Protein-surface interactions are fundamentally important in a broad range of applications in biomedical engineering and biotechnology. The adsorption behavior of a protein is governed by the complex set of interactions between the atoms making up the protein, surface, and surrounding solution. Molecular simulation provides a means of theoretically viewing, studying, and understanding these types of interactions at the atomic level. However, as with any application, molecular simulation methods must be properly developed and applied if protein-surface interactions are to be accurately portrayed. This chapter provides an overview of the basics of molecular simulation with a focus on the simulation of protein-surface interactions using molecular dynamics. Important issues such as force field transferability, solvation effects, and statistical sampling are addressed, as well as directions for further development. Molecular simulation methods have the potential to greatly enhance our ability to understand protein–surface interactions, leading to improvements in biomaterials design to control cellular response and to improve the sensitivity of biosensors and other bioanalytical systems.
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Abbreviations
- b :
-
bond length
- b 0 :
-
force field parameter: bond length at zero energy
- CM:
-
classical mechanics
- E :
-
potential energy
- F :
-
force
- f ij :
-
force vector between atoms i and j
- GB:
-
generalized Born
- K.E.:
-
kinetic energy
- k B :
-
Boltzmann’s constant
- k b :
-
force field parameter: bond stretching stiffness
- k u :
-
stiffness constant for an umbrella-sampling simulation
- k ϕ :
-
force field parameter: dihedral angle rotational stiffness
- k θ :
-
force field parameter: bond angle bending stiffness
- L-J:
-
Lennard–Jones
- m :
-
mass
- MC:
-
Monte Carlo
- MD:
-
molecular dynamics
- MM:
-
molecular mechanics
- N :
-
number of degrees of freedom
- N c :
-
number of constraints on the degrees of freedom
- NPT:
-
constant number of atoms, pressure, and temperature
- NVT:
-
constant number of atoms, volume, and temperature
- P :
-
pressure
- P-B:
-
Poisson–Boltzmann
- p i :
-
probability of system to be in state i
- q :
-
partial charge
- Q :
-
configurational partition function of the system
- QM:
-
quantum mechanics
- REMD:
-
replica-exchange molecular dynamics
- r ij :
-
distance between atoms i and j
- SAM:
-
self-assembled monolayer
- T :
-
temperature
- TIGER:
-
temperature intervals with global energy reassignment
- TIGER2:
-
temperature intervals with global exchange of replicas-2
- TIP3P:
-
name of a type of three-site water model
- U :
-
internal energy
- V :
-
velocity
- V :
-
volume
- x :
-
coordinate position
- DB ij :
-
biasing energy function between states i and j
- Dt :
-
time-step increment for a molecular dynamics simulation
- δ :
-
force field parameter: rotational dihedral shift
- ε r :
-
relative dielectric constant
- ε ij :
-
well-depth for Lennard–Jones interactions
- ε 0 :
-
permittivity of free space
- θ :
-
bond angle
- θ 0 :
-
force field parameter: bond angle at zero energy
- λ :
-
variable coordinate parameter for an umbrella-sampling simulation
- λ h :
-
fixed coordinate parameter for an umbrella-sampling simulation
- σ ij :
-
collision diameter between atoms i and j ϕdihedral angle
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Acknowledgments
I thank my colleague Dr. Steven Stuart, Department of Chemistry, Clemson University, for numerous helpful discussions over the years regarding molecular simulation and statistical thermodynamics, Mr. Galen Collier, a current doctoral student in my group for assistance with Fig. 4.5, and Dr. Feng Wang, a former doctoral student in my group, for helpful discussions regarding the protein-folding funnel and protein adsorption. I also thank the NIH and NSF for providing funding support for my research program on the development of molecular simulation methods to simulate protein-surface interactions: NIH R01 EB006163, R01 GM074511, the NJ Center for Biomaterials RESBIO (NIH, P41 EB001046), and the Center for Advanced Engineering Fibers and Films (CAEFF, NSF-ERC, EPS-0296165).
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Latour, R.A. (2009). Molecular Simulation of Protein-Surface Interactions. In: Puleo, D., Bizios, R. (eds) Biological Interactions on Materials Surfaces. Springer, New York, NY. https://doi.org/10.1007/978-0-387-98161-1_4
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