Protein binding energies

This gives the following estimate for the protein-protein binding energy in an assembly,... 

Most protein-protein binding energies are related only to a group of a few amino acids at intermolecular protein interfaces the hot spots. The characterization of the energetics of molecular complexes, especially the detection of these hot spots is essential to structure-based drug design. 

Bouzida D, Rejto PA, Verkhivker GM(1999) Monte Carlo simulations of ligand-protein binding energy landscapes with the weighted histogram analysis method, Int I Quantum Chem, 73 113—121... 

Bound water is not a unique species because there is a distribution of the water protein binding energies (s p), which according to simulation studies... 

The direct resolution of functionally important in situ, cofactor-protein binding energies is accomplished by comparison of binding free energies of parent (AG(P)) and substituted (AG(PX)) compounds measured in hexane solution according to the expression derived by Jencks (2) ... 

Until now, we have discussed the use of additivity schemes to estimate global properties of a molecule such as its mean molecular polarizability, its heat of formation, or its average binding energy to a protein receptor. 

Gilson M K and B Honig 1988. Calculation of the Total Electrostatic Energy of a Macromoleculai System Solvation Energies, Binding Energies and Conformational Analysis. Proteins Structure Function and Genetics 4 7-18. 

MK Gilson, B Homg. Calculation of the total electrostatic energy of a macromolecular system Solution energies, binding energies, and conformational analysis. Proteins 4 7-18, 1988. 

Section 6.1 considered the noncovalent binding energies that stabilize a protein strnctnre. However, the folding of a protein depends ultimately on the difference in Gibbs free energy (AG) between the folded (F) and unfolded (U) states at some temperature T ... 

More detailed aspects of protein function can be obtained also by force-field based approaches. Whereas protein function requires protein dynamics, no experimental technique can observe it directly on an atomic scale, and motions have to be simulated by molecular dynamics (MD) simulations. Also free energy differences (e.g. between binding energies of different protein ligands) can be characterised by MD simulations. Molecular mechanics or molecular dynamics based approaches are also necessary for homology modelling and for structure refinement in X-ray crystallography and NMR structure determination. 

Retention in HIC can be described in terms of the solvophobic theory, in which the change in free energy on protein binding to the stationary phase with the salt concentration in the mobile phase is determined mainly by the contact surface area between the protein and stationary phase and the nature of the salt as measured by its propensity to increase the surface tension of aqueous solutions [331,333-338]. In simple terms the solvopbobic theory predicts that the log u ithn of the capacity factor should be linearly dependent on the surface tension of the mobile phase, which in turn, is a llne2u function of the salt concentration. At sufficiently high salt concentration the electrostatic contribution to retention can be considered constant, and in the absence of specific salt-protein interactions, log k should depend linearly on salt concentration as described by equation (4.21)... 

Figure 2-7. Origins of the increased O2 binding energy in IPNS when the protein is included in an ONIOM model. (A) A comparison of the optimized geometries from an active-site model (silver) and an ONIOM protein model (dark grey), show that the artificial structural relaxation of the active-site model is more pronounced for the reactant state than for the product state. (B) Contributions to O2 binding from the surrounding protein, evaluated only at the MM level (Adapted from Lundberg and Morokuma [26], Reprinted with permission. Copyright 2007 American Chemical Society.)...

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