1
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Sanchez‐Martinez S, Nguyen K, Biswas S, Nicholson V, Romanyuk AV, Ramirez J, Kc S, Akter A, Childs C, Meese EK, Usher ET, Ginell GM, Yu F, Gollub E, Malferrari M, Francia F, Venturoli G, Martin EW, Caporaletti F, Giubertoni G, Woutersen S, Sukenik S, Woolfson DN, Holehouse AS, Boothby TC. Labile assembly of a tardigrade protein induces biostasis. Protein Sci 2024; 33:e4941. [PMID: 38501490 PMCID: PMC10949331 DOI: 10.1002/pro.4941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 03/20/2024]
Abstract
Tardigrades are microscopic animals that survive desiccation by inducing biostasis. To survive drying tardigrades rely on intrinsically disordered CAHS proteins, which also function to prevent perturbations induced by drying in vitro and in heterologous systems. CAHS proteins have been shown to form gels both in vitro and in vivo, which has been speculated to be linked to their protective capacity. However, the sequence features and mechanisms underlying gel formation and the necessity of gelation for protection have not been demonstrated. Here we report a mechanism of fibrillization and gelation for CAHS D similar to that of intermediate filament assembly. We show that in vitro, gelation restricts molecular motion, immobilizing and protecting labile material from the harmful effects of drying. In vivo, we observe that CAHS D forms fibrillar networks during osmotic stress. Fibrillar networking of CAHS D improves survival of osmotically shocked cells. We observe two emergent properties associated with fibrillization; (i) prevention of cell volume change and (ii) reduction of metabolic activity during osmotic shock. We find that there is no significant correlation between maintenance of cell volume and survival, while there is a significant correlation between reduced metabolism and survival. Importantly, CAHS D's fibrillar network formation is reversible and metabolic rates return to control levels after CAHS fibers are resolved. This work provides insights into how tardigrades induce reversible biostasis through the self-assembly of labile CAHS gels.
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Affiliation(s)
| | - K. Nguyen
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - S. Biswas
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - V. Nicholson
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - A. V. Romanyuk
- School of ChemistryUniversity of BristolBristolUK
- Max Planck‐Bristol Centre for Minimal BiologyUniversity of BristolBristolUK
| | - J. Ramirez
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - S. Kc
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - A. Akter
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - C. Childs
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - E. K. Meese
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - E. T. Usher
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - G. M. Ginell
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - F. Yu
- Quantitative Systems Biology ProgramUniversity of California MercedMercedCaliforniaUSA
| | - E. Gollub
- Department of Chemistry and BiochemistryUniversity of California MercedMercedCaliforniaUSA
| | - M. Malferrari
- Dipartimento di Chimica “Giacomo Ciamician”Università di BolognaBolognaItaly
| | - F. Francia
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiTUniversità di BolognaBolognaItaly
| | - G. Venturoli
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiTUniversità di BolognaBolognaItaly
- Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), c/o Dipartimento di Fisica e Astronomia (DIFA)Università di BolognaBolognaItaly
| | - E. W. Martin
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTennesseeUSA
| | - F. Caporaletti
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - G. Giubertoni
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - S. Woutersen
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - S. Sukenik
- Quantitative Systems Biology ProgramUniversity of California MercedMercedCaliforniaUSA
- Department of Chemistry and BiochemistryUniversity of California MercedMercedCaliforniaUSA
| | - D. N. Woolfson
- School of ChemistryUniversity of BristolBristolUK
- Max Planck‐Bristol Centre for Minimal BiologyUniversity of BristolBristolUK
- School of BiochemistryUniversity of Bristol, Biomedical Sciences BuildingBristolUK
| | - A. S. Holehouse
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - T. C. Boothby
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
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2
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Giubertoni G, Feng L, Klein K, Giannetti G, Rutten L, Choi Y, van der Net A, Castro-Linares G, Caporaletti F, Micha D, Hunger J, Deblais A, Bonn D, Sommerdijk N, Šarić A, Ilie IM, Koenderink GH, Woutersen S. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proc Natl Acad Sci U S A 2024; 121:e2313162121. [PMID: 38451946 PMCID: PMC10945838 DOI: 10.1073/pnas.2313162121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/30/2023] [Indexed: 03/09/2024] Open
Abstract
Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water-collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H[Formula: see text]O/D[Formula: see text]O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H[Formula: see text]O and D[Formula: see text]O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D[Formula: see text]O than in H[Formula: see text]O, and collagen in D[Formula: see text]O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H[Formula: see text]O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D[Formula: see text]O is less hydrated than in H[Formula: see text]O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen-water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly.
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Affiliation(s)
- Giulia Giubertoni
- Van ’t Hoff Institute for Molecular Sciences, Department of Molecular Photonics, University of Amsterdam, Amsterdam1090 GD, The Netherlands
| | - Liru Feng
- Van ’t Hoff Institute for Molecular Sciences, Department of Molecular Photonics, University of Amsterdam, Amsterdam1090 GD, The Netherlands
| | - Kevin Klein
- Institute of Science and Technology Austria, Division of Mathematical and Physical Sciences, Klosterneuburg3400, Austria
- University College London, Division of Physics and Astronomy, LondonWC1E 6BT, United Kingdom
| | - Guido Giannetti
- Van ’t Hoff Institute for Molecular Sciences, Department of Molecular Photonics, University of Amsterdam, Amsterdam1090 GD, The Netherlands
| | - Luco Rutten
- Electron Microscopy Center, Radboud Technology Center Microscopy, Department of Medical BioSciences, Radboud University Medical Center, Nijmegen6525 GA, The Netherlands
| | - Yeji Choi
- Max Planck Institute for Polymer Research, Molecular Spectroscopy Department, Mainz55128, Germany
| | - Anouk van der Net
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft2628 HZ, The Netherlands
| | - Gerard Castro-Linares
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft2628 HZ, The Netherlands
| | - Federico Caporaletti
- Van ’t Hoff Institute for Molecular Sciences, Department of Molecular Photonics, University of Amsterdam, Amsterdam1090 GD, The Netherlands
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, Amsterdam1090 GL, The Netherlands
| | - Dimitra Micha
- Amsterdam University Medical Centers, Human Genetics Department, Vrije Universiteit, Amsterdam1007 MB, The Netherlands
| | - Johannes Hunger
- Max Planck Institute for Polymer Research, Molecular Spectroscopy Department, Mainz55128, Germany
| | - Antoine Deblais
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, Amsterdam1090 GL, The Netherlands
| | - Daniel Bonn
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, Amsterdam1090 GL, The Netherlands
| | - Nico Sommerdijk
- Electron Microscopy Center, Radboud Technology Center Microscopy, Department of Medical BioSciences, Radboud University Medical Center, Nijmegen6525 GA, The Netherlands
| | - Andela Šarić
- Institute of Science and Technology Austria, Division of Mathematical and Physical Sciences, Klosterneuburg3400, Austria
| | - Ioana M. Ilie
- Van ’t Hoff Institute for Molecular Sciences, Department of Molecular Photonics, University of Amsterdam, Amsterdam1090 GD, The Netherlands
- Amsterdam Center for Multiscale Modeling, University of Amsterdam, Amsterdam1090 GD, The Netherlands
| | - Gijsje H. Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft2628 HZ, The Netherlands
| | - Sander Woutersen
- Van ’t Hoff Institute for Molecular Sciences, Department of Molecular Photonics, University of Amsterdam, Amsterdam1090 GD, The Netherlands
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3
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Giubertoni G, Bonn M, Woutersen S. D 2O as an Imperfect Replacement for H 2O: Problem or Opportunity for Protein Research? J Phys Chem B 2023; 127:8086-8094. [PMID: 37722111 PMCID: PMC10544019 DOI: 10.1021/acs.jpcb.3c04385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/28/2023] [Indexed: 09/20/2023]
Abstract
D2O is commonly used as a solvent instead of H2O in spectroscopic studies of proteins, in particular, in infrared and nuclear-magnetic-resonance spectroscopy. D2O is chemically equivalent to H2O, and the differences, particularly in hydrogen-bond strength, are often ignored. However, replacing solvent water with D2O can affect not only the kinetics but also the structure and stability of biomolecules. Recent experiments have shown that even the mesoscopic structures and the elastic properties of biomolecular assemblies, such as amyloids and protein networks, can be very different in D2O and H2O. We discuss these findings, which probably are just the tip of the iceberg, and which seem to call for obtaining a better understanding of the H2O/D2O-isotope effect on water-water and water-protein interactions. Such improved understanding may change the differences between H2O and D2O as biomolecular solvents from an elephant in the room to an opportunity for protein research.
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Affiliation(s)
- Giulia Giubertoni
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Mischa Bonn
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sander Woutersen
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
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4
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Schmidt R, Giubertoni G, Caporaletti F, Kolpakov P, Shahidzadeh N, Ariese F, Woutersen S. Raman Diffusion-Ordered Spectroscopy. J Phys Chem A 2023; 127:7638-7645. [PMID: 37656920 PMCID: PMC10510375 DOI: 10.1021/acs.jpca.3c03232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/25/2023] [Indexed: 09/03/2023]
Abstract
The Stokes-Einstein relation, which relates the diffusion coefficient of a molecule to its hydrodynamic radius, is commonly used to determine molecular sizes in chemical analysis methods. Here, we combine the size sensitivity of such diffusion-based methods with the structure sensitivity of Raman spectroscopy by performing Raman diffusion-ordered spectroscopy (Raman-DOSY). The core of the Raman-DOSY setup is a flow cell with a Y-shaped channel containing two inlets: one for the sample solution and one for the pure solvent. The two liquids are injected at the same flow rate, giving rise to two parallel laminar flows in the channel. After the flow stops, the solute molecules diffuse from the solution-filled half of the channel into the solvent-filled half at a rate determined by their hydrodynamic radius. The arrival of the solute molecules in the solvent-filled half of the channel is recorded in a spectrally resolved manner by Raman microspectroscopy. From the time series of Raman spectra, a two-dimensional Raman-DOSY spectrum is obtained, which has the Raman frequency on one axis and the diffusion coefficient (or equivalently, hydrodynamic radius) on the other. In this way, Raman-DOSY spectrally resolves overlapping Raman peaks arising from molecules of different sizes. We demonstrate Raman-DOSY on samples containing up to three compounds and derive the diffusion coefficients of small molecules, proteins, and supramolecules (micelles), illustrating the versatility of Raman-DOSY. Raman-DOSY is label-free and does not require deuterated solvents and can thus be applied to samples and matrices that might be difficult to investigate with other diffusion-based spectroscopy methods.
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Affiliation(s)
- Robert
W. Schmidt
- Vrije
Universiteit Amsterdam, De Boelelaan 1105, 1081HV Amsterdam, The Netherlands
- University
of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Giulia Giubertoni
- University
of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Federico Caporaletti
- University
of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
- Université
Libre de Bruxelles, Av.
Franklin Roosevelt 50, 1050 Bruxelles, Belgium
| | - Paul Kolpakov
- University
of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | | | - Freek Ariese
- Vrije
Universiteit Amsterdam, De Boelelaan 1105, 1081HV Amsterdam, The Netherlands
| | - Sander Woutersen
- University
of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
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5
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Giubertoni G, Caporaletti F, Van Diest R, Woutersen S. Multidimensional Infrared Diffusion-Ordered Spectroscopy in depletion mode distinguishes protein amyloids and monomers. J Chem Phys 2023; 158:124202. [PMID: 37003753 DOI: 10.1063/5.0140132] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023] Open
Abstract
Conventional and two-dimensional infrared (2D-IR) spectroscopy are well suited to study amyloid aggregates, because the amide I mode is a sensitive probe of the aggregate structure. However, these methods are not so useful to study mixtures of aggregates and monomers, which generally have overlapping amide I spectra. Here, we show that IR-Diffusion-Ordered Spectroscopy (IR-DOSY) can disentangle the contributions of protein monomers and aggregates in FTIR and 2D-IR spectra by separating the spectral contributions based on molecular size. We rely on the fact that the diffusion coefficient of a molecule is determined by its size through the Stokes-Einstein relation, and achieve sensitivity to the diffusion coefficient by creating a concentration gradient inside an infrared sample cell and tracking its equilibration in an IR-frequency resolved manner. The protein-aggregate diffusion is too slow to be experimentally observable, so instead of tracking the arrival of molecular species diffusing into the initially empty region of the sample cell, we track the depletion of the more rapidly diffusing species as they leave the sample-filled region. In this way, we can still obtain the spectrum of very slowly diffusing species, although we cannot determine their diffusion coefficient. We first demonstrate this depletion method on a mixture of two small organic molecules, and then show how it can be used to separate the spectrum of a mixture of bovine-serum-albumin amyloids and monomers into its component spectra, both in the FTIR and 2D-IR case.
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Affiliation(s)
- Giulia Giubertoni
- University of Amsterdam Van 't Hoff Institute for Molecular Sciences, Netherlands
| | | | - Rianne Van Diest
- University of Amsterdam Van 't Hoff Institute for Molecular Sciences, Netherlands
| | - Sander Woutersen
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam Van 't Hoff Institute for Molecular Sciences, Netherlands
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6
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Giubertoni G, Hilbers M, Caporaletti F, Laity P, Groen H, Van der Weide A, Bonn D, Woutersen S. Hydrogen Bonds under Stress: Strain-Induced Structural Changes in Polyurethane Revealed by Rheological Two-Dimensional Infrared Spectroscopy. J Phys Chem Lett 2023; 14:940-946. [PMID: 36688732 PMCID: PMC9900637 DOI: 10.1021/acs.jpclett.2c03109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
The remarkable elastic properties of polymers are ultimately due to their molecular structure, but the relation between the macroscopic and molecular properties is often difficult to establish, in particular for (bio)polymers that contain hydrogen bonds, which can easily rearrange upon mechanical deformation. Here we show that two-dimensional infrared spectroscopy on polymer films in a miniature stress tester sheds new light on how the hydrogen-bond structure of a polymer is related to its viscoelastic response. We study thermoplastic polyurethane, a block copolymer consisting of hard segments of hydrogen-bonded urethane groups embedded in a soft matrix of polyether chains. The conventional infrared spectrum shows that, upon deformation, the number of hydrogen bonds increases, a process that is largely reversible. However, the 2DIR spectrum reveals that the distribution of hydrogen-bond strengths becomes slightly narrower after a deformation cycle, due to the disruption of weak hydrogen bonds, an effect that could explain the strain-cycle induced softening (Mullins effect) of polyurethane. These results show how rheo-2DIR spectroscopy can bridge the gap between the molecular structure and the macroscopic elastic properties of (bio)polymers.
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Affiliation(s)
- Giulia Giubertoni
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Michiel Hilbers
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Federico Caporaletti
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
- Van
der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098XH Amsterdam, The Netherlands
| | - Peter Laity
- Department
of Materials Science and Engineering, University
of Sheffield, Sir Robert
Hadfield Building, Mappin Street, Sheffield S1 3JD, U.K.
| | - Hajo Groen
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Anne Van der Weide
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Daniel Bonn
- Van
der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098XH Amsterdam, The Netherlands
| | - Sander Woutersen
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
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7
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Giubertoni G, Rombouts G, Caporaletti F, Deblais A, van Diest R, Reek JNH, Bonn D, Woutersen S. Infrared Diffusion-Ordered Spectroscopy Reveals Molecular Size and Structure. Angew Chem Int Ed Engl 2023; 62:e202213424. [PMID: 36259515 PMCID: PMC10107201 DOI: 10.1002/anie.202213424] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Indexed: 11/07/2022]
Abstract
Inspired by ideas from NMR, we have developed Infrared Diffusion-Ordered Spectroscopy (IR-DOSY), which simultaneously characterizes molecular structure and size. We rely on the fact that the diffusion coefficient of a molecule is determined by its size through the Stokes-Einstein relation, and achieve sensitivity to the diffusion coefficient by creating a concentration gradient and tracking its equilibration in an IR-frequency resolved manner. Analogous to NMR-DOSY, a two-dimensional IR-DOSY spectrum has IR frequency along one axis and diffusion coefficient (or equivalently, size) along the other, so the chemical structure and the size of a compound are characterized simultaneously. In an IR-DOSY spectrum of a mixture, molecules with different sizes are nicely separated into distinct sets of IR peaks. Extending this idea to higher dimensions, we also perform 3D-IR-DOSY, in which we combine the conformation sensitivity of femtosecond multi-dimensional IR spectroscopy with size sensitivity.
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Affiliation(s)
- Giulia Giubertoni
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Gijs Rombouts
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Federico Caporaletti
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands.,Institute of Physics, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Antoine Deblais
- Institute of Physics, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Rianne van Diest
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Joost N H Reek
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Daniel Bonn
- Institute of Physics, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Sander Woutersen
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
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8
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Giubertoni G, Caporaletti F, Roeters SJ, Chatterley AS, Weidner T, Laity P, Holland C, Woutersen S. In Situ Identification of Secondary Structures in Unpurified Bombyx mori Silk Fibrils Using Polarized Two-Dimensional Infrared Spectroscopy. Biomacromolecules 2022; 23:5340-5349. [PMID: 36437734 DOI: 10.1021/acs.biomac.2c01156] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanical properties of biomaterials are dictated by the interactions and conformations of their building blocks, typically proteins. Although the macroscopic behavior of biomaterials is widely studied, our understanding of the underlying molecular properties is generally limited. Among the noninvasive and label-free methods to investigate molecular structures, infrared spectroscopy is one of the most commonly used tools because the absorption bands of amide groups strongly depend on protein secondary structure. However, spectral congestion usually complicates the analysis of the amide spectrum. Here, we apply polarized two-dimensional (2D) infrared spectroscopy (IR) to directly identify the protein secondary structures in native silk films cast from Bombyx mori silk feedstock. Without any additional peak fitting, we find that the initial effect of hydration is an increase of the random coil content at the expense of the helical content, while the β-sheet content is unchanged and only increases at a later stage. This paper demonstrates that 2D-IR can be a valuable tool for characterizing biomaterials.
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Affiliation(s)
- Giulia Giubertoni
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XHAmsterdam, The Netherlands.,Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XHAmsterdam, The Netherlands
| | - Federico Caporaletti
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XHAmsterdam, The Netherlands.,Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XHAmsterdam, The Netherlands
| | - Steven J Roeters
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XHAmsterdam, The Netherlands.,Department of Chemistry, Aarhus University, 8000Aarhus C, Denmark
| | | | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000Aarhus C, Denmark
| | - Peter Laity
- Department of Materials Science and Engineering, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, SheffieldS1 3JD, U.K
| | - Chris Holland
- Department of Materials Science and Engineering, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, SheffieldS1 3JD, U.K
| | - Sander Woutersen
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XHAmsterdam, The Netherlands
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9
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Giubertoni G, Rombouts G, Caporaletti F, Deblais A, Van Diest R, Reek J, Bonn D, Woutersen S. Infrared Diffusion‐Ordered Spectroscopy Reveals Molecular Size and Structure. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202213424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Giulia Giubertoni
- University of Amsterdam: Universiteit van Amsterdam FNWI NETHERLANDS
| | - Gijs Rombouts
- University of Amsterdam: Universiteit van Amsterdam FNWI NETHERLANDS
| | | | - Antoine Deblais
- University of Amsterdam: Universiteit van Amsterdam FNWI NETHERLANDS
| | - Rianne Van Diest
- University of Amsterdam: Universiteit van Amsterdam FNWI NETHERLANDS
| | - Joost Reek
- University of Amsterdam: Universiteit van Amsterdam FNWI NETHERLANDS
| | - Daniel Bonn
- University of Amsterdam: Universiteit van Amsterdam FNWI NETHERLANDS
| | - Sander Woutersen
- Universiteit van Amsterdam HIMS Science Park 904 1098XH Amsterdam NETHERLANDS
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10
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Chatterley AS, Laity P, Holland C, Weidner T, Woutersen S, Giubertoni G. Broadband Multidimensional Spectroscopy Identifies the Amide II Vibrations in Silkworm Films. Molecules 2022; 27:molecules27196275. [PMID: 36234809 PMCID: PMC9571984 DOI: 10.3390/molecules27196275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
We used two-dimensional infrared spectroscopy to disentangle the broad infrared band in the amide II vibrational regions of Bombyx mori native silk films, identifying the single amide II modes and correlating them to specific secondary structure. Amide I and amide II modes have a strong vibrational coupling, which manifests as cross-peaks in 2D infrared spectra with frequencies determined by both the amide I and amide II frequencies of the same secondary structure. By cross referencing with well-known amide I assignments, we determined that the amide II (N-H) absorbs at around 1552 and at 1530 cm–1 for helical and β-sheet structures, respectively. We also observed a peak at 1517 cm−1 that could not be easily assigned to an amide II mode, and instead we tentatively assigned it to a Tyrosine sidechain. These results stand in contrast with previous findings from linear infrared spectroscopy, highlighting the ability of multidimensional spectroscopy for untangling convoluted spectra, and suggesting the need for caution when assigning silk amide II spectra.
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Affiliation(s)
| | - Peter Laity
- Department of Materials Science and Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Chris Holland
- Department of Materials Science and Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Sander Woutersen
- Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Giulia Giubertoni
- Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
- Correspondence:
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11
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Moll CJ, Giubertoni G, van Buren L, Versluis J, Koenderink GH, Bakker HJ. Molecular Structure and Surface Accumulation Dynamics of Hyaluronan at the Water-Air Interface. Macromolecules 2021; 54:8655-8663. [PMID: 34602653 PMCID: PMC8482758 DOI: 10.1021/acs.macromol.1c00366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 02/15/2021] [Indexed: 11/30/2022]
Abstract
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Hyaluronan is a biopolymer
that is essential for many biological
processes in the human body, like the regulation of tissue lubrication
and inflammatory responses. Here, we study the behavior of hyaluronan
at aqueous surfaces using heterodyne-detected vibrational sum-frequency
generation spectroscopy (HD-VSFG). Low-molecular-weight hyaluronan
(∼150 kDa) gradually covers the water–air interface
within hours, leading to a negatively charged surface and a reorientation
of interfacial water molecules. The rate of surface accumulation strongly
increases when the bulk concentration of low-molecular-weight hyaluronan
is increased. In contrast, high-molecular-weight hyaluronan (>1
MDa)
cannot be detected at the surface, even hours after the addition of
the polymer to the aqueous solution. The strong dependence on the
polymer molecular weight can be explained by entanglements of the
hyaluronan polymers. We also find that for low-molecular-weight hyaluronan
the migration kinetics of hyaluronan in aqueous media shows an anomalous
dependence on the pH of the solution, which can be explained from
the interplay of hydrogen bonding and electrostatic interactions of
hyaluronan polymers.
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Affiliation(s)
- Carolyn J Moll
- Amolf, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Giulia Giubertoni
- Amolf, Science Park 104, 1098 XG Amsterdam, The Netherlands.,Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Lennard van Buren
- Amolf, Science Park 104, 1098 XG Amsterdam, The Netherlands.,Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jan Versluis
- Amolf, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Gijsje H Koenderink
- Amolf, Science Park 104, 1098 XG Amsterdam, The Netherlands.,Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Huib J Bakker
- Amolf, Science Park 104, 1098 XG Amsterdam, The Netherlands
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12
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Sun Y, Giubertoni G, Bakker HJ, Liu J, Wagner M, Ng DYW, Devries AL, Meister K. Disaccharide Residues are Required for Native Antifreeze Glycoprotein Activity. Biomacromolecules 2021; 22:2595-2603. [PMID: 33957041 PMCID: PMC8207503 DOI: 10.1021/acs.biomac.1c00313] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Antifreeze glycoproteins
(AFGPs) are able to bind to ice, halt
its growth, and are the most potent inhibitors of ice recrystallization
known. The structural basis for AFGP’s unique properties remains
largely elusive. Here we determined the antifreeze activities of AFGP
variants that we constructed by chemically modifying the hydroxyl
groups of the disaccharide of natural AFGPs. Using nuclear magnetic
resonance, two-dimensional infrared spectroscopy, and circular dichroism,
the expected modifications were confirmed as well as their effect
on AFGPs solution structure. We find that the presence of all the
hydroxyls on the disaccharides is a requirement for the native AFGP
hysteresis as well as the maximal inhibition of ice recrystallization.
The saccharide hydroxyls are apparently as important as the acetyl
group on the galactosamine, the α-linkage between the disaccharide
and threonine, and the methyl groups on the threonine and alanine.
We conclude that the use of hydrogen-bonding through the hydroxyl
groups of the disaccharide and hydrophobic interactions through the
polypeptide backbone are equally important in promoting the antifreeze
activities observed in the native AFGPs. These important criteria
should be considered when designing synthetic mimics.
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Affiliation(s)
- Yuling Sun
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Giulia Giubertoni
- NWO Institute AMOLF, 1098 XG Amsterdam, The Netherlands.,University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Huib J Bakker
- NWO Institute AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Jie Liu
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Manfred Wagner
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - David Y W Ng
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Arthur L Devries
- University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Konrad Meister
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany.,University of Alaska Southeast, Juneau, Alaska 99801, United States
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13
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Giubertoni G, Pérez de Alba Ortíz A, Bano F, Zhang X, Linhardt RJ, Green DE, DeAngelis PL, Koenderink GH, Richter RP, Ensing B, Bakker HJ. Strong Reduction of the Chain Rigidity of Hyaluronan by Selective Binding of Ca 2+ Ions. Macromolecules 2021; 54:1137-1146. [PMID: 33583956 PMCID: PMC7879427 DOI: 10.1021/acs.macromol.0c02242] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 10/05/2020] [Revised: 12/08/2020] [Indexed: 01/09/2023]
Abstract
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The
biological functions of natural polyelectrolytes are strongly
influenced by the presence of ions, which bind to the polymer chains
and thereby modify their properties. Although the biological impact
of such modifications is well recognized, a detailed molecular picture
of the binding process and of the mechanisms that drive the subsequent
structural changes in the polymer is lacking. Here, we study the molecular
mechanism of the condensation of calcium, a divalent cation, on hyaluronan,
a ubiquitous polymer in human tissues. By combining two-dimensional
infrared spectroscopy experiments with molecular dynamics simulations,
we find that calcium specifically binds to hyaluronan at millimolar
concentrations. Because of its large size and charge, the calcium
cation can bind simultaneously to the negatively charged carboxylate
group and the amide group of adjacent saccharide units. Molecular
dynamics simulations and single-chain force spectroscopy measurements
provide evidence that the binding of the calcium ions weakens the
intramolecular hydrogen-bond network of hyaluronan, increasing the
flexibility of the polymer chain. We also observe that the binding
of calcium to hyaluronan saturates at a maximum binding fraction of
∼10–15 mol %. This saturation indicates that the binding
of Ca2+ strongly reduces the probability of subsequent
binding of Ca2+ at neighboring binding sites, possibly
as a result of enhanced conformational fluctuations and/or electrostatic
repulsion effects. Our findings provide a detailed molecular picture
of ion condensation and reveal the severe effect of a few, selective
and localized electrostatic interactions on the rigidity of a polyelectrolyte
chain.
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Affiliation(s)
| | - Alberto Pérez de Alba Ortíz
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Fouzia Bano
- School of Biomedical Sciences, Faculty of Biological Sciences, School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, Astbury Centre of Structural Molecular Biology, and Bragg Centre for Materials Research, University of Leeds, LS2 9JT Leeds, U.K
| | - Xing Zhang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, 12180 New York, United States
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, 12180 New York, United States
| | - Dixy E Green
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., Oklahoma, 73104 Oklahoma, United States
| | - Paul L DeAngelis
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., Oklahoma, 73104 Oklahoma, United States
| | - Gijsje H Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Ralf P Richter
- School of Biomedical Sciences, Faculty of Biological Sciences, School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, Astbury Centre of Structural Molecular Biology, and Bragg Centre for Materials Research, University of Leeds, LS2 9JT Leeds, U.K
| | - Bernd Ensing
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Huib J Bakker
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
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14
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Giubertoni G, Burla F, Bakker HJ, Koenderink GH. Connecting the Stimuli-Responsive Rheology of Biopolymer Hydrogels to Underlying Hydrogen-Bonding Interactions. Macromolecules 2020; 53:10503-10513. [PMID: 33335340 PMCID: PMC7735748 DOI: 10.1021/acs.macromol.0c01742] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 07/27/2020] [Revised: 11/04/2020] [Indexed: 11/29/2022]
Abstract
Many biopolymer hydrogels are environmentally responsive because they are held together by physical associations that depend on pH and temperature. Here, we investigate how the pH and temperature responses of the rheology of hyaluronan hydrogels are connected to the underlying molecular interactions. Hyaluronan is an essential structural biopolymer in the human body with many applications in biomedicine. Using two-dimensional infrared spectroscopy, we show that hyaluronan chains become connected by hydrogen bonds when the pH is changed from 7.0 to 2.5 and that the bond density at pH 2.5 is independent of temperature. Temperature-dependent rheology measurements show that because of this hydrogen bonding the stress relaxation at pH 2.5 is strongly slowed down in comparison to pH 7.0, consistent with the sticky reptation model of associative polymers. From the flow activation energy, we conclude that each polymer is cross-linked by multiple (5-15) hydrogen bonds to others, causing slow macroscopic stress relaxation, despite the short time scale of breaking and reformation of each individual hydrogen bond. Our findings can aid the design of stimuli-responsive hydrogels with tailored viscoelastic properties for biomedical applications.
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Affiliation(s)
| | - Federica Burla
- AMOLF, Science Park 104, Amsterdam 1098 XG, The Netherlands
| | - Huib J. Bakker
- AMOLF, Science Park 104, Amsterdam 1098 XG, The Netherlands
| | - Gijsje H. Koenderink
- AMOLF, Science Park 104, Amsterdam 1098 XG, The Netherlands
- Department of Bionanoscience, Kavli Institute
of Nanoscience Delft, Delft University of
Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
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15
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Giubertoni G, Sofronov OO, Bakker HJ. Effect of intramolecular hydrogen-bond formation on the molecular conformation of amino acids. Commun Chem 2020; 3:84. [PMID: 36703397 PMCID: PMC9814578 DOI: 10.1038/s42004-020-0329-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/21/2020] [Indexed: 01/29/2023] Open
Abstract
The molecular conformation of the carboxyl group can be crucial for its chemical properties and intermolecular interactions, especially in complex molecular environments such as polypeptides. Here, we study the conformational behaviour of the model amino acid N-acetylproline in solution at room temperature with two-dimensional infrared spectroscopy. We find that the carboxyl group of N-acetylproline adopts two distinct conformations, syn- and anti-. In the syn-conformer the O-H group is oriented at ~60∘ with respect to the C=O and in the anti-conformer the O-H is anti-parallel to the C=O. In hydrogen-bond accepting solvents such as dimethyl sulfoxide or water, we observe that, similar to simple carboxylic acids, around 20% of the -COOH groups adopt an anti-conformation. However, when N-acetylproline is dissolved in a weakly hydrogen-bond accepting solvent (acetonitrile), we observe the formation of a strong intramolecular hydrogen bond between the carboxyl group in the anti-conformation and the amide group, which stabilizes the anti-conformer, increasing its relative abundance to ~60%.
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Affiliation(s)
- Giulia Giubertoni
- grid.417889.b0000 0004 0646 2441AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Oleksandr O. Sofronov
- grid.417889.b0000 0004 0646 2441AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Huib J. Bakker
- grid.417889.b0000 0004 0646 2441AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
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16
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Sofronov O, Giubertoni G, Pérez de Alba Ortíz A, Ensing B, Bakker HJ. Peptide Side-COOH Groups Have Two Distinct Conformations under Biorelevant Conditions. J Phys Chem Lett 2020; 11:3466-3472. [PMID: 32293901 PMCID: PMC7212517 DOI: 10.1021/acs.jpclett.0c00711] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
The carboxyl (COOH) side chain groups of amino acids, such as aspartic acid, play an important role in biochemical processes, including enzymatic proton transport. In many theoretical studies, it was found that the (bio)chemical reactivity of the carboxyl group strongly depends on the conformation of this group. Interestingly, up to now there has been no experimental investigation of the geometry and the stability of different COOH conformers under biorelevant conditions. Here, we investigate the conformational isomerism of the side chain COOH group of N-acetyl aspartic acid amide using polarization-resolved two-dimensional infrared spectroscopy. We find that the carboxyl group shows two distinct near-planar conformers (syn and anti) when dissolved in water at room temperature. Both conformers are significantly populated in aqueous solution (75 ± 10% and 25 ± 10% for syn and anti, respectively). Molecular dynamics simulations show that the anti conformer interacts more strongly with water molecules than the syn conformer, explaining why this conformer is significantly present in aqueous solution.
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Affiliation(s)
| | | | - Alberto Pérez de Alba Ortíz
- Amsterdam
Center for Multiscale Modeling and Van ’t Hoff Institute for
Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Bernd Ensing
- Amsterdam
Center for Multiscale Modeling and Van ’t Hoff Institute for
Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Huib J. Bakker
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
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17
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van Dam EP, Giubertoni G, Burla F, Koenderink GH, Bakker HJ. Hyaluronan biopolymers release water upon pH-induced gelation. Phys Chem Chem Phys 2020; 22:8667-8671. [DOI: 10.1039/d0cp00215a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We measure the reorientation dynamics of water in hyaluronan solutions, and find that, upon pH-induced gelation, these biopolymers release water.
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Affiliation(s)
| | | | | | - Gijsje H. Koenderink
- AMOLF
- 1098 XG Amsterdam
- The Netherlands
- Department of Bionanoscience
- Kavli Institute of Nanoscience Delft
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18
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Abstract
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We use two-dimensional
infrared spectroscopy to study the interactions
between the amide and carboxylate anion groups of hyaluronan polymers
at neutral pH. The spectra reveal the presence of intrachain hydrogen
bonds between the amide and carboxylate anion groups in aqueous solution.
We determine the relative orientation of the amide and carboxylate
anion groups when forming this hydrogen bond and quantify the fraction
of amide groups that participate in hydrogen bonding. We find that
a variation of the pH and/or temperature has a negligible effect on
this fraction, whereas the persistence length of the hyaluronan chains
and the associated viscosity of hyaluronan solutions are known to
change significantly. We conclude that the hydrogen bonding between
the amide and carboxylate anion groups does not significantly contribute
to the chain rigidity of hyaluronan polymers.
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Affiliation(s)
| | | | - Huib J Bakker
- AMOLF , Science Park 104 , 1098 XG Amsterdam , The Netherlands
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19
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Giubertoni G, Sofronov OO, Bakker HJ. Observation of Distinct Carboxylic Acid Conformers in Aqueous Solution. J Phys Chem Lett 2019; 10:3217-3222. [PMID: 31125521 PMCID: PMC6589744 DOI: 10.1021/acs.jpclett.9b00915] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/24/2019] [Indexed: 05/26/2023]
Abstract
We investigate the molecular geometry of the carboxyl group of formic acid in acetonitrile and aqueous solutions at room temperature with two-dimensional infrared spectroscopy (2D-IR). We found that the carboxyl group adopts two distinct configurations: a configuration in which the carbonyl group is oriented antiparallel to the hydroxyl (anti-conformer), and a configuration in which the carbonyl group is oriented at an angle of ∼60° with respect to the hydroxyl (syn-conformer). These results constitute the first experimental evidence that carboxyl groups exist as two distinct and long-living conformational isomers in aqueous solution at room temperature.
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20
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Giubertoni G, Burla F, Martinez-Torres C, Dutta B, Pletikapic G, Pelan E, Rezus YLA, Koenderink GH, Bakker HJ. Molecular Origin of the Elastic State of Aqueous Hyaluronic Acid. J Phys Chem B 2019; 123:3043-3049. [PMID: 30888176 PMCID: PMC6466474 DOI: 10.1021/acs.jpcb.9b00982] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 01/10/2023]
Abstract
The macroscopic mechanical properties of biological hydrogels are broadly studied and successfully mimicked in synthetic materials, but little is known about the molecular interactions that mediate these properties. Here, we use two-dimensional infrared spectroscopy to study the pH-induced gelation of hyaluronic acid, a ubiquitous biopolymer, which undergoes a transition from a viscous to an elastic state in a narrow pH range around 2.5. We find that the gelation originates from the enhanced formation of strong interchain connections, consisting of a double amide-COOH hydrogen bond and an N-D-COO- hydrogen bond on the adjacent sugars of the hyaluronan disaccharide unit. We confirm the enhanced interchain connectivity in the elastic state by atomic force microscopy imaging.
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Affiliation(s)
| | - Federica Burla
- AMOLF , Science Park 104 , 1098 XG Amsterdam , The Netherlands
| | | | - Biplab Dutta
- AMOLF , Science Park 104 , 1098 XG Amsterdam , The Netherlands
| | | | - Eddie Pelan
- Unilever Research and Development Vlaardingen B.V , Olivier van Noortlaan 120 , 3133 AT Vlaardingen , The Netherlands
| | - Yves L A Rezus
- AMOLF , Science Park 104 , 1098 XG Amsterdam , The Netherlands
| | | | - Huib J Bakker
- AMOLF , Science Park 104 , 1098 XG Amsterdam , The Netherlands
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21
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Giubertoni G, Meister K, DeVries AL, Bakker HJ. Determination of the Solution Structure of Antifreeze Glycoproteins Using Two-Dimensional Infrared Spectroscopy. J Phys Chem Lett 2019; 10:352-357. [PMID: 30615465 PMCID: PMC6369719 DOI: 10.1021/acs.jpclett.8b03468] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/07/2019] [Indexed: 05/20/2023]
Abstract
We study the solution structure of antifreeze glycoproteins (AFGPs) with linear and two-dimensional infrared spectroscopy (2D-IR). With 2D-IR, we study the coupling between the amide I and amide II vibrations of AFGPs. The measured nonlinear spectral response constitutes a much more clearly resolved amide I spectrum than the linear absorption spectrum of the amide I vibrations and allows us to identify the different structural elements of AFGPs in solution. We find clear evidence for the presence of polyproline II (PPII) helical structures already at room temperature, and we find that the fraction of PPII structures increases when the temperature is decreased to the biological working temperature of AFGP. We observe that inhibition of the antifreeze activity of AFGP using borate buffer or enhancing the antifreeze activity using sulfate buffer does not lead to significant changes in the protein conformation. This finding indicates that AFGPs bind to ice with their sugar side chains.
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Affiliation(s)
| | - Konrad Meister
- Max-Planck
Institute for Polymer Research, D-55128 Mainz, Germany
| | - Arthur L. DeVries
- University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Huib J. Bakker
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
- E-mail:
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22
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Gallop NP, Selig O, Giubertoni G, Bakker HJ, Rezus YLA, Frost JM, Jansen TLC, Lovrincic R, Bakulin AA. Rotational Cation Dynamics in Metal Halide Perovskites: Effect on Phonons and Material Properties. J Phys Chem Lett 2018; 9:5987-5997. [PMID: 30260646 DOI: 10.1021/acs.jpclett.8b02227] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The dynamics of organic cations in metal halide hybrid perovskites (MHPs) have been investigated using numerous experimental and computational techniques because of their suspected effects on the properties of MHPs. In this Perspective, we summarize and reconcile key findings and present new data to synthesize a unified understanding of the dynamics of the cations. We conclude that theory and experiment collectively paint a relatively complete picture of rotational dynamics within MHPs. This picture is then used to discuss the consequences of structural dynamics for electron-phonon interactions and their effect on material properties by providing a brief account of key studies that correlate cation dynamics with the dynamics of the inorganic sublattice and overall device properties.
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Affiliation(s)
- Nathaniel P Gallop
- Ultrafast Optoelectronics Group, Department of Chemistry , Imperial College London , London SW7 2AZ , U.K
| | - Oleg Selig
- AMOLF , Science Park 104 , 1098 XG Amsterdam , The Netherlands
| | | | - Huib J Bakker
- AMOLF , Science Park 104 , 1098 XG Amsterdam , The Netherlands
| | - Yves L A Rezus
- AMOLF , Science Park 104 , 1098 XG Amsterdam , The Netherlands
| | - Jarvist M Frost
- Department of Physics , Kings College London , London WC2R 2LS , U.K
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands
| | - Robert Lovrincic
- InnovationLab Heidelberg and TU Braunschweig , Speyerer Str. 4 , 69115 Heidelberg , Germany
| | - Artem A Bakulin
- Ultrafast Optoelectronics Group, Department of Chemistry , Imperial College London , London SW7 2AZ , U.K
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23
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Yuan H, Xu J, van Dam EP, Giubertoni G, Rezus YLA, Hammink R, Bakker HJ, Zhan Y, Rowan AE, Xing C, Kouwer PHJ. Strategies To Increase the Thermal Stability of Truly Biomimetic Hydrogels: Combining Hydrophobicity and Directed Hydrogen Bonding. Macromolecules 2017; 50:9058-9065. [PMID: 29213150 PMCID: PMC5707627 DOI: 10.1021/acs.macromol.7b01832] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [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] [Received: 08/24/2017] [Revised: 11/08/2017] [Indexed: 01/29/2023]
Abstract
Enhancing the thermal stability of proteins is an important task for protein engineering. There are several ways to increase the thermal stability of proteins in biology, such as greater hydrophobic interactions, increased helical content, decreased occurrence of thermolabile residues, or stable hydrogen bonds. Here, we describe a well-defined polymer based on β-helical polyisocyanotripeptides (TriPIC) that uses biological approaches, including hydrogen bonding and hydrophobic interactions for its exceptional thermal stability in aqueous solutions. The multiple hydrogen bonding arrays along the polymer backbone shield the hydrophobic core from water. Variable temperature CD and FTIR studies indicate that, on heating, a better packed polymer conformation further stiffens the backbone. Driven by hydrophobic interactions, TriPIC solutions give fully reversible hydrogels that can withstand high temperatures (80 °C) for extended times. Cryo-scanning electron microscopy (cryo-SEM), small-angle X-ray scattering (SAXS), and thorough rheological analysis show that the hydrogel has a bundled architecture, which gives rise to strain stiffening effects on deformation of the gel, analogous to many biological hydrogels.
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Affiliation(s)
- Hongbo Yuan
- School of Materials Science and Engineering, Hebei University of Technology, Tianjin 300401, P. R. China.,Institute for Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands
| | - Jialiang Xu
- School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Tianjin 300350, P. R. China.,Institute for Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands
| | | | | | - Yves L A Rezus
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Roel Hammink
- Institute for Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands
| | - Huib J Bakker
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Yong Zhan
- School of Materials Science and Engineering, Hebei University of Technology, Tianjin 300401, P. R. China
| | - Alan E Rowan
- Institute for Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Chengfen Xing
- School of Materials Science and Engineering, Hebei University of Technology, Tianjin 300401, P. R. China
| | - Paul H J Kouwer
- Institute for Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands
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Castelli M, Zanca A, Giubertoni G, Zanca A, Bertolini A. Griseofulvin-methisoprinol combination in the treatment of herpes zoster. Pharmacol Res Commun 1986; 18:991-6. [PMID: 2433701 DOI: 10.1016/0031-6989(86)90101-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A total of 57 herpes zoster patients (28 men and 28 women) were randomly assigned to one of the following four treatments: griseofulvin, 125 mg four times daily; methisoprinol, 1 g four times daily; griseofulvin plus methisoprinol (dosage schedules as above); placebo, four times daily. Griseofulvin had no effect at all, methisoprinol both significantly accelerated drying of vesicles and reduced pain, and the combination of griseofulvin and methisoprinol turned out to be significantly more effective in reducing pain than methisoprinol alone. The present results suggest a new effective treatment for herpes zoster disease.
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25
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Zanca A, Giubertoni G. [Medicosocial study of burns. (Statistical review of burned patients confined to bed in the dermatologic department of the C. Poma hospital institutes in Mantua in the period 1966-70)]. G Ital Dermatol Minerva Dermatol 1972; 47:62-71. [PMID: 5067554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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