Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation

Bahar, İvet; Chennubhotla, Chakra; Tobi, Dror

doi:10.1016/j.sbi.2007.09.011

Cited by 285 publications

(307 citation statements)

References 65 publications

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“…2), into the Nterminal region of BtuB (see Methods). The X-band EPR spectra from spin labels placed at positions [1][2][3][4][5] in BtuB are shown in Figure 3, along with the position of these sites in the BtuB meso structure. These spectra are similar to those published previously, 22 and are composed of two components resulting from populations of spin labels that have different dynamics.…”

Section: Resultsmentioning

confidence: 99%

“…[3][4][5] Dynamics also underlies protein-protein recognition, which is often mediated by conserved and highly dynamic or unstructured regions of proteins. 6,7 It is not precisely understood how structural fluctuations facilitate and mediate recognition, but there is considerable interest in characterizing the dynamics and conformation substates in regions that function in recognition.…”

Section: Introductionmentioning

confidence: 99%

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Osmolytes modulate conformational exchange in solvent‐exposed regions of membrane proteins

Jiménez¹,

Cao²,

Kim³

et al. 2010

Protein Science

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Site-directed spin labeling (SDSL) was used to investigate local structure and conformational exchange in two bacterial outer-membrane TonB-dependent transporters, BtuB and FecA. Protecting osmolytes, such as polyethylene glycols (PEGs) are known to modulate a substrate-dependent conformational equilibrium in the energy coupling motif (Ton box) of BtuB. Here, we demonstrate that a segment that is N-terminal to the Ton box in BtuB, is in conformational exchange between ordered and disordered states with or without substrate. Protecting osmolytes shift this equilibrium to favor the more ordered, folded state. However, a segment of BtuB that is C-terminal to the Ton box that is not solvent exposed is insensitive to PEGs. Protecting osmolytes also modulate a conformational equilibrium in the Ton box of FecA, with larger molecular weight PEGs producing the largest shifts in the conformational free energy. These data indicate that solvent-exposed regions of these transporters undergo conformational exchange and that regions of these transporters that are involved in protein-protein interactions sample multiple conformational substates. The sensitivity to solute provides an explanation for differences seen between two high-resolution structures of BtuB, which each likely represent one conformation from a subset of states that are normally sampled by the protein. This work also illustrates how SDSL and osmolytes may be used to characterize and quantitate conformational equilibria in membrane proteins.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Osmolytes modulate conformational exchange in solvent‐exposed regions of membrane proteins

Jiménez¹,

Cao²,

Kim³

et al. 2010

Protein Science

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“…Transdomain "cross-talk" between a catalytic center and a distal loop is an emerging theme by which single domains can transmit cellular signals (7,(53)(54)(55). In the single-domain protein interleukin-1β, point mutations that are distal to the receptor binding interface have no effect on stability, yet they have significant effects on the binding properties (55).…”

Section: Discussionmentioning

confidence: 99%

Allostery in the ferredoxin protein motif does not involve a conformational switch

Nechushtai

Lammert²,

Michaeli³

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Regulation of protein function via cracking, or local unfolding and refolding of substructures, is becoming a widely recognized mechanism of functional control. Oftentimes, cracking events are localized to secondary and tertiary structure interactions between domains that control the optimal position for catalysis and/or the formation of protein complexes. Small changes in free energy associated with ligand binding, phosphorylation, etc., can tip the balance and provide a regulatory functional switch. However, understanding the factors controlling function in single-domain proteins is still a significant challenge to structural biologists. We investigated the functional landscape of a single-domain planttype ferredoxin protein and the effect of a distal loop on the electron-transfer center. We find the global stability and structure are minimally perturbed with mutation, whereas the functional properties are altered. Specifically, truncating the L1,2 loop does not lead to large-scale changes in the structure, determined via X-ray crystallography. Further, the overall thermal stability of the protein is only marginally perturbed by the mutation. However, even though the mutation is distal to the iron-sulfur cluster (∼20 Å), it leads to a significant change in the redox potential of the ironsulfur cluster (57 mV). Structure-based all-atom simulations indicate correlated dynamical changes between the surface-exposed loop and the iron-sulfur cluster-binding region. Our results suggest intrinsic communication channels within the ferredoxin fold, composed of many short-range interactions, lead to the propagation of long-range signals. Accordingly, protein interface interactions that involve L1,2 could potentially signal functional changes in distal regions, similar to what is observed in other allosteric systems.electron transfer | functional energy landscape | iron-sulfur proteins | protein folding O ver the last several decades, our understanding of protein function has evolved from a rather static perspective, where signaling and function have been understood through surface complementarity arguments, such as the "lock and key" paradigm (1, 2), to a more dynamic view where protein conformational fluctuations are inextricably linked to function (3). As our understanding of protein dynamics expands, we are revealing many mechanisms by which proteins exploit conformational fluctuations to perform cellular function. In multidomain proteins, relative repositioning of domains is often linked to their levels of activity. For example, large-scale domain rearrangements in the four-domain Src kinase (4) and C-terminal Src kinase (5, 6) lead to these proteins being in so-called "on" or "off" states, and functional regulation may be obtained by adjusting the balance between these conformations (7). In proteins such as adenylate kinase, domain rearrangements can be rate limiting during each round of catalysis (8), where the enzyme cycles between ligandcompetent and ligand-release conformations. Because the kinetics of these tra...

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“…Such long distance coupling is at the very heart of allosteric regulation (3). Experimental and computational studies of many regulatory complexes support the current view that they possess the intrinsic ability to undergo conformational transitions, conferred by the 3-dimensional network of interresidue interactions (4)(5)(6)(7)(8). The pathways of signal transduction favored by the network of interresidue contacts and the role conservation plays in these pathways remain to be established.…”

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confidence: 94%

Dynamical networks in tRNA:protein complexes

Sethi¹,

Eargle

Black³

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

722

1,091

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Community network analysis derived from molecular dynamics simulations is used to identify and compare the signaling pathways in a bacterial glutamyl-tRNA synthetase (GluRS):tRNA Glu and an archaeal leucyl-tRNA synthetase (LeuRS):tRNA Leu complex. Although the 2 class I synthetases have remarkably different interactions with their cognate tRNAs, the allosteric networks for charging tRNA with the correct amino acid display considerable similarities. A dynamic contact map defines the edges connecting nodes (amino acids and nucleotides) in the physical network whose overall topology is presented as a network of communities, local substructures that are highly intraconnected, but loosely interconnected. Whereas nodes within a single community can communicate through many alternate pathways, the communication between monomers in different communities has to take place through a smaller number of critical edges or interactions. Consistent with this analysis, there are a large number of suboptimal paths that can be used for communication between the identity elements on the tRNAs and the catalytic site in the aaRS:tRNA complexes. Residues and nucleotides in the majority of pathways for intercommunity signal transmission are evolutionarily conserved and are predicted to be important for allosteric signaling. The same monomers are also found in a majority of the suboptimal paths. Modifying these residues or nucleotides has a large effect on the communication pathways in the protein:RNA complex consistent with kinetic data.aminoacyl-tRNA synthetase ͉ communication networks ͉ community ͉ suboptimal paths

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Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation

Cited by 285 publications

References 65 publications

Osmolytes modulate conformational exchange in solvent‐exposed regions of membrane proteins

Osmolytes modulate conformational exchange in solvent‐exposed regions of membrane proteins

Allostery in the ferredoxin protein motif does not involve a conformational switch

Dynamical networks in tRNA:protein complexes

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