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

Jonathan H Zippin,Mahesh Koirala,Bohua Wu,H B Mihiri Shashikala,Stacie K Loftus,Emil Alexov,Jacob Jeffries

doi:10.3390/ijms22158273

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.

Highlights

The pH of a solution is an important characteristic for many biological processes
In this work, we focus on several proteins participating in melanosome formation, with the goal of contrasting their stability pH dependence and the effect of pathogenic variants
Using methods established in our previous work on the correlation between pH optimum of activity and the pH optimum of stability [1], we predict protein stability over varying pH and infer the activity of each protein

Summary

Introduction

The pH of a solution is an important characteristic for many biological processes. For every macromolecule, there is a particular pH at which the macromolecule is the most stable and activity is maximum, termed the pH optimum [1,2]. Macromolecular interactions are pH-dependent [3,4,5], and there is typically a pH optimum at which the binding affinity is maximum [4]. Subcellular compartments have different pH, reflecting their function, from low pH in lysosomes to high pH in peroxisomes. Macromolecules tend to have a pH optimum that is ideal for the pH of the subcellular compartment where they reside [3]. All above examples indicate that the regulation and maintenance of pH is essential for many biological phenomena

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