HYDRONMR: Prediction of NMR Relaxation of Globular Proteins from Atomic-Level Structures and Hydrodynamic Calculations

Torre, José Garcı́a de la; Huertas, M.L.; Carrasco, Beatriz

doi:10.1006/jmre.2000.2170

Cited by 513 publications

(493 citation statements)

References 41 publications

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“…The uncertainties on the values of the isotropic correlation times are obtained by a Monte‐Carlo simulation procedure implemented in TENSOR2, which assumes that the stochastic fluctuations of the measured relaxation rates are described by their experimental errors. Isotropic correlation time projections were obtained by the program HYDRONMR (Garcia de la Torre et al , 2000). …”

Section: Methodsmentioning

confidence: 99%

Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity

et al. 2016

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TRIM E3 ubiquitin ligases regulate a wide variety of cellular processes and are particularly important during innate immune signalling events. They are characterized by a conserved tripartite motif in their N‐terminal portion which comprises a canonical RING domain, one or two B‐box domains and a coiled‐coil region that mediates ligase dimerization. Self‐association via the coiled‐coil has been suggested to be crucial for catalytic activity of TRIMs; however, the precise molecular mechanism underlying this observation remains elusive. Here, we provide a detailed characterization of the TRIM ligases TRIM25 and TRIM32 and show how their oligomeric state is linked to catalytic activity. The crystal structure of a complex between the TRIM25 RING domain and an ubiquitin‐loaded E2 identifies the structural and mechanistic features that promote a closed E2~Ub conformation to activate the thioester for ubiquitin transfer allowing us to propose a model for the regulation of activity in the full‐length protein. Our data reveal an unexpected diversity in the self‐association mechanism of TRIMs that might be crucial for their biological function.

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Section: Methodsmentioning

confidence: 99%

Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity

et al. 2016

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“…The rotational correlation time τ c of the protein−peptide complex was estimated to be 5 ns, using the software hydroNMR 39 and a structure of chicken Src SH3 bound to a similar peptide [RALPPLPRY, Protein Data Bank (PDB) entry 1RLQ]. 17 The R 2,para H values obtained with eq 3 for peptide nuclei are a population-weighted average of PREs in the free peptide (no PRE) and the bound form, so they were first extrapolated to the 100% bound form of the peptide.…”

Section: ■ Experimental Proceduresmentioning

confidence: 99%

A Focal Adhesion Kinase-Derived Peptide Binds the Src SH3 Domain in Two Orientations, As Demonstrated Using Paramagnetic Nuclear Magnetic Resonance

et al. 2015

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SH3 binding peptides contain polyproline helices and are classified according to their binding orientations as N-to-C-terminal or C-to-N-terminal. We have tested the hypothesis that such a peptide binds in both orientations but with different populations. A focal adhesion kinase (FAK)-derived peptide was tested for its binding orientation on the Src SH3 domain. Paramagnetic tags were introduced at several positions on the SH3 domain, and on the basis of the paramagnetic relaxation enhancements (PREs) of the amide protons, the positions of the paramagnetic centers were determined. Two peptides were synthesized with 13 C-enriched Ala or Pro, at the N-terminal or C-terminal side of the peptide, and the intermolecular PREs were measured. The results provide compelling evidence that the FAK-derived peptide binds the SH3 domain in two orientations. In the major state, the SH3 domain binds the peptide in the N−C orientation, whereas 20% of the time, the peptide binds in the C−N orientation. We conclude that the distinction between N− C and C−N orientations, which is based on crystal structures, might be artificial. The pseudosymmetric nature of the polyproline helix might allow for binding in both orientations in the solution state.

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“…Our DOSY experiments on HBD2 and HBD2 in complex with FX 0.99 (1.51) ---a calculated values were determined using HYDRONMR and monomeric or dimeric X-ray structures of HBD2 (14) . To interpret our data more rigorously, we calculated theoretical correlation times and diffusion coefficients using the program HYDRONMR (52,53) . Monomeric and dimeric X-ray structures of HBD2 (14) were used to approximate the [GAG-HBD2] complexes.…”

Section: Diffusion Coefficients Of Hbd2 and Its Complexes With Gags mentioning

confidence: 99%

Interaction of Human β-Defensin 2 (HBD2) with Glycosaminoglycans

et al. 2010

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Human -defensin 2 (HBD2) is a member of the defensin family of antimicrobial peptides that plays important roles in the innate and adaptive immune system of both vertebrates and invertebrates. In addition to their direct bactericidal action, defensins are also involved in chemotaxis and Toll-like receptor activation. In analogy to chemokine/glycosaminoglycan (GAG) interactions, GAG-defensin complexes are likely to play an important role in chemotaxis and in presenting defensins to their receptors. Using a gel mobility shift assay, we found that HBD2 bound to a range of GAGs including heparin/heparan sulfate (HS), dermatan sulfate (DS) and chondroitin sulfate. We used NMR nESI, nano-electrospray ionization.

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HYDRONMR: Prediction of NMR Relaxation of Globular Proteins from Atomic-Level Structures and Hydrodynamic Calculations

Cited by 513 publications

References 41 publications

Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity

Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity

A Focal Adhesion Kinase-Derived Peptide Binds the Src SH3 Domain in Two Orientations, As Demonstrated Using Paramagnetic Nuclear Magnetic Resonance

Interaction of Human β-Defensin 2 (HBD2) with Glycosaminoglycans

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