| | - Jing He
- Department of Anatomy and Neurobiology, Tongji University School of Medicine, Shanghai 201804, China.
| | - Chuncai Zhou
- School of Materials Science and Engineering, Tongji University, 4800 Caoan Road, Shanghai 201804, China.
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