Hinge bending potentials

Figure 5. The hinge-bending potential for free and bound lysozyme systems (from Bruccoleri et al. 1986) (a) steepest descents protocol (b) spatially constrained protocol. The circles are the points calculated by the protocols, the line is the least-squares fit parabola. All plots are on the same scale with energies in units of kcal/mole and angles in degrees. Positive angles correspond to closing.

E-fS ES ES. The standard deviation of the distribution, (Atopen ) = 8.3 2ms, reflects the distribution bandwidth. For the individual T4 lysozyme molecules examined under the same enz unatic reaction conditions, we found that the first and second moments of the single-molecule topen distributions are homogeneous, within the error bars. The hinge-bending motion allows sufficient structural flexibility for the enzyme to optimize its domain conformation the donor fluorescence essentially reaches the same intensity in each turnover, reflecting the domain conformation reoccurrence. The distribution with a defined first moment and second moment shows typical oscillatory conformational motions. The nonequilibrium conformational motions in forming the active enzymatic reaction intermediate states intrinsically define a recurrence of the essentially similar potential surface for the enzymatic reaction to occur, which represents a memory effect in the enzymatic reaction conformational dynamics [12,41,42]. 

Free energy of solvation Absolute and ApK Free energy of binding Redox potentials PB forces Electrostatics for Brownian dynamics calculations Rate constants Loop and hinge bending motions Polymer dynamics Protein-surface dynamics... 

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