Calmodulin Readily Switches Conformation upon Protonating High pK_aAcidic Residues

Abstract

We investigate protonation as a possible route for triggering conformational change in proteins by focusing on the calmodulin (CaM) example. Two hundred nanosecond molecular dynamics (MD) simulations are performed on both the extended and compact forms of calcium loaded CaM. The stability of both structures is confirmed under prevailing conditions. Protonation of nine acidic residues with upshifted pK(a) values leads to a large conformational change in less than 100 ns. The structure attained is consistent with fluorescence resonance energy transfer experimental results as well as structures from an ensemble compatible with NMR data. Analysis of the MD trajectories summing up to one microsecond implies that the key events leading to the completion of the conformational change begins with an initial formation of a salt bridge between the N-lobe and the linker, followed by the bending of the C-lobe and the organization of a stabilizing hydrophobic patch between the lobes. We find that CaM utilizes its Ca(2+) ions to harden/soften different regions so as to achieve various conformations. Thus, barrier crossing between extended and compact forms of CaM which is normally a rare event due to the repulsive electrostatic interactions between the two lobes is facilitated by protonation of high pK(a) residues. The results delineate how pH changes might be utilized in the cell to achieve different conformation-related functions.

Protonation States of Remote Residues Affect Binding–Release Dynamics of the Ligand but Not the Conformation of Apo Ferric Binding Protein

“…We note that our perturbation-response scanning method [14,28] can pinpoint such positions, as exemplified here by D52 and another charged surface residue, E31 in our previous work on calmodulin [47]. In contrast to the current work, the latter study demonstrated that large conformational changes related to calmodulin function were induced by the perturbation of the single residue [44], or the protonation of a group of residues mimicking the low pH environment [48].…”

Designing Molecular Dynamics Simulations to Shift Populations of the Conformational States of Calmodulin

“…We do not go into the details of these runs since we have already published a detailed account of the conformations sampled and key events leading to the conformational change [24]. However, it suffices to say that the same sequence of states I→II→III are followed in both runs.…”

Effect of Calcium Ion Removal, Ionic Strength, and Temperature on the Conformation Change in Calmodulin Protein at Physiological pH

“…For this we monitor the distance distribution between the residues numbers 34 and 110 throughout the simulation. A normalized cumulative distance distribution is then calculated which shows a trend similar to what is observed in the lower pH case [ 15 , 16 ]. These normalized distance distributions are calculated at the end of the 100 ns simulations of the native structure.…”

“…The distance distributions are calculated between the residues 34 and 110, observed at the end of 100 ns as in [ 12 , 15 , 16 ] which gives a measure of the compactness of the protein structure. The respective normalized distance distributions are as seen in Figure 3 with different stages of the calcium ion removal from the protein shown in different colors.…”

“…In our earlier work [ 15 , 16 ] we studied the effect of varying pH and observed a conformation change in CaM triggered by protonating nine acidic residues of the protein. Four different servers H++ [ 17 , 18 ], pKd [ 19 , 20 ], propKa 3.1 [ 21 ], and PHEMTO [ 22 , 23 ] were used to calculate the pKa values of all the titratable groups.…”