Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication

Abstract

Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks and signaling pathways. We found that functional sites involved in allosteric regulation of Hsp70 may be characterized by structural stability, proximity to global hinge centers and local structural environment that is enriched by highly coevolving flexible residues. These specific characteristics may be necessary for regulation of allosteric structural transitions and could distinguish regulatory sites from nonfunctional conserved residues. The observed confluence of dynamics correlations and coevolutionary residue couplings with global networking features may determine modular organization of allosteric interactions and dictate localization of key mediating sites. Community analysis of the residue interaction networks revealed that concerted rearrangements of local interacting modules at the inter-domain interface may be responsible for global structural changes and a population shift in the DnaK chaperone. The inter-domain communities in the Hsp70 structures harbor the majority of regulatory residues involved in allosteric signaling, suggesting that these sites could be integral to the network organization and coordination of structural changes. Using a network-based formalism of allostery, we introduced a community-hopping model of allosteric communication. Atomistic reconstruction of signaling pathways in the DnaK structures captured a direction-specific mechanism and molecular details of signal transmission that are fully consistent with the mutagenesis experiments. The results of our study reconciled structural and functional experiments from a network-centric perspective by showing that global properties of the residue interaction networks and coevolutionary signatures may be linked with specificity and diversity of allosteric regulation mechanisms.

The Hsp70 interdomain linker is a dynamic switch that enables allosteric communication between two structured domains

“…Our work also points to the importance of these residues, but we find the dynamics of the linker to be better characterized as ordered segments with connecting hinges at Lys 387 and Leu 391 . Stetz and Verkhivker (13,14) also posit that several linker residues interact with the SBD, which is consistent with the observations made here. Similarly, Penkler et al (15) observed linker interactions with the SBD consistent with our observations.…”

“…We note, however, that both the ADP-bound and substrate-, ADPbound forms of DnaK simulated by Chiappori et al (11,12) were significantly more collapsed than would be consistent with experiments. Stetz and Verkhivker (13,14) propose that several linker residues are important in allostery based on a combination of evolutionary co-variance and dynamic character. Among these are Gly 384 , Asp 385 , Val 386 , Lys 387 , Leu 390 , Asp 393 , and Thr 395 , which they propose to be hinge residues, in either forward or reverse allosteric pathways.…”

“…For ADP and substrate-bound DnaK (12), these authors observed a state with the two domains collapsed on one another and several contacts between the linker and the SBD. Stetz and Verkhiver (13,14) applied a novel network model that incorporates evolutionary sequence information and MD-derived trajectories to elucidate potential allosteric communication mechanisms. Their approach identified several candidate residue interaction patterns that may be important in allostery.…”

Two-step mechanism of J-domain action in driving Hsp70 function

“…Though no model for the mechanistic role of the D HPD -R NBD interaction per se has been previously put forth, the functional connection between these residues is well supported by genetic and biochemical data. Alteration of either R NBD or residues interacting with it (D SBD and D Lk ) 10, 11,14,17,34,38 disrupt allosteric communication between domains, resulting in a somewhat increased basal activity and ineffective stimulation by its JDP partner, DnaJ in the case of DnaK 14 and Hsc20 in the case of Ssc1 ( Supplementary Fig. S4).…”

Protein synthesis as an object of physical and mathematical research and modeling

“…Текущая задача исследователей синтеза белка (трансляции) в этом контексте формулируется так: «our understanding of how basic ribosome processes, including mRNA decoding, peptide bond formation, mRNA, and tRNA translocation and cotranslational transport of the nascent peptide, are regulated» [24]. С этим трудно и нет смысла спорить, и слава тем специалистам, которые двигаются в этом направлении, применяя самые современные методы микроскопии, рентгеноструктурного анализа, направленного мутагенеза и самых изощренных компьютерных симуляций [25,26,27,28,29].…”