Download Rev 08 Supplementary Materials_TW_11517

Supplementary Material for
“Understanding the Interfacial Behavior of Lysozyme on Au (111) Surfaces
with Atomistic Multiscale Simulations”
Mohammadreza Samieegohar1, Heng Ma1, Feng Sha2, Md Symon Jahan Sajib1, G. Iván
Guerrero-García3 and Tao Wei1
1
Dan F. Smith Department of Chemical Engineering, Lamar University, Beaumont, TX 77710,
USA
2
Network Information Center, Xiamen University of Technology, Xiamen, 361024, China
3
CONACYT-Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí,
78000, México
MD Simulations
In full-atom MD simulations, the velocity Verlet algorithm with a time step of 1.0 fs was used
to solve the trajectory. A Nosé-Hoover thermostat was adopted to maintain a constant
temperature at 298 K. The particle mesh Ewald summation (PME) was used to calculate longrange electrostatic interactions with a cut-off distance of 1.2 nm for the separation of the direct
and reciprocal spaces. A spherical cut-off at 1.2 nm was imposed on Lennard-Jones interactions.
The long-range dispersion effect was calibrated. A 3.0-nm vacuum slab of was inserted at the
bottom of the cell in order to remove the interactions between atoms inside the cell and their
PBC image atoms along the Z direction (see Figure S1).
Figure S1. Snapshot of MD simulation (NA+ ions (green), CL- ions (Grey), Water molecules (grey) and
Au atoms (orange).
LD Simulations
LD simulations are presented by
𝑑𝑣̅𝑝
𝑚𝑝
= 𝐹̅𝐷 + 𝐹̅𝑔 + 𝐹̅𝐵 + 𝐹̅𝑃−𝑃 + 𝐹̅𝑃−𝑆
(S1)
with protein mass 𝑚𝑝 , protein velocity 𝑣̅𝑝 , drag force 𝐹̅𝐷 , gravity 𝐹̅𝑔 , Brownian force 𝐹̅𝐵 , proteinprotein 𝐹̅𝑃−𝑃 and protein-surface interactions forces 𝐹̅𝑃−𝑆 in both static environment and flowing
𝑑𝑡
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microchannel (see Figure S2). Drag force (𝐹̅𝐷 ), which is dependent on the relative velocity
between proteins and fluid, is calculated by using the Stokes law,
𝐹̅𝐷 = 6𝜇𝜋𝑟𝑝 (𝑢̅𝑓 − 𝑣̅𝑝 )
(S2)
with fluid velocity 𝑢̅𝑓 , protein radius 𝑟𝑝 , fluid density 𝜌𝑓 and dynamic viscosity 𝜇. The randomw
Brownian force 𝐹̅𝐵 on proteins can be estimated from the Einstein theory as
12𝜋𝐾𝑏 𝜇𝑇𝑟𝑝
𝐹𝐵 = 𝜁 √
(S3)
∆𝑡′
with a normalized random number 𝜁, the Boltzmann constant 𝐾𝑏 , temperature T (=298.15 K),
dynamic viscosity 𝜇 and the timescale ∆𝑡′ . The net force on a protein submerged in fluid
emanates from gravity force and buoyancy force,
𝑚𝑝 𝑔̅(𝜌𝑓 −𝜌𝑝 )
𝐹̅𝑔 =
(S4)
𝜌𝑝
where 𝜌𝑓 and 𝜌𝑝 are fluid density at 298.15 K and protein density respectively. Protein-surface
forces (𝐹̅𝑃−𝑠 ) and protein-protein forces (𝐹̅𝑃−𝑃 ), were presented as PMF. The properties of the
components in the system and the dimensions are listed in Table S1.
Table S1. Simulation Parameters
Height H (nm)
120
Length L (nm)
100
Width W (nm)
30
Protein diameter 𝑑𝑝 (nm)
2.8
Particle density 𝜌𝑝 (kg/m3)
1200
Fluid density 𝜌𝑓 (kg/m3)
1000
Initial concentration CA0 (mg/ml)
28.6
Figure S2. Snapshot of Langevin dynamic simulation in a static fluidic environment.
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PMF fitting with hydration effect
Gaussian function is added in equation 2 in manuscript for prediction of hydration effect
1.368 33
)
𝑍
PMF = 81.744 ((
1.368 3
) )+
𝑍
−(
5.2Exp (−
(z−1.558)2
0.0008
) + 52.037
(S5)
Figure S3. PMF profiles: data of PMF (blue) from umbrella sampling and the fitting (red).
Adsorption kinetic profile
Protein adsorption kinetic on the surface of Au is performed with hydration effect for 20 µs.
Figure S4. Adsorption kinetic of the first layer: with hydration effect (blue) and without hydration effect
(red).
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Interaction Energies
LJ and electrostatic interaction energies of protein, water and ions with Au(111) surfaces as a
function of protein-surface distance are shown in Fig. S5.
b
a
Figure S5. Itemized energies (protein, water and ions) for LJ (a) and electrostatic (b) interactions with
Au(111) surface as a function of displacement distance Zcom.
Protein adsorption process
Protein adsorption is monitored in 30 µs. Protein surface aggregation is observed before first
layer saturation.
Figure S6. Side and top views of protein adsorption process
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Distribution of proteins residue time in the 2nd layer
The distribution of proteins’ residence time inside the 2nd layer is statistically analyzed.
Figure S7. Histogram of protein residue time in the 2nd layer
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