Hello everyone, I am in-need for a good explanation regarding the molecular energy. I'm curious how the highest negative number could have a stable energy and the less negative number have instable energy? For example, if I have -15kjol and -10kjol, the -15kjol is the smallest number and instable energy... Am I correct? Next, how can minimisation determine energy since minimisation is an arrangement process in a space? Please help me to understand this. Thank you so much in advance.
System with the lowest Gibbs free energy is the most stable. If a system has more Gibbs free energy than another system than the first system will react to form the second one.
Entropy of the universe is increasing and going towards equilibrium and this tendency towards equilibrium is fulfilled when total energy of a system is minimized.
Negative=favorable. Positive=unfavorable.
Energy minimization is the process of finding a satisfactorily low-energy arrangement in space of a collection of atoms according to a computational model of bonded and non-bonded interactions (e.g., a molecular mechanical force field).
Energy minimization tries to adjust the structural geometry in such a way that the (predicted) Gibbs free energy of folding is minimized. Normal energy minimization will lead your structure to the nearest local minimum in the energy landscape. Molecular dynamics adds thermal energy to the system to allow the molecule to overcome some of the energy barriers separating the local minimum from other minima (simulated melting and annealing). Entropic contributions, especially pertaining to solvent interaction, are usually approximated based on the solvent exposed surface area.
Energy minimization performed under a certain force field helps to obtain local or global minima. A minimum energy structure is the optimized geometry of the conformation wherein forces of attraction and repulsion are more balanced and hence stable.
For example, if I have -15kjol and -10kjol, the -15kjol is the smallest number and instable energy... Am I correct?
Consider negative sign indicates, favorable energy or good binding energy or attractive energy. Now the number looks fine, the highest "good energy" is the stable energy/favorable energy.
The more negative the number is, the more stable your protein.
deltaG relates to the equilibrium constant of a reaction by:
deltaG=-RT ln(Keq)
for the reaction:
Unfolded Folded
a large negative delta G signifies that the equilibrium is far to the side of the product, that is, the folded state.
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