Reaction mechanisms, catalysis, and movement

Combining multi-mutant and modular thermodynamic cycles to measure energetic coupling networks in enzyme catalysis

“…Perhaps the clearest discussion of these underlying issues is that by Jencks, 13,14 who outlined how sequential changes in ligand-binding affinity lead to profound changes in the overall free energy of ATP hydrolysis, and recognized the necessity for understanding what he called the “coupling rules.” As the structural landscape of transducing enzymes was as yet unknown, Jencks was mute about what mechanisms actually linked conformational changes to catalysis, and this issue remains unresolved 81 . Identifying 24,40 and mutating 29 key residues associated with the conformational transition state(s), together with modular thermodynamic cycles 44 to measure energetic coupling between domains, now enhance the understanding of how idiosyncratic structural and mechanistic details implement the coupling rules.…”

“…Nonetheless, many enzymes, especially NTP (nucleotide triphosphate)-dependent motors, synthetases, polymerases, and signaling GTPases, exhibit multi-state, vectorial behavior 13–19 in which biological function depends critically on coupling catalysis to conformational changes. Purposes served by such coupling include many of the most interesting aspects of biology.…”

High-Dimensional Mutant and Modular Thermodynamic Cycles, Molecular Switching, and Free Energy Transduction

“…Jencks (57, 59, 61) recognized the challenge of understanding how nucleoside triphosphate (NTP) hydrolysis drives vectorial processes. Astumian (3–5) summarized relationships between conformation and ligand-binding specificity necessary for free energy transduction by diffusive molecular machines.…”

“…Here, I attempt to ( a ) define molecular switches and conformational transition states (60, 61, 109); ( b ) emphasize how higher-dimensional thermodynamic cycles constructed between side chains within modules (96, 109, 111, 112) and between modules (67) connected by molecular switches deepen our understanding of allosteric phenomena; and ( c ) relate long-range coupling to conformational equilibria and catalysis by transducing enzymes (52). A second goal is to introduce experimental studies of the voltage-gated K channel and Bacillus geostearothermophilus tryptophanyl-tRNA synthetase (TrpRS) to a wider audience.…”

“…A second goal is to introduce experimental studies of the voltage-gated K channel and Bacillus geostearothermophilus tryptophanyl-tRNA synthetase (TrpRS) to a wider audience. Experimental coupling energies from the two systems furnish new understanding of free energy transduction mechanisms important in channels, NTP-dependent motors, synthetases, polymerases, and signaling GTPases that exhibit multistate, vectorial behavior (4, 5, 57, 60, 61, 83, 96), enabling them to convert energy sources into work and information (27, 53, 90). …”