MIAX: a new paradigm for modeling biomacromolecular interactions and complex formation in condensed phases

A new paradigm is proposed for modeling biomacromolecular interactions and complex formation in solution (protein-protein interactions so far in this report) that constitutes the scaffold of the automatic system MIAX (acronym for Macromolecular Interaction Assessment X). It combines in a rational way a series of computational methodologies, the goal being the prediction of the most native-like protein complex that may be formed when two isolated (unbound) protein monomers interact in a liquid environment. The overall strategy consists of first inferring putative precomplex structures by identification of binding sites or epitopes on the proteins surfaces and a simultaneous rigid-body docking process using geometric instances alone. Precomplex configurations are defined here as all those decoys the interfaces of which comply substantially with the inferred binding sites and whose free energy values are lower. Retaining all those precomplex configurations with low energies leads to a reasonable number of decoys for which a flexible treatment is amenable. A novel algorithm is introduced here for automatically inferring binding sites in proteins given their 3-D structure. The procedure combines an unsupervised learning algorithm based on the self-organizing map or Kohonen network with a 2-D Fourier spectral analysis. To model interaction, the potential function proposed here plays a central role in the system and is constituted by empirical terms expressing well-characterized factors influencing biomacromolecular interaction processes, essentially electrostatic, van der Waals, and hydrophobic. Each of these procedures is validated by comparing results with observed instances. Finally, the more demanding process of flexible docking is performed in MIAX embedding the potential function in a simulated annealing optimization procedure. Whereas search of the entire configuration hyperspace is a major factor precluding hitherto systems from efficiently modeling macromolecular interaction modes and complex structures, the paradigm presented here may constitute a step forward in the field because it is shown that a rational treatment of the information available from the 3-D structure of the interacting monomers combined with conveniently selected computational techniques can assist to elude search of regions of low probability in configuration space and indeed lead to a highly efficient system oriented to solve this intriguing and fundamental biologic problem.     

Clustering of Human Chromosome Fragments on the Mouse Genome by Chromosome-Mediated Gene Transfer

Pieces of metaphase chromosomes prepared from mouse cells containingneo-tagged human chromosome 7 were transferred to mouse cellswith calcium phosphate to isolate G418-resistant clones. FISHanalysis revealed that the majority of them contained humanDNA at a single site on their genome. These transformants containedSTS markers mapped to various regions of chromosome 7. It isthus suggested that pieces of human chromosomes tend to assembleand integrate on the mouse genome.     

Seasonal and diurnal use of eight different call types by Indian peafowl (<Emphasis Type="Italic">Pavo cristatus</Emphasis>)

The vocal displays of male Indian peafowl (Pavo cristatus) are thought to be sexually selected traits. To clarify the specific call types involved in breeding, as well as to provide basic information on the vocalisations of Indian peafowl, we conducted monthly daytime recordings in a large feral population in Japan. Based on 13,420 records, we identified seven different call types made only by males and six alarm calls uttered by both sexes. Furthermore, we found seasonal and diurnal changes in the calling activity of peafowl. Three of the male call types (keow, ka and hoot-call) were particularly important for breeding, as sexually mature males produced them only during the breeding season, in a similar diurnal pattern to other breeding behaviours. A digital video image relating to the article is available at .     

Monkeys with disabilities: prevalence and severity of congenital limb malformations in <Emphasis Type="Italic">Macaca fuscata</Emphasis> on Awaji Island

The Awajishima Monkey Center (AMC) free-ranging, provisioned population of Japanese macaques has included individuals with congenital limb malformations (CLMs) for at least 40 years. Including new data from this study, 16.1% of AMC infants from 1969 to 2007 (185 of 1,150) were born with CLMs. However, relatively little is known about the demographics of CLMs in the population, particularly the relationships among occurrence and severity of CLMs and age-sex demographics after infancy. In 2004, we conducted a census at AMC. Of the 199 monkeys censused, 34 individuals (17.1%) had CLMs. To estimate the severity of CLMs, we created an index that ranks individuals on a scale of 0 to 1 based on affected and absent limbs and digits. The severity of CLMs varied greatly (index range = 0.01-0.79, mean = 0.29), with similar variation in severity in each age-sex class (Student t-test, P > 0.05).     

Cloning and characterization of Kin5, a novel Tetrahymena ciliary kinesin II

Two Tetrahymena kinesin-like proteins (klps) of the kinesin II subfamily, Kin1 and Kin2, were first identified by Brown et al. [1999: Mol Biol Cell 10: 3081-3096] and shown to be involved in ciliary morphogenesis probably as molecular motors in intraciliary transport (ICT). Using Tetrahymena genomic DNA as a template, we cloned Kin5, another kinesin II subfamily member. Kin5 is upregulated upon deciliation, suggesting that Kin5 is a ciliary protein. Kin5 is most closely related to Osm3, a Caenorhabditis elegans kinesin II; Osm3 and Kin5 have a 56% identity, which rises to 60.4% in the motor domain and a 45% identity in a 60 amino acid region of the C-terminal FERM (4.1, Ezrin, Radixin, Moesin) domain, not present in Kin1 or Kin2, which we hypothesize to be a critical domain either for dimerization or for cargo recognition in ICT. An antibody to a peptide sequence from the tail region of Kin5 localizes in a punctate pattern along the ciliary axoneme, colocalizing with an antibody to the raft protein IFT139. These findings suggest that Kin5 is an ICT motor like Osm3. Osm3 orthologs apparently transport membrane proteins and Kin5 may be the homodimeric kinesin II that performs this function in Tetrahymena cilia.     

Production of multiple extracellular enzyme activities by novel submerged culture of <Emphasis Type="Italic">Aspergillus kawachii</Emphasis> for ethanol production from raw cassava flour

Cassava is a starch-containing root crop that is widely used as a raw material in a variety of industrial applications, most recently in the production of fuel ethanol. In the present study, ethanol production from raw (uncooked) cassava flour by simultaneous saccharification and fermentation (SSF) using a preparation consisting of multiple enzyme activities from Aspergillus kawachii FS005 was investigated. The multi-activity preparation was obtained from a novel submerged fermentation broth of A. kawachii FS005 grown on unmilled crude barley as a carbon source. The preparation was found to consist of glucoamylase, acid-stable α-amylase, acid carboxypeptidase, acid protease, cellulase and xylanase activities, and exhibited glucose and free amino nitrogen (FAN) production rates of 37.7 and 118.7 mg/l/h, respectively, during A. kawachii FS005-mediated saccharification of uncooked raw cassava flour. Ethanol production from 18.2% (w/v) dry uncooked solids of raw cassava flour by SSF with the multi-activity enzyme preparation yielded 9.0% (v/v) of ethanol and 92.3% fermentation efficiency. A feasibility study for ethanol production by SSF with a two-step mash using raw cassava flour and the multi-activity enzyme preparation manufactured on-site was verified on a pilot plant scale. The enzyme preparation obtained from the A. kawachii FS005 culture broth exhibited glucose and FAN production rates of 41.1 and 135.5 mg/l/h, respectively. SSF performed in a mash volume of about 1,612 l containing 20.6% (w/v) dry raw cassava solids and 106 l of on-site manufactured A. kawachii FS005 culture broth yielded 10.3% (v/v) ethanol and a fermentation efficiency of 92.7%.     

Isolation of mitochondrial and plastid ftsZ genes and analysis of the organelle targeting sequence in the diatom Chaetoceros neogracile (Diatoms,Bacillariophyceae)

Mitochondria and plastids multiply by division in eukaryotic cells. Recently, the eukaryotic homolog of the bacterial cell division protein FtsZ was identified and shown to play an important role in the organelle division process inside the inner membrane. To explore the evolution of FtsZ proteins, and to accumulate data on the protein import system in mitochondria and plastids of the red algal lineage, one mitochondrial and three plastid ftsZ genes were isolated from the diatom Chaetoceros neogracile, whose plastids were acquired by secondary endosymbiotic uptake of a red alga. Protein import into organelles depends on the N‐terminal organelle targeting sequences. N‐terminal bipartite presequences consisting of an endoplasmic reticulum signal peptide and a plastid transit peptide are required for protein import into diatom plastids. To characterize the organelle targeting peptides of C. neogracile, we observed the localization of each green fluorescent protein‐tagged predicted organelle targeting peptide in cultured tobacco cells and diatom cells. Our data suggested that each targeting sequences functioned both in tobacco cultured cells and diatom cells.     

Differential regulation of intracellular redox state by extracellular matrix proteins in glomerular mesangial cells: potential role in diabetic nephropathy

Advanced diabetic nephropathy is characterized by abnormal synthesis of extracellular matrix (ECM) proteins, such as collagen I (COL I). The present experiments were designed to test the hypothesis that the presence of abnormal ECM proteins may be responsible for increased generation of reactive oxygen species (ROS) that are thought to have an important role in the pathogenesis of diabetic nephropathy. SV40 MES 13 murine mesangial cells were plated on COL I or collagen IV (COL IV) for 3 h at 5.5 or 25 mM D-glucose concentration. Increased intracellular ROS generation and reduced intracellular nitric oxide (NO) production was measured in cells attached to COL I compared with cells attached to COL IV. Treatment with N(omega)-nitro-L-arginine methyl ester hydrochloride (L-NAME), an inhibitor of NO synthase, reduced this difference in ROS generation between cells attached to either COL I or IV. The results using antibodies against integrins also indicated that an alpha(2) integrin-mediated pathway was involved in the different response in ROS generation caused by ECM proteins. These results suggest that contact between altered ECM proteins that are present in advanced diabetic nephropathy and mesangial cells has the potential to increase intracellular oxidative stress, leading to progressive glomerular damage.     

Antinecrotic and antiapoptotic effects of hepatocyte growth factor on cholestatic hepatitis in a mouse model of bile-obstructive diseases

Cholestasis, an impairment of bile outflux, frequently occurs in liver diseases. In this process, an overaccumulation of bile acids causes hepatocyte necrosis and apoptosis, leading to advanced hepatitis. Hepatocyte growth factor (HGF) is mitogenic toward hepatocytes, but it is still unclear whether HGF has physiological and therapeutic functions during the progression of cholestasis. Using anti-HGF IgG or recombinant HGF in mice that had undergone bile duct ligation (BDL), we investigated the involvement of HGF in cholestasis-induced hepatitis. After the BDL surgery, HGF and c-Met mRNA levels transiently increased in livers during the progression of cholestatic hepatitis. When c-Met tyrosine phosphorylation was blocked in the livers of BDL-treated mice by anti-HGF IgG, hepatic dysfunction became evident, associated with the acceleration of hepatocyte necrosis and apoptosis. Inversely, administration of recombinant HGF into the mice led to the prevention of cholestasis-induced inflammation: HGF suppressed the hepatic expression of intracellular adhesion molecule-1 and neutrophil infiltration in BDL-treated mice. As a result, parenchymal necrosis was suppressed in the HGF-injected BDL mice. In addition, HGF supplement therapy reduced the number of apoptotic hepatocytes in cholestatic mice, associated with the early induction of Bcl-xL. The administration of HGF enhanced hepatic repair, via accelerating G1/S progression in hepatocytes. Our study showed that 1) upregulation of HGF production is required for protective mechanisms against cholestatic hepatitis and 2) enhancement of the intrinsic defense system by adding HGF may be a reasonable strategy to attenuate hepatic inflammation, necrosis, and apoptosis under bile-congestive conditions.     

Mechanisms and significance of bifunctional NK4 in cancer treatment

Based on the background that hepatocyte growth factor (HGF) and c-Met/HGF receptor tyrosine kinase play a definite role in tumor invasion and metastasis, NK4, four-kringles containing intramolecular fragment of HGF, was isolated as a competitive antagonist for the HGF-c-Met system. Independent of its HGF-antagonist action, NK4 inhibited angiogenesis induced by vascular endothelial cell growth factor and basic fibroblast growth factor, as well as HGF, indicating that NK4 is a bifunctional molecule that acts as an HGF-antagonist and angiogenesis inhibitor. Interestingly, kringle domains in distinct types of proteins, e.g., plasminogen, prothrombin, plasminogen activators, apolipoprotein(a), and HGF, share angioinhibitory actions. In experimental models of distinct types of cancers, NK4 protein administration or NK4 gene therapy inhibited tumor invasion, metastasis, and angiogenesis-dependent tumor growth. Cancer treatment with NK4 may prove to suppress malignant tumors to be 'static' in both tumor growth and spreading, as based on biological characteristics of malignant tumors.