Computational Investigation of the pH Dependence of Stability of Melanosome Proteins: Implication for Melanosome formation and Disease

Abstract

Intravesicular pH plays a crucial role in melanosome maturation and function. Melanosomal pH changes during maturation from very acidic in the early stages to neutral in late stages. Neutral pH is critical for providing optimal conditions for the rate-limiting, pH-sensitive melanin-synthesizing enzyme tyrosinase (TYR). This dramatic change in pH is thought to result from the activity of several proteins that control melanosomal pH. Here, we computationally investigated the pH-dependent stability of several melanosomal membrane proteins and compared them to the pH dependence of the stability of TYR. We confirmed that the pH optimum of TYR is neutral, and we also found that proteins that are negative regulators of melanosomal pH are predicted to function optimally at neutral pH. In contrast, positive pH regulators were predicted to have an acidic pH optimum. We propose a competitive mechanism among positive and negative regulators that results in pH equilibrium. Our findings are consistent with previous work that demonstrated a correlation between the pH optima of stability and activity, and they are consistent with the expected activity of positive and negative regulators of melanosomal pH. Furthermore, our data suggest that disease-causing variants impact the pH dependence of melanosomal proteins; this is particularly prominent for the OCA2 protein. In conclusion, melanosomal pH appears to affect the activity of multiple melanosomal proteins.

Electrostatics in Computational Biophysics and Its Implications for Disease Effects

“…Thus, a recent work computationally studied the pH-dependent stability of several melanosome membrane proteins. The authors found that disease-causing variants impact the pH-dependence of melanosome proteins [ 8 ]. Substitution of wild-type His with Gln was found to alter the function of CLIC2 protein and to cause X-linked channelopathy with cardiomegaly [ 108 ].…”

“…( b ) Mutation of D196G (SARS-CoV-2 spike protein) caused the loss of the hydrogen bond between THR and ASP (PDB: 7KMS [ 100 ]). ( c ) The pH-dependence of folding free energy for the melanosome of oculocutaneous albinism-2 [ 8 ]. ( d ) The image shows p53 protein–DNA and 1-[2-(1,3-benzodioxol-5-yl) pyrazolo[1,5-a] pyrazin-4-yl]-3-piperidinamine.…”

“…The electrostatic features in biological molecules are described in this review within three functions: long-range effects [ 1 , 2 ]; short-range effects [ 3 , 4 , 5 ]; and pH-dependent effects [ 6 , 7 , 8 ]. The long-range electrostatic force is the main force making biomolecules travel and bind to other biomolecules over a long distance [ 1 , 9 ].…”