Structure dictates the mechanism of ligand recognition in the histidine and maltose binding proteins

Abstract

Two mechanisms, induced fit (IF) and conformational selection (CS), have been proposed to explain ligand recognition coupled conformational changes. The histidine binding protein (HisJ) adopts the CS mechanism, in which a pre-equilibrium is established between the open and the closed states with the ligand binding to the closed state. Despite being structurally similar to HisJ, the maltose binding protein (MBP) adopts the IF mechanism, in which the ligand binds the open state and induces a transition to the closed state. To understand the molecular determinants of this difference, we performed molecular dynamics (MD) simulations of coarse-grained dual structure based models. We find that intra-protein contacts unique to the closed state are sufficient to promote the conformational transition in HisJ, indicating a CS-like mechanism. In contrast, additional ligand-mimicking contacts are required to “induce” the conformational transition in MBP suggesting an IF-like mechanism. In agreement with experiments, destabilizing modifications to two structural features, the spine helix (SH) and the balancing interface (BI), present in MBP but absent in HisJ, reduce the need for ligand-mimicking contacts indicating that SH and BI act as structural restraints that keep MBP in the open state. We introduce an SH like element into HisJ and observe that this can impede the conformational transition increasing the importance of ligand-mimicking contacts. Similarly, simultaneous mutations to BI and SH in MBP reduce the barrier to conformational transitions significantly and promote a CS-like mechanism. Together, our results show that structural restraints present in the protein structure can determine the mechanism of conformational transitions and even simple models that correctly capture such structural features can predict their positions. MD simulations of such models can thus be used, in conjunction with mutational experiments, to regulate protein ligand interactions, and modulate ligand binding affinities.

The role of C-terminal helix in the conformational transition of an arginine binding protein

“…The results from MD simulations obtained by applying a dual-Gaussian SBM model are presented first followed by results from all-atom MD simulation. The native centric Cα-SBMs offers a distinct advantage in studying conformational transition with the assumption that the mechanism of conformational transition depends solely on the two end states and its posit lies in taking advantage of the difference in the distribution of contacts between them ( Jayanthi et al, 2020 , Okazaki et al, 2006 , Ramírez-Sarmiento et al, 2015 , Whitford et al, 2007 ). In this study a dual-Gaussian SBM potential is defined from the knowledge of common contacts from both the open- and closed-states of TmArgBP and the structural information unique to both the states are encoded as specific contacts.…”

“…In the conformational selection scenario the protein is flexible enough to transiently gain access to the closed-state and the ligand then selects this conformation to bind. Hence, in the induced-fit mechanism the ligand is essential to unlock the closed-state conformation, while in the conformational selection it appears that the protein possesses inbuilt intrinsic flexibility to access the closed-state at least for a very short span ( Jayanthi et al, 2020 ). In the absence of the ligand many multi-domain proteins exist in their open-state, which undergo a conformational change to the closed-state upon ligand binding and these systems provide an ideal set-up to understand conformational changes.…”

“…Salt-bridge interactions of CTH with L2 were observed in the simulation of os-TmArgBP CTH , and we hypothesized that these interactions link the CTH with the protein, thereby stabilizing the open-state conformation. A CTH-like helix called the spine-helix (SH) has been observed to perform a similar role in MBP (maltose-binding protein), a structurally similar family of periplasmic binding protein ( Jayanthi et al, 2020 ). It has been demonstrated that changing the SH residues to more bulky ones (I329W) lengthens the distance between the SH and the N -terminal domain at the back of the binding pocket ( Telmer and Shilton, 2003 ).…”