Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm
- RIKEN, Japan
- RIKEN Quantitative Biology Center, Japan
- RIKEN Advanced Institute for Computational Science, Japan
- Michigan State University, United States
Figures
Figure 1 with 3 supplements
Molecular model of a bacterial cytoplasm.
(A) Schematic illustration of Mycoplasma genitalium (MG). (B) Equilibrated MGh system highlighted with proteins, tRNA, GroEL, and ribosomes. (C) MGh cl ose-up showing atomistic level of detail. See …
Figure 1—figure supplement 1
Macromolecular components.
Structures of macromolecular complexes colored by residues index with tag, Stokes radius, and name.
Figure 1—figure supplement 2
Structure of metabolites in MGh.
For each metabolite, the abbreviation used in the text and its full name are given. Phosphates are highlighted in red.
Figure 1—figure supplement 3
Initial configurations of simulated systems.
Initial simulation boxes with colors indicating different macromolecular types.
Figure 2 with 3 supplements
Conformational stability of macromolecules in crowded and dilute environments.
(A) Time-averaged RMSDs (from starting structures) and radii of gyration (Rg) for selected macromolecules in MGm1(red), in dilute solution with only counterions (blue) and with KCl excess salt …
Figure 2—figure supplement 1
Time series of structural stability measures for selected macromolecules.
Root mean square deviations (RMSD) relative to initial structures based on Cα or P atoms of core structures as explained in Analysis Details (A); and radii of gyration based on all Cα or P atoms (Rg;…
Figure 2—figure supplement 2
Influence of local crowding environment on the structure of PDHA in MGm1.
(A) Denatured (green) conformation of one of the 39 copies of PDHA (denoted as PDHA*) due to contacts with other cytoplasmic proteins (PYK (red), PGK (gray), ENO (orange), PTA (black), and METK …
Figure 2—figure supplement 3
Influence of metabolite binding and local crowding environment on the structure of PGK in MGm1.
(A) Atoms in two ligand binding sites (yellow and green licorice) of one of the 18 copies of PGK (denoted as PGK*) (gray tube) in the MGm1 system. The distance between the center of mass for Cα …
Figure 3 with 1 supplement
Association of metabolic proteins in crowded environments.
(A) Intermolecular distance changes between initial and final time (ΔdAB) for pairs of glycolytic enzymes, other regular proteins, RNAs, and ribosomes/GroEL (huge). (B) Solvation free energies ΔGsol …
Figure 3—figure supplement 1
Influence of large macromolecules on the association of small proteins.
(A−D) Two-component mixtures of small Lennard-Jones particles ‘A’ (2 Å, white) in the presence of same size particles ‘B’ (LJ_AB) or in the presence of larger particles ‘C’ (3.509 Å, LJ_AC) or ‘D’ …
Figure 4 with 2 supplements
Translational diffusion of macromolecules in MGm1 slows down as a function of Stokes radius and is dependent on local crowding.
(A) Translational diffusion coefficients (Dtr) of macromolecules in MGm1 vs. Stokes radii (Rs) from MD, and SD compared with experimental data for green fluorescent protein (GFP) and GFP-attached …
Figure 4—figure supplement 1
Dependency of translational diffusion coefficient Dtr on the maximum observation time τmax.
Dtr for macromolecules ATRN, PDHA, PDHD and PGK (see Figure 1—figure supplement 1 for abbreviations) and metabolites NAD, COA, ATP, VAL, GLN, G1P, ETOH, and ACE (see Figure 1—figure supplement 2 for …
Figure 4—figure supplement 2
Influence of local crowding environment on Dtr.
Dtr for macromolecules PGK, PDHA, PDHD, NOX, ENO, ACKA, and ATRN in MGm1 as a function of coordination number of crowder Cα atoms Nc. For each type of macromolecule, Dtr and Nc at given time windows …
Figure 5 with 1 supplement
Rotational diffusion of macromolecules.
(A) Averaged angular velocity (ω) of macromolecules in MGm1 as a function of their Stokes radii (Rs) (gray squares with IF1, ATRN, PDHD, PDHA, and PGK highlighted in purple, red, blue, yellow, and …
Figure 5—figure supplement 1
Influence of local crowding environment on angular velocity ω.
Averaged angular velocities ω for macromolecules PGK, PDHA, PDHD, NOX, ENO, ACKA, and ATRN in MGm1 as a function of coordinate number of crowder Cα atoms Nc. Normalized angular velocities as a …
Figure 6 with 1 supplement
Metabolites in cytoplasmic environments interact extensively with macromolecules resulting in significantly reduced diffusion.
(A) Translational diffusion coefficients (Dtr) for metabolites in MGm1 as a function of molecular weight (phosphates: diamond; amino acids: triangles; others: circles; color reflects charge). For …
Figure 6—figure supplement 1
ATP distribution in cytoplasmic environments.
(A) Schematic representation of theoretically accessible volume, V(r), in crowded environments. The large square box represents the size of the periodic system. The yellow objects represent …
Videos
Video 1
Nanosecond dynamics of the MGm1 system in atomistic detail.
Macromolecules are shown with both cartoon and lines. Metabolites and ions are shown with stick or sphere. Macromolecules in back ground are shown with surface representation.
Video 2
Conformational dynamics highlighting partial denaturation of one copy of PDHA (green, tube) due to interactions with proteins in the vicinity.
https://doi.org/10.7554/eLife.19274.014
Video 3
Diffusive motion of macromolecules during the last 130 ns of the MGm1 system.
Macromolecules are shown with surface representation. Ribosomes and GroELs are colored violet and yellow respectively. Other groups of molecules are colored differently for each individual …
Video 4
Diffusive motion of metabolites during the last 130 ns of the MGm1 system.
Macromolecules are shown with surface representation. Metabolites and ions are shown with van der Waals spheres. Phosphates, amino acids, ions, and other metabolites are highlighted with red, green, …
Tables
Table 1
Simulated cytoplasmic systems.
System | MGh | MGm1 | MGm2 | MGcg |
|---|---|---|---|---|
Cubic box length (nm) | 99.8 | 48.2 | 48.2 | 106.2 |
Program | GENESIS | GENESIS | NAMD | GENESIS |
Simulation time | 20 ns | 140 ns | 60 ns | 10 × 20 μs |
number of molecules | ||||
Ribosomes | 31 | 3 | 3 | 24 |
GroELs | 20 | 3 | 3 | 24 |
Proteins | 1238 | 182 | 133 | 1927 |
RNAs | 284 | 28 | 44 | 298 |
Metabolites | 41,006 | 5.005 | 5.072 | |
Ions | 214,000 | 23,049 | 27,415 | |
Waters | 26,263,505 | 2,944,143 | 2,893,830 | |
Total # of atoms | 103,708,785 | 11,737,298 | 11,706,962 | |
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See also Figure 1—figure supplement 3 showing initial configurations and supplementary material with lists of the individual molecular components.
Table 2
Simulated single protein reference systems.
System | Cubic box [nm] | # of waters | # of ions | # of metabolites | # of atoms | Simulation time* [ns] |
|---|---|---|---|---|---|---|
PGK_w | 9.89 | 30,787 | Cl−: 8 | 0 | 98,886 | 4 × 140 |
PGK_i | 9.87 | 30,374 | K+: 217, Cl−: 225 | 0 | 98,081 | 4 × 140 |
PDHA_w | 9.90 | 31,032 | Na+: 7 | 0 | 98,779 | 2 × 140 |
PDHA_i | 9.98 | 30,627 | K+: 224, Cl−: 217 | 0 | 97,998 | 2 × 140 |
IF1_w | 9.92 | 32,785 | Cl-: 4 | 0 | 99,535 | 2 × 140 |
IF1_i | 9.90 | 32,312 | K+: 233, Cl−: 237 | 0 | 98,582 | 2 × 140 |
NOX_w | 9.89 | 30,473 | Cl−: 3 | 0 | 98,708 | 2 × 140 |
NOX_i | 9.87 | 30,007 | K+: 222, Cl−: 225 | 0 | 97,754 | 2 × 140 |
ENO_w | 9.85 | 28,050 | Na+: 2 | 0 | 98,330 | 2 × 140 |
ENO_i | 9.84 | 27,648 | K+: 203, Cl−: 201 | 0 | 97,526 | 2 × 140 |
ATRN_i | 9.88 | 31,734 | K+: 231, Cl−: 156 | 0 | 98,032 | 2 × 140 |
ACKA_m | 14.71 | 102,379 | K+: 231, Cl−: 156 | 168 | 325,691 | 2 × 510 |
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*The first 10 ns of each trajectory was discarded as equilibration.
Table 3
Diffusion of water and ions. Translational diffusion constants [Å2/ps] in the cytoplasm (Mgm1) and dilute solvent (simulation of PGK in excess salt matching cytoplasmic concentration).
Cytoplasm | Dilute solvent | |||
|---|---|---|---|---|
τmax 1.0 (ns) | τmax 10 (ns) | τmax 1.0 (ns) | τmax 10 (ns) | |
water | 0.32 | 0.29 | 0.42 | 0.41 |
K+ | 0.079 | 0.068 | 0.22 | 0.21 |
Na+ | 0.017 | 0.015 | N/A | N/A |
Cl− | 0.17 | 0.14 | 0.22 | 0.21 |
Mg2+ | 0.0073 | 0.0051 | N/A | N/A |
Additional files
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Supplementary file 1
Detailed lists of system components.
List of Macromolecules. Copy numbers for each macromolecule (represented by tag name) in four simulation systems. The Stokes radius Rs is given in the last column. Groups and types of metabolites. Net charge and number of copies for each metabolite (represented by tag name) in three simulation systems. Phosphates are highlighted with a pink background.
- https://doi.org/10.7554/eLife.19274.027
