NIH, NIDDK, LBG
Travis Hoppe, Allen Minton, Di Wu
Background interactions: Weak, nonspecific interactions between macromolecular species and local constituents. Does not depends on detailed structure of interaction but only on gross physical properties like size, shape, hydrophobicity, net charge, dipole moment, ...
Three terms: change of chemical potential & enthalpy/entropy of absorption
Thermodynamic cost of cavity formation
Hard-sphere case: Integrand can be evaluated exactly for close distances,
and approximated with the Percus-Yevick closure
of the Orstein-Zernike equation.
Sphereocylinder into hard-spheres
Free rotation in bulk
Free rotation near the surface
Activity coefficients depend only on excluded volume
Use Monte-Carlo to estimate , i.e. the
dependence of crowding concentration.
Sample conformational states of hard-spheres near a boundary.
Two approaches to improve sampling, DMD (Discrete molecular dynamics) and particle displacement.
Split into , sample over "test" particle:
Location of critical phenomena and extent of cooperatively is
sensitive to details of the model (adsorption/association).
If fibrillation and/or adsorption is linked to biological function,
crowding can act as a sensitive form of biochemical regulation.
Laboratory of Biochemistry and Genetics
Physical Biochemistry Section