Which conditions affect protein secondary and tertiary structure?

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The stability of protein structure rests on a network of noncovalent interactions—hydrogen bonds, ionic interactions, hydrophobic packing, and van der Waals forces—that shape both the local backbone folds (secondary structure) and the overall 3D arrangement (tertiary structure). High temperature increases molecular motion and can break these noncovalent bonds, especially the backbone hydrogen bonds that hold helices and sheets together and the interactions that maintain the folded shape, leading to unfolding. Changes in pH shift the ionization states of acidic and basic side chains, which can disrupt salt bridges and other electrostatic interactions that help hold the tertiary structure in place; these changes can also perturb hydrogen-bond networks, indirectly affecting secondary structure as well. A high concentration of polar molecules can perturb the solvent environment and hydration shell around the protein, and chaotropic polar solutes (like urea) specifically disrupt hydrogen bonding and destabilize the folded state, promoting unfolding and loss of both secondary and tertiary structure. Because all three factors can destabilize the same structural features, they each influence protein folding and stability, making the combination of effects capable of altering both secondary and tertiary structures.