Riboswitches: natural SELEXion

Gilbert, S.D.; Batey, Robert T.

doi:10.1007/s00018-005-5345-3

Cited by 16 publications

(9 citation statements)

References 22 publications

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“…On average, 90% of the metabolite surface area is solvent inaccessible, which is greater than that of ligands bound to artificial aptamers (71%) (Edwards et al, 2007). At first glance, this might be attributed to the need to discriminate between closely related metabolites in the cell (Gilbert and Batey, 2005). However, in vitro selected RNAs can easily achieve comparable specificities for their ligands without the need for extensive burial.…”

Section: Recognition Of Effector Molecules By Riboswitch Receptorsmentioning

confidence: 99%

Riboswitches: Structures and Mechanisms

Garst¹,

Edwards²,

Batey³

2010

Cold Spring Harbor Perspectives in Biology

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Section: Recognition Of Effector Molecules By Riboswitch Receptorsmentioning

confidence: 99%

Riboswitches: Structures and Mechanisms

Garst¹,

Edwards²,

Batey³

2010

Cold Spring Harbor Perspectives in Biology

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334

264

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“…For example, pore-forming toxin proteins exist in a wide range of organisms including bacteria, fungi, plant and animal cells. [16] By binding at particular sites on a membrane, toxins can create pores via oligomerizing on the membrane surface. The pores created by toxin proteins are of limited sizes.…”

Section: Introductionmentioning

confidence: 99%

Shapes of pored membranes

et al. 2012

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We study the shapes of pored membranes within the framework of the Helfrich theory under the constraints of fixed area and pore size. We show that the mean curvature term leads to a budding- like structure, while the Gaussian curvature term tends to flatten the membrane near the pore; this is corroborated by simulation. We propose a scheme to deduce the ratio of the Gaussian rigidity to the bending rigidity simply by observing the shape of the pored membrane. This ratio is usually difficult to measure experimentally. In addition, we briefly discuss the stability of a pore by relaxing the constraint of a fixed pore size and adding the line tension. Finally, the flattening effect due to the Gaussian curvature as found in studying pored membranes is extended to two-component membranes. We find that sufficiently high contrast between the components' Gaussian rigidities leads to budding which is distinct from that due to the line tension.Comment: 8 pages, 9 figure

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“…It has been known for nearly two decades that sulfated proteoglycans are major contributors to the repulsive nature of the glial scar (15); however, the precise inhibitory mechanism remains poorly understood. Because the identification of specific neuronal receptors for CSPGs has been lacking, relatively nonspecific mechanisms brought about by arrays of negatively charged sulfate (16) or the occlusion of substrate adhesion molecules (17) have been suggested.…”

mentioning

confidence: 99%

“…The CS moiety plays an important role in CSPG-mediated inhibition of neural regeneration (10, 12, 15, 16). We therefore tested whether the CS moiety of neurocan is involved in its interaction with PTPσ.…”

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confidence: 99%

PTPσ Is a Receptor for Chondroitin Sulfate Proteoglycan, an Inhibitor of Neural Regeneration

Shen

Tenney

Busch

et al. 2009

Science

606

552

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Chondroitin sulfate proteoglycans (CSPGs) present a barrier to axon regeneration. However, no specific receptor for the inhibitory effect of CSPGs has been identified. We showed that a transmembrane protein tyrosine phosphatase, PTPσ, binds with high affinity to neural CSPGs. Binding involves the chondroitin sulfate chains and a specific site on the first immunoglobulin-like domain of PTPσ. In culture, PTPσ −/− neurons show reduced inhibition by CSPG. A PTPσ fusion protein probe can detect cognate ligands that are up-regulated specifically at neural lesion sites. After spinal cord injury, PTPσ gene disruption enhanced the ability of axons to penetrate regions containing CSPG. These results indicate that PTPσ can act as a receptor for CSPGs and may provide new therapeutic approaches to neural regeneration.Recovery after central nervous system (CNS) injury is minimal, leading to substantial current interest in potential strategies to overcome this challenge (1-5). Chondroitin sulfate proteoglycans (CSPGs) show dramatic up-regulation after neural injury, within the extracellular matrix of scar tissue and in the perineuronal net within more-distant targets of the severed axons (6,7). The inhibitory nature of CSPGs is reflected not only in the formation of dystrophic axonal retraction bulbs that fail to regenerate through the lesion (8), but also in the limited capacity for collateral sprouting of spared fibers (8,9). This inhibition can be relieved by chondroitinase ABC digestion of the chondroitin sulfate (CS) side chains, which can promote regeneration and sprouting and restore lost function (10)(11)(12)(13)(14). It has been known for nearly two decades that sulfated proteoglycans are major contributors to the repulsive nature of the glial scar (15); however, the precise inhibitory mechanism remains poorly understood. Because the identification of specific neuronal receptors for CSPGs has been lacking, relatively nonspecific mechanisms brought about by arrays of negatively charged sulfate (16) or the occlusion of substrate adhesion molecules (17) have been suggested.Transmembrane protein tyrosine phosphatases (PTPs) form a large and diverse molecular family and have a structure typical of transmembrane cell-surface receptors (18,19). In previous work, we and others have found that PTPσ and other PTPs in the leukocyte antigen-related (LAR) subfamily can act as receptors for heparan sulfate proteoglycans (HSPGs) (20)(21)(22), and these PTPs are involved in axon guidance and synapse formation during development (18- ‡To whom correspondence should be addressed. flanagan@hms.harvard.edu. * These authors contributed equally to this work. † Present address: Motor Neuron Center, Columbia University, New York, NY 10032, USA. (Fig. 1A). Using a cell-free system with recombinant fusion proteins of the PTPσ extra-cellular domain with an immunoglobulin Fc tag (PTPσ-Fc) and neurocan with an alkaline phosphatase tag (Ncn-AP), a binding interaction was indeed identified (P < 0.001) (Fig. 1B). Genuine biological ligand-re...

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Riboswitches: natural SELEXion

Cited by 16 publications

References 22 publications

Riboswitches: Structures and Mechanisms

Riboswitches: Structures and Mechanisms

Shapes of pored membranes

PTPσ Is a Receptor for Chondroitin Sulfate Proteoglycan, an Inhibitor of Neural Regeneration

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