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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] [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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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] [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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Pica A, Graziano G. Effect of heavy water on the conformational stability of globular proteins. Biopolymers 2017; 109:e23076. [PMID: 29068056 DOI: 10.1002/bip.23076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 09/30/2017] [Accepted: 10/10/2017] [Indexed: 01/08/2023]
Abstract
It is well established from the experimental point of view that the native state of globular proteins is more stable in heavy water than in water. No robust explanation, however, has been provided up to now. The application of the theoretical approach, originally devised to rationalize the general occurrence of cold denaturation, indicates that the magnitude of the solvent-excluded volume effect is slightly smaller in heavy water than in water and cannot explain the observed protein stabilization. The latter has to be due to the strength of protein-water van der Waals attractions which are weaker in heavy water due to the smaller molecular polarizability of D2 O compared with that of H2 O molecules. Since protein-water van der Waals attractions occur more in the denatured than in the native state, this contribution leads to a stabilization of the latter through a destabilization of the former.
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Affiliation(s)
- Andrea Pica
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, Napoli, 80126, Italy
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Via Port'Arsa 11, Benevento, 82100, Italy
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Eklouh-Molinier C, Happillon T, Bouland N, Fichel C, Diébold MD, Angiboust JF, Manfait M, Brassart-Pasco S, Piot O. Investigating the relationship between changes in collagen fiber orientation during skin aging and collagen/water interactions by polarized-FTIR microimaging. Analyst 2016; 140:6260-8. [PMID: 26120602 DOI: 10.1039/c5an00278h] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Upon chronological aging, human skin undergoes structural and molecular modifications, especially at the level of type I collagen. This macromolecule is one of the main dermal structural proteins and presents several age-related alterations. It exhibits a triple helical structure and assembles itself to form fibrils and fibers. In addition, water plays an important role in stabilizing the collagen triple helix by forming hydrogen-bonds between collagen residues. However, the influence of water on changes of dermal collagen fiber orientation with age has not been yet understood. Polarized-Fourier Transform Infrared (P-FTIR) imaging is an interesting biophotonic approach to determine in situ the orientation of type I collagen fibers, as we have recently shown by comparing skin samples of different ages. In this work, P-FTIR spectral imaging was performed on skin samples from two age groups (35- and 38-year-old on the one hand, 60- and 66-year-old on the other hand), and our analyses were focused on the effect of H2O/D2O substitution. Spectral data were processed with fuzzy C-means (FCM) clustering in order to distinguish different orientations of collagen fibers. We demonstrated that the orientation was altered with aging, and that D2O treatment, affecting primarily highly bound water molecules, is more marked for the youngest skin samples. Collagen-bound water-related spectral markers were also highlighted. Our results suggest a weakening of water/collagen interactions with age. This non-destructive and label-free methodology allows us to understand better the importance of bound water in collagen fiber orientation alterations occurring with skin aging. Obtaining such structural information could find benefits in dermatology as well as in cosmetics.
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Affiliation(s)
- Christophe Eklouh-Molinier
- Equipe MéDIAN-Biophotonique et Technologies pour la Santé, UFR de Pharmacie, Université de Reims Champagne-Ardenne, Reims, France.
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