1
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Schaeffer G, Eleveld MJ, Ottelé J, Kroon PC, Frederix PWJM, Yang S, Otto S. Stochastic Emergence of Two Distinct Self-Replicators from a Dynamic Combinatorial Library. J Am Chem Soc 2022; 144:6291-6297. [PMID: 35357150 PMCID: PMC9011346 DOI: 10.1021/jacs.1c12591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Unraveling how chemistry
can give rise to biology is one of the
greatest challenges of contemporary science. Achieving life-like properties
in chemical systems is therefore a popular topic of research. Synthetic
chemical systems are usually deterministic: the outcome is determined
by the experimental conditions. In contrast, many phenomena that occur
in nature are not deterministic but caused by random fluctuations
(stochastic). Here, we report on how, from a mixture of two synthetic
molecules, two different self-replicators emerge in a stochastic fashion.
Under the same experimental conditions, the two self-replicators are
formed in various ratios over several repeats of the experiment. We
show that this variation is caused by a stochastic nucleation process
and that this stochasticity is more pronounced close to a phase boundary.
While stochastic nucleation processes are common in crystal growth
and chiral symmetry breaking, it is unprecedented for systems of synthetic
self-replicators.
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Affiliation(s)
- Gaël Schaeffer
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marcel J Eleveld
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jim Ottelé
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Peter C Kroon
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Pim W J M Frederix
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Shuo Yang
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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2
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Tsanai M, Frederix PWJM, Schroer CFE, Souza PCT, Marrink SJ. Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model. Chem Sci 2021; 12:8521-8530. [PMID: 34221333 PMCID: PMC8221187 DOI: 10.1039/d1sc00374g] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/17/2021] [Indexed: 01/30/2023] Open
Abstract
Complex coacervates are liquid-liquid phase separated systems, typically containing oppositely charged polyelectrolytes. They are widely studied for their functional properties as well as their potential involvement in cellular compartmentalization as biomolecular condensates. Diffusion and partitioning of solutes into a coacervate phase are important to address because their highly dynamic nature is one of their most important functional characteristics in real-world systems, but are difficult to study experimentally or even theoretically without an explicit representation of every molecule in the system. Here, we present an explicit-solvent, molecular dynamics coarse-grain model of complex coacervates, based on the Martini 3.0 force field. We demonstrate the accuracy of the model by reproducing the salt dependent coacervation of poly-lysine and poly-glutamate systems, and show the potential of the model by simulating the partitioning of ions and small nucleotides between the condensate and surrounding solvent phase. Our model paves the way for simulating coacervates and biomolecular condensates in a wide range of conditions, with near-atomic resolution.
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Affiliation(s)
- Maria Tsanai
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen 9747AG Groningen The Netherlands
| | - Pim W J M Frederix
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen 9747AG Groningen The Netherlands
| | - Carsten F E Schroer
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen 9747AG Groningen The Netherlands
| | - Paulo C T Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen 9747AG Groningen The Netherlands
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, University of Lyon Lyon France
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen 9747AG Groningen The Netherlands
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3
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Maity S, Ottelé J, Santiago GM, Frederix PWJM, Kroon P, Markovitch O, Stuart MCA, Marrink SJ, Otto S, Roos WH. Caught in the Act: Mechanistic Insight into Supramolecular Polymerization-Driven Self-Replication from Real-Time Visualization. J Am Chem Soc 2020; 142:13709-13717. [PMID: 32786814 PMCID: PMC7426903 DOI: 10.1021/jacs.0c02635] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
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Self-assembly features
prominently in fields ranging from materials
science to biophysical chemistry. Assembly pathways, often passing
through transient intermediates, can control the outcome of assembly
processes. Yet, the mechanisms of self-assembly remain largely obscure
due to a lack of experimental tools for probing these pathways at
the molecular level. Here, the self-assembly of self-replicators into
fibers is visualized in real-time by high-speed atomic force microscopy
(HS-AFM). Fiber growth requires the conversion of precursor molecules
into six-membered macrocycles, which constitute the fibers. HS-AFM
experiments, supported by molecular dynamics simulations, revealed
that aggregates of precursor molecules accumulate at the sides of
the fibers, which then diffuse to the fiber ends where growth takes
place. This mechanism of precursor reservoir formation, followed by
one-dimensional diffusion, which guides the precursor molecules to
the sites of growth, reduces the entropic penalty associated with
colocalizing precursors and growth sites and constitutes a new mechanism
for supramolecular polymerization.
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Affiliation(s)
- Sourav Maity
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Jim Ottelé
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Guillermo Monreal Santiago
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Pim W J M Frederix
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | - Peter Kroon
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | - Omer Markovitch
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands.,Origins Center, Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | - Marc C A Stuart
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Wouter H Roos
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
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4
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Debnath S, Roy S, Abul‐Haija YM, Frederix PWJM, Ramalhete SM, Hirst AR, Javid N, Hunt NT, Kelly SM, Angulo J, Khimyak YZ, Ulijn RV. Tunable Supramolecular Gel Properties by Varying Thermal History. Chemistry 2019; 25:7881-7887. [DOI: 10.1002/chem.201806281] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Sisir Debnath
- WestCHEMDepartment of Pure and Applied ChemistryUniversity of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK
- Current Address: Department of ChemistrySerampore College 9, William Carey Sarani Serampore, Hooghly West Bengal Pin-712201 India
| | - Sangita Roy
- WestCHEMDepartment of Pure and Applied ChemistryUniversity of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK
| | - Yousef M. Abul‐Haija
- WestCHEMDepartment of Pure and Applied ChemistryUniversity of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK
- Current Address: WestCHEMSchool of ChemistryUniversity of Glasgow Glasgow G12 8QQ UK
| | - Pim W. J. M. Frederix
- WestCHEMDepartment of Pure and Applied ChemistryUniversity of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK
- SUPADepartment of PhysicsUniversity of Strathclyde 107 Rottenrow East Glasgow G4 0NG UK
| | - Susana M. Ramalhete
- School of PharmacyUniversity of East Anglia Norwich Research Park Norwich NR4 7TJ UK
| | - Andrew R. Hirst
- WestCHEMDepartment of Pure and Applied ChemistryUniversity of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK
- Current Address: Department of ChemistryUniversity of York York YO10 5DD UK
| | - Nadeem Javid
- WestCHEMDepartment of Pure and Applied ChemistryUniversity of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK
- Current Address: School of Chemistry and BiosciencesUniversity of Bradford Bradford BD7 1DP UK
| | - Neil T. Hunt
- SUPADepartment of PhysicsUniversity of Strathclyde 107 Rottenrow East Glasgow G4 0NG UK
- Current Address: Department of ChemistryUniversity of York York YO10 5DD UK
| | - Sharon M. Kelly
- Institute of Molecular Cell and Systems BiologyUniversity of Glasgow Glasgow G12 8QQ UK
| | - Jesús Angulo
- School of PharmacyUniversity of East Anglia Norwich Research Park Norwich NR4 7TJ UK
| | - Yaroslav Z. Khimyak
- School of PharmacyUniversity of East Anglia Norwich Research Park Norwich NR4 7TJ UK
| | - Rein V. Ulijn
- WestCHEMDepartment of Pure and Applied ChemistryUniversity of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK
- Advanced Science Research Center (ASRC) at the Graduate Center of the City University of New York (CUNY) 85 St Nicholas Terrace New York 10031 USA
- Department of ChemistryHunter CollegeCity University of New York 695 Park Avenue New York 10065 USA
- Ph.D. programs in Biochemistry and ChemistryThe Graduate Center of the City University of New York New York 10016 USA
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5
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Angelerou MGF, Frederix PWJM, Wallace M, Yang B, Rodger A, Adams DJ, Marlow M, Zelzer M. Correction to "Supramolecular Nucleoside-Based Gel: Molecular Dynamics Simulation and Characterization of Its Nanoarchitecture and Self-Assembly Mechanism". Langmuir 2019; 35:2885. [PMID: 30730748 PMCID: PMC8154873 DOI: 10.1021/acs.langmuir.9b00009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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6
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Angelerou MF, Frederix PWJM, Wallace M, Yang B, Rodger A, Adams DJ, Marlow M, Zelzer M. Supramolecular Nucleoside-Based Gel: Molecular Dynamics Simulation and Characterization of Its Nanoarchitecture and Self-Assembly Mechanism. Langmuir 2018; 34:6912-6921. [PMID: 29757652 PMCID: PMC6078381 DOI: 10.1021/acs.langmuir.8b00646] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/09/2018] [Indexed: 05/27/2023]
Abstract
Among the diversity of existing supramolecular hydrogels, nucleic acid-based hydrogels are of particular interest for potential drug delivery and tissue engineering applications because of their inherent biocompatibility. Hydrogel performance is directly related to the nanostructure and the self-assembly mechanism of the material, an aspect that is not well-understood for nucleic acid-based hydrogels in general and has not yet been explored for cytosine-based hydrogels in particular. Herein, we use a broad range of experimental characterization techniques along with molecular dynamics (MD) simulation to demonstrate the complementarity and applicability of both approaches for nucleic acid-based gelators in general and propose the self-assembly mechanism for a novel supramolecular gelator, N4-octanoyl-2'-deoxycytidine. The experimental data and the MD simulation are in complete agreement with each other and demonstrate the formation of a hydrophobic core within the fibrillar structures of these mainly water-containing materials. The characterization of the distinct duality of environments in this cytidine-based gel will form the basis for further encapsulation of both small hydrophobic drugs and biopharmaceuticals (proteins and nucleic acids) for drug delivery and tissue engineering applications.
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Affiliation(s)
| | - Pim W. J. M. Frederix
- Faculty
of Science and Engineering, University of
Groningen, Groningen 9747 AG, The Netherlands
| | - Matthew Wallace
- School
of Pharmacy, University of East Anglia, Norwich NR4 7TJ, U.K.
| | - Bin Yang
- School
of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Alison Rodger
- Department
of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Dave J. Adams
- School
of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K.
| | - Maria Marlow
- School
of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Mischa Zelzer
- School
of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K.
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Lampel A, McPhee SA, Park HA, Scott GG, Humagain S, Hekstra DR, Yoo B, Frederix PWJM, Li TD, Abzalimov RR, Greenbaum SG, Tuttle T, Hu C, Bettinger CJ, Ulijn RV. Polymeric peptide pigments with sequence-encoded properties. Science 2018; 356:1064-1068. [PMID: 28596363 DOI: 10.1126/science.aal5005] [Citation(s) in RCA: 203] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 05/08/2017] [Indexed: 12/19/2022]
Abstract
Melanins are a family of heterogeneous polymeric pigments that provide ultraviolet (UV) light protection, structural support, coloration, and free radical scavenging. Formed by oxidative oligomerization of catecholic small molecules, the physical properties of melanins are influenced by covalent and noncovalent disorder. We report the use of tyrosine-containing tripeptides as tunable precursors for polymeric pigments. In these structures, phenols are presented in a (supra-)molecular context dictated by the positions of the amino acids in the peptide sequence. Oxidative polymerization can be tuned in a sequence-dependent manner, resulting in peptide sequence-encoded properties such as UV absorbance, morphology, coloration, and electrochemical properties over a considerable range. Short peptides have low barriers to application and can be easily scaled, suggesting near-term applications in cosmetics and biomedicine.
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Affiliation(s)
- Ayala Lampel
- Advanced Science Research Center at the Graduate Center of the City University of New York, 85 Saint Nicholas Terrace, New York, NY 10031, USA
| | - Scott A McPhee
- Advanced Science Research Center at the Graduate Center of the City University of New York, 85 Saint Nicholas Terrace, New York, NY 10031, USA
| | - Hang-Ah Park
- Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Gary G Scott
- WestCHEM and Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - Sunita Humagain
- Department of Physics and Astronomy, Hunter College, City University of New York, 695 Park Avenue, New York, NY 10065, USA.,Ph.D. programs in Biochemistry, Chemistry and Physics, The Graduate Center of the City University of New York, NY 10016, USA
| | - Doeke R Hekstra
- Department of Molecular and Cellular Biology, School of Engineering and Applied Sciences, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Barney Yoo
- Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, New York, NY 10065, USA
| | - Pim W J M Frederix
- Groningen Biomolecular Sciences and Biotechnology Institute, Rijksuniversiteit Groningen, Groningen, Netherlands
| | - Tai-De Li
- Advanced Science Research Center at the Graduate Center of the City University of New York, 85 Saint Nicholas Terrace, New York, NY 10031, USA
| | - Rinat R Abzalimov
- Advanced Science Research Center at the Graduate Center of the City University of New York, 85 Saint Nicholas Terrace, New York, NY 10031, USA
| | - Steven G Greenbaum
- Department of Physics and Astronomy, Hunter College, City University of New York, 695 Park Avenue, New York, NY 10065, USA.,Ph.D. programs in Biochemistry, Chemistry and Physics, The Graduate Center of the City University of New York, NY 10016, USA
| | - Tell Tuttle
- WestCHEM and Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - Chunhua Hu
- Department of Chemistry, Silver Center for Arts and Science, 100 Washington Square East, New York University, New York, NY 10003, USA
| | - Christopher J Bettinger
- Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.,Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.,McGowan Institute of Regenerative Medicine, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219, USA
| | - Rein V Ulijn
- Advanced Science Research Center at the Graduate Center of the City University of New York, 85 Saint Nicholas Terrace, New York, NY 10031, USA. .,Ph.D. programs in Biochemistry, Chemistry and Physics, The Graduate Center of the City University of New York, NY 10016, USA.,Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, New York, NY 10065, USA
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9
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Van Eerden FJ, Melo MN, Frederix PWJM, Marrink SJ. Prediction of Thylakoid Lipid Binding Sites on Photosystem II. Biophys J 2018; 113:2669-2681. [PMID: 29262360 PMCID: PMC5770566 DOI: 10.1016/j.bpj.2017.09.039] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/11/2017] [Accepted: 09/29/2017] [Indexed: 11/20/2022] Open
Abstract
The thylakoid membrane has a unique lipid composition, consisting mostly of galactolipids. These thylakoid lipids have important roles in photosynthesis. Here, we investigate to what extent these lipids bind specifically to the Photosystem II complex. To this end, we performed coarse-grain MD simulations of the Photosystem II complex embedded in a thylakoid membrane with realistic composition. Based on >85 μs simulation time, we find that monogalactosyldiacylglycerol and sulfoquinovosyldiacylglycerol lipids are enriched in the annular shell around the protein, and form distinct binding sites. From the analysis of residue contacts, we conclude that electrostatic interactions play an important role in stabilizing these binding sites. Furthermore, we find that chlorophyll a has a prevalent role in the coordination of the lipids. In addition, we observe lipids to diffuse in and out of the plastoquinone exchange cavities, allowing exchange of cocrystallized lipids with the bulk membrane and suggesting a more open nature of the plastoquinone exchange cavity. Together, our data provide a wealth of information on protein-lipid interactions for a key protein in photosynthesis.
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Affiliation(s)
- Floris J Van Eerden
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands.
| | - Manuel N Melo
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Pim W J M Frederix
- 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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10
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Frederix PWJM, Idé J, Altay Y, Schaeffer G, Surin M, Beljonne D, Bondarenko AS, Jansen TLC, Otto S, Marrink SJ. Structural and Spectroscopic Properties of Assemblies of Self-Replicating Peptide Macrocycles. ACS Nano 2017; 11:7858-7868. [PMID: 28723067 PMCID: PMC5616102 DOI: 10.1021/acsnano.7b02211] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Self-replication at the molecular level is often seen as essential to the early origins of life. Recently a mechanism of self-replication has been discovered in which replicator self-assembly drives the process. We have studied one of the examples of such self-assembling self-replicating molecules to a high level of structural detail using a combination of computational and spectroscopic techniques. Molecular Dynamics simulations of self-assembled stacks of peptide-derived replicators provide insights into the structural characteristics of the system and serve as the basis for semiempirical calculations of the UV-vis, circular dichroism (CD) and infrared (IR) absorption spectra that reflect the chiral organization and peptide secondary structure of the stacks. Two proposed structural models are tested by comparing calculated spectra to experimental data from electron microscopy, CD and IR spectroscopy, resulting in a better insight into the specific supramolecular interactions that lead to self-replication. Specifically, we find a cooperative self-assembly process in which β-sheet formation leads to well-organized structures, while also the aromatic core of the macrocycles plays an important role in the stability of the resulting fibers.
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Affiliation(s)
- Pim W. J. M. Frederix
- University
of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 7, 9747AG Groningen, The Netherlands
- University
of Groningen, Center for Systems Chemistry, Stratingh Institute for
Chemistry, Nijenborgh
4, 9747AG Groningen, The Netherlands
- E-mail:
| | - Julien Idé
- Laboratory
of Chemistry of Novel Materials, University
of Mons − UMONS, Place du Parc 20, B-7000 Mons, Belgium
| | - Yigit Altay
- University
of Groningen, Center for Systems Chemistry, Stratingh Institute for
Chemistry, Nijenborgh
4, 9747AG Groningen, The Netherlands
| | - Gaël Schaeffer
- University
of Groningen, Center for Systems Chemistry, Stratingh Institute for
Chemistry, Nijenborgh
4, 9747AG Groningen, The Netherlands
| | - Mathieu Surin
- Laboratory
of Chemistry of Novel Materials, University
of Mons − UMONS, Place du Parc 20, B-7000 Mons, Belgium
| | - David Beljonne
- Laboratory
of Chemistry of Novel Materials, University
of Mons − UMONS, Place du Parc 20, B-7000 Mons, Belgium
| | - Anna S. Bondarenko
- University
of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Thomas L. C. Jansen
- University
of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Sijbren Otto
- University
of Groningen, Center for Systems Chemistry, Stratingh Institute for
Chemistry, Nijenborgh
4, 9747AG Groningen, The Netherlands
- University
of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG Groningen, The Netherlands
- E-mail:
| | - Siewert J. Marrink
- University
of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 7, 9747AG Groningen, The Netherlands
- University
of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG Groningen, The Netherlands
- E-mail:
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11
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Van Eerden FJ, Melo MN, Frederix PWJM, Periole X, Marrink SJ. Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex. Nat Commun 2017; 8:15214. [PMID: 28489071 PMCID: PMC5436218 DOI: 10.1038/ncomms15214] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/01/2017] [Indexed: 11/09/2022] Open
Abstract
Plastoquinone (PLQ) acts as an electron carrier between photosystem II (PSII) and the cytochrome b6f complex. To understand how PLQ enters and leaves PSII, here we show results of coarse grained molecular dynamics simulations of PSII embedded in the thylakoid membrane, covering a total simulation time of more than 0.5 ms. The long time scale allows the observation of many spontaneous entries of PLQ into PSII, and the unbinding of plastoquinol (PLQol) from the complex. In addition to the two known channels, we observe a third channel for PLQ/PLQol diffusion between the thylakoid membrane and the PLQ binding sites. Our simulations point to a promiscuous diffusion mechanism in which all three channels function as entry and exit channels. The exchange cavity serves as a PLQ reservoir. Our simulations provide a direct view on the exchange of electron carriers, a key step of the photosynthesis machinery.
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Affiliation(s)
- Floris J Van Eerden
- Groningen Biomolecular Sciences and Biotechnology Institute &Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Manuel N Melo
- Groningen Biomolecular Sciences and Biotechnology Institute &Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Pim W J M Frederix
- Groningen Biomolecular Sciences and Biotechnology Institute &Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Xavier Periole
- Groningen Biomolecular Sciences and Biotechnology Institute &Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute &Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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12
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van Eerden FJ, van den Berg T, Frederix PWJM, de Jong DH, Periole X, Marrink SJ. Molecular Dynamics of Photosystem II Embedded in the Thylakoid Membrane. J Phys Chem B 2016; 121:3237-3249. [PMID: 27624992 DOI: 10.1021/acs.jpcb.6b06865] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Photosystem II (PSII) is one of the key protein complexes in photosynthesis. We introduce a coarse grained model of PSII and present the analysis of 60 μs molecular dynamics simulations of PSII in both monomeric and dimeric form, embedded in a thylakoid membrane model that reflects its native lipid composition. We describe in detail the setup of the protein complex and the many natural cofactors and characterize their mobility. Overall we find that the protein subunits and cofactors are more flexible toward the periphery of the complex as well as near the PLQ exchange cavity and at the dimer interface. Of all cofactors, β-carotenes show the highest mobility. Some of the β-carotenes diffuse in and out of the protein complex via the thylakoid membrane. In contrast with the PSII dimer, the monomeric form adopts a tilted conformation in the membrane, with strong interactions between the soluble PsbO subunit and the glycolipid headgroups. Interestingly, the tilted conformation causes buckling of the membrane. Together, our results provide an unprecedented view of PSII dynamics on a microsecond time scale. Our data may be used as basis for the interpretation of experimental data as well as for theoretical models describing exciton energy transfer.
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Affiliation(s)
- Floris J van Eerden
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Tom van den Berg
- Department of Physics and Astronomy, Faculteit der Exacte Wetenschappen, Vrije Universiteit , De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Pim W J M Frederix
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Djurre H de Jong
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Xavier Periole
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG, Groningen, The Netherlands
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13
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Shaw DJ, Adamczyk K, Frederix PWJM, Simpson N, Robb K, Greetham GM, Towrie M, Parker AW, Hoskisson PA, Hunt NT. Multidimensional infrared spectroscopy reveals the vibrational and solvation dynamics of isoniazid. J Chem Phys 2015; 142:212401. [DOI: 10.1063/1.4914097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Daniel J. Shaw
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
- Strathclyde Institute for Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, United Kingdom
| | - Katrin Adamczyk
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
| | - Pim W. J. M. Frederix
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
| | - Niall Simpson
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
| | - Kirsty Robb
- Strathclyde Institute for Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, United Kingdom
| | - Gregory M. Greetham
- STFC Rutherford Appleton Laboratory, Central Laser Facility, Research Complex at Harwell, Didcot OX11 0QX, United Kingdom
| | - Michael Towrie
- STFC Rutherford Appleton Laboratory, Central Laser Facility, Research Complex at Harwell, Didcot OX11 0QX, United Kingdom
| | - Anthony W. Parker
- STFC Rutherford Appleton Laboratory, Central Laser Facility, Research Complex at Harwell, Didcot OX11 0QX, United Kingdom
| | - Paul A. Hoskisson
- Strathclyde Institute for Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, United Kingdom
| | - Neil T. Hunt
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
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14
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Pappas CG, Frederix PWJM, Mutasa T, Fleming S, Abul-Haija YM, Kelly SM, Gachagan A, Kalafatovic D, Trevino J, Ulijn RV, Bai S. Alignment of nanostructured tripeptide gels by directional ultrasonication. Chem Commun (Camb) 2015; 51:8465-8. [DOI: 10.1039/c5cc02049b] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We demonstrate an in situ ultrasonic approach to generate anisotropic organo- and hydrogels consisting of oriented tripeptides self-assembled structures.
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15
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Kalafatovic D, Nobis M, Javid N, Frederix PWJM, Anderson KI, Saunders BR, Ulijn RV. MMP-9 triggered micelle-to-fibre transitions for slow release of doxorubicin. Biomater Sci 2014. [PMID: 26218115 DOI: 10.1039/c4bm00297k] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Phenylacetyl-peptide amphiphiles were designed, which upon cleavage by a disease-associated enzyme reconfigure from micellar aggregates to fibres. Upon this morphological change, a doxorubicin payload could be retained in the fibres formed, which makes them valuable carriers for localised formation of nanofibre depots for slow release of hydrophobic anticancer drugs.
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Affiliation(s)
- Daniela Kalafatovic
- West CHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
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16
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Nalluri SKM, Shivarova N, Kanibolotsky AL, Zelzer M, Gupta S, Frederix PWJM, Skabara PJ, Gleskova H, Ulijn RV. Conducting nanofibers and organogels derived from the self-assembly of tetrathiafulvalene-appended dipeptides. Langmuir 2014; 30:12429-37. [PMID: 25259412 DOI: 10.1021/la503459y] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We demonstrate the nonaqueous self-assembly of a low-molecular-mass organic gelator based on an electroactive p-type tetrathiafulvalene (TTF)-dipeptide bioconjugate. We show that a TTF moiety appended with diphenylalanine amide derivative (TTF-FF-NH2) self-assembles into one-dimensional nanofibers that further lead to the formation of self-supporting organogels in chloroform and ethyl acetate. Upon doping of the gels with electron acceptors (TCNQ/iodine vapor), stable two-component charge transfer gels are produced in chloroform and ethyl acetate. These gels are characterized by various spectroscopy (UV-vis-NIR, FTIR, and CD), microscopy (AFM and TEM), rheology, and cyclic voltammetry techniques. Furthermore, conductivity measurements performed on TTF-FF-NH2 xerogel nanofiber networks formed between gold electrodes on a glass surface indicate that these nanofibers show a remarkable enhancement in the conductivity after doping with TCNQ.
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Affiliation(s)
- Siva Krishna Mohan Nalluri
- WestCHEM, Department of Pure & Applied Chemistry, University of Strathclyde , Glasgow G1 1XL, United Kingdom
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17
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Frederix PWJM, Adamczyk K, Wright JA, Tuttle T, Ulijn RV, Pickett CJ, Hunt NT. Investigation of the Ultrafast Dynamics Occurring during Unsensitized Photocatalytic H2 Evolution by an [FeFe]-Hydrogenase Subsite Analogue. Organometallics 2014. [DOI: 10.1021/om500521w] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Pim W. J. M. Frederix
- Department
of Physics, University of Strathclyde, SUPA, Glasgow G4 0NG, United Kingdom
- WestCHEM,
Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, United Kingdom
| | - Katrin Adamczyk
- Department
of Physics, University of Strathclyde, SUPA, Glasgow G4 0NG, United Kingdom
| | - Joseph A. Wright
- Energy
Materials Laboratory, School of Chemistry, University of East Anglia, Norwich Research
Park, Norwich NR4 7TJ, United Kingdom
| | - Tell Tuttle
- WestCHEM,
Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, United Kingdom
| | - Rein V. Ulijn
- WestCHEM,
Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, United Kingdom
| | - Christopher J. Pickett
- Energy
Materials Laboratory, School of Chemistry, University of East Anglia, Norwich Research
Park, Norwich NR4 7TJ, United Kingdom
| | - Neil T. Hunt
- Department
of Physics, University of Strathclyde, SUPA, Glasgow G4 0NG, United Kingdom
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18
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Bai S, Pappas C, Debnath S, Frederix PWJM, Leckie J, Fleming S, Ulijn RV. Stable emulsions formed by self-assembly of interfacial networks of dipeptide derivatives. ACS Nano 2014; 8:7005-13. [PMID: 24896538 DOI: 10.1021/nn501909j] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We demonstrate the use of dipeptide amphiphiles that, by hand shaking of a biphasic solvent system for a few seconds, form emulsions that remain stable for months through the formation of nanofibrous networks at the organic/aqueous interface. Unlike absorption of traditional surfactants, the interfacial networks form by self-assembly through π-stacking interactions and hydrogen bonding. Altering the dipeptide sequence has a dramatic effect on the properties of the emulsions formed, illustrating the possibility of tuning emulsion properties by chemical design. The systems provide superior long-term stability toward temperature and salts compared to with sodium dodecyl sulfate (SDS) and can be enzymatically disassembled causing on-demand demulsification under mild conditions. The interfacial networks facilitate highly tunable and stable encapsulation and compartmentalization with potential applications in cosmetics, therapeutics, and food industry.
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19
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Bai S, Debnath S, Javid N, Frederix PWJM, Fleming S, Pappas C, Ulijn RV. Differential self-assembly and tunable emission of aromatic peptide bola-amphiphiles containing perylene bisimide in polar solvents including water. Langmuir 2014; 30:7576-84. [PMID: 24911955 DOI: 10.1021/la501335e] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We demonstrate the self-assembly of bola-amphiphile-type conjugates of dipeptides and perylene bisimide (PBI) in water and other polar solvents. Depending on the nature of the peptide used (glycine-tyrosine, GY, or glycine-aspartic acid, GD), the balance between H-bonding and aromatic stacking can be tailored. In aqueous buffer, PBI-[GY]2 forms chiral nanofibers, resulting in the formation of a hydrogel, while for PBI-[GD]2 achiral spherical aggregates are formed, demonstrating that the peptide sequence has a profound effect on the structure formed. In water and a range of other polar solvents, self-assembly of these two PBI-peptides conjugates results in different nanostructures with highly tunable fluorescence performance depending on the peptide sequence employed, e.g., fluorescent emission and quantum yield. Organogels are formed for the PBI-[GD]2 derivative in DMF and DMSO while PBI-[GY]2 gels in DMF. To the best of our knowledge, this is the first successful strategy for using short peptides, specifically, their sequence/structure relationships, to manipulate the PBI nanostructure and consequent optical properties. The combination of controlled self-assembly, varied optical properties, and formation of aqueous and organic gel-phase materials may facilitate the design of devices for various applications related to light harvesting and sensing.
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Affiliation(s)
- Shuo Bai
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde , Glasgow G1 1XL, U.K
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20
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Abstract
Aromatic peptide amphiphile hydrogelators commonly utilise the fluorenyl-9-methoxycarbonyl moiety as an N-terminal capping group. Material properties and spectroscopic techniques show the influence of alternative linkers between the fluorenyl moiety and the peptide. This study establishes whether methoxycarbonyl is an optimal or mainly convenient linker, for this class of self-assembling systems.
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Affiliation(s)
- Scott Fleming
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, UK.
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21
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Nalluri SKM, Berdugo C, Javid N, Frederix PWJM, Ulijn RV. Biocatalytic Self-Assembly of Supramolecular Charge-Transfer Nanostructures Based on n-Type Semiconductor-Appended Peptides. Angew Chem Int Ed Engl 2014; 53:5882-7. [DOI: 10.1002/anie.201311158] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 03/27/2014] [Indexed: 12/20/2022]
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22
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Nalluri SKM, Berdugo C, Javid N, Frederix PWJM, Ulijn RV. Biocatalytic Self-Assembly of Supramolecular Charge-Transfer Nanostructures Based on n-Type Semiconductor-Appended Peptides. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201311158] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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23
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Abul-Haija YM, Roy S, Frederix PWJM, Javid N, Jayawarna V, Ulijn RV. Biocatalytically triggered co-assembly of two-component core/shell nanofibers. Small 2014; 10:973-979. [PMID: 24027125 DOI: 10.1002/smll.201301668] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 07/29/2013] [Indexed: 06/02/2023]
Abstract
For the development of applications and novel uses for peptide nanostructures, robust routes for their surface functionalization, that ideally do not interfere with their self-assembly properties, are required. Many existing methods rely on covalent functionalization, where building blocks are appended with functional groups, either pre- or post-assembly. A facile supramolecular approach is demonstrated for the formation of functionalized nanofibers by combining the advantages of biocatalytic self-assembly and surfactant/gelator co-assembly. This is achieved by enzymatically triggered reconfiguration of free flowing micellar aggregates of pre-gelators and functional surfactants to form nanofibers that incorporate and display the surfactants' functionality at the surface. Furthermore, by varying enzyme concentration, the gel stiffness and supramolecular organization of building blocks can be varied.
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Affiliation(s)
- Yousef M Abul-Haija
- Pure and Applied Chemistry Department/WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
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24
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Fleming S, Debnath S, Frederix PWJM, Hunt NT, Ulijn RV. Insights into the coassembly of hydrogelators and surfactants based on aromatic peptide amphiphiles. Biomacromolecules 2014; 15:1171-84. [PMID: 24568678 DOI: 10.1021/bm401720z] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The coassembly of small molecules is a useful means of increasing the complexity and functionality of their resultant supramolecular constructs in a modular fashion. In this study, we explore the assembly and coassembly of serine surfactants and tyrosine-leucine hydrogelators, capped at the N-termini with either fluorenyl-9-methoxycarbonyl (Fmoc) or pyrene. These systems all exhibit self-assembly behavior, which is influenced by aromatic stacking interactions, while the hydrogelators also exhibit β-sheet-type arrangements, which reinforce their supramolecular structures. We provide evidence for three distinct supramolecular coassembly models; cooperative, disruptive, and orthogonal. The coassembly mode adopted depends on whether the individual constituents (I) are sufficiently different, such that effective segregation and orthogonal assembly occurs; (II) adhere to a communal mode of self-assembly; or (III) act to compromise the assembly of one another via incorporation and disruption. We find that a greater scope for controllable coassembly exists within orthogonal systems; which show minimal relative changes in the native gelator's supramolecular structure by Fourier transform infrared spectroscopy (FTIR), circular dichroism (CD), and fluorescence spectroscopy. This is indicative of the segregation of orthogonal coassembly constituents into distinct domains, where surfactant chemical functionality is presented at the surface of the gelator's supramolecular fibers. Overall, this work provides new insights into the design of modular coassembly systems, which have the potential to augment the chemical and physical properties of existing gelator systems.
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Affiliation(s)
- Scott Fleming
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde , 295 Cathedral Street, Glasgow, G1 1XL, United Kingdom
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25
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Pappas CG, Abul-Haija YM, Flack A, Frederix PWJM, Ulijn RV. Tuneable Fmoc–Phe–(4-X)–Phe–NH2 nanostructures by variable electronic substitution. Chem Commun (Camb) 2014; 50:10630-3. [DOI: 10.1039/c4cc04926h] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We show enzymatic introduction of non-natural amino acids with different electronic substituents with a dramatic influence on morphology in self-assembled nanostructures.
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Affiliation(s)
- Charalampos G. Pappas
- WestCHEM
- Department of Pure and Applied Chemistry
- Thomas Graham Building
- Glasgow G1 1XL, UK
| | - Yousef M. Abul-Haija
- WestCHEM
- Department of Pure and Applied Chemistry
- Thomas Graham Building
- Glasgow G1 1XL, UK
| | - Angela Flack
- WestCHEM
- Department of Pure and Applied Chemistry
- Thomas Graham Building
- Glasgow G1 1XL, UK
| | - Pim W. J. M. Frederix
- WestCHEM
- Department of Pure and Applied Chemistry
- Thomas Graham Building
- Glasgow G1 1XL, UK
- SUPA
| | - Rein V. Ulijn
- WestCHEM
- Department of Pure and Applied Chemistry
- Thomas Graham Building
- Glasgow G1 1XL, UK
- Advanced Science Research Center (ASRC)
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26
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Simpson N, Shaw DJ, Frederix PWJM, Gillies AH, Adamczyk K, Greetham GM, Towrie M, Parker AW, Hoskisson PA, Hunt NT. Infrared spectroscopy of nicotinamide adenine dinucleotides in one and two dimensions. J Phys Chem B 2013; 117:16468-78. [PMID: 24313706 DOI: 10.1021/jp411091f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The development of multidimensional spectroscopic tools capable of resolving site-specific information about proteins and enzymes in the solution phase is an important aid to our understanding of biomolecular mechanisms, structure, and dynamics. Nicotinamide adenine dinucleotide (NAD) is a common biological substrate and so offers significant potential as an intrinsic vibrational probe of protein-ligand interactions but its complex molecular structure and incompletely characterized infrared spectrum currently limit its usefulness. Here, we report the FTIR spectroscopy of the oxidized and reduced forms of NAD at a range of pD values that relate to the "folded" and "unfolded" forms of the molecules that exist in solution. Comparisons with structural analogs and the use of density functional theory simulations provide a full assignment of the observed modes and their complex pD dependencies. Finally, ultrafast two-dimensional infrared spectra of the oxidized and reduced forms of NAD are reported and their usefulness as biomolecular probes is discussed.
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Affiliation(s)
- Niall Simpson
- Department of Physics, University of Strathclyde , SUPA, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
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27
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Fleming S, Frederix PWJM, Ramos Sasselli I, Hunt NT, Ulijn RV, Tuttle T. Assessing the utility of infrared spectroscopy as a structural diagnostic tool for β-sheets in self-assembling aromatic peptide amphiphiles. Langmuir 2013; 29:9510-5. [PMID: 23805919 DOI: 10.1021/la400994v] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
β-Sheets are a commonly found structural motif in self-assembling aromatic peptide amphiphiles, and their characteristic "amide I" infrared (IR) absorption bands are routinely used to support the formation of supramolecular structure. In this paper, we assess the utility of IR spectroscopy as a structural diagnostic tool for this class of self-assembling systems. Using 9-fluorene-methyloxycarbonyl dialanine (Fmoc-AA) and the analogous 9-fluorene-methylcarbonyl dialanine (Fmc-AA) as examples, we show that the origin of the band around 1680-1695 cm(-1) in Fourier transform infrared (FTIR) spectra, which was previously assigned to an antiparallel β-sheet conformation, is in fact absorption of the stacked carbamate group in Fmoc-peptides. IR spectra from (13)C-labeled samples support our conclusions. In addition, DFT frequency calculations on small stacks of aromatic peptides help to rationalize these results in terms of the individual vibrational modes.
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Affiliation(s)
- Scott Fleming
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, UK
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28
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Vidma KV, Frederix PWJM, Parker DH, Baklanov AV. Photodissociation of van der Waals clusters of isoprene with oxygen, C5H8-O2, in the wavelength range 213-277 nm. J Chem Phys 2012; 137:054305. [PMID: 22894346 DOI: 10.1063/1.4737856] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The speed and angular distribution of O atoms arising from the photofragmentation of C(5)H(8)-O(2), the isoprene-oxygen van der Waals complex, in the wavelength region of 213-277 nm has been studied with the use of a two-color dissociation-probe method and the velocity map imaging technique. Dramatic enhancement in the O atoms photo-generation cross section in comparison with the photodissociation of individual O(2) molecules has been observed. Velocity map images of these "enhanced" O atoms consisted of five channels, different in their kinetic energy, angular distribution, and wavelength dependence. Three channels are deduced to be due to the one-quantum excitation of the C(5)H(8)-O(2) complex into the perturbed Herzberg III state ((3)Δ(u)) of O(2). This excitation results in the prompt dissociation of the complex giving rise to products C(5)H(8)+O+O when the energy of exciting quantum is higher than the complex photodissociation threshold, which is found to be 41740 ± 200 cm(-1) (239.6±1.2 nm). This last threshold corresponds to the photodissociation giving rise to an unexcited isoprene molecule. The second channel, with threshold shifted to the blue by 1480 ± 280 cm(-1), corresponds to dissociation with formation of rovibrationally excited isoprene. A third channel was observed at wavelengths up to 243 nm with excitation below the upper photodissociation threshold. This channel is attributed to dissociation with the formation of a bound O atom C(5)H(8)-O(2) + hv → C(5)H(8)-O(2)((3)Δ(u)) → C(5)H(8)O + O and/or to dissociation of O(2) with borrowing of the lacking energy from incompletely cooled complex internal degrees of freedom C(5)H(8)*-O(2) + hv → C(5)H(8)*-O(2)((3)Δ(u)) → C(5)H(8) + O + O. The kinetic energy of the O atoms arising in two other observed channels corresponds to O atoms produced by photodissociation of molecular oxygen in the excited a (1)Δ(g) and b (1)Σ(g)(+) singlet states as the precursors. This indicates the formation of singlet oxygen O(2)(a (1)Δ(g)) and O(2)(b (1)Σ(g)(+)) after excitation of the C(5)H(8)-O(2) complex. Cooperative excitation of the complex with a simultaneous change of the spin of both partners (1)X-(3)O(2) + hν → (3)X-(1)O(2) → (3)X + (1)O(2) is suggested as a source of singlet oxygen O(2)(a (1)Δ(g)) and O(2)(b (1)Σ(g)(+)). This cooperative excitation is in agreement with little or no vibrational excitation of O(2)(a (1)Δ(g)), produced from the C(5)H(8)-O(2) complex as studied in the current paper as well as from the C(3)H(6)-O(2) and CH(3)I-O(2) complexes reported in our previous paper [Baklanov et al., J. Chem. Phys. 126, 124316 (2007)]. The formation of O(2)(a (1)Δ(g)) from C(5)H(8)-O(2) was observed at λ(pump) = 213-277 nm with the yield going down towards the long wavelength edge of this interval. This spectral profile is interpreted as the red-side wing of the band of a cooperative transition (1)X-(3)O(2) + hν → (3)X(T(2))-(1)O(2)(a (1)Δ(g)) in the C(5)H(8)-O(2) complex.
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Affiliation(s)
- Konstantin V Vidma
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 ED Nijmegen, The Netherlands
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Roy S, Javid N, Frederix PWJM, Lamprou DA, Urquhart AJ, Hunt NT, Halling PJ, Ulijn RV. Dramatic Specific-Ion Effect in Supramolecular Hydrogels. Chemistry 2012; 18:11723-31. [DOI: 10.1002/chem.201201217] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Indexed: 11/06/2022]
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Kania R, Frederix PWJM, Wright JA, Ulijn RV, Pickett CJ, Hunt NT. Solution-phase photochemistry of a [FeFe]hydrogenase model compound: Evidence of photoinduced isomerisation. J Chem Phys 2012; 136:044521. [DOI: 10.1063/1.3679387] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Frederix PWJM, Kania R, Wright JA, Lamprou DA, Ulijn RV, Pickett CJ, Hunt NT. Encapsulating [FeFe]-hydrogenase model compounds in peptide hydrogels dramatically modifies stability and photochemistry. Dalton Trans 2012; 41:13112-9. [DOI: 10.1039/c2dt30307h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Frederix PWJM, Ulijn RV, Hunt NT, Tuttle T. Virtual Screening for Dipeptide Aggregation: Toward Predictive Tools for Peptide Self-Assembly. J Phys Chem Lett 2011; 2:2380-2384. [PMID: 23795243 PMCID: PMC3688361 DOI: 10.1021/jz2010573] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 09/01/2011] [Indexed: 05/22/2023]
Abstract
Several short peptide sequences are known to self-assemble into supramolecular nanostructures with interesting properties. In this study, coarse-grained molecular dynamics is employed to rapidly screen all 400 dipeptide combinations and predict their ability to aggregate as a potential precursor to their self-assembly. The simulation protocol and scoring method proposed allows a rapid determination of whether a given peptide sequence is likely to aggregate (an indicator for the ability to self-assemble) under aqueous conditions. Systems that show strong aggregation tendencies in the initial screening are selected for longer simulations, which result in good agreement with the known self-assembly or aggregation of dipeptides reported in the literature. Our extended simulations of the diphenylalanine system show that the coarse-grain model is able to reproduce salient features of nanoscale systems and provide insight into the self-assembly process for this system.
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Affiliation(s)
- Pim W. J. M. Frederix
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, United Kingdom
- SUPA, Department of Physics, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, United Kingdom
| | - Rein V. Ulijn
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, United Kingdom
| | - Neil T. Hunt
- SUPA, Department of Physics, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, United Kingdom
| | - Tell Tuttle
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, United Kingdom
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Frederix PWJM, Yang CH, Groenenboom GC, Parker DH, Alnama K, Western CM, Orr-Ewing AJ. Photodissociation Imaging of Diatomic Sulfur (S2). J Phys Chem A 2009; 113:14995-5005. [DOI: 10.1021/jp905104u] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | - Koutayba Alnama
- Laboratoire de Photophysique Moléculaire, Université de Paris-Sud, 91405 ORSAY CEDEX, France
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