Mechanisms that fine tune the activity of potassium channels are crucial to a cell's ability to integrate and respond to a plethora of internal and external signals. Peptide toxins from venomous creatures have served as vital tools to define the molecular mechanisms underlying K ϩ channel function (1, 2). It has been suggested that toxins evolved from endogenous genes that function in normal cellular pathways (3, 4). Indeed, venomous creatures possess toxins with homology to several proteins, including acetylcholinesterases (5), phospholipases (6, 7), nerve growth factor (8), endothelins (9), Lynx-1 (10, 11), Kunitz-type serine protease inhibitors (12), and the ion channel regulatory (ICR) 5 domains of cysteinerich secretory proteins (CRISPs) (3,13,14). Mammalian proteins containing toxin-like domains (TxDs) that block K ϩ channels have not been characterized previously.BgK, a 37-residue peptide toxin from the sea anemone Bunodosoma granulifera (15,16), and ShK, a 35-residue peptide toxin from the sea anemone Stichodactyla helianthus (17,18) are potent inhibitors of K ϩ channels. The Simple Modular Architecture Research Tool (SMART) (available on the World Wide Web) predicts the existence of a large superfamily of proteins that contain domains (referred to as ShKT domains in the SMART data base) resembling these two toxins (Fig. 1A). Many of these proteins (ϳ70 proteins) are metallopeptidases, whereas others are prolyl-4-hydroxylases, tyrosinases, peroxidases, oxidoreductases, or proteins containing epidermal growth factor-like domains, thrombospondin-type repeats, or trypsin-like serine protease domains (Fig. 1B). The only human protein containing a ShKT domain in the SMART data base is MMP23 (matrix metalloprotease 23). Matrix metalloproteases belong to the metzincin superfamily and play important roles in tissue remodeling, development, and the immune response (19).MMP23 is expressed in many tissues and exists either as a type II transmembrane protein in ER/nuclear membranes or as a secreted form following cleavage of the RRRRY motif just N-terminal to the Zn 2ϩ -dependent metalloprotease domain (20 -23). The ShKT domain of MMP23 (MMP23 TxD ) lies between the metalloprotease domain and an immunoglobulinlike cell adhesion molecule (IgCAM) domain ( Fig. 2A). MMP23 has been implicated in prostate, brain, and breast cancer (24 -26). In humans, two related sequences, MMP23A (a pseudogene) and MMP23B, are co-located on chromosome 1p36 (20). We have investigated MMP23 to gain insight into the structure and physiological functions of ShKT toxin domains and describe the solution structure of the MMP23 TxD domain, its * This work was supported, in whole or in part, by National Institutes of Health

MS-271, produced by Streptomyces sp. M-271, is a lasso peptide natural product comprising 21 amino acid residues with a d-tryptophan at its C terminus. Because lasso peptides are ribosomal peptides, the biosynthesis of MS-271, especially the mechanism of d-Trp introduction, is of great interest. The MS-271 biosynthetic gene cluster was identified by draft genome sequencing of the MS-271 producer, and it was revealed that the precursor peptide contains all 21 amino acid residues including the C-terminal tryptophan. This suggested that the d-Trp residue is introduced by epimerization. Genes for modification enzymes such as a macrolactam synthetase (mslC), precursor peptide recognition element (mslB1), cysteine protease (mslB2), disulfide oxidoreductases (mslE, mslF), and a protein of unknown function (mslH) were found in the flanking region of the precursor peptide gene. Although obvious epimerase genes were absent in the cluster, heterologous expression of the putative MS-271 cluster in Streptomyces lividans showed that it contains all the necessary genes for MS-271 production including a gene for a new peptide epimerase. Furthermore, a gene-deletion experiment indicated that MslB1, -B2, -C and -H were indispensable for MS-271 production and that some interactions of the biosynthetic enzymes were essential for the biosynthesis of MS-271.

Background: Many proteins contain disordered regions that lack fixed three-dimensional (3D) structure under physiological conditions but have important biological functions. Prediction of disordered regions in protein sequences is important for understanding protein function and in high-throughput determination of protein structures. Machine learning techniques, including neural networks and support vector machines have been widely used in such predictions. Predictors designed for long disordered regions are usually less successful in predicting short disordered regions. Combining prediction of short and long disordered regions will dramatically increase the complexity of the prediction algorithm and make the predictor unsuitable for large-scale applications. Efficient batch prediction of long disordered regions alone is of greater interest in large-scale proteome studies.

The biosynthesis of d-tryptophan containing lasso peptide MS-271 involves the epimerization of a ribosomal peptide MslA catalyzed by a novel class of metal- and cofactor-independent peptide epimerase MslH.

Receiver domains are key molecular switches in bacterial signaling. Structural studies have shown that the receiver domain of the nitrogen regulatory protein C (NtrC) exists in a conformational equilibrium encompassing both inactive and active states, with phosphorylation of Asp54 allosterically shifting the equilibrium towards the active state. To analyze dynamical fluctuations and correlations in NtrC as it undergoes activation, we have applied a coarse-grained dynamics algorithm using elastic network models. Normal mode analysis reveals possible dynamical pathways for the transition of NtrC from the inactive state to the active state. The diagonalized correlation between the inactive and the active (phosphorylated) state shows that most correlated motions occur around the active site of Asp54 and in the region Thr82 to Tyr101. This indicates a coupled correlation of dynamics in the "Thr82-Tyr101" motion. With phosphorylation inducing significant flexibility changes around the active site and alpha3 and alpha4 helices, we find that this activation makes the active-site region and the loops of alpha3/beta4 and alpha4/beta5 more stable. This means that phosphorylation entropically favors the receiver domain in its active state, and the induced conformational changes occur in an allosteric manner. Analyses of the local flexibility and long-range correlated motion also suggest a dynamics criterion for determining the allosteric cooperativity of NtrC, and may be applicable to other proteins.