MEDOC: A Fast, Scalable, and Mathematically Exact Algorithm for the Site-Specific Prediction of the Protonation Degree in Large Disordered Proteins

Intrinsically disordered regions are found in most eukaryotic proteins and are enriched with positively and negatively charged residues. While it is often convenient to assume that these residues follow their model-compound p<i>K</i>_a values, recent work has shown that local charge effects (charge regulation) can upshift or downshift side chain p<i>K</i>_a values with major consequences for molecular function. Despite this, charge regulation is rarely considered when investigating disordered regions. The number of potential charge microstates that can be populated through acid/base regulation of a given number of ionizable residues in a sequence, <i>N</i>, scales as ∼2^<i>N</i>. This exponential scaling makes the assessment of the full charge landscape of most proteins computationally intractable. To address this problem, we developed "multisite extent of deprotonation originating from context" (MEDOC) to determine the degree of protonation of a protein based on the local sequence context of each ionizable residue. We show that we can drastically reduce the number of parameters necessary to determine the full, analytical Boltzmann partition function of the charge landscape at both global and site-specific levels. Our algorithm applies the structure of the <i>q</i>-canonical ensemble, combined with novel strategies to rapidly obtain the minimal set of parameters, thereby circumventing the combinatorial explosion of the number of charge microstates even for proteins containing a large number of ionizable amino acids. We apply MEDOC to several sequences, including a global analysis of the distribution of p<i>K</i>_a values across the entire DisProt database. Our results show differences in the distribution of predicted p<i>K</i>_a values for different amino acids and good agreement with NMR-measured p<i>K</i>_a values in proteins.