Propagation of Dynamic Changes in Barnase Upon Binding of Barstar: An NMR and Computational Study

Mapping allostery through the covariance analysis of NMR chemical shifts

“…Such subtle changes may include minor readjustments in backbone and/or side-chain structure and/or dynamics, e.g., in the energy landscape of the interconverting states within the conformational ensemble. Although these variations often escape direct structural observation, they are sensed through chemical shift differences and underlie the modulations in dynamics that are critical for the allosteric signal propagation (7,24). It is therefore essential to not only identify such allosterically relevant minor chemical shift changes through AC of the R matrix (Fig.…”

“…However, what remains experimentally challenging is often defining the networks of residues that mediate the cross-talk between distal sites. Such clusters of coupled residues are particularly elusive in allosteric processes with a significant dynamically driven component (11)(12)(13)(14)(15)(16)(17), as in this case the allosteric signal propagation relies on subtle, but critical, conformational and side-chain packing rearrangements that often fall below the resolution of common X-ray or NMR structure determination methods (2,7,24).…”

“…The chemical shift covariance analysis (CHESCA) is based on two simple but general notions. The first assumption is that the subtle but functionally relevant structural changes that underlie the allosteric modulations of dynamics are effectively probed by accurately measured NMR chemical shift variations, even when they escape detection through traditional structure determination methods (24)(25)(26)(27). The second general assumption of the CHESCA approach is that when a system is subject to a set of perturbations, residues that belong to the same effectordependent allosteric network exhibit a concerted response to the perturbation set.…”

Compensatory and Long-Range Changes in Picosecond–Nanosecond Main-Chain Dynamics upon Complex Formation: 15N Relaxation Analysis of the Free and Bound States of the Ubiquitin-like Domain of Human Plexin-B1 and the Small GTPase Rac1

“…Such changes in dynamics can reflect subtle structural alterations or may occur without substantial changes in protein structure, given that the protein structure is already a dynamic ensemble of subtly different conformations that interconvert. 46,54,55 To address this issue, we investigated a possible correlation between changes in chemical shift and picosecond-nanosecond protein dynamics, but found no significant correlation. It should be noted that in the case of protein-protein interactions such a comparison may not be straightforward, as chemical shifts are also substantially perturbed by the new protein-protein contacts, which may occur without any change in internal protein dynamics.…”

NMR reveals novel mechanisms of protein activity regulation

“…[33][34][35] Numerous examples are currently available highlighting the inextricable link between protein dynamics and allostery 8,36 . Long-range allosteric coupling between sites through changes in internal dynamics were seen between the nucleotide-binding cleft and the preprotein-binding site in SecA ATPase, 37 between the coordination Na þ site and exosite I in thrombin that regulates enzyme's specificity, 38 between the substrate-binding site and distal loop in dihydrofolate reductase, 39 between the mixed lineage leukemia)-and c-Myb binding sites of the KIX domain of CREB-binding protein, 40 in PDZ signaling domains, 41 the serine protease inhibitor eglin c, 42 upon binding of barstar to the RNase barnase, 43 in the interaction between the Rho GTPasebinding domain and Rac1, 44 upon cyclic nucleotide binding to the exchange protein activated by cAMP, 45,46 a in V-type allosteric enzyme, 47 and in protein kinase A, 48,49 only to mention few recent examples from a long list of systems characterized over the years. Dynamic changes in these systems were accompanied by varying extent of structural changes, ranging from minimal to substantial.…”