Role of pKA in Charge Regulation and Conformation of Various Peptide Sequences

Abstract

Peptides containing amino acids with ionisable side chains represent a typical example of weak ampholytes, that is, molecules with multiple titratable acid and base groups, which generally exhibit charge regulating properties upon changes in pH. Charged groups on an ampholyte interact electrostatically with each other, and their interaction is coupled to conformation of the (macro)molecule, resulting in a complex feedback loop. Their charge-regulating properties are primarily determined by the pKA of individual ionisable side-chains, modulated by electrostatic interactions between the charged groups. The latter is determined by the amino acid sequence in the peptide chain. In our previous work we introduced a simple coarse-grained model of a flexible peptide. We validated it against experiments, demonstrating its ability to quantitatively predict charge on various peptides in a broad range of pH. In the current work, we investigated two types of peptide sequences: diblock and alternating, each of them consisting of an equal number of amino acids with acid and base side-chains. We showed that changing the sequence while keeping the same overall composition has a profound effect on the conformation, whereas it practically does not affect total charge on the peptide. Nevertheless, the sequence significantly affects the charge state of individual groups, showing that the zero net effect on the total charge is a consequence of unexpected cancellation of effects. Furthermore, we investigated how the difference between the pKA of acid and base side chains affects the charge and conformation of the peptide, showing that it is possible to tune the charge-regulating properties by following simple guiding principles based on the pKA and on the amino acid sequence. Our current results provide a theoretical basis for understanding of the complex coupling between the ionisation and conformation in flexible polyampholytes, including synthetic polymers, biomimetic materials and biological molecules, such as intrinsically disordered proteins, whose function can be regulated by changes in the pH.

Electrostatically Cross-Linked Reversible Gels—Effects of pH and Ionic Strength

“…As a result the net charge of the monomer is negative. As discussed in ref , the net charge of such a polyampholyte block should be almost indistinguishable from that of a polyacid block with the same p K A .…”

Anionically-functionalized glycogen encapsulates melittin by multivalent interactions

“…This last simplification was validated a posteriori by agreement between the trends observed in simulations and in experiments, suggesting that the neglected interactions are not dominant in the studied system. Similar coarse-grained models are ubiquitous in polymer science and have been used in our previous publications to model short peptides 29,30 or disordered proteins. 31 The simulation box length was chosen such that one hyperbranched polymer in the simulation box corresponds to cglyc = 1.5 mg/mL, assuming that one bead corresponds to one glucose unit of glycogen.…”

Interfacial Peptides as Affinity Modulating Agents of Protein-Protein Interactions

“…Srivastava and co-authors demonstrated that the charge regulation mechanism is the most important contributor in protein-polyelectrolyte complexation regardless of pH and other physical chemistry parameters using constant-pH Monte-Carlo simulations [ 71 ]. In addition, it has also been recently shown that the presence of “charged patches” along the polyelectrolyte is also an important factor in the stability of the protein/peptide interactions [ 72 , 73 ].…”