ZF21 protein, a regulator of the disassembly of focal adhesions and cancer metastasis, contains a novel noncanonical pleckstrin homology domain.

Directional migration of adherent cells on an extracellular matrix requires repeated formation and disassembly of focal adhesions (FAs). Directional migration of adherent cells We have identified ZF21 as a regulator of disassembly of FAs and cell migration, and increased expression of the gene has been linked to metastatic colon cancer. ZF21 is a member of a protein family characterized by the presence of the FYVE domain, which is conserved among Fab1p, YOPB, Vps27p, and EEA1 proteins, and has been shown to mediate the binding of such proteins to phosphoinositides in the lipid layers of cell membranes.

Structural basis for the recognition of nucleophosmin-anaplastic lymphoma kinase oncoprotein by the phosphotyrosine binding domain of Suc1-associated neurotrophic factor-induced tyrosine-phosphorylated target-2.

The nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) fusion oncoprotein, formed by the t(2;5) chromosomal translocation in anaplastic large-cell lymphomas, has constitutive tyrosine kinase activity and interacts with a number of signaling molecules. One of the interacting partners of NPM-ALK is the adaptor protein, Suc1-associated neurotrophic factor-induced tyrosine-phosphorylated target (SNT), and mutations that deprive NPM-ALK of all three of the SNT-binding sites significantly reduced the transforming activity. In this study, the interactions of the three binding sites in NPM-ALK with the phosphotyrosine binding (PTB) domain of SNT-2 were analyzed.

The NMR solution structures of the five constituent cold-shock domains (CSD) of the human UNR (upstream of N-ras) protein.

Upon cold shock, the amounts of most proteins dramatically decrease from normal levels, but those of cold shock proteins (CSPs) and proteins containing cold-shock domains (CSDs) greatly increase. Although their biological function is still not completely clear, cold-shock proteins might control translation via RNA chaperoning. Many cold-shock proteins contain the motifs (Y/F)GFI and (V/F)(V/F)H, which are known as ribonucleoprotein (RNP)-1 and RNP-2 motifs implicated in RNA/DNA binding.

NMR solution structures of actin depolymerizing factor homology domains.

Actin is one of the most conserved proteins in nature. Its assembly and disassembly are regulated by many proteins, including the family of actin-depolymerizing factor homology (ADF-H) domains. ADF-H domains can be divided into five classes: ADF/cofilin, glia maturation factor (GMF), coactosin, twinfilin, and Abp1/drebrin.

Functional and structural basis of the nuclear localization signal in the ZIC3 zinc finger domain.

Disruptions in ZIC3 cause heterotaxy, a congenital anomaly of the left-right axis. ZIC3 encodes a nuclear protein with a zinc finger (ZF) domain that contains five tandem C2H2 ZF motifs. Missense mutations in the first ZF motif (ZF1) result in defective nuclear localization, which may underlie the pathogenesis of heterotaxy.

Structure of the C-terminal phosphotyrosine interaction domain of Fe65L1 complexed with the cytoplasmic tail of amyloid precursor protein reveals a novel peptide binding mode.

Fe65L1, a member of the Fe65 family, is an adaptor protein that interacts with the cytoplasmic domain of Alzheimer amyloid precursor protein (APP) through its C-terminal phosphotyrosine interaction/phosphotyrosine binding (PID/PTB) domain. In the present study, the solution structures of the C-terminal PID domain of mouse Fe65L1, alone and in complex with a 32-mer peptide (DAAVTPEERHLSKMQQNGYENPTYKFFEQMQN) derived from the cytoplasmic domain of APP, were determined using NMR spectroscopy. The C-terminal PID domain of Fe65L1 alone exhibits a canonical PID/PTB fold, whereas the complex structure reveals a novel mode of peptide binding.

Structural basis for controlling the dimerization and stability of the WW domains of an atypical subfamily.

The second WW domain in mammalian Salvador protein (SAV1 WW2) is quite atypical, as it forms a beta-clam-like homodimer. The second WW domain in human MAGI1 (membrane associated guanylate kinase, WW and PDZ domain containing 1) (MAGI1 WW2) shares high sequence similarity with SAV1 WW2, suggesting comparable dimerization. However, an analytical ultracentrifugation study revealed that MAGI1 WW2 (Leu355-Pro390) chiefly exists as a monomer at low protein concentrations, with an association constant of 1.

KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies.

The recent expansion of structural genomics has increased the demands for quick and accurate protein structure determination by NMR spectroscopy. The conventional strategy without an automated protocol can no longer satisfy the needs of high-throughput application to a large number of proteins, with each data set including many NMR spectra, chemical shifts, NOE assignments, and calculated structures. We have developed the new software KUJIRA, a package of integrated modules for the systematic and interactive analysis of NMR data, which is designed to reduce the tediousness of organizing and manipulating a large number of NMR data sets.

Solution structure of an atypical WW domain in a novel beta-clam-like dimeric form.

The WW domain is known as one of the smallest protein modules with a triple-stranded beta-sheet fold. Here, we present the solution structure of the second WW domain from the mouse salvador homolog 1 protein. This WW domain forms a homodimer with a beta-clam-like motif, as evidenced by size exclusion chromatography, analytical ultracentrifugation and NMR spectroscopy.

Global structure analysis of acid-unfolded myoglobin with consideration to effects of intermolecular coulomb repulsion on solution X-ray scattering.

To obtain information on the global structure of protein in the acid-unfolded (AU) state, the structure of apomyoglobin (apoMb) was analyzed by using the solution X-ray scattering (SXS) method. SXS profiles were obtained over a wide range of protein concentrations, 1-18 mg mL-1, under strongly acidic conditions. From analysis of the SXS profile extrapolated to a zero protein concentration, the mean square radius, Rsq, of AU-apoMb at 20 mM HCl was estimated to be 4.

Contribution of solvent water to the solution X-ray scattering profile of proteins.

A theoretical framework is presented to analyze how solvent water contributes to the X-ray scattering profile of protein solution. Molecular dynamics simulations were carried out on pure water and an aqueous solution of myoglobin to determine the spatial distribution of water molecules in each of them. Their solution X-ray scattering (SXS) profiles were numerically evaluated with obtained atomic-coordinate data.