Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain

Many important protein-protein interactions are mediated by peptide recognition modular domains, such as the Src homology 3 (SH3), SH2, PDZ, and WW domains. Characterizing the interaction interface of domain-peptide complexes and predicting binding specificity for modular domains are critical for deciphering protein-protein interaction networks. Here, we propose the use of an energetic decomposition analysis to characterize domain-peptide interactions and the molecular interaction energy components (MIECs), including van der Waals, electrostatic, and desolvation energy between residue pairs on the binding interface. We show a proof-of-concept study on the amphiphysin-1 SH3 domain interacting with its peptide ligands. The structures of the human amphiphysin-1 SH3 domain complexed with 884 peptides were first modeled using virtual mutagenesis and optimized by molecular mechanics (MM) minimization. Next, the MIECs between domain and peptide residues were computed using the MM/generalized Born decomposition analysis. We conducted two types of statistical analyses on the MIECs to demonstrate their usefulness for predicting binding affinities of peptides and for classifying peptides into binder and non-binder categories. First, combining partial least squares analysis and genetic algorithm, we fitted linear regression models between the MIECs and the peptide binding affinities on the training data set. These models were then used to predict binding affinities for peptides in the test data set; the predicted values have a correlation coefficient of 0.81 and an unsigned mean error of 0.39 compared with the experimentally measured ones. The partial least squares-genetic algorithm analysis on the MIECs revealed the critical interactions for the binding specificity of the amphiphysin-1 SH3 domain. Next, a support vector machine (SVM) was employed to build classification models based on the MIECs of peptides in the training set. A rigorous training-validation procedure was used to assess the performances of different kernel functions in SVM and different combinations of the MIECs. The best SVM classifier gave satisfactory predictions for the test set, indicated by average prediction accuracy rates of 78% and 91% for the binding and non-binding peptides, respectively. We also showed that the performance of our approach on both binding affinity prediction and binder/non-binder classification was superior to the performances of the conventional MM/Poisson-Boltzmann solvent-accessible surface area and MM/generalized Born solvent-accessible surface area calculations. Our study demonstrates that the analysis of the MIECs between peptides and the SH3 domain can successfully characterize the binding interface, and it provides a framework to derive integrated prediction models for different domain-peptide systems.     

Neurotrophin receptor homolog-2 regulates nerve growth factor signaling

The neurotrophin receptor homolog (NRH2) is closely related to the p75 neurotrophin receptor (p75NTR); however, its function and role in neurotrophin signaling are unclear. NRH2 does not bind to nerve growth factor (NGF), however, is able to form a receptor complex with tropomyosin-related kinase receptor A (TrkA) and to generate high-affinity NGF binding sites. Despite this, the mechanisms underpinning the interaction between NRH2 and TrkA remain unknown. Here, we identify that the intracellular domain of NRH2 is required to form an association with TrkA. Our data suggest extensive intracellular interaction between NRH2 and TrkA, as either the juxtamembrane or death domain regions of NRH2 are sufficient for interaction with TrkA. In addition, we demonstrate that TrkA signaling is dramatically influenced by the co-expression of NRH2. Importantly, NRH2 did not influence all downstream TrkA signaling pathways, but rather exerted a specific effect, enhancing src homology 2 domain-containing transforming protein (Shc) activation. Moreover, downstream of Shc, the co-expression of NRH2 resulted in TrkA specifically modulating mitogen-activated protein kinase pathway activation, but not the phosphatidylinositol 3-kinase/Akt pathway. These results indicate that NRH2 utilizes intracellular mechanisms to not only regulate NGF binding to TrkA, but also specifically modulate TrkA receptor signaling, thus adding further layers of complexity and specificity to neurotrophin signaling.     

Refining molluscan characters: morphology, character coding and a phylogeny of the Caenogastropoda

Midgut morphology of gastropod molluscs has been underutilized as a resource of characters for phylogenetic analysis. The exclusion of these features reflects the inference that they will be uninformative in determining phylogenetic relationships because they are functionally correlated. In general, it has been hypothesized that the style sac form of midgut is an adaptation to microphagy and becomes secondarily simplified in taxa that have adopted a macrophagous/carnivorous habit with a corresponding increase in extracellular digestion (i.e. radular trituration, gizzards and/or foregut glands). This assumption has resulted in the formulation of adaptive scenarios concerning gastropod alimentary systems, which are mapped onto phylogenetic hypotheses derived from other characters. However, any conclusions regarding phylogenetic utility, and therefore homology, must be realized within a cladistic context. For this analysis, a multi‐organ system anatomical data set was assembled for 16 caenogastropods and two outgroups. The data matrix comprises 64 characters and includes many systems poorly represented in previous broad‐based comparative surveys, such as the alimentary and reno‐pericardial systems. In addition, several taxa were included for which no comprehensive anatomical studies have been available (Cyclophoroidea, Ptenoglossa). Phylogenetic analysis with NONA 1.6 resulted in two most‐parsimonious trees with length 188, CI = 0.53 and RI = 0.63, differing only in the placement of Prunum apicinum and Conus jaspideus. The topology of the strict consensus (Macleaniella Theodoxus((Neocyclotus Marisa)((Lampanella((Petaloconchus Strombus)(Crepidula Bithyia)))(Littorina(Neverita(Cypraea(Nitidiscala(Panarona(Prunum Conus(Ilyanassa Urosalpinx)))))))))), is largely congruent with several independent estimates based on both morphological and molecular data, supporting caenogastropod monophyly and monphyly of the Architaenioglossa, Sorbeoconcha and Neogastropoda. To evaluate phylogenetic utility of the midgut, a broad sampling of taxa was included representing a diversity of feeding modes, food preferences and alimentary morphologies. Character optimization revealed that the evolution of midgut structure is highly mosaic, cutting broadly across patterns of feeding, diet and foregut complexity, to a degree previously unappreciated. In addition, features from the foregut (subradular organ, oesophageal folding) and midgut (position of gastric shield) are broadly distributed among large clades of caenogastropods, providing critical basal synapomorphies within the group. This demonstrates that the gut is an unexploited resource for important and informative characters in higher order systematics of caenogastropods. © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society, 2003, 137 , 447–554.     

Analysis of the Glycyrrhizic Acid-Binding Sites with Phage Display

Phages that expose peptides specifically interacting with glycyrrhizic acid (GA) were selected from a phage peptide library by affinity selection and ELISA. Amino acid sequence analysis of the selected peptides and human proteins with the SIM program revealed homology to tyrosine protein kinases, serine/threonine protein kinases, tyrosine phosphatases, and some receptors. Analysis of the peptide and virus protein sequences with the BLAST program showed that GA has affinity for various surface proteins of several human viruses such as HIV-1, hepatitis C virus, and herpesviruses.     

The Chemoreceptive Lattice Organs in Cypris Larvae Develop from Naupliar Setae (Thecostraca: Cirripedia, Ascothoracida and Facetotecta)

Lattice organs are peculiar chemoreceptors found only in the Crustacea Thecostraca (Facetotecta, Ascothoracida, Cirripedia). In these taxa, five pairs occur in the head shield (carapace) of the terminal larval instar (y-cyprid, ascothoracid larva, cyprid), which is the settlement stage. Lattice organs represent an autapomorphy for the Thecostraca but their evolutionary origin and possible homologues in other Crustacea remain obscure. We have used scanning electron microscopy to describe the setation pattern of the head shield in late nauplii of one species of Ascothoracida, one species of Facetotecta and several species of the Cirripedia Thoracica, Acrothoracica, and Rhizocephala. The naupliar head shield always carries two pairs setae situated anteriorly near the midline. Each of these setae carry a single pore, and positional, structural and ontogenetic evidence show that these setae are homologous in all the examined species and that they represent precursors of the two anterior pairs of lattice organs of the succeeding larval stage, viz., the ascothoracid larva (Ascothoracida), y-cyprid (Facetotecta), and cyprid (Cirripedia). This leads us to infer that lattice organs are among the most highly modified sensilla in all Crustacea and they have in most cases lost all external resemblance to a seta. The nauplii of the Rhizocephala carry an additional three pairs of setae situated more posteriorly on the head shield and they could be precursors of the three posterior pairs of lattice organs. All other species examined lack these posterior setae, except the Facetotecta which have one posteriorly situated pair.     

外加紫杉醇对悬浮培养东北红豆杉细胞的诱导效应

研究表明外加紫杉醇能够诱导悬浮培养的东北红豆杉(Taxus cuspidata)细胞总DNA发生梯带化降解。利用mRNA差异显示技术比较了紫杉醇诱导凋亡与不诱导凋亡的东北红豆杉细胞基因表达的差异,得到了8个特异表达的cDNA克隆,经Northern杂交证实其中3个在不发生凋亡的细胞中表达,5个在凋亡的细胞中表达。对这8个cDNA克隆单向序列测定后,与GenBank/EMBL/DDBJ中同源序列进行了比较,结果表明：1个cDNA片段与拟南芥中ABA应答蛋白基因的保守区有86%的同源性;2个cDNA片段与番茄内切壳聚糖酶前体基因的保守区有50%的同源性;其他5个cDNA片段无明显的同源基因,可能是新基因。     

Ancient repeat sequence derived from U6 snRNA in primate genomes

LINE-1 (L1) is the most represented sequence of the human genome (17% of the total genomic mass). Moreover, it has been proposed for many years and demonstrated more recently that L1 has contributed to the mobilization of pseudogenes, small non-coding RNAs, such as tRNAs or snRNAs, and SINEs. In fact, it is estimated that L1 is responsible for at least 30% of our genome. The mobilization of non-L1 RNAs can occur in different ways and at different steps of the retrotransposition cycle. Here, by looking at U6 snRNA sequences mobilized by L1, we have observed an ancient repeat sequence derived from U6, present in all primate genomes. We were able to trace its origin in Euarchota genomes, most likely during the divergence of the four orders; Scandentia, Dermoptera, Plesiadapiform (extinct) and Primates.     

Substrate Selectivity of Glycerol-3-phosphate Acyl Transferase in Rice

Substrate selectivity of glycerol-3-phosphate acyltransferase （EC 2. 3. 1. 15） of rice （Oryza sativa L.） was explored in a comparative study of acyltransferases from seven plant species. In vitro labeling of acyl carrier protein （ACP） with ^14C or 3H showed that acyltransferase from chill-sensitive plants, such as rice that uses either oleic （18：1） or palmitic acid （16：0） as acyl donor at comparable rates, displays lower selectivity than the enzyme from chill-resistant plants, such as spinach, which preferentially uses oleic acid （18：1） rather than palmitic acid （16：0） as an acyl donor. This may be a result of the size and character of the substrate-binding pocket of acyltransferase. Homology modeling and protein structure-based sequence alignment of acyltransferases revealed that proteins from either chill-sensitive or chill-tolerant plants shared a highly conserved domain containing the proposed substrate-binding pocket. However, the aligned residues surrounding the substrate-binding pocket are highly heterogeneous and may have an influence mainly on the size of the substrate binding pockets of acyltransferases. The substrate selectivity of acyltransferase of rice can be improved by enlarging the substrate-binding pocket using molecular biological methods.     

Ternary oxovanadium(IV) complexes of ONO-donor Schiff base and polypyridyl derivatives as protein tyrosine phosphatase inhibitors: synthesis, characterization, and biological activities

Abstract  A series of oxovanadium complexes with mixed ligands, a tridentate ONO-donor Schiff base ligand [viz., salicylidene anthranilic acid (SAA)], and a bidentate NN ligand [viz., 2,2′-bipyridine (bpy), 1,10-phenanthroline (phen), dipyrido[3,2-d:2′,3′-f]quinoxaline (dpq), dipyrido[3,2-a:2′,3′-c]phenazine (dppz), or 7-methyldipyrido[3,2-a:2′,3′-c]phenazine (dppm)], have been synthesized and characterized by elemental analysis, electrospray ionization mass spectrometry, UV–vis spectroscopy, Fourier transform IR spectroscopy, EPR spectroscopy, and X-ray crystallography. Crystal structures of both complexes, [V^IVO(SAA)(bpy)]·0.25bpy and [V^IVO(SAA)(phen)]·0.33H₂O, reveal that oxovanadium(IV) is coordinated with one nitrogen and two oxygen atoms from the Schiff base and two nitrogen atoms from the bidentate planar ligands, in a distorted octahedral geometry (VO₃N₃). The oxidation state of V(IV) with d ¹ configuration was confirmed by EPR spectroscopy. The speciation of VO–SAA–bpy in aqueous solution was investigated by potentiomtreic pH titrations, and the results revealed that the main species are two ternary complexes at a pH range of 7.0–7.4, and one is the isolated crystalline complex. The complexes have been found to be potent inhibitors against human protein tyrosine phosphatase 1B (PTP1B) (IC₅₀ approximately 30–61 nM), T-cell protein tyrosine phosphatase (TCPTP), and Src homology phosphatase 1 (SHP-1) in vitro. Interestingly, the [V^IVO(SAA)(bpy)] complex selectively inhibits PTP1B over the other two phosphatases (approximate ninefold selectivity against SHP-1 and about twofold selectivity against TCPTP). Kinetics assays suggest that the complexes inhibit PTP1B in a competitive and reversible manner. These suggest that the complexes may be promising candidates as novel antidiabetic agents. Graphical Abstract   Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Homology modeling of phosphoryl thymidine kinase of enterohemorrhagic Escherichia coli OH: 157

Enterohemorrhagic Escherichia coli (EHEC) are source of emerging infectious disease in India. Escherichia coli O157:H7 is an EHEC strain showing multiple antibiotic resistances and the cause of infantile diarrhea and hemolytic uremic syndrome worldwide. A novel strategy to counteract multiple antibiotic resistant organisms is to design drugs which specifically target metabolic pathways such as thiamine biosynthetic pathways found exclusively in prokaryotes. Homology modeling was used for model building of a terminal thiamine biosynthesis enzyme phosphoryl thymidine kinase (Thi E) using Geno3D, Swiss Model and Modeller. The best model was selected based on overall stereochemical quality. The potential ligand binding sites in the model were identified by CASTp server. The validated theoretical model of the 3D structure of the thiE protein of E. coli O157:H7 was predicted using a thiamine phosphate pyrophosphatase from Pyrococcus furiosus (PDB ID: 1X13_A) as template. The active pockets of ligand binding sites in the enzyme were identified. In this study, phosphoryl thymidine kinase (thi E), a terminal enzyme in the thiamine biosynthesis pathway in the pathogen has been modeled to be used in future as a potential drug target by the design of suitable inhibitors.