Energies of macromolecules

Schaefer, M. Froemmel, C., A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution, J. Mol. Biol. 1990, 216, 1045-1066... 

According to the current state of the theory, the deformation of polymeric networks must be accompanied not only by the intrachain conformational entropy changes but intrachain energy changes which depend on the conformational energies of macromolecules. Therefore, reliable experimental determination of these intrachain energy changes and their interpretation by means of isomeric state theory is of fundamental importance for polymer physics. 

A few authors have moved away from the standard GBSA formalism to derive approximated (GBSA-based) methods designed to provide rough but very fast estimates of solvation free energy of macromolecules, something that can be very useful, for example,... 

These results are particularly interesting not only in preparing various methods for obtaining conformations of the same macromolecules at an interface but also because they indicate the possibility of comparing energies of macromolecules in the two-dimensional phase with those in the three-dimensional phase. 

Scarsi, M., Apostolakis, J., Gaflisch, A. Continuum electrostatic energies of macromolecules in aqueous solutions. J. Rhys. Chem. A1997,101,8098-106. 

M. Scarsi, J. Apostolakis, and A. Caflisch,/. Phys. Chem. A, 101, 8098 (1997). Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions. 

Thus, one can calculate the free energy of the macromolecule in a given ionization state, provided that pK and AAG° p are known. 

For a given potential energy function, one may take a variety of approaches to study the dynamics of macromolecules. The most exact and detailed information is provided by MD simulations in which one solves the equations of motion for the atoms constituting the macromolecule and any surrounding environment. With currently available techniques and methods it is possible... 

The electrostatic free energy of a macromolecule embedded in a membrane in the presence of a membrane potential V can be expressed as the sum of three separate terms involving the capacitance C of the system, the reaction field Orffr), and the membrane potential field p(r) [73],... 

The well-known difficulties in calculating tliree-dimensional structures of macromolecules from NMR data mentioned above (sparseness of the data, imprecision of the restraints due to spin diffusion and internal dynamics) also make the validation of the structures a challenging task. The quality of the data [88] and the energy parameters used in the refinement [89] can be expected to influence the quality of structures. Several principles can be used to validate NMR structures. 

Energy for maintenance is the energy required for survival, or non-growth related purposes. It includes activities such as active transport across membranes and turnover (replacement synthesis) of macromolecules. 

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