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Cited by 12Protein Structure and DynamicsEnzyme Structure and FunctionHigh-pressure geophysics and materials

The DOI matches its Crossref record; 84 of the 84 references it cites were found in a registry or an index.

Unravelling the Adaptation Mechanisms to High Pressure in Proteins

Open access
Caliò, Antonino, Dubois, Cécile, Fontanay, Stéphane, Koza, Michael Marek, Hoh, François, Roumestand, Christian, Oger, Philippe, Peters, Judith·2022·International Journal of Molecular Sciences
DOI 10.3390/ijms23158469PMC PMC9369236

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Abstract

Life is thought to have appeared in the depth of the sea under high hydrostatic pressure. Nowadays, it is known that the deep biosphere hosts a myriad of life forms thriving under high-pressure conditions. However, the evolutionary mechanisms leading to their adaptation are still not known. Here, we show the molecular bases of these mechanisms through a joint structural and dynamical study of two orthologous proteins. We observed that pressure adaptation involves the decoupling of protein–water dynamics and the elimination of cavities in the protein core. This is achieved by rearranging the charged residues on the protein surface and using bulkier hydrophobic residues in the core. These findings will be the starting point in the search for a complete genomic model explaining high-pressure adaptation.

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Figures

Figure 1 Crystal structures of Tba PMI (a) and Tko PMI (b) with labelled substituted residues for comparison. Residues are color-coded for polarity (red for acidic, blue for basic, green for polar, and yellow for hydrophobic), and the active site is also shown (details in Figure S7).
Figure 1 Crystal structures of Tba PMI (a) and Tko PMI (b) with labelled substituted residues for comparison. Residues are color-coded for polarity (red for acidic, blue for basic, green for polar, and yellow for hydrophobic), and the active site is also shown (details in Figure S7).CC BY · PubMed Central
Figure 2 Internal cavities in the two proteins located near Ile-Val substitutions in the protein core (a,b) and at the dimer interface (c,d) after the relaxation of the crystal structures by MD at 310 K and 1 bar.
Figure 2 Internal cavities in the two proteins located near Ile-Val substitutions in the protein core (a,b) and at the dimer interface (c,d) after the relaxation of the crystal structures by MD at 310 K and 1 bar.CC BY · PubMed Central
Figure 3 Scattering curves for Tba PMI at 150 bar and at some representative temperatures, with the corresponding two-state model fits. The decrease of the elastic intensity with temperature is expected, as more motions enter the time window of the experiment and the involved atoms scatter neutrons inelastically.
Figure 3 Scattering curves for Tba PMI at 150 bar and at some representative temperatures, with the corresponding two-state model fits. The decrease of the elastic intensity with temperature is expected, as more motions enter the time window of the experiment and the involved atoms scatter neutrons inelastically.CC BY · PubMed Central
Figure 4 Total MSD (full circles) and MSD into the single wells (Δx0², open circles) for Tba PMI (a) and Tko PMI (b), lines are a guide to the eye. The absolute value of the MSD reports on the amplitude of hydrogen atoms motion, while the slope of the curve as a function of temperature indicates how much energy is necessary to increase said amplitude, i.e., the resilience of the protein [32].
Figure 4 Total MSD (full circles) and MSD into the single wells (Δx0², open circles) for Tba PMI (a) and Tko PMI (b), lines are a guide to the eye. The absolute value of the MSD reports on the amplitude of hydrogen atoms motion, while the slope of the curve as a function of temperature indicates how much energy is necessary to increase said amplitude, i.e., the resilience of the protein [32].CC BY · PubMed Central
Figure 5 Temperature-independent parameters extracted from the two-state model as a function of pressure for Tba PMI (black symbols) and Tko PMI (red symbols): distance between the two wells (d, (a)), enthalpy (ΔH, (b)) and entropy (ΔS, (c)) difference, lines are a guide to the eye. (b) also contains a pictorial representation of the model showing how the different parameters influence the shape of a proteins’ energy landscape.
Figure 5 Temperature-independent parameters extracted from the two-state model as a function of pressure for Tba PMI (black symbols) and Tko PMI (red symbols): distance between the two wells (d, (a)), enthalpy (ΔH, (b)) and entropy (ΔS, (c)) difference, lines are a guide to the eye. (b) also contains a pictorial representation of the model showing how the different parameters influence the shape of a proteins’ energy landscape.CC BY · PubMed Central
Figure 6 Fit example of Tba PMI at 1 bar and 286 K, at a q value of 1.14 Å−1. Black circles represent the corrected data, the two Lorentzian contributions owing to localized motions and jump–diffusion are shown respectively as blue and green solid lines, and the total fit is shown as a red solid line. The resolution function is also shown. Error bars are smaller than the symbol size.
Figure 6 Fit example of Tba PMI at 1 bar and 286 K, at a q value of 1.14 Å−1. Black circles represent the corrected data, the two Lorentzian contributions owing to localized motions and jump–diffusion are shown respectively as blue and green solid lines, and the total fit is shown as a red solid line. The resolution function is also shown. Error bars are smaller than the symbol size.CC BY · PubMed Central
Figure 7 Natural logarithm of the broad component HWHM as a function of inverse temperature for Tba PMI (a) and Tko PMI (b) at all pressure values. Lines are linear fittings assuming an Arrhenius behaviour. Activation energy values are reported on the figure color-coded with the plots. Mean jump length from the Hall–Ross model as a function of temperature and pressure for Tba PMI (c) and Tko PMI (d). Natural logarithm of the residence time as a function of inverse temperature at all pressure values. Lines are fits to the Arrhenius law ((e), Tba PMI) or to the Vogel–Fulcher–Tamman law ((f), Tko PMI). Values for the activation energy (Tba PMI) and the fragility index (Tko PMI) are reported on the figure color-coded with the plots. Values of confinement radius R for Tba PMI (g) and Tko PMI (h).
Figure 7 Natural logarithm of the broad component HWHM as a function of inverse temperature for Tba PMI (a) and Tko PMI (b) at all pressure values. Lines are linear fittings assuming an Arrhenius behaviour. Activation energy values are reported on the figure color-coded with the plots. Mean jump length from the Hall–Ross model as a function of temperature and pressure for Tba PMI (c) and Tko PMI (d). Natural logarithm of the residence time as a function of inverse temperature at all pressure values. Lines are fits to the Arrhenius law ((e), Tba PMI) or to the Vogel–Fulcher–Tamman law ((f), Tko PMI). Values for the activation energy (Tba PMI) and the fragility index (Tko PMI) are reported on the figure color-coded with the plots. Values of confinement radius R for Tba PMI (g) and Tko PMI (h).CC BY · PubMed Central
Figure 8 Representation of internal (magenta) and solvent-accessible (cyan) cavities for Tba PMI (a–c) and Tko PMI (d–f) at different T and P conditions. Structures are represented in cartoons, and substituted residues are evidenced in sticks (with the corresponding part of the ribbon coloured for residue type, blue for basic, red for acidic, green for polar and yellow for hydrophobic). Red arrows follow the evolution of some cavities, and the opposite behaviour of the internal cavities in the dimer interface of the two proteins is highlighted by red circles. Another red circle in (f) also shows how the ligand pocket in one monomer of Tko PMI has actually become a channel from side to side under extreme conditions.
Figure 8 Representation of internal (magenta) and solvent-accessible (cyan) cavities for Tba PMI (a–c) and Tko PMI (d–f) at different T and P conditions. Structures are represented in cartoons, and substituted residues are evidenced in sticks (with the corresponding part of the ribbon coloured for residue type, blue for basic, red for acidic, green for polar and yellow for hydrophobic). Red arrows follow the evolution of some cavities, and the opposite behaviour of the internal cavities in the dimer interface of the two proteins is highlighted by red circles. Another red circle in (f) also shows how the ligand pocket in one monomer of Tko PMI has actually become a channel from side to side under extreme conditions.CC BY · PubMed Central
Figure 9 (a) sequence alignment of the two proteins, substitutions are highlighted (red for acidic, blue for basic, green for polar and yellow for hydrophobic residues). (b) schematic representation of the two proteins and effect of high pressure on them. (c) cartoon representation of Tba PMI, substitutions are represented in sticks with the same color-code as (b). (d) vertical cut on the surface representation of Tba PMI, highlighting the ligand pocket.
Figure 9 (a) sequence alignment of the two proteins, substitutions are highlighted (red for acidic, blue for basic, green for polar and yellow for hydrophobic residues). (b) schematic representation of the two proteins and effect of high pressure on them. (c) cartoon representation of Tba PMI, substitutions are represented in sticks with the same color-code as (b). (d) vertical cut on the surface representation of Tba PMI, highlighting the ligand pocket.CC BY · PubMed Central

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Citations

Cites

Research works printed but not linked: 1

  1. 1884, Sur un Énoncé gènèral des lois des Équilibres chimiques, C. R. Acad. Sci., 99, 786

Metadata

Authors
Caliò, A., Dubois, C., Fontanay, S., Koza, M. M., Hoh, F., Roumestand, C., Oger, P., & Peters, J.
Affiliations
  • Lyon 1 Université (FR)
  • Centre National de la Recherche Scientifique (FR)
  • Institut Laue-Langevin (FR)
Corresponding author
  • Oger, Philippe
  • Peters, Judith
ORCID
Venue
International Journal of Molecular Sciences
Publisher
MDPI AG
Published
2022-07-30
Volume
23
Issue
15
Pages
8469
ISSN
1422-0067 (ISSN-L)
DOI
10.3390/ijms23158469
PMC
PMC9369236
OpenAlex
W4289175460
Cited by
12
References
84
Citations by year
2026: 1 · 2025: 3 · 2024: 3 · 2023: 4 · 2022: 1
FWCI
0.90
Type
journal article
Language
en
Open access
Licence
Locations
  • International Journal of Molecular Sciences (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, other-oa)
  • HAL (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • French National Research Agency (ANR 17-CE11-0012-01)
  • Mission pour les Initiatives Transverses et Interdisciplinaires of the CNRS (ANR 17-CE11-0012-01)
  • French Ministry of Science and Technology (ANR 17-CE11-0012-01)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Physical Sciences › Earth and Planetary Sciences › Geophysics › High-pressure geophysics and materials
Keywords
high-pressure adaptation, deep-sea fauna, deep biosphere, protein cavities, charged residues, hydrophobic core, protein structure and dynamics, orthologous proteins, adaptive evolution
MeSH terms
Acclimatization, Adaptation, Physiological, Hydrostatic Pressure

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