Considering Protonation as a Posttranslational Modification Regulating Protein Structure and Function

Abstract

Post-translational modification of proteins is an evolutionarily conserved mechanism for regulating activity, binding affinities and stability. Compared with established post-translational modifications such as phosphorylation or uniquitination, post-translational modification by protons within physiological pH ranges is a less recognized mechanism for regulating protein function. By changing the charge of amino acid side chains, post-translational modification by protons can drive dynamical changes in protein conformation and function. Addition and removal of a proton is rapid and reversible and in contrast to most other post-translational modifications does not require an enzyme. Signaling specificity is achieved by only a minority of sites in proteins titrating within the physiological pH range. Here, we examine the structural mechanisms and functional consequences of proton post-translational modification of pH-sensing proteins regulating different cellular processes.

The chemistry, physiology and pathology of pH in cancer

“…negative feedback) effect of H þ ions on CA activity [33][34][35]. 2 and H þ -lactate diffusion away from the surface of cells is expected to produce a more alkaline pH i that better supports cell proliferation. Indeed, facilitated CO 2 venting appears to be a major role for CAIX and CAXII in tumour physiology [25,36], possibly explaining the faster growth rates measured in tumours expressing catalytically active enzyme [35,37].…”

“…As most fixed buffers reside on the surface of membranes, buffering capacity will depend on the degree of cell-cell packing (decreasing in 'looser' regions). Combined with weak diffusional coupling across the tumour interstitium, pH e changes may be considerable and add to the acidosis imposed by CO 2 and H þ -lactate venting (explaining why glycolysis-deficient tumours still generate low pH e [57,58]). Displacements of pH e can slow the transport cycle, either by means of trans inhibition or activation of allosteric sites [51,55,59].…”

“…Secondly, a sustained change in pH alters the [HA]/[A] ratio, which could have secondary effects if the biological properties of HA and A differ substantially. The sensitivity of proteins to pH has exceptional bearing on cells because proteins act as pH buffers, and their function can change substantially if ionization state is altered by the binding or release of H þ ions (a form of post-translational modification) [2]. It is therefore not surprising that only a narrow range of pH is compatible with eukaryotic function.…”

Ratiometric Imaging of pH Probes

“…The narrow pH range of the cytosol allows for the optimal activity, stability, structure, and interactions of cytoplasmic macromolecules. The activity of select regulatory proteins, especially enzymes, is sensitive to small physiological changes in pH (Schönichen, Webb, Jacobson, & Barber, 2013), which Increase of mCherry-pHluorin fluorescence ratio due to different photobleaching rates. Tissue was imaged every 5 s (300 ms exposure) over 30 min for a total laser exposure of 108 s. Following background subtraction, fluorescence intensity was measured at five regions and averaged.…”

Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems

“…Even specifically for ionization equilibria in biomolecules, a number of both macroscopic (e.g., potentiometric titrations) and spectroscopic methods [e.g., nuclear magnetic resonance (NMR), infrared, ultraviolet and visible spectroscopy] are routinely used. Here, we point the reader to specific texts (Schlichter 1980;Bartik et al 1994;Legault and Pardi 1994;Borkovec et al 2001;Harris and Turner 2002;Thurlkill et al 2006).…”