Multiple open forms of ribose-binding protein trace the path of its conformational change

Bjorkman, A.J.; Mowbray, Sherry L.

doi:10.1006/jmbi.1998.1785

Cited by 155 publications

(226 citation statements)

References 35 publications

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“…The literature hinges are based on the comparison of the closed structure with several open structures. 15 StoneHinge predictions agree with the two gold standard hinges. FlexProt detects the first hinge region, but misses the second.…”

Section: Ribose Binding Proteinsupporting

confidence: 56%

“…12 Such pivot-like hinges are known for proteins including adenylate kinase, 13 inorganic pyrophosphatase, 14 and ribose binding protein. 15 To account for backbone flexibility during ligand docking, programs such as FlexDock have been developed to sample hinge rotations. 3 FlexDock partitions a protein into rigid regions with intervening hinges and docks the other molecule against each rigid region.…”

Section: Introductionmentioning

confidence: 99%

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StoneHinge: Hinge prediction by network analysis of individual protein structures

et al. 2009

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Hinge motions are important for molecular recognition, and knowledge of their location can guide the sampling of protein conformations for docking. Predicting domains and intervening hinges is also important for identifying structurally self-determinate units and anticipating the influence of mutations on protein flexibility and stability. Here we present StoneHinge, a novel approach for predicting hinges between domains using input from two complementary analyses of noncovalent bond networks: StoneHingeP, which identifies domain-hinge-domain signatures in ProFlex constraint counting results, and StoneHingeD, which does the same for DomDecomp Gaussian network analyses. Predictions for the two methods are compared to hinges defined in the literature and by visual inspection of interpolated motions between conformations in a series of proteins. For StoneHingeP, all the predicted hinges agree with hinge sites reported in the literature or observed visually, although some predictions include extra residues. Furthermore, no hinges are predicted in six hinge-free proteins. On the other hand, StoneHingeD tends to overpredict the number of hinges, while accurately pinpointing hinge locations. By determining the consensus of their results, StoneHinge improves the specificity, predicting 11 of 13 hinges found both visually and in the literature for nine different open protein structures, and making no false-positive predictions. By comparison, a popular hinge detection method that requires knowledge of both the open and closed conformations finds 10 of the 13 known hinges, while predicting four additional, false hinges.

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Section: Ribose Binding Proteinsupporting

confidence: 56%

Section: Introductionmentioning

confidence: 99%

StoneHinge: Hinge prediction by network analysis of individual protein structures

et al. 2009

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“…The known motions of the RBP/ALBP cluster are dominated by movements of connections I and II, while the movements of connection III seem to reflect attempts to adjust to motions in the other two. However, even RBP and ALBP, which have 35% amino acid sequence identity, have differences of 30 -40°in the preferred directions of motion (23,26). The available structures clearly show that some conformational routes are highly preferred for a particular protein, but changes in water and protein structure can allow many different outcomes in the various proteins.…”

Section: Resultsmentioning

confidence: 99%

X-ray Structures of the Leucine-binding Protein Illustrate Conformational Changes and the Basis of Ligand Specificity

Magnusson

Salopek‐Sondi

Luck

et al. 2004

Journal of Biological Chemistry

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The periplasmic leucine-binding protein is the primary receptor for the leucine transport system in Escherichia coli. We report here the structure of an open ligand-free form solved by molecular replacement and refined at 1.5-Å resolution. In addition, two closed ligand-bound structures of the same protein are presented, a phenylalanine-bound form at 1.8 Å and a leucine-bound structure at a nominal resolution of 2.4 Å. These structures show the basis of this protein's ligand specificity, as well as illustrating the conformational changes that are associated with ligand binding. Comparison with earlier structures provides further information about solution conformations, as well as the different specificity of the closely related leucine/ isoleucine/valine-binding protein.

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“…Crystal structures of RBP and other periplasmic binding proteins demonstrated that these proteins undergo a large conformational change upon ligand binding (33)(34)(35). Specifically, the connector regions of the two ␣/␤ domains of the receptor serve as a hinge, allowing substantial rigid-body motions of the two domains with respect to one another during ligand binding.…”

Section: Table 2 Oligonucleotide Primers Used For Rt-pcr In This Studymentioning

confidence: 99%

The PnrA (Tp0319; TmpC) Lipoprotein Represents a New Family of Bacterial Purine Nucleoside Receptor Encoded within an ATP-binding Cassette (ABC)-like Operon in Treponema pallidum

Deka

Brautigam

Yang

et al. 2006

Journal of Biological Chemistry

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Treponema pallidum, the bacterial agent of syphilis, cannot be cultivated in vitro. This constraint has severely impeded the study of the membrane biology of this complex human pathogen. A structure-to-function approach thus was adopted as a means of discerning the likely function of Tp0319, a 35-kDa cytoplasmic membraneassociated lipoprotein of T. pallidum formerly designated as TmpC. A 1.7-Å crystal structure showed that recombinant Tp0319 (rTp0319) consists of two ␣/␤ domains, linked by three crossovers, with a deep cleft between them akin to ATP-binding cassette (ABC) receptors. In the cleft, a molecule of inosine was bound. Isothermal titration calorimetry demonstrated that rTp0319 specifically binds purine nucleosides (dissociation constant (K d ) ϳ10 ؊7 M). This predilection for purine nucleosides by rTp0319 is consistent with its likely role as a receptor component of a cytoplasmic membraneassociated transporter system. Reverse transcription-PCR analysis of RNA isolated from rabbit tissue-extracted T. pallidum additionally showed that tp0319 is transcriptionally linked to four other downstream open reading frames, thereby supporting the existence of an ABC-like operon (tp0319 -0323). We herein thus re-name tp0319 as purine nucleoside receptor A (pnrA), with its operonic partners tp0320 -0323 designated as pnrB-E, respectively. Our study not only infers that PnrA transports purine nucleosides essential for the survival of T. pallidum within its obligate human host, but to our knowledge, this is the first description of an ABC-type nucleoside transport system in any bacterium. PnrA has been grouped with a functionally uncharacterized protein family (HBG016869), thereby implying that other members of the family may have similar nucleoside-binding function(s).Treponema pallidum, the bacterial agent of syphilis, cannot be cultivated continuously in vitro (1). Historically, this constraint has severely hampered progress in understanding many features of this enigmatic pathogen. More specifically, key aspects of the membrane biology of T. pallidum, particularly as it pertains to the interaction of the pathogen with its human host, remain poorly defined (2-4). The initial discovery of membrane lipoproteins in T. pallidum (5, 6) spawned new avenues of investigation into treponemal membrane biology, inasmuch as in other bacteria, lipoproteins have importance as virulence factors, modular components of ATP-binding cassette (ABC) 3 transporters, receptors, protective immune targets, and proinflammatory agonists that elicit innate immune responses (7-14). In fact, genome analysis predicts that T. pallidum devotes as much as 3% of its genetic coding capacity to lipoproteins (15). However, to date, with one exception (9, 16), comparative sequence analyses have not been fruitful for predicting the functions of treponemal lipoproteins, and the inability to cultivate (and thus genetically manipulate) the organism has precluded using classical gene inactivation approaches (17) for investigating the functions of treponemal ...

show abstract

Multiple open forms of ribose-binding protein trace the path of its conformational change

Cited by 155 publications

References 35 publications

StoneHinge: Hinge prediction by network analysis of individual protein structures

StoneHinge: Hinge prediction by network analysis of individual protein structures

X-ray Structures of the Leucine-binding Protein Illustrate Conformational Changes and the Basis of Ligand Specificity

The PnrA (Tp0319; TmpC) Lipoprotein Represents a New Family of Bacterial Purine Nucleoside Receptor Encoded within an ATP-binding Cassette (ABC)-like Operon in Treponema pallidum

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