Decoupling of the onset of anharmonicity between a protein and its surface water around 200 K

  1. Lirong Zheng
  2. Bingxin Zhou  Is a corresponding author
  3. Banghao Wu
  4. Yang Tan
  5. Juan Huang
  6. Madhusudan Tyagi
  7. Victoria García Sakai
  8. Takeshi Yamada
  9. Hugh O'Neill
  10. Qiu Zhang
  11. Liang Hong  Is a corresponding author
  1. Institute of Natural Sciences, Shanghai Jiao Tong University, China
  2. Department of Cell and Developmental Biology & Michigan Neuroscience Institute, University of Michigan Medical School, United States
  3. Shanghai National Center for Applied Mathematics (SJTU Center), Shanghai Jiao Tong University, China
  4. School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, China
  5. Department of Materials Science and Engineering, University of Maryland, United States
  6. NIST Center for Neutron Research, National Institute of Standards and Technology (NIST), United States
  7. ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Science & Technology Facilities Council, United Kingdom
  8. Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society, Japan
  9. Biology and Soft Matter Division, Oak Ridge National Laboratory, United States
  10. Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong Univeristy, China
  11. Shanghai Artificial Intelligence Laboratory, China
4 figures, 7 tables and 1 additional file

Figures

Figure 1 with 2 supplements
Resolution dependence of the onset of protein dynamical transition.

Neutron spectrometers with different resolutions (1, 13, 25.4, and 100 μeV) were applied. Elatic intensity S(q, Δt) of (a, b) dry H-LYS and H-LYS in D2O at h = 0.3, (c, d) dry H-MYO and H-MYO in D2O …

Figure 1—figure supplement 1
Structures of proteins studied in this work.

Structures of (a) lysozyme (LYS), (b) myoglobin (MYO), (c) cytochrome P450 (CYP), and (d) green fluorescent protein (GFP).

Figure 1—figure supplement 2
Resolution dependence of the onset of protein dynamical transition.

Mean-squared atomic displacements <x2t)> derived from Figure 1 using Gaussian approximation, of (a, b) dry H-LYS and H-LYS in D2O at h = 0.3, (c, d) dry H-MYO and H-MYO in D2O at h = 0.3, and (eg)…

Figure 2 with 3 supplements
Hydration dependence of the onset of protein dynamical transition.

S(q, Δt) of (a) dry H-CYP and H-CYP in D2O at h = 0.2 and 0.4 and (c) dry H-LYS and H-LYS in D2O at h = 0.18, 0.30, and 0.45, all measured using HFBS with the instrumental resolution of 1 μeV. All …

Figure 2—figure supplement 1
Resolution dependence of the onset of protein dynamical transition.

<x2(Δt)>, derived from Figure 2c using Gaussian approximation, of dry H-CYP and H-CYP in D2O at h = 0.2 and 0.4.

Figure 2—figure supplement 2
The three-dimensional (3D) structure of cytochrome P450 (CYP) protein at different hydration levels obtained from molecular dynamics (MD) simulations (PDB ID: 2ZAX).
Figure 2—figure supplement 3
The potential energy as a function of MD trajectory time of cytochrome P450 (CYP).
Figure 3 with 1 supplement
Resolution dependence of the anharmonic onset of hydration water.

Neutron spectrometers with different resolutions (1, 25.4, and 100 μeV) were applied. S(q, Δt) of (a, b) dry D-GFP and D-GFP in H2O at h = 0.4, and (c–e) dry D-CYP and D-CYP in H2O at h = 0.4.

Figure 3—figure supplement 1
Resolution dependence of the anharmonic onset of hydration water.

Mean-squared atomic displacements <x2t)>, derived from Figure 3 using Gaussian approximation, of (a, b) dry D-GFP and D-GFP in H2O at h = 0.4, (c–e) dry D-CYP and D-CYP in H2O at h = 0.4.

Figure 4 with 1 supplement
Hydration dependence of the anharmonic onset of hydration water.

S(q, Δt), for dry D-CYP and D-CYP in H2O at h = 0.2 and 0.4, measured using HFBS neutron instrument with an energy resolution of 1 μeV.

Figure 4—figure supplement 1
Hydration dependence of the anharmonic onset of hydration water.

<x2t)>, derived from Figure 4 using Gaussian approximation, of dry D-CYP and D-CYP in H2O at h = 0.2 and 0.4.

Tables

Table 1
Relative content of each secondary structure in the proteins.
ProteinLysozymeMyoglobinCytochrome P450Green fluorescent protein
AbbreviationLYSMYOCYPGFP
PDB ID1AKI2V1K2ZAX1EMB
Alpha-helix*40%76%52%7%
Beta-sheet*12%0%11%50%
Loop and turn*48%24%37%43%
  1. *

    The relative content of each secondary structure is defined by mass fraction.

Table 2
The secondary structure content of cytochrome P450 (CYP) protein at different hydration levels.
Alpha-helixBeta-sheetLoop and turn
CYP (h = 0.2)52%11%37%
CYP (h = 0.4)52%11%37%
Table 3
Ton of protein in q-ranges from q = 0.45–0.9 Å−1.
1 ns80 ps40 ps10 ps
LYS213 K213 K--
MYO198 K198 K--
CYP228 K-228 K228 K
Table 4
Ton of protein in q-ranges from q = 1.1–1.75 Å−1.
1 ns80 ps40 ps10 ps
LYS212 K213 K--
MYO197 K199 K--
CYP228 K-227 K228 K
Table 5
Ton of protein at different time resolution.
1 ns80 ps40 ps10 ps
LYS (h = 0.3)213 K213 K--
MYO (h = 0.3)198 K198 K--
CYP (h = 0.4)228 K-228 K228 K
Table 6
Ton of protein at different hydration level.
0.180.20.30.40.45
LYS (1 ns)225 K-213 K-195 K
CYP (1 ns)-248 K-228 K-
CYP (TDSC)-245 K-225 K-
Key resources table
Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional information
Strain, strain background (Escherichia coli)Escherichia coli, BL21(DE3)Sigma-AldrichCMC0016
Peptide, Recombinant proteinLysozyme, chicken egg whiteSigma-AldrichCAS: 12650-88-3
Peptide, Recombinant proteinMyoglobin, equine skeletal muscleSigma-AldrichCAS: 100684-32-0
Chemical compound, drugH2OMillipore
Chemical compound, drugD2OSigma-AldrichCAS: 7789-20-0

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