1
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Piskorz T, Perez-Chirinos L, Qiao B, Sasselli IR. Tips and Tricks in the Modeling of Supramolecular Peptide Assemblies. ACS OMEGA 2024; 9:31254-31273. [PMID: 39072142 PMCID: PMC11270692 DOI: 10.1021/acsomega.4c02628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/30/2024]
Abstract
Supramolecular peptide assemblies (SPAs) hold promise as materials for nanotechnology and biomedicine. Although their investigation often entails adapting experimental techniques from their protein counterparts, SPAs are fundamentally distinct from proteins, posing unique challenges for their study. Computational methods have emerged as indispensable tools for gaining deeper insights into SPA structures at the molecular level, surpassing the limitations of experimental techniques, and as screening tools to reduce the experimental search space. However, computational studies have grappled with issues stemming from the absence of standardized procedures and relevant crystal structures. Fundamental disparities between SPAs and protein simulations, such as the absence of experimentally validated initial structures and the importance of the simulation size, number of molecules, and concentration, have compounded these challenges. Understanding the roles of various parameters and the capabilities of different models and simulation setups remains an ongoing endeavor. In this review, we aim to provide readers with guidance on the parameters to consider when conducting SPA simulations, elucidating their potential impact on outcomes and validity.
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Affiliation(s)
| | - Laura Perez-Chirinos
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 182, 20014 Donostia-San Sebastián, Spain
| | - Baofu Qiao
- Department
of Natural Sciences, Baruch College, City
University of New York, New York, New York 10010, United States
| | - Ivan R. Sasselli
- Centro
de Física de Materiales (CFM), CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
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2
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Jayamaha H, Ugras TJ, Page KA, Hanrath T, Robinson RD, Shepherd LM. Chiroptical Strain Sensors from Electrospun Cadmium Sulfide Quantum-Dot Fibers. ACS APPLIED MATERIALS & INTERFACES 2024; 16:17757-17765. [PMID: 38535523 PMCID: PMC11009915 DOI: 10.1021/acsami.3c17623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 04/12/2024]
Abstract
Controllable synthesis of homochiral nano/micromaterials has been a constant challenge for fabricating various stimuli-responsive chiral sensors. To provide an avenue to this goal, we report electrospinning as a simple and economical strategy to form continuous homochiral microfibers with strain-sensitive chiroptical properties. First, electrospun homochiral microfibers from self-assembled cadmium sulfide (CdS) quantum dot magic-sized clusters (MSCs) are produced. Highly sensitive and reversible strain sensors are then fabricated by embedding these chiroptically active fibers into elastomeric films. The chiroptical response on stretching is indicated quantitatively as reversible changes in magnitude, spectral position (wavelength), and sign in circular dichroism (CD) and linear dichroism (LD) signals and qualitatively as a prominent change in the birefringence features under cross-polarizers. The observed periodic twisted helical fibrils at the surface of fibers provide insights into the origin of the fibers' chirality. The measurable shifts in CD and LD are caused by elastic deformations of these helical fibrillar structures of the fiber. To elucidate the origin of these chiroptical properties, we used field emission-electron microscopy (FE-SEM), atomic force microscopy (AFM), synchrotron X-ray analysis, polarized optical microscopy, as well as measurements to isolate the true CD, and contributions from photoelastic modulators (PEM) and LD. Our findings thus offer a promising strategy to fabricate chiroptical strain-sensing devices with multiple measurables/observables using electric-field-assisted spinning of homochiral nano/microfibers.
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Affiliation(s)
- Hansadi Jayamaha
- Department
of Human Centered Design, Cornell University, Ithaca, New York 14853, United States
| | - Thomas J. Ugras
- School
of Applied and Engineering Physics, Cornell
University, Ithaca, New York 14853, United States
| | - Kirt A. Page
- Materials
and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
- UES,
Inc., Beavercreek, Ohio 45432, United States
- Cornell
High Energy Synchrotron Source, Cornell
University, Ithaca, New York 14853, United States
| | - Tobias Hanrath
- Robert F.
Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Richard D. Robinson
- Department
of Materials Science and Engineering, Cornell
University, Ithaca, New York 14853, United States
| | - Larissa M. Shepherd
- Department
of Human Centered Design, Cornell University, Ithaca, New York 14853, United States
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3
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Sasselli IR, Coluzza I. Assessment of the MARTINI 3 Performance for Short Peptide Self-Assembly. J Chem Theory Comput 2024; 20:224-238. [PMID: 38113378 PMCID: PMC10782451 DOI: 10.1021/acs.jctc.3c01015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023]
Abstract
The coarse-grained MARTINI force field, initially developed for membranes, has proven to be an exceptional tool for investigating supramolecular peptide assemblies. Over the years, the force field underwent refinements to enhance accuracy, enabling, for example, the reproduction of protein-ligand interactions and constant pH behavior. However, these protein-focused improvements seem to have compromised its ability to model short peptide self-assembly. In this study, we assess the performance of MARTINI 3 in reproducing peptide self-assembly using the well-established diphenylalanine (FF) as our test case. Unlike its success in version 2.1, FF does not even exhibit aggregation in version 3. By systematically exploring parameters for the aromatic side chains and charged backbone beads, we established a parameter set that effectively reproduces tube formation. Remarkably, these parameter adjustments also replicate the self-assembly of other di- and tripeptides and coassemblies. Furthermore, our analysis uncovers pivotal insights for enhancing the performance of MARTINI in modeling short peptide self-assembly. Specifically, we identify issues stemming from overestimated hydrophilicity arising from charged termini and disruptions in π-stacking interactions due to insufficient planarity in aromatic groups and a discrepancy in intermolecular distances between this and backbone-backbone interactions. This investigation demonstrates that strategic modifications can harness the advancements offered by MARTINI 3 for the realm of short peptide self-assembly.
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Affiliation(s)
- Ivan R. Sasselli
- Centro
de Física de Materiales (CFM), CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research
and Technology Alliance (BRTA), Paseo de Miramón 182, 20014 Donostia-San Sebastián, Spain
| | - Ivan Coluzza
- Ikerbasque,
Basque Foundation for Science, Plaza de Euskadi 5, 48009 Bilbao, Spain
- BCMaterials,
Basque Center for Materials, Applications and Nanostructures, UPV/EHU Science Park, 48940 Leioa, Spain
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4
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Somasundaran SM, Kompella SVK, Mohan T M N, Das S, Abdul Vahid A, Vijayan V, Balasubramanian S, Thomas KG. Structurally Induced Chirality of an Achiral Chromophore on Self-Assembled Nanofibers: A Twist Makes It Chiral. ACS NANO 2023. [PMID: 37220308 DOI: 10.1021/acsnano.3c03892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The surface domains of self-assembled amphiphiles are well-organized and can perform many physical, chemical, and biological functions. Here, we present the significance of chiral surface domains of these self-assemblies in transferring chirality to achiral chromophores. These aspects are probed using l- and d-isomers of alkyl alanine amphiphiles which self-assemble in water as nanofibers, possessing a negative surface charge. When bound on these nanofibers, positively charged cyanine dyes (CY524 and CY600), each having two quinoline rings bridged by conjugated double bonds, show contrasting chiroptical features. Interestingly, CY600 displays a bisignated circular dichroic (CD) signal with mirror-image symmetry, while CY524 is CD silent. Molecular dynamics simulations reveal that the model cylindrical micelles (CM) derived from the two isomers exhibit surface chirality and the chromophores are buried as monomers in mirror-imaged pockets on their surfaces. The monomeric nature of template-bound chromophores and their binding reversibility are established by concentration- and temperature-dependent spectroscopies and calorimetry. On the CM, CY524 displays two equally populated conformers with opposite sense, whereas CY600 is present as two pairs of twisted conformers in each of which one is in excess, due to differences in weak dye-amphiphile hydrogen bonding interactions. Infrared and NMR spectroscopies support these findings. Reduction of electronic conjugation caused by the twist establishes the two quinoline rings as independent entities. On-resonance coupling between the transition dipoles of these units generates bisignated CD signals with mirror-image symmetry. The results presented herein provide insight on the little-known structurally induced chirality of achiral chromophores through transfer of chiral surface information.
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Affiliation(s)
- Sanoop Mambully Somasundaran
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
| | - Srinath V K Kompella
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India
| | - Nila Mohan T M
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
| | - Sudip Das
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India
| | - Arshad Abdul Vahid
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
| | - Vinesh Vijayan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
| | - Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India
| | - K George Thomas
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
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5
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Hao B, Wei L, Cheng Y, Ma Z, Wang J. Advanced nanomaterial for prostate cancer theranostics. Front Bioeng Biotechnol 2022; 10:1046234. [DOI: 10.3389/fbioe.2022.1046234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
Prostate cancer (PC) has the second highest incidence in men, according to global statistical data. The symptoms of PC in the early stage are not obvious, causing late diagnosis in most patients, which is the cause for missing the optimal treatment time. Thus, highly sensitive and precise early diagnosis methods are very important. Additionally, precise therapy regimens for good targeting and innocuous to the body are indispensable to treat cancer. This review first introduced two diagnosis methods, containing prostate-specific biomarkers detection and molecular imaging. Then, it recommended advanced therapy approaches, such as chemotherapy, gene therapy, and therapeutic nanomaterial. Afterward, we summarized the development of nanomaterial in PC, highlighting the importance of integration of diagnosis and therapy as the future direction against cancer.
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6
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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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7
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Lebedenko CG, Banerjee IA. Investigation of Self‐Assembly of Symmetric and Asymmetric Peptide Bolaamphiphiles by COSMO‐RS and Atomistic Simulations and Their Interactions with POPC Bilayers. MACROMOL THEOR SIMUL 2021. [DOI: 10.1002/mats.202100066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Ipsita A. Banerjee
- Department of Chemistry Fordham University 441 East Fordham Road Bronx NY 10458 USA
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8
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Xiong Q, Stupp SI, Schatz GC. Molecular Insight into the β-Sheet Twist and Related Morphology of Self-Assembled Peptide Amphiphile Ribbons. J Phys Chem Lett 2021; 12:11238-11244. [PMID: 34762436 DOI: 10.1021/acs.jpclett.1c03243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Self-assembly of high-aspect-ratio filaments containing β-sheets has attracted much attention due to potential use in bioengineering and biomedicine. However, precisely predicting the assembled morphologies remains a grand challenge because of insufficient understanding of the self-assembly process. We employed an atomistic model to study the self-assembly of peptide amphiphiles (PAs) containing valine-glutamic acid (VE) dimeric repeats. By changing of the sequence length, the assembly morphology changes from flat ribbon to left-handed twisted ribbon, implying a relationship between β-sheet twist and strength of interstrand hydrogen bonds. The calculations are used to quantify this relationship including both magnitude and sign of the ribbon twist angle. Interestingly, a change in chirality is observed when we introduce the RGD epitope into the C-terminal of VE repeats, suggesting arginine and glycine's role in suppressing right-handed β-sheet formation. This study provides insight into the relationship between β-sheet twist and self-assembled nanostructures including a possible design rule for PA self-assembly.
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Affiliation(s)
- Qinsi Xiong
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Samuel I Stupp
- Department of Chemistry, Center for BioInspired Energy Science, and Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Medicine, Northwestern University, Chicago, Illinois 60611, United States
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
| | - George C Schatz
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
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9
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Sangji MH, Sai H, Chin SM, Lee SR, R Sasselli I, Palmer LC, Stupp SI. Supramolecular Interactions and Morphology of Self-Assembling Peptide Amphiphile Nanostructures. NANO LETTERS 2021; 21:6146-6155. [PMID: 34259001 DOI: 10.1021/acs.nanolett.1c01737] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The morphology of supramolecular peptide nanostructures is difficult to predict given their complex energy landscapes. We investigated peptide amphiphiles containing β-sheet forming domains that form twisted nanoribbons in water. We explained the morphology based on a balance between the energetically favorable packing of molecules in the center of the nanostructures, the unfavorable packing at the edges, and the deformations due to packing of twisted β-sheets. We find that morphological polydispersity of PA nanostructures is determined by peptide sequences, and the twisting of their internal β-sheets. We also observed a change in the supramolecular chirality of the nanostructures as the peptide sequence was modified, although only amino acids with l-configuration were used. Upon increasing charge repulsion between molecules, we observed a change in morphology to long cylinders and then rodlike fragments and spherical micelles. Understanding the self-assembly mechanisms of peptide amphiphiles into nanostructures should be useful to optimize their well-known functions.
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Affiliation(s)
- M Hussain Sangji
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Center for Bio-Inspired Energy Science, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Hiroaki Sai
- Simpson Querrey Institute, Northwestern University, 303 E Superior, Chicago, Illinois 60611, United States
- Center for Bio-Inspired Energy Science, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Stacey M Chin
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Sieun Ruth Lee
- Department of Materials Science and Engineering, 2220 Campus Drive, Evanston, Illinois 60208, United States
| | - Ivan R Sasselli
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Simpson Querrey Institute, Northwestern University, 303 E Superior, Chicago, Illinois 60611, United States
| | - Liam C Palmer
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Simpson Querrey Institute, Northwestern University, 303 E Superior, Chicago, Illinois 60611, United States
- Center for Bio-Inspired Energy Science, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Samuel I Stupp
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Materials Science and Engineering, 2220 Campus Drive, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Medicine, Northwestern University, 676 N St. Clair, Chicago, Illinois 60611, United States
- Simpson Querrey Institute, Northwestern University, 303 E Superior, Chicago, Illinois 60611, United States
- Center for Bio-Inspired Energy Science, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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10
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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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11
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Dana A, Tekinay AB, Tekin ED. A comparison of peptide amphiphile nanofiber macromolecular assembly strategies. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:63. [PMID: 31115713 DOI: 10.1140/epje/i2019-11827-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
Supramolecular peptide nanofibers that are composed of peptide amphiphile molecules have been widely used for many purposes from biomedical applications to energy conversion. The self-assembly mechanisms of these peptide nanofibers also provide convenient models for understanding the self-assembly mechanisms of various biological supramolecular systems; however, the current theoretical models that explain these mechanisms do not sufficiently explain the experimental results. In this study, we present a new way of modeling these nanofibers that better fits with the experimental data. Molecular dynamics simulations were applied to create model fibers using two different layer models and two different tilt angles. Strikingly, the fibers which were modeled to be tilting the peptide amphiphile molecules and/or tilting the plane were found to be more stable and consistent with the experiments.
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Affiliation(s)
- Aykutlu Dana
- Spilker Engineering & Applied Sciences, Stanford University, 94305, Stanford, CA, USA
| | - Ayse B Tekinay
- Eryigit Medical Devices, Research and Development Center, 06378, Ankara, Turkey
| | - E Deniz Tekin
- Faculty of Engineering, University of Turkish Aeronautical Association, 06790, Ankara, Turkey.
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12
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Lampel A, Ulijn RV, Tuttle T. Guiding principles for peptide nanotechnology through directed discovery. Chem Soc Rev 2018; 47:3737-3758. [PMID: 29748676 DOI: 10.1039/c8cs00177d] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Life's diverse molecular functions are largely based on only a small number of highly conserved building blocks - the twenty canonical amino acids. These building blocks are chemically simple, but when they are organized in three-dimensional structures of tremendous complexity, new properties emerge. This review explores recent efforts in the directed discovery of functional nanoscale systems and materials based on these same amino acids, but that are not guided by copying or editing biological systems. The review summarises insights obtained using three complementary approaches of searching the sequence space to explore sequence-structure relationships for assembly, reactivity and complexation, namely: (i) strategic editing of short peptide sequences; (ii) computational approaches to predicting and comparing assembly behaviours; (iii) dynamic peptide libraries that explore the free energy landscape. These approaches give rise to guiding principles on controlling order/disorder, complexation and reactivity by peptide sequence design.
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Affiliation(s)
- A Lampel
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), New York, NY, USA.
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13
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Frederix PWJM, Patmanidis I, Marrink SJ. Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments. Chem Soc Rev 2018; 47:3470-3489. [PMID: 29688238 PMCID: PMC5961611 DOI: 10.1039/c8cs00040a] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Indexed: 01/01/2023]
Abstract
In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation.
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Affiliation(s)
- Pim W. J. M. Frederix
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Ilias Patmanidis
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
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Zhang Z, Yang H, Bi J, Zhang A, Fang Y, Feng Y, An L, Liang L, Zhang C, Pu J. The leading role of the steric hindrance effect and dipole–dipole interaction in superlattice nanostructures formed via the assembly of discotic liquid crystals. NEW J CHEM 2018. [DOI: 10.1039/c8nj05405c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of steric hindrance and dipole–dipole interactions are a prerequisite for the formation of ordered plastic phases.
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