Migfilin, a molecular switch in regulation of integrin activation.

The linkage of heterodimeric (alpha/beta) integrin receptors with their extracellular matrix ligands and intracellular actin cytoskeleton is a fundamental step for controlling cell adhesion and migration. Binding of the actin-linking protein, talin, to integrin beta cytoplasmic tails (CTs) induces high affinity ligand binding (integrin activation), whereas binding of another actin-linking protein, filamin, to the integrin beta CTs negatively regulates this process by blocking the talin-integrin interaction. Here we show structurally that migfilin, a novel cytoskeletal adaptor highly enriched in the integrin adhesion sites, strongly interacts with the same region in filamin where integrin beta CTs bind. We further demonstrate that the migfilin interaction dissociates filamin from integrin and promotes the talin/integrin binding and integrin activation. Migfilin thus acts as a molecular switch to disconnect filamin from integrin for regulating integrin activation and dynamics of extracellular matrix-actin linkage.

Molecular basis for PKR activation by PACT or dsRNA.

The mammalian protein kinase PKR is a critical component of the innate immune response against virus infection. Its cellular actions are mediated by modulating cell signaling and translational regulation. To be enzymatically active, latent PKR needs to be activated by binding to one of its activators, dsRNA or PACT protein. Although the structures of the N-terminal dsRNA-binding domain and the C-terminal kinase domain of PKR have been separately determined, the mode of activation of the enzyme remains unknown. To address this problem, we used biochemical, genetic, and NMR analyses to identify the PACT-binding motif (PBM) located in the kinase domain and demonstrated an intramolecular interaction between PBM and dsRNA-binding domain. This interaction is responsible for keeping PKR in an inactive conformation, because its disruption by point mutations of appropriate residues produced constitutively active PKR. Furthermore, a short decoy peptide, representing PBM, was able to activate PKR by interfering with the intramolecular interaction. These observations suggest a model for PKR activation upon binding of dsRNA or PACT.

Three-dimensional correlated accordion NMR spectroscopy of proteins.

A major step toward the protein structure determination by nuclear magnetic resonance (NMR) spectroscopy is the assignment of multidimensional NMR signals that provide through-bond and through-space inter-atomic correlations. Ambiguities often occur during the assignment process due to resonance degeneracy, which challenges high resolution and larger size protein structure determination. Here, we present a method that will significantly improve the efficiency and accuracy of the NMR signal assignment. The method is based on a correlated accordion principle that, when incorporated into conventional three-dimensional (3D) heteronuclear NMR experiments, allows the retrieval of additional frequency correlation information at high resolution. We show that 3D spectra derived from this method are as effective as the impractical high resolution four-dimensional (4D) spectra with substantially reduced signal ambiguity as compared to their conventional counterparts. The approach promises increased accuracy and size of protein structures determined by NMR.

Protein Backbone 1H(N)-13Calpha and 15N-13Calpha residual dipolar and J couplings: new constraints for NMR structure determination.

A simple, sensitivity-enhanced experiment was devised for accurate measurement of backbone 15N-13Calpha and 1HN-13Calpha couplings in proteins. The measured residual dipolar couplings 2DHCA, 1DNCA, 3DHCA, and 2DNCA for protein GB1 display very good agreement with the refined NMR structure (PDB code: 3GB1). A Karplus-type relationship between the one-bond 1JNCA couplings and the backbone dihedral psi angles holds, and on the basis of the two-bond 2JNCA couplings a secondary structure index can be established.

Sensitivity-enhanced IPAP experiments for measuring one-bond 13C'-13Calpha and 13Calpha-1Halpha residual dipolar couplings in proteins.

Sensitivity-enhanced 2D IPAP experiments using the accordion principle for measuring one-bond 13C'-13Calpha and 1Halpha-13Calpha dipolar couplings in proteins are presented. The resolution of the resulting spectra is identical to that of the decoupled HSQC spectra and the sensitivity of the corresponding 1D acquisitions are only slightly lower than those obtained with 3D HNCO and 3D HN(COCA)HA pulse sequences due to an additional delay 2Delta. For cases of limited resolution in the 2D 15N-1HN HSQC spectrum the current pulse sequences can easily be modified into 3D versions by introducing a poorly digitized third dimension, if so desired. The experiments described here are a valuable addition to the suites available for determination of residual dipolar couplings in biological systems.

Insights into conformation and dynamics of protein GB1 during folding and unfolding by NMR.

Understanding protein stability requires characterization of structural determinants of the folded and unfolded states. Many proteins are capable of populating partially folded states under specific solution conditions. Occasionally, coexistence of the folded and an unfolded state under non- or mildly denaturing conditions can be observed by NMR, allowing us to structurally probe these states under identical conditions. Here we report on a destabilized mutant of the B1 domain of protein G (GB1) whose equilibrium unfolding was systematically investigated. Backbone amide residual dipolar couplings (RDCs), the tryptophan Nepsilon-H resonance and the amide nitrogen transverse relaxation rates (R2s) for varying pH values and different temperatures were measured. The backbone amide RDCs indicate that prior to complete unfolding, two melting hot spots are formed at the turn around T11, L12 and K13 and the N terminus of the helix at A24 and T25. The RDCs for the low pH, thermally unfolded state of GB1 are very small and do not indicate the presence of any native-like structure. Amide nitrogen transverse relaxation rates for GB1 in the folded state at different temperatures exhibit large contributions from exchange processes and the associated dynamics display considerable heterogeneity. Our data provide clear evidence for intermediate conformations and multi-state equilibrium un/folding for this GB1 variant.

Simultaneous and accurate determination of one-bond (15)N-(13)C' and two-bond (1)H(N)--(13)C' dipolar couplings.

Using the echo-anti-echo manipulation, the 15N-1HN cross-peaks split in the E.COSY spectrum by the 13CO couplings are separated into different, distinct regions in the HSQC spectrum. From this novel E.COSY 15N-1HN HSQC spectrum, the small one-bond 15N-13C' and two-bond 1HN-13C' residual dipolar couplings can be extracted easily and accurately. These dipolar couplings provide a set of important long-range constraints for protein structure determination.

Sensitivity-enhanced 2D IPAP, TROSY-anti-TROSY, and E.COSY experiments: alternatives for measuring dipolar 15N-1HN couplings.

Sensitivity-enhanced versions of the IPAP, TROSY-anti-TROSY, and E.COSY experiments for measuring one-bond 15N-1HN couplings are presented. Together with the previously developed sensitivity-enhanced E.COSY-type HSQC experiment they comprise a suite of sensitivity-enhanced experiments that allows one to chose the optimal spectrum for accurate measurement of one-bond 15N-1HN residual dipolar couplings in proteins. Since one-bond 15N-1HN residual dipolar couplings play uniquely important roles in structural NMR, these additional methods provide further tools for improving structure determination of proteins and other biological macromolecules.

Reduction of pentavalent antimony by trypanothione and formation of a binary and ternary complex of antimony(III) and trypanothione.

Several pentavalent antimony compounds have been used for the treatment of leishmaniasis for decades. However, the mechanism of these antimony drugs still remains unclear. One of their targets is thought to be trypanothione, a major low molecular mass thiol inside the parasite. We show that pentavalent antimony (Sb(V)) can be rapidly reduced to its trivalent state by trypanothione at mildly acidic conditions and 310 K ( k=4.42 M(-1) x min(-1) at pH 6.4), and that Sb(III) can be bound to trypanothione to form an Sb(III)-trypanothione complex. NMR data demonstrate that Sb(III) binds to trypanothione at the two thiolates of the cysteine residues, and that the binding is pH dependent and is strongest at biological pH with a stability constant log K=23.6 at 298 K (0.1 M NaNO(3)). The addition of low molecular monothiol ligands such as glutathione and cysteine to the Sb(III)-trypanothione complex results in the formation of a ternary complex. Thiolates from both trypanothione and monothiol bind to the Sb(III) center. The formation of the ternary complex is important, as the antileishmanial properties of the drugs are probably due to a complex between of Sb(III)-trypanothione and enzymes. Although thermodynamically stable, the complex is kinetically labile and the free and bound forms of thiolates exchange on the (1)H NMR timescale. Such a facile exchange may be crucial for the transport of Sb(III) within parasites.

Sensitivity-enhanced E.COSY-type HSQC experiments for accurate measurements of one-bond 15N-1H(N) and 15N-13C' and two-bond 13C'-1H(N) residual dipolar couplings in proteins.

Novel E.COSY-type HSQC experiments are presented for the accurate measurement of one-bond 15N-1H(N) and 15N-13C(') and two-bond 13C(')-1H(N) residual dipolar couplings in proteins. Compared with existing experiments, the (delta,J)-E.COSY experiments described here are composed of fewer pulses and the resulting spectra exhibit 1.4 times the sensitivity of coupled HSQC spectra. Since residual dipolar couplings play increasingly important roles in structural NMR, the proposed methods should find wide spread application for structure determination of proteins and other biological macromolecules.

Novel 2D triple-resonance NMR experiments for sequential resonance assignments of proteins.

We present 2D versions of the popular triple resonance HN(CO) CACB, HN(COCA)CACB, HN(CO)CAHA, and HN(COCA) CAHA experiments, commonly used for sequential resonance assignments of proteins. These experiments provide information about correlations between amino proton and nitrogen chemical shifts and the alpha- and beta-carbon and alpha-proton chemical shifts within and between amino acid residues. Using these 2D spectra, sequential resonance assignments of H(N), N, C(alpha), C(beta), and H(alpha) nuclei are easily achieved. The resolution of these spectra is identical to the well-resolved 2D (15)N-(1)H HSQC and H(NCO)CA spectra, with slightly reduced sensitivity compared to their 3D and 4D versions. These types of spectra are ideally suited for exploitation in automated assignment procedures and thereby constitute a fast and efficient means for NMR structural determination of small and medium-sized proteins in solution in structural genomics programs.