Article pubs.acs.org/JPCB
Allosteric Fine-Tuning of the Binding Pocket Dynamics in the ITK SH2 Domain by a Distal Molecular Switch: An Atomistic Perspective Mohamed Momin,† Yao Xin,† and Donald Hamelberg*,†,‡ †
Department of Chemistry and ‡Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302-3965, United States S Supporting Information *
ABSTRACT: Although the regulation of function of proteins by allosteric interactions has been identified in many subcellular processes, molecular switches are also known to induce long-range conformational changes in proteins. A less well understood molecular switch involving cis−trans isomerization of a peptidyl−prolyl bond could induce a conformational change directly to the backbone that is propagated to other parts of the protein. However, these switches are elusive and hard to identify because they are intrinsic to biomolecules that are inherently dynamic. Here, we explore the conformational dynamics and free energy landscape of the SH2 domain of interleukin-2-inducible T-cell or tyrosine kinase (ITK) to fully understand the conformational coupling between the distal cis− trans molecular switch and its binding pocket of the phosphotyrosine motif. We use multiple microsecond-long all-atom molecular dynamics simulations in explicit water for over a total of 60 μs. We show that cis−trans isomerization of the Asn286− Pro287 peptidyl−prolyl bond is directly coupled to the dynamics of the binding pocket of the phosphotyrosine motif, in agreement with previous NMR experiments. Unlike the cis state that is localized and less dynamic in a single free energy basin, the trans state samples two distinct conformations of the binding pocketone that recognizes the phosphotyrosine motif and the other that is somewhat similar to that of the cis state. The results provide an atomic-level description of a less well understood allosteric regulation by a peptidyl−prolyl cis−trans molecular switch that could aid in the understanding of normal and aberrant subcellular processes and the identification of these elusive molecular switches in other proteins.
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INTRODUCTION The regulation of biomolecular function as a result of transient molecular interactions to modulate the dynamics or conformational changes at a distal site is central to many subcellular biological processes.1,2 The binding of an allosteric effector, conformational changes, or mutations at an allosteric site could lead to modulation of binding affinity or enzymatic activity at a distal site.2−6 The allosteric pathways are different from protein to protein, and understanding these processes on the atomic level could help in the design and development of new classes of allosteric drugs, for example.7 Although the regulation of biomolecular function by allosteric ligands has been identified in many subcellular processes, molecular switches are also thought to be one of the leading triggers of intracellular signaling.8,9 Molecular switches have been sought as the “holy grail” of how conformational changes intrinsic to biomolecules could allosterically control distal sites. Molecular switches are in stark contrast to allosteric regulation by effector binding.10 These switches are elusive and hard to identify because they are intrinsic to inherently dynamic biomolecules. They are known to be an integral part of a good number of subcellular signaling processes.10 Molecular switches are usually part of protein motifs that undergo reversible changes between two or more metastable states. © 2017 American Chemical Society
Thermodynamically, peptide amide bonds involving all amino acids favor the lower free energy trans conformation in linear and folded proteins.11,12 Unlike other amino acids, peptide bonds preceding proline residues have a smaller free energy difference of
