Conformational Equilibria and Free Energy Profiles for the Allosteric Transition of the Ribose-binding Protein

Ravindranathan, Krishna Pratap; Gallicchio, Emilio; Levy, Ronald M.

doi:10.1016/j.jmb.2005.08.009

Cited by 71 publications

(123 citation statements)

References 48 publications

(70 reference statements)

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“…In the apo state, open-like conformations are by far the most probable, although the protein is still able adopt a closed conformation, albeit less frequently. This is consistent with theoretical and experimental studies for the maltose, ribose, and vitamin B 12 SBPs (3,(37)(38)(39). The presence of ectoine in the binding cleft reverses this balance, and cleft opening is seen to have a very significant energy cost.…”

Section: A Proline Mutant In α9 Is Conformationally Unbiased and Thussupporting

confidence: 87%

Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins

Marinelli

Kuhlmann

Grell

et al. 2011

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

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Numerous membrane importers rely on accessory water-soluble proteins to capture their substrates. These substrate-binding proteins (SBP) have a strong affinity for their ligands; yet, substrate release onto the low-affinity membrane transporter must occur for uptake to proceed. It is generally accepted that release is facilitated by the association of SBP and transporter, upon which the SBP adopts a conformation similar to the unliganded state, whose affinity is sufficiently reduced. Despite the appeal of this mechanism, however, direct supporting evidence is lacking. Here, we use experimental and theoretical methods to demonstrate that an allosteric mechanism of enhanced substrate release is indeed plausible. First, we report the atomic-resolution structure of apo TeaA, the SBP of the Na -coupled ectoine TRAP transporter TeaBC from Halomonas elongata DSM2581 T , and compare it with the substrate-bound structure previously reported. Conformational freeenergy landscape calculations based upon molecular dynamics simulations are then used to dissect the mechanism that couples ectoine binding to structural change in TeaA. These insights allow us to design a triple mutation that biases TeaA toward apo-like conformations without directly perturbing the binding cleft, thus mimicking the influence of the membrane transporter. Calorimetric measurements demonstrate that the ectoine affinity of the conformationally biased triple mutant is 100-fold weaker than that of the wild type. By contrast, a control mutant predicted to be conformationally unbiased displays wild-type affinity. This work thus demonstrates that substrate release from SBPs onto their membrane transporters can be facilitated by the latter through a mechanism of allosteric modulation of the former.binding thermodynamics | periplasmic binding protein | secondary transporter | ABC transporter | replica-exchange metadynamics

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Section: A Proline Mutant In α9 Is Conformationally Unbiased and Thussupporting

confidence: 87%

Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins

Marinelli

Kuhlmann

Grell

et al. 2011

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

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“…From an evolutionary perspective, it is generally accepted that the biological function of a protein has been selected by evolution, and accordingly, the dynamic characteristics of a protein are the result of evolutionary selection 10 . It has been suggested that various periplasmic-binding proteins have their own dynamic characteristics along with their particular purposes [21][22][23][24] . MBP, for example, is involved in the uptake of various sugars in Gramnegative bacteria, and maltose uptake in vivo has been shown to be modulated by a change in the dynamic property of MBP 25 .…”

Section: Discussionmentioning

confidence: 99%

Protein conformational dynamics dictate the binding affinity for a ligand

et al. 2014

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Interactions between a protein and a ligand are essential to all biological processes. Binding and dissociation are the two fundamental steps of ligand-protein interactions, and determine the binding affinity. Intrinsic conformational dynamics of proteins have been suggested to play crucial roles in ligand binding and dissociation. Here, we demonstrate how protein dynamics dictate the binding and dissociation of a ligand through a single-molecule kinetic analysis for a series of maltose-binding protein mutants that have different intrinsic conformational dynamics and dissociation constants for maltose. Our results provide direct evidence that the ligand dissociation is determined by the intrinsic opening rate of the protein.

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“…The end result of extracellular and periplasmic pectin deesterification and polygalacturonate depolymerization is the production of small (di-and tri-) oligogalacturonides (33,54). The ultimate goal for these carbohydrates is to be passaged into the cytoplasm where intracellular metabolic pathways dedicated for the catabolism of both saturated and unsaturated oligogalacturonides converge to produce KDG (57).…”

Section: Intracellular Transport Is An Active and Selective Processmentioning

confidence: 99%

“…7B). This isomerization proceeds along a two-order coordinate, with transitions in a hinge and twist vector (1,7,54,68). In its "closed" state, the ligand is completely inaccessible to bulk solvent (Fig.…”

Section: Intracellular Transport Is An Active and Selective Processmentioning

confidence: 99%

Structural Biology of Pectin Degradation byEnterobacteriaceae

Abbott

Boraston

2008

Microbiol Mol Biol Rev

157

105

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SUMMARY Pectin is a structural polysaccharide that is integral for the stability of plant cell walls. During soft rot infection, secreted virulence factors from pectinolytic bacteria such as Erwinia spp. degrade pectin, resulting in characteristic plant cell necrosis and tissue maceration. Catabolism of pectin and its breakdown products by pectinolytic bacteria occurs within distinct cellular environments. This process initiates outside the cell, continues within the periplasmic space, and culminates in the cytoplasm. Although pectin utilization is well understood at the genetic and biochemical levels, an inclusive structural description of pectinases and pectin binding proteins by both extracellular and periplasmic enzymes has been lacking, especially following the recent characterization of several periplasmic components and protein-oligogalacturonide complexes. Here we provide a comprehensive analysis of the protein folds and mechanisms of pectate lyases, polygalacturonases, and carbohydrate esterases and the binding specificities of two periplasmic pectic binding proteins from Enterobacteriaceae. This review provides a structural understanding of the molecular determinants of pectin utilization and the mechanisms driving catabolite selectivity and flow through the pathway.

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Conformational Equilibria and Free Energy Profiles for the Allosteric Transition of the Ribose-binding Protein

Cited by 71 publications

References 48 publications

Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins

Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins

Protein conformational dynamics dictate the binding affinity for a ligand

Structural Biology of Pectin Degradation byEnterobacteriaceae

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