Dynamic Aspects of Protein Structure

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to loss of function. A change in conformation of a single side chain in the active site of an enzyme or a change in protonation of a side chain can result in loss of activity, but does not lead to a complete loss of the native protein structure.
Even though conformational differences between denatured and native structures may be substantial, the free energy difference between such structures can in some cases be as low as the free energy of three or four noncovalent bonds. Thus the loss of a single hydrogen bond or electrostatic or hydrophobic interaction can lead to destabilization of a folded structure. A change in stability of a noncovalent bond can, in turn, be caused by a change in pH, ionic strength, or temperature. Binding of prosthetic groups, cofactors, and substrates also affects stability of the native conformation.
Figure 2.53 Steady­state concentration of a protein is due to its rates of synthesis and denaturation.
The statement that the breaking of a single noncovalent bond in a protein can cause denaturation apparently conflicts with the observation that the amino acid sequence can often be extensively varied without loss of a protein's structure. The key to the resolution of this apparent conflict is the word ''essential." Many noncovalent interactions are not essential to the structural stability of the native conformation of a protein. However, substitution or modification of an essential amino acid that provides a critical noncovalent interaction dramatically affects the stability of a native protein structure.
The concentration of a protein in a cell is controlled by its rate of synthesis and degradation (Figure 2.53). Understanding the processes that control protein degradation is therefore as equally important as an understanding of the processes that regulate protein synthesis. Under many circumstances the denaturation of a protein is the rate­controlling step in its degradation. Cellular enzymes and organelles that digest proteins "recognize" denatured protein conformations and eliminate them rapidly. In experimental situations, protein denaturation occurs on addition of urea or detergents (sodium dodecyl sulfate or guanidine hydrochloride) that weaken hydrophobic bonding in proteins. These reagents stabilize the denatured state and shift the equilibrium toward the denatured form of the protein. Addition of strong base, acid, or organic solvent, or heating to temperatures above 60°C are also common ways to denature a protein.
2.8— Dynamic Aspects of Protein Structure
While high­resolution X­ray diffraction experiments yield atomic coordinates for each atom in a protein structure, experimental evidence from NMR, fluorescence spectroscopy, and the temperature dependence of the X­ray diffraction reveals that the atoms in a folded protein molecule have a fluid­like dynamic motion and do not exist in a single static position. Rather than an exact location, the atomic coordinates obtained by X­ray diffraction represent the time­averaged position for each atom. The time frame for position averaging is the length of time for data collection, which may be several days. Thus the active conformation may differ from the average conformation. An X­ray structure also shows small "defects" in packing of the folded structure, indicating the existence of "holes" in the structure that will allow the protein space for flexibility. The concept that each atom in a protein is in constant motion such as molecules within a fluid, although constrained by its covalent bonds and the secondary and tertiary structure, is an important aspect of protein structure.
Theoretical molecular dynamics calculations describe the changes in coordinates of atoms in a folded protein structure, with corresponding changes in position of regions of the structure due to summation of the movements of atoms in that region. The dynamic motion computation is based on the solving of Newton's equations of motion simultaneously for all the atoms of the protein and the solvent that interacts with the protein. The energy functions used in the equation include representations of covalent and noncovalent bonding energies due to electrostatic forces, hydrogen bonding, and van der Waals