1
|
Bassotti E, Gabrielli S, Paradossi G, Chiessi E, Telling M. An experimentally representative in-silico protocol for dynamical studies of lyophilised and weakly hydrated amorphous proteins. Commun Chem 2024; 7:83. [PMID: 38609466 PMCID: PMC11014950 DOI: 10.1038/s42004-024-01167-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Characterization of biopolymers in both dry and weakly hydrated amorphous states has implications for the pharmaceutical industry since it provides understanding of the effect of lyophilisation on stability and biological activity. Atomistic Molecular Dynamics (MD) simulations probe structural and dynamical features related to system functionality. However, while simulations in homogenous aqueous environments are routine, dehydrated model assemblies are a challenge with systems investigated in-silico needing careful consideration; simulated systems potentially differing markedly despite seemingly negligible changes in procedure. Here we propose an in-silico protocol to model proteins in lyophilised and weakly hydrated amorphous states that is both more experimentally representative and routinely applicable. Since the outputs from MD align directly with those accessed by neutron scattering, the efficacy of the simulation protocol proposed is shown by validating against experimental neutron data for apoferritin and insulin. This work also highlights that without cooperative experimental and simulative data, development of simulative procedures using MD alone would prove most challenging.
Collapse
Affiliation(s)
- Elisa Bassotti
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica I, 00133, Rome, Italy
| | - Sara Gabrielli
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica I, 00133, Rome, Italy
| | - Gaio Paradossi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica I, 00133, Rome, Italy
| | - Ester Chiessi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica I, 00133, Rome, Italy.
| | - Mark Telling
- STFC, ISIS Facility, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11OQX, UK.
- Department of Materials, University of Oxford, Parks Road, Oxford, UK.
| |
Collapse
|
2
|
Peters J, Oliva R, Caliò A, Oger P, Winter R. Effects of Crowding and Cosolutes on Biomolecular Function at Extreme Environmental Conditions. Chem Rev 2023; 123:13441-13488. [PMID: 37943516 DOI: 10.1021/acs.chemrev.3c00432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
The extent of the effect of cellular crowding and cosolutes on the functioning of proteins and cells is manifold and includes the stabilization of the biomolecular systems, the excluded volume effect, and the modulation of molecular dynamics. Simultaneously, it is becoming increasingly clear how important it is to take the environment into account if we are to shed light on biological function under various external conditions. Many biosystems thrive under extreme conditions, including the deep sea and subseafloor crust, and can take advantage of some of the effects of crowding. These relationships have been studied in recent years using various biophysical techniques, including neutron and X-ray scattering, calorimetry, FTIR, UV-vis and fluorescence spectroscopies. Combining knowledge of the structure and conformational dynamics of biomolecules under extreme conditions, such as temperature, high hydrostatic pressure, and high salinity, we highlight the importance of considering all results in the context of the environment. Here we discuss crowding and cosolute effects on proteins, nucleic acids, membranes, and live cells and explain how it is possible to experimentally separate crowding-induced effects from other influences. Such findings will contribute to a better understanding of the homeoviscous adaptation of organisms and the limits of life in general.
Collapse
Affiliation(s)
- Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, 140 rue de la physique, 38400 St Martin d'Hères, France
- Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France
- Institut Universitaire de France, 75005 Paris, France
| | - Rosario Oliva
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy
| | - Antonino Caliò
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38000 Grenoble, France
| | - Philippe Oger
- INSA Lyon, Universite Claude Bernard Lyon1, CNRS, UMR5240, 69621 Villeurbanne, France
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Dortmund, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| |
Collapse
|
3
|
Bertini L, Libera V, Ripanti F, Natali F, Paolantoni M, Orecchini A, Nucara A, Petrillo C, Comez L, Paciaroni A. Polymorphism and Ligand Binding Modulate Fast Dynamics of Human Telomeric G-Quadruplexes. Int J Mol Sci 2023; 24:ijms24054280. [PMID: 36901712 PMCID: PMC10001961 DOI: 10.3390/ijms24054280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/07/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
Telomeric G-quadruplexes (G4s) are promising targets in the design and development of anticancer drugs. Their actual topology depends on several factors, resulting in structural polymorphism. In this study, we investigate how the fast dynamics of the telomeric sequence AG3(TTAG3)3 (Tel22) depends on the conformation. By using Fourier transform Infrared spectroscopy, we show that, in the hydrated powder state, Tel22 adopts parallel and mixed antiparallel/parallel topologies in the presence of K+ and Na+ ions, respectively. These conformational differences are reflected in the reduced mobility of Tel22 in Na+ environment in the sub-nanosecond timescale, as probed by elastic incoherent neutron scattering. These findings are consistent with the G4 antiparallel conformation being more stable than the parallel one, possibly due to the presence of ordered hydration water networks. In addition, we study the effect of Tel22 complexation with BRACO19 ligand. Despite the quite similar conformation in the complexed and uncomplexed state, the fast dynamics of Tel22-BRACO19 is enhanced compared to that of Tel22 alone, independently of the ions. We ascribe this effect to the preferential binding of water molecules to Tel22 against the ligand. The present results suggest that the effect of polymorphism and complexation on the G4 fast dynamics is mediated by hydration water.
Collapse
Affiliation(s)
- Luca Bertini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Valeria Libera
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- CNR-IOM c/o Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Correspondence: (F.R.); (L.C.)
| | - Francesca Natali
- CNR-IOM and INSIDE@ILL c/o OGG, 71 avenue des Martyrs, CEDEX 9, 38042 Grenoble, France
| | - Marco Paolantoni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 6, 06123 Perugia, Italy
| | - Andrea Orecchini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- CNR-IOM c/o Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Alessandro Nucara
- Department of Physics, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Roma, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Lucia Comez
- CNR-IOM c/o Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Correspondence: (F.R.); (L.C.)
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| |
Collapse
|
4
|
Bertini L, Libera V, Ripanti F, Seydel T, Paolantoni M, Orecchini A, Petrillo C, Comez L, Paciaroni A. Role of fast dynamics in the complexation of G-quadruplexes with small molecules. Phys Chem Chem Phys 2022; 24:29232-29240. [PMID: 36445842 DOI: 10.1039/d2cp03602a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
G-quadruplexes (G4s) formed by the human telomeric sequence AG3 (TTAG3)3 (Tel22) play a key role in cancer and aging. We combined elastic incoherent neutron scattering (EINS) and quasielastic incoherent neutron scattering (QENS) to characterize the internal dynamics of Tel22 G4s and to assess how it is affected by complexation with two standard ligands, Berberine and BRACO19. We show that the interaction with the two ligands induces an increase of the overall mobility of Tel22 as quantified by the mean squared displacements (MSD) of hydrogen atoms. At the same time, the complexes display a lower stiffness than G4 alone. Two different types of motion characterize the G4 nanosecond timescale dynamics. Upon complexation, an increasing fraction of G4 atomic groups participate in this fast dynamics, along with an increase in the relevant characteristic length scales. We suggest that the entropic contribution to the conformational free energy of these motions might be crucial for the complexation mechanisms.
Collapse
Affiliation(s)
- Luca Bertini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Valeria Libera
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy. .,Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Tilo Seydel
- Institut Max von Laue - Paul Langevin (ILL) 71 avenue des Martyrs, 38042 Grenoble, France
| | - Marco Paolantoni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto, 6, 06123 Perugia, Italy
| | - Andrea Orecchini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Lucia Comez
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
| |
Collapse
|
5
|
Rosi BP, D’Angelo A, Buratti E, Zanatta M, Tavagnacco L, Natali F, Zamponi M, Noferini D, Corezzi S, Zaccarelli E, Comez L, Sacchetti F, Paciaroni A, Petrillo C, Orecchini A. Impact of the Environment on the PNIPAM Dynamical Transition Probed by Elastic Neutron Scattering. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Benedetta P. Rosi
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Arianna D’Angelo
- Laboratoire de Physique des Solides, CNRS, Université Paris-Saclay, 510 Rue André Rivière, 91405 Orsay, France
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, Cedex 9, France
| | - Elena Buratti
- Dipartimento di Fisica, CNR-ISC c/o Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Marco Zanatta
- Dipartimento di Fisica, Università di Trento, via Sommarive 14, 38123 Trento, Italy
| | - Letizia Tavagnacco
- Dipartimento di Fisica, CNR-ISC c/o Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Francesca Natali
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, Cedex 9, France
- CNR-IOM, OGG, 71 Avenue des Martyrs, 38043 Grenoble, Cedex 9, France
| | - Michaela Zamponi
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Daria Noferini
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, 85747 Garching, Germany
- European Spallation Source ERIC, Box 176, 221 00 Lund, Sweden
| | - Silvia Corezzi
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Emanuela Zaccarelli
- Dipartimento di Fisica, CNR-ISC c/o Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Lucia Comez
- Dipartimento di Fisica e Geologia, CNR-IOM c/o Università di Perugia, via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesco Sacchetti
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Alessandro Paciaroni
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Caterina Petrillo
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Andrea Orecchini
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Dipartimento di Fisica e Geologia, CNR-IOM c/o Università di Perugia, via Alessandro Pascoli, 06123 Perugia, Italy
| |
Collapse
|
6
|
Berlie A, Terry I, Szablewski M, Telling M, Apperley D, Hodgkinson P, Zeller D. A study of the dynamics and structure of the dielectric anomaly within the molecular solid TEA(TCNQ) 2. Phys Chem Chem Phys 2022; 24:7481-7492. [PMID: 35274651 DOI: 10.1039/d2cp00142j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
With rising interest in organic-based functional materials, it is important to understand the nature of magnetic and electrical transitions within these types of systems. One intriguing material is triethylammonium bis-7,7,8,8-tetracyanoquinodimethane (TEA(TCNQ)2) where there is an order-disorder transition at ∼220 K. This work focuses on novel neutron scattering techniques to understand the motion of the TEA cations at this transition and explain why we see the dielectric behaviour and possible ferroelectricity within this type of system. We show that the motion of the methyl groups of the TEA cation is spatially restricted below 220 K, whereas above the dielectric anomaly at 220 K, they are free to re-orientate, which ultimately leads to some rich behaviour that could be further exploited. Lastly, we also study the dynamics at this transition using a variety of additional techniques, helping to provide a consistent picture of the motions of the cations.
Collapse
Affiliation(s)
- Adam Berlie
- ISIS Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Chilton, Oxfordshire, OX11 0QX, UK.
| | - Ian Terry
- Department of Physics, Durham University, South Road, Durham, DH1 3LE, UK
| | - Marek Szablewski
- Department of Physics, Durham University, South Road, Durham, DH1 3LE, UK
| | - Mark Telling
- ISIS Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Chilton, Oxfordshire, OX11 0QX, UK.
| | - David Apperley
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK
| | - Paul Hodgkinson
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK
| | - Dominik Zeller
- Institut Laue Langevin, BP 156, 38042 Grenoble Cedex 9, France
| |
Collapse
|
7
|
Matsuo T, De Francesco A, Peters J. Molecular Dynamics of Lysozyme Amyloid Polymorphs Studied by Incoherent Neutron Scattering. Front Mol Biosci 2022; 8:812096. [PMID: 35111814 PMCID: PMC8801425 DOI: 10.3389/fmolb.2021.812096] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/03/2021] [Indexed: 11/22/2022] Open
Abstract
Lysozyme amyloidosis is a hereditary disease, which is characterized by the deposition of lysozyme amyloid fibrils in various internal organs. It is known that lysozyme fibrils show polymorphism and that polymorphs formed at near-neutral pH have the ability to promote more monomer binding than those formed at acidic pH, indicating that only specific polymorphs become dominant species in a given environment. This is likely due to the polymorph-specific configurational diffusion. Understanding the possible differences in dynamical behavior between the polymorphs is thus crucial to deepen our knowledge of amyloid polymorphism and eventually elucidate the molecular mechanism of lysozyme amyloidosis. In this study, molecular dynamics at sub-nanosecond timescale of two kinds of polymorphic fibrils of hen egg white lysozyme, which has long been used as a model of human lysozyme, formed at pH 2.7 (LP27) and pH 6.0 (LP60) was investigated using elastic incoherent neutron scattering (EINS) and quasi-elastic neutron scattering (QENS). Analysis of the EINS data showed that whereas the mean square displacement of atomic motions is similar for both LP27 and LP60, LP60 contains a larger fraction of atoms moving with larger amplitudes than LP27, indicating that the dynamical difference between the two polymorphs lies not in the averaged amplitude, but in the distribution of the amplitudes. Furthermore, analysis of the QENS data showed that the jump diffusion coefficient of atoms is larger for LP60, suggesting that the atoms of LP60 undergo faster diffusive motions than those of LP27. This study thus characterizes the dynamics of the two lysozyme polymorphs and reveals that the molecular dynamics of LP60 is enhanced compared with that of LP27. The higher molecular flexibility of the polymorph would permit to adjust its conformation more quickly than its counterpart, facilitating monomer binding.
Collapse
Affiliation(s)
- Tatsuhito Matsuo
- Univ. Grenoble Alpes, CNRS, LiPhy, Grenoble, France
- Institut Laue-Langevin, Grenoble, France
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Tokai, Japan
- *Correspondence: Tatsuhito Matsuo, ; Judith Peters,
| | - Alessio De Francesco
- Institut Laue-Langevin, Grenoble, France
- CNR-IOM and INSIDE@ILL C/O Operative Group in Grenoble (OGG), Grenoble, France
| | - Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, Grenoble, France
- Institut Laue-Langevin, Grenoble, France
- Institut Universitaire de France, Paris, France
- *Correspondence: Tatsuhito Matsuo, ; Judith Peters,
| |
Collapse
|
8
|
Misuraca L, Demé B, Oger P, Peters J. Alkanes increase the stability of early life membrane models under extreme pressure and temperature conditions. Commun Chem 2021; 4:24. [PMID: 36697785 PMCID: PMC9814696 DOI: 10.1038/s42004-021-00467-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/14/2021] [Indexed: 01/31/2023] Open
Abstract
Terrestrial life appeared on our planet within a time window of [4.4-3.5] billion years ago. During that time, it is suggested that the first proto-cellular forms developed in the surrounding of deep-sea hydrothermal vents, oceanic crust fractures that are still present nowadays. However, these environments are characterized by extreme temperature and pressure conditions that question the early membrane compartment's capability to endure a stable structural state. Recent studies proposed an adaptive strategy employed by present-day extremophiles: the use of apolar molecules as structural membrane components in order to tune the bilayer dynamic response when needed. Here we extend this hypothesis on early life protomembrane models, using linear and branched alkanes as apolar stabilizing molecules of prebiotic relevance. The structural ordering and chain dynamics of these systems have been investigated as a function of temperature and pressure. We found that both types of alkanes studied, even the simplest linear ones, impact highly the multilamellar vesicle ordering and chain dynamics. Our data show that alkane-enriched membranes have a lower multilamellar vesicle swelling induced by the temperature increase and are significantly less affected by pressure variation as compared to alkane-free samples, suggesting a possible survival strategy for the first living forms.
Collapse
Affiliation(s)
- Loreto Misuraca
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, LIPhy, Grenoble, France ,grid.156520.50000 0004 0647 2236Institut Laue - Langevin, Grenoble, France
| | - Bruno Demé
- grid.156520.50000 0004 0647 2236Institut Laue - Langevin, Grenoble, France
| | - Philippe Oger
- grid.7849.20000 0001 2150 7757Univ Lyon, INSA Lyon, CNRS UMR5240, Villeurbanne, France
| | - Judith Peters
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, LIPhy, Grenoble, France ,grid.156520.50000 0004 0647 2236Institut Laue - Langevin, Grenoble, France
| |
Collapse
|
9
|
Lushchekina SV, Inidjel G, Martinez N, Masson P, Trovaslet-Leroy M, Nachon F, Koza MM, Seydel T, Peters J. Impact of Sucrose as Osmolyte on Molecular Dynamics of Mouse Acetylcholinesterase. Biomolecules 2020; 10:biom10121664. [PMID: 33322722 PMCID: PMC7763276 DOI: 10.3390/biom10121664] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 01/28/2023] Open
Abstract
The enzyme model, mouse acetylcholinesterase, which exhibits its active site at the bottom of a narrow gorge, was investigated in the presence of different concentrations of sucrose to shed light on the protein and water dynamics in cholinesterases. The study was conducted by incoherent neutron scattering, giving access to molecular dynamics within the time scale of sub-nano to nanoseconds, in comparison with molecular dynamics simulations. With increasing sucrose concentration, we found non-linear effects, e.g., first a decrease in the dynamics at 5 wt% followed by a gain at 10 wt% sucrose. Direct comparisons with simulations permitted us to understand the following findings: at 5 wt%, sugar molecules interact with the protein surface through water molecules and damp the motions to reduce the overall protein mobility, although the motions inside the gorge are enhanced due to water depletion. When going to 10 wt% of sucrose, some water molecules at the protein surface are replaced by sugar molecules. By penetrating the protein surface, they disrupt some of the intra-protein contacts, and induce new ones, creating new pathways for correlated motions, and therefore, increasing the dynamics. This exhaustive study allowed for an explanation of the detail interactions leading to the observed non-linear behavior.
Collapse
Affiliation(s)
- Sofya V. Lushchekina
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Gaetan Inidjel
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
- Université Grenoble Alpes, UFR PhITEM, LiPhy, CNRS, 38000 Grenoble, France
| | - Nicolas Martinez
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
- Université Grenoble Alpes, UFR PhITEM, LiPhy, CNRS, 38000 Grenoble, France
| | - Patrick Masson
- Neuropharmacology Laboratory, Kazan Federal University, Kremlevskaya str 18, 480002 Kazan, Russia;
| | - Marie Trovaslet-Leroy
- Institut de Recherche Biomédicale des Armées, 91223 Brétigny sur Orge, France; (M.T.-L.); (F.N.)
| | - Florian Nachon
- Institut de Recherche Biomédicale des Armées, 91223 Brétigny sur Orge, France; (M.T.-L.); (F.N.)
| | - Michael Marek Koza
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
| | - Tilo Seydel
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
| | - Judith Peters
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
- Université Grenoble Alpes, UFR PhITEM, LiPhy, CNRS, 38000 Grenoble, France
- Correspondence: ; Tel.: +33-4-7620-7560
| |
Collapse
|
10
|
Matsarskaia O, Bühl L, Beck C, Grimaldo M, Schweins R, Zhang F, Seydel T, Schreiber F, Roosen-Runge F. Evolution of the structure and dynamics of bovine serum albumin induced by thermal denaturation. Phys Chem Chem Phys 2020; 22:18507-18517. [PMID: 32780038 DOI: 10.1039/d0cp01857k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein denaturation in concentrated solutions consists of the unfolding of the native protein structure, and subsequent cross-linking into clusters or gel networks. While the kinetic evolution of structure has been studied for some cases, the underlying microscopic dynamics of proteins has so far been neglected. However, protein dynamics is essential to understand the specific nature of assembly processes, such as diffusion-limited growth, or vitrification of dense liquids. Here, we present a study on thermal denaturation of concentrated solutions of bovine serum albumin (BSA) in D2O with and without NaCl. Using small-angle scattering, we provide information on structure before, during and after denaturation. Using quasi-elastic neutron scattering, we monitor in real-time the microscopic dynamics and dynamical confinement throughout the entire denaturation process covering protein unfolding and cross-linking. After denaturation, the protein dynamics is slowed down in salty solutions compared to those in pure water, while the stability and dynamics of the native solution appears unaffected by salt. The approach presented here opens opportunities to link microscopic dynamics to emerging structural properties, with implications for assembly processes in soft and biological matter.
Collapse
Affiliation(s)
- Olga Matsarskaia
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France.
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Frieberg BR, Glynos E, Sakellariou G, Tyagi M, Green PF. Effect of Molecular Stiffness on the Physical Aging of Polymers. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Emmanouil Glynos
- Institute of Electronic Structure and Laser, Foundation for Research and Technology—Hellas, P.O. Box 1385, 71110 Heraklion, Crete, Greece
| | - Georgios Sakellariou
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis
Zografou, 15771 Athens, Greece
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
- Department of Materials Science, University of Maryland, College Park, Maryland 20742, United States
| | | |
Collapse
|
12
|
Zeller D, Tan P, Hong L, Di Bari D, Garcia Sakai V, Peters J. Differences between calcium rich and depleted alpha-lactalbumin investigated by molecular dynamics simulations and incoherent neutron scattering. Phys Rev E 2020; 101:032415. [PMID: 32289905 DOI: 10.1103/physreve.101.032415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/21/2020] [Indexed: 11/07/2022]
Abstract
We present a study comparing atomic motional amplitudes in calcium rich and depleted alpha-lactalbumin. The investigations were performed by elastic incoherent neutron scattering (EINS) and molecular dynamics (MD) simulations. As the variations were expected to be very small, three different hydration levels and timescales (instrumental resolutions) were measured. In addition, we used two models to extract the mean square displacements (MSDs) from the EINS data, one taking into account the motional heterogeneity of the MSD. At a timescale of several nanoseconds, small differences in the amplitudes between the calcium enriched and depleted alpha-lactalbumin are visible, whereas at lower timescales no changes can be concluded within the statistics. The results are compared to MD simulations at 280 and 300 K by extracting the MSDs of the trajectories in two separate ways: first by direct calculation, and second by a virtual neutron experiment using the same models as for the experimental data. We show that the simulated data give qualitatively similar results as the experimental data but quantitatively there are differences. Furthermore, the distribution of the MSDs in the simulations suggests that the inclusion of heterogeneity is reasonable for alpha-lactalbumin, but a bi-or trimodal approach may be sufficient.
Collapse
Affiliation(s)
- Dominik Zeller
- University Grenoble Alpes, LiPhy, CNRS, F-38000 Grenoble, France and Institut Laue Langevin, F-38042 Grenoble Cedex 9, France
| | - Pan Tan
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liang Hong
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniele Di Bari
- University Grenoble Alpes, LiPhy, CNRS, F-38000 Grenoble, France and Institut Laue Langevin, F-38042 Grenoble Cedex 9, France.,Physics Department, University of Perugia, 06123 Perugia, Italy
| | - Victoria Garcia Sakai
- ISIS Pulsed Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Chilton, Oxfordshire OX11 0QX, United Kingdom
| | - Judith Peters
- University Grenoble Alpes, LiPhy, CNRS, F-38000 Grenoble, France and Institut Laue Langevin, F-38042 Grenoble Cedex 9, France
| |
Collapse
|
13
|
Golub M, Guillon V, Gotthard G, Zeller D, Martinez N, Seydel T, Koza MM, Lafaye C, Clavel D, von Stetten D, Royant A, Peters J. Dynamics of a family of cyan fluorescent proteins probed by incoherent neutron scattering. J R Soc Interface 2019; 16:20180848. [PMID: 30836899 DOI: 10.1098/rsif.2018.0848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cyan fluorescent proteins (CFPs) are variants of green fluorescent proteins in which the central tyrosine of the chromophore has been replaced by a tryptophan. The increased bulk of the chromophore within a compact protein and the change in the positioning of atoms capable of hydrogen bonding have made it difficult to optimize their fluorescence properties, which took approximately 15 years between the availability of the first useable CFP, enhanced cyan fluorescent protein (ECFP), and that of a variant with almost perfect fluorescence efficiency, mTurquoise2. To understand the molecular bases of the progressive improvement in between these two CFPs, we have studied by incoherent neutron scattering the dynamics of five different variants exhibiting progressively increased fluorescence efficiency along the evolution pathway. Our results correlate well with the analysis of the previously determined X-ray crystallographic structures, which show an increase in flexibility between ECFP and the second variant, Cerulean, which is then hindered in the three later variants, SCFP3A (Super Cyan Fluorescent Protein 3A), mTurquoise and mTurquoise2. This confirms that increasing the rigidity of the direct environment of the fluorescent chromophore is not the sole parameter leading to brighter fluorescent proteins and that increased flexibility in some cases may be helpful.
Collapse
Affiliation(s)
- Maksym Golub
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | - Virginia Guillon
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | | | - Dominik Zeller
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,4 Laboratoire Interdisciplinaire de Physique, Univ. Grenoble Alpes, CNRS , 38000 Grenoble , France
| | - Nicolas Martinez
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | - Tilo Seydel
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France
| | - Michael M Koza
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France
| | - Céline Lafaye
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | - Damien Clavel
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | | | - Antoine Royant
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France.,3 European Synchrotron Radiation Facility , 38043 Grenoble , France
| | - Judith Peters
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,4 Laboratoire Interdisciplinaire de Physique, Univ. Grenoble Alpes, CNRS , 38000 Grenoble , France
| |
Collapse
|