Increase in Backbone Mobility of the VTS1p-SAM Domain on Binding to SRE–RNA

Ravindranathan, Sapna; Oberstrass, Florian C.; Allain, Frédéric H.‐T.

doi:10.1016/j.jmb.2009.12.004

Cited by 24 publications

(25 citation statements)

References 47 publications

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“…Deletion of the nucleotide indicated in parentheses does not alter binding affinity indicating that penta-or tetra loop RNAs can bind to the VTS1p SAM domain. 15 N relaxation studies of the backbone dynamics indicate that in its free state the VTS1p SAM domain is mostly rigid with no significant motion in the fast and slow time scales [372]. This is consistent with the idea of a conformationally pre-organized binding surface on the protein which can accommodate the RNA loop.…”

Section: Protein Dynamicssupporting

confidence: 77%

“…Detailed analysis of relaxation rates in both protein and RNA in their free and bound states, along with dynamics changes following binding have been reported for two systems, human U1A protein interaction with the 3' untranslated region (UTR) of its own pre-mRNA and VTS1p sterile alpha motif (SAM) domain interaction with the smaug recognition element (SRE) stem-loop RNA [368][369][370][371][372]. Other studies have examined dynamics in the free and RNA bound states of the cleavage stimulation factor (Cstf-64) and the ribosomal protein L11 [46,373].…”

mentioning

confidence: 99%

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Structure determination and dynamics of protein–RNA complexes by NMR spectroscopy

Dominguez

Schubert

Duss

et al. 2011

Progress in Nuclear Magnetic Resonance Spectroscopy

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Section: Protein Dynamicssupporting

confidence: 77%

mentioning

confidence: 99%

Structure determination and dynamics of protein–RNA complexes by NMR spectroscopy

Dominguez

Schubert

Duss

et al. 2011

Progress in Nuclear Magnetic Resonance Spectroscopy

Self Cite

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“…In this approach, the relaxation data for each residue were fitted with five internal motions of increasing complexity as described previously [45], [64] and the model giving the best fit was assigned to each residue. Most of the residues could be fitted with Model 2, 4, 5 while only a few residues could be fitted with Model 1 and 3 (Materials and Methods).…”

Section: Resultsmentioning

confidence: 99%

“…Exclusively for experiments recorded at 500 MHz the CPMG experiments were repeated with the 15 N carrier positioned at 103, 116, 120, 129 ppm in order to take into account the errors arising from large resonances [45], [59], [60].…”

Section: Methodsmentioning

confidence: 99%

“…The data obtained at 950 MHz and 500 MHz were fitted separately at each field or simultaneously. As previously described, the relaxation rates of each residue were fitted to five models of increasing complexity [45], [64], [68]. The spectral densities J() were calculated using as parameters, a uniform value d CSA of −172 ppm for chemical shift anisotropy (CSA) and a value of 1.02 Å for the N-H bond length [69].…”

Section: Methodsmentioning

confidence: 99%

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Dynamics of Linker Residues Modulate the Nucleic Acid Binding Properties of the HIV-1 Nucleocapsid Protein Zinc Fingers

Zargarian

Tisné

et al. 2014

PLoS ONE

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The HIV-1 nucleocapsid protein (NC) is a small basic protein containing two zinc fingers (ZF) separated by a short linker. It is involved in several steps of the replication cycle and acts as a nucleic acid chaperone protein in facilitating nucleic acid strand transfers occurring during reverse transcription. Recent analysis of three-dimensional structures of NC-nucleic acids complexes established a new property: the unpaired guanines targeted by NC are more often inserted in the C-terminal zinc finger (ZF2) than in the N-terminal zinc finger (ZF1). Although previous NMR dynamic studies were performed with NC, the dynamic behavior of the linker residues connecting the two ZF domains remains unclear. This prompted us to investigate the dynamic behavior of the linker residues. Here, we collected 15N NMR relaxation data and used for the first time data at several fields to probe the protein dynamics. The analysis at two fields allows us to detect a slow motion occurring between the two domains around a hinge located in the linker at the G35 position. However, the amplitude of motion appears limited in our conditions. In addition, we showed that the neighboring linker residues R29, A30, P31, R32, K33 displayed restricted motion and numerous contacts with residues of ZF1. Our results are fully consistent with a model in which the ZF1-linker contacts prevent the ZF1 domain to interact with unpaired guanines, whereas the ZF2 domain is more accessible and competent to interact with unpaired guanines. In contrast, ZF1 with its large hydrophobic plateau is able to destabilize the double-stranded regions adjacent to the guanines bound by ZF2. The linker residues and the internal dynamics of NC regulate therefore the different functions of the two zinc fingers that are required for an optimal chaperone activity.

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Discerning intersecting fusion‐activation pathways in the Nipah virus using machine learning

2014

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The fusion of Nipah with host cells is facilitated by two of their glycoproteins, the G and the F proteins. The binding of cellular ephrins to the G head domain causes the G stalk domain to interact differently with F, which activates F to mediate virus-host fusion. To gain insight into how the ephrin-binding signal transduces from the head to the stalk domain of G, we examine quantitatively the differences between the conformational ensembles of the G head domain in its ephrin-bound and unbound states. We consider the human ephrins B2 and B3, and a double mutant of B2, all of which trigger fusion. The ensembles are generated using molecular dynamics, and the differences between them are quantified using a new machine learning method. We find that the portion of the G head domain whose conformational density is altered equivalently by the three ephrins is large, and comprises ∼25% of the residues in the G head domain. This subspace also includes the residues that are known to be important to F activation, which suggests that it contains at least one common signaling pathway. The spatial distribution of the residues constituting this subspace supports the model of signal transduction in which the signal transduces via the G head dimer interface. This study also adds to the growing list of examples where signaling does not depend solely on backbone deviations. In general, this study provides an approach to filter out conserved patterns in protein dynamics.

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Increase in Backbone Mobility of the VTS1p-SAM Domain on Binding to SRE–RNA

Cited by 24 publications

References 47 publications

Structure determination and dynamics of protein–RNA complexes by NMR spectroscopy

Structure determination and dynamics of protein–RNA complexes by NMR spectroscopy

Dynamics of Linker Residues Modulate the Nucleic Acid Binding Properties of the HIV-1 Nucleocapsid Protein Zinc Fingers

Discerning intersecting fusion‐activation pathways in the Nipah virus using machine learning

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