Conserved internal hydration motifs in protein kinases

Abstract

Crystal structures of diverse protein kinase catalytic subunits reveal a number of water molecules whose positions within the protein core are better preserved than amino acid types in many functionally important locations. It remains unknown whether they play any particular role, and whether their removal, disturbing local interaction patterns to no smaller degree than amino acid mutations, can affect kinase stability and function. In this study, we apply an array of computational approaches to characterize hydration of kinase catalytic subunits. First, we systematically screen multiple crystal structures with the use of a simplified hydration model in order to determine the distribution of internal solvent and the degree of its conservation. Second, we analyze water structure, dynamics and binding affinity to buried hydration sites in a number of kinases, also taking into account their variable functional state. We find that a large portion of buried solvent is dynamic, possibly contributing to kinase conformational changes related to the activation process. In turn, binding free energies of some of tightly bound conserved water molecules to different kinases tend to shift in a similar manner following the change of their functional state. This finding highlights the likely specific role of internal solvent in fine tuning local protein plasticity.

Exploring Covalent Docking Mechanisms of Boron-Based Inhibitors to Class A, C and D β-Lactamases Using Time-dependent Hybrid QM/MM Simulations

“…For a review of the first experimental observations and quantum-mechanical analysis of the “flip-flop” hydrogen bonds see ( Saenger et al, 1985 ; Jeffrey and Saenger, 1991 ). Below are some representative publications analyzing the mechanisms of delocalized hydrogen bonds and “water wires” ( Cui and Karplus, 2003 ; Cukierman, 2003; Marx, 2006 ; Yan et al, 2007 ; Sakti et al, 2019 ; Setny, 2020 ). The analysis of structural conformational changes coupled with proton transfer processes shows that the covalent docking reactions described in this study are highly cooperative processes, and future studies should probably also take into account the quantum-dynamical effects associated with cooperative proton transfer mechanisms.…”

Drugging the Undruggable: How Isoquinolines and PKA Initiated the Era of Designed Protein Kinase Inhibitor Therapeutics

“…This residue reaches across the active site cleft and in the active conformation shields the γphosphate from water. 26 The activation loop (A-loop; residues 184−197) is part of the activation segment in PKA (residues 184−208). The A-loop includes several highly conserved features (Figure 2A).…”

“…Another key feature of the G-loop is a conserved aromatic amino acid in the β-hairpin turn, usually phenylalanine. This residue reaches across the active site cleft and in the active conformation shields the γ-phosphate from water …”

Emerging Role of Aurora A in Radioresistance: A Comprehensive Review

“…The C-terminal region of the kinase domain consists of seven α-helices and a two-stranded β-sheet, and contains the catalytic aspartic acid of the HRD motif (sequence histidine, arginine, and aspartate at positions 254-256) and the mobile activation loop, whose position and conformation determine whether a kinase is active or inactive. 22,23 The Aurora A activation loop (the most crucial part required for functional activation of the protein) spans 274-299 amino acid residues, beginning with an aspartate, phenylalanine, and glycine sequence motif and ending with an alanine, proline, and glutamate motif (sequence proline, proline, and glutamate in Aurora A). Aurora A becomes active by its autophosphorylation (discussed in detail later) and trans-phosphorylation at threonine 287 and threonine 288 residues by targeting protein for Xenopus kinesin-like protein 2, 24 p21 activated kinase, 25 protein kinase A, 26 or atypical protein kinase C. 27…”