Locomotion of Gymnarchus Niloticus： Experiment and Kinematics

In addition to forward undulatory swimming, Gymnarchus niloticus can swim via undulations of the dorsal fin while the body axis remains straight; furthermore, it swims forward and backward in a similar way, which indicates that the undulation of the dorsal fin can simultaneously provide bidirectional propulsive and maneuvering forces with the help of the tail fin. A high-resolution Charge-Coupled Device （CCD） imaging camera system is used to record kinematics of steady swimming as well as maneuvering in G. niloticus. Based on experimental data, this paper discusses the kinematics （cruising speed, wave speed, cycle frequency, amplitude, lateral displacement） of forward as well as backward swimming and maneuvering. During forward swimming, the propulsive force is generated mainly by undulations of the dorsal fin while the body axis remains straight. The kinematic parameters （wave speed, wavelength, cycle frequency, amplitude） have statistically significant correlations with cruising speed. In addition, the yaw at the head is minimal during steady swimming. From experimental data, the maximal lateral displacement of head is not more than 1% of the body length, while the maximal lateral displacement of the whole body is not more than 5% of the body length. Another important feature is that G. niloticus swims backwards using an undulatory mechanism that resembles the forward undulatory swimming mechanism. In backward swimming, the increase of lateral displacement of the head is comparatively significant; the amplitude profiles of the propulsive wave along the dorsal fin are significantly different from those in forward swimming. When G. niloticus does fast maneuvering, its body is first bent into either a C shape or an S shape, then it is rapidly unwound in a travelling wave fashion. It rarely maneuvers without the help of the tail fin and body bending.     

Enhancing the Activity of a Protein by Stereospecific Unfolding: CONFORMATIONAL LIFE CYCLE OF INSULIN AND ITS EVOLUTIONARY ORIGINS*S??

A central tenet of molecular biology holds that the function of a protein is mediated by its structure. An inactive ground-state conformation may nonetheless be enjoined by the interplay of competing biological constraints. A model is provided by insulin, well characterized at atomic resolution by x-ray crystallography. Here, we demonstrate that the activity of the hormone is enhanced by stereospecific unfolding of a conserved structural element. A bifunctional β-strand mediates both self-assembly (within β-cell storage vesicles) and receptor binding (in the bloodstream). This strand is anchored by an invariant side chain (Phe^B24); its substitution by Ala leads to an unstable but native-like analog of low activity. Substitution by d-Ala is equally destabilizing, and yet the protein diastereomer exhibits enhanced activity with segmental unfolding of the β-strand. Corresponding photoactivable derivatives (containing l- or d-para-azido-Phe) cross-link to the insulin receptor with higher d-specific efficiency. Aberrant exposure of hydrophobic surfaces in the analogs is associated with accelerated fibrillation, a form of aggregation-coupled misfolding associated with cellular toxicity. Conservation of Phe^B24, enforced by its dual role in native self-assembly and induced fit, thus highlights the implicit role of misfolding as an evolutionary constraint. Whereas classical crystal structures of insulin depict its storage form, signaling requires engagement of a detachable arm at an extended receptor interface. Because this active conformation resembles an amyloidogenic intermediate, we envisage that induced fit and self-assembly represent complementary molecular adaptations to potential proteotoxicity. The cryptic threat of misfolding poses a universal constraint in the evolution of polypeptide sequences.How insulin binds to the insulin receptor (IR)² is not well understood despite decades of investigation. The hormone is a globular protein containing two chains, A (21 residues) and B (30 residues) (Fig. 1A). In pancreatic β-cells, insulin is stored as Zn²⁺-stabilized hexamers (Fig. 1B), which form microcrystal-line arrays within specialized secretory granules (1). The hexamers dissociate upon secretion into the portal circulation, enabling the hormone to function as a zinc-free monomer. The monomer is proposed to undergo a change in conformation upon receptor binding (2). In this study, we investigated a site of conformational change in the B-chain (Phe^B24) (arrow in Fig. 1A). In classical crystal structures, this invariant aromatic side chain (tawny in Fig. 1B) anchors an antiparallel β-sheet at the dimer interface (blue in Fig. 1C). Total chemical synthesis is exploited to enable comparison of corresponding d- and l-amino acid substitutions at this site, an approach designated “chiral mutagenesis” (3-5). In the accompanying article, the consequences of this conformational change are investigated by photomapping of the receptor-binding surface (6). Together, these studies redefine the interrelation of structure and activity in a protein central to the hormonal control of metabolism.Open in a separate windowFIGURE 1.Sequence and structure of insulin. A, sequences of the B-chain (upper) and A-chain (lower) with disulfide bridges as indicated. The arrow indicates invariant Phe^B24. The B24-B28 β-strand is highlighted in blue. B, crystal structure of the T₆ zinc insulin hexamer (Protein Data Bank code 4INS): ribbon model (left) and space-filling model (right). The B24-B28 β-strand is shown in blue, and the side chain of Phe^B24 is highlighted in tawny. The B-chain is otherwise dark gray; the A-chain, light gray; and zinc ions, magenta. Also shown at the left are the side chains of His^B10 at the axial zinc-binding sites. C, cylinder model of the insulin dimer showing the B24-B26 antiparallel β-sheet (blue) anchored by the B24 side chain (tawny circle). The A- and B-chains are shown in light and dark gray, respectively. The protomer at the left is shown in the R-state, in which the central α-helix of the B-chain is elongated (B3-B19 in the frayed R^f protomer of T₃R^f₃ hexamers and B1-B19 in the R protomer of R₆ hexamers). The three types of zinc insulin hexamers share similar B24-B26 antiparallel β-sheets as conserved dimerization elements.The structure of an insulin monomer in solution resembles a crystallographic protomer (Fig. 2A) (7-9). The A-chain contains an N-terminal α-helix, non-canonical turn, and second helix; the B-chain contains an N-terminal segment, central α-helix, and C-terminal β-strand. The β-strand is maintained in an isolated monomer wherein the side chain of Phe^B24 (tawny in Fig. 2A), packing against the central α-helix of the B-chain, provides a “plug” to seal a crevice in the hydrophobic core (Fig. 2B). Anomalies encountered in previous studies of insulin analogs suggest that Phe^B24 functions as a conformational switch (4, 7, 10-14). Whereas l-amino acid substitutions at B24 generally impair activity (even by such similar residues as l-Tyr) (15), a seeming paradox is posed by the enhanced activities of nonstandard analogs containing d-amino acids (10-12).

TABLE 1

Previous studies of insulin analogs

Reduced Expression of the Hyaluronan and Proteoglycan Link Proteins in Malignant Gliomas

Malignant gliomas have a distinctive ability to infiltrate the brain parenchyma and disrupt the neural extracellular matrix that inhibits motility of axons and normal neural cells. Chondroitin sulfate proteoglycans (CSPGs) are among the major inhibitory components in the neural matrix, but surprisingly, some are up-regulated in gliomas and act as pro-invasive signals. In the normal brain, CSPGs are thought to associate with hyaluronic acid and glycoproteins such as the tenascins and link proteins to form the matrix scaffold. Here, we examined for the first time the expression of link proteins in human brain and malignant gliomas. Our results indicate that HAPLN4 and HAPLN2 are the predominant members of this family in the adult human brain but are strongly reduced in the tumor parenchyma. To test if their absence was related to a pro-invasive gain of function of CSPGs, we expressed HAPLN4 in glioma cells in combination with the CSPG brevican. Surprisingly, HAPLN4 increased glioma cell adhesion and migration and even potentiated the motogenic effect of brevican. Further characterization revealed that HAPLN4 expressed in glioma cells was largely soluble and did not reproduce the strong, hyaluronan-independent association of the native protein to brain subcellular membranes. Taken together, our results suggest that the tumor parenchyma is rich in CSPGs that are not associated to HAPLNs and could instead interact with other extracellular matrix proteins produced by glioma cells. This dissociation may contribute to changes in the matrix scaffold caused by invasive glioma cells.The extracellular matrix (ECM)² of the adult central nervous system lacks most fibrous proteins (collagens, fibronectin, and laminins) that are present in the matrices of other tissues and is formed instead by a scaffold of hyaluronic acid (HA) with associated glycoproteins (1). The major family of HA binding matrix glycoproteins in the central nervous system is formed by the chondroitin sulfate proteoglycans of the lectican family (aggrecan, versican, neurocan, and brevican), the last two expressed almost exclusively in neural tissue (2). These proteoglycans bind both to HA and to cell-surface receptors (3), regulating the cross-linking and compressibility of the matrix scaffold and, therefore, modulating many neural processes including cell motility during development, axonal navigation, and the stabilization of synapses (4). The lecticans have been identified as a major class of molecules that restrict cellular and axonal motility in neural tissue and are a major component of the glial scar that forms after neural injury and prevents axonal regeneration (5).A second family of HA-binding proteins expressed in the central nervous system is formed by small glycoproteins known as HA- and proteoglycan-link proteins (HAPLNs) or, simply, “link proteins.” These glycoproteins bind both to HA and to the lecticans, forming ternary complexes (6, 7). The structure of the link proteins is remarkably similar to the N-terminal region of the lecticans, and the highly homologous HA binding domains from HAPLNs and lecticans are indistinctly known as proteoglycan tandem repeats or link-protein modules.In a striking example of molecular evolution, the genes of the four HAPLNs are located adjacent to the genes of the four lecticans, indicating a common molecular origin by gene duplication (8). Two of the link proteins, HAPLN2 and HAPLN4, have only been detected in neural tissue, and their genes are adjacent to the neural-specific proteoglycans, brevican and neurocan, respectively (8). Both HAPLN2 and HAPLN4, also known as brain-specific link protein (Bral-1) and Bral-2, are up-regulated in the adult central nervous system and match the temporal expression profile of brevican, which is the most abundant CSPG in adult neural tissue (9, 10).Current evidence suggests that the HAPLNs may be key components in the organization of the HA-based matrix scaffold. HAPLN1, the best studied member of the family, increases the affinity of the lecticans for HA (11, 12) and stabilizes lectican-HA matrix aggregates (6, 13). Moreover, the increased expression of lecticans and HAPLNs in the adult central nervous system correlates temporally and spatially with changes in ECM solubility and with appearance of ECM aggregates around subsets of neurons, known as “perineuronal nets.” These changes have been associated with restricted cellular motility and decreased synaptic plasticity (14).The role of the lectican CSPGs as inhibitors of motility in the adult central nervous system contrasts starkly with their pro-invasive role in the highly aggressive brain tumors known as malignant gliomas. These are the most common primary tumors of the brain and are characterized by their extensive and diffuse infiltration of the brain parenchyma (15), which makes them impossible to completely remove and facilitates tumor recurrence even after long term therapies. The invasive ability of gliomas is restricted to neural tissue and is not observed in other tumors that metastasize to the brain, suggesting that glioma invasion may be supported in part by unique mechanisms to remodel the neural microenvironment (16).Two lectican CSPGs, versican and the neural-specific CSPG brevican, are highly up-regulated in gliomas compared with normal brain tissue (3). Although these proteoglycans are thought to inhibit the motility of normal glial cells (17, 18), they instead promote glioma cell adhesion and migration. The underlying molecular mechanisms for this unusual effect are poorly understood, although we and others have demonstrated that these lecticans can activate epidermal growth factor receptor signaling in glioma cells, which leads to an increase of cell-surface adhesion molecules (19). Both brevican and versican can also form adhesive complexes with mesenchymal matrix proteins that are present in the glioma ECM but absent from the normal neural ECM (19, 20).Although the role of CSPGs in brain tumors is starting to become better defined, their HAPLN partners have never been analyzed in human brain or in neuropathologies. Therefore, we still have a highly incomplete picture of the molecular changes that occur in the tumor ECM and of how those changes could affect critical aspects of glioma biology such as invasion of the surrounding tissue.We hypothesized that the gain of function of CSPGs in gliomas could be associated with changes in the levels or molecular associations of specific HAPLNs in the ECM of gliomas. Thus, we studied here the expression and biochemical properties of the HAPLN family in human normal brain and glioma tissue. Our results provide the first biochemical characterization of the brain-specific human HAPLN4 and, in addition, show that both neural-specific link proteins HAPLN2 and HAPLN4, which are abundant in adult brain, are virtually absent from the ECM of malignant gliomas.     

Examining Hedgehog pathway genes GLI3, SHH, and PTCH1 and the p53 target GLIPR1/GLIPR1L1/GLIPR1L2 gene cluster using fluorescence in situ hybridization uncovers GLIPR1/GLIPR1L1/GLIPR1L2 deletion in 9% of patients with multiple myeloma

Mutations in genes regulating cell cycle and apoptosis are considered major culprits for the malignant transformation of cancer cells. Aberrant activation of the Hedgehog (HH) signaling pathway which primarily regulates genes involved in cell growth, proliferation, survival and apoptosis has been demonstrated in multiple myeloma. Mutations resulting in defective components of the p53 pathway, which serves a critical role in mediating cellular stress response by triggering DNA repair, cell cycle arrest, senescence and apoptosis, have also been identified. This study focuses on detecting copy number variations for the GLIPR1/GLIPR1L1/GLIPR1L2 gene cluster of the p53 pathway and three elements of the HH pathway, SHH, PTCH1 and GLI3 in multiple myeloma (MM) using fluorescence in situ hybridization (FISH). In eighteen samples, there was no evidence of abnormal copy number for PTCH1, GLI3 or SHH. Thus, it is unlikely that copy number variations of these genes are linked to multiple myeloma. However, a deletion of the GLIPR1/GLIPR1L1/ GLIPR1L2 gene cluster, all p53 targets, was found in three of 32 samples (9.4%) indicating that these deleted genes may have significant implications in MM. Further studies should be performed to determine the role of the GLIPR1/GLIPR1L1/GLIPR1L2 gene cluster in the pathogenesis of multiple myeloma.     

Contribution of Residue B5 to the Folding and Function of Insulin and IGF-I: CONSTRAINTS AND FINE-TUNING IN THE EVOLUTION OF A PROTEIN FAMILY*

Proinsulin exhibits a single structure, whereas insulin-like growth factors refold as two disulfide isomers in equilibrium. Native insulin-related growth factor (IGF)-I has canonical cystines (A6—A11, A7–B7, and A20—B19) maintained by IGF-binding proteins; IGF-swap has alternative pairing (A7–A11, A6—B7, and A20—B19) and impaired activity. Studies of mini-domain models suggest that residue B5 (His in insulin and Thr in IGFs) governs the ambiguity or uniqueness of disulfide pairing. Residue B5, a site of mutation in proinsulin causing neonatal diabetes, is thus of broad biophysical interest. Here, we characterize reciprocal B5 substitutions in the two proteins. In insulin, His^B5 → Thr markedly destabilizes the hormone (ΔΔG_u 2.0 ± 0.2 kcal/mol), impairs chain combination, and blocks cellular secretion of proinsulin. The reciprocal IGF-I substitution Thr^B5 → His (residue 4) specifies a unique structure with native ¹H NMR signature. Chemical shifts and nuclear Overhauser effects are similar to those of native IGF-I. Whereas wild-type IGF-I undergoes thiol-catalyzed disulfide exchange to yield IGF-swap, His^B5-IGF-I retains canonical pairing. Chemical denaturation studies indicate that His^B5 does not significantly enhance thermodynamic stability (ΔΔG_u 0.2 ± 0.2 kcal/mol), implying that the substitution favors canonical pairing by destabilizing competing folds. Whereas the activity of Thr^B5-insulin is decreased 5-fold, His^B5-IGF-I exhibits 2-fold increased affinity for the IGF receptor and augmented post-receptor signaling. We propose that conservation of Thr^B5 in IGF-I, rescued from structural ambiguity by IGF-binding proteins, reflects fine-tuning of signal transduction. In contrast, the conservation of His^B5 in insulin highlights its critical role in insulin biosynthesis.     

Response of growth and fatty acid compositions of Nannochloropsis sp. to environmental factors under elevated CO2 concentration

Nannochloropsis sp. was grown with different levels of nitrate, phosphate, salinity and temperature with CO₂ at 2,800 μl l⁻¹. Increased levels of NaNO₃ and KH₂PO₄ raised protein and polyunsaturated fatty acids (PUFAs) contents but decreased carbohydrate, total lipid and total fatty acids (TFA) contents. Nannochloropsis sp. grew well at salinities from 22 to 49 g l⁻¹, and lowering salinity enhanced TFA and PUFAs contents. TFA contents increased with the increasing temperature but PUFAs contents decreased. The highest eicosapentaenoic acid (EPA, 20:5ω3) content based on the dry mass was above 3% under low N (150 μM NaNO₃) or high N (3000 μM NaNO₃) condition. Excessive nitrate, low salinity and temperature are thus favorable factors for improving EPA yields in Nannochloropsis sp.     

The symptom difference induced by <Emphasis Type="Italic">Tobacco mosaic virus</Emphasis> and <Emphasis Type="Italic">Tomato mosaic virus</Emphasis> in tobacco plants containing the <Emphasis Type="Italic">N</Emphasis> gene is determined by movement protein gene

Tobacco mosaic virus (TMV) and Tomato mosaic virus (ToMV) are two closely related viruses in the genus Tobamovirus, but they induce obviously different sizes of necrotic lesions in tobacco plants containing the N gene. Comparison of the symptoms produced by TMV, ToMV and a chimaeric virus (T/OMP), in which the TMV movement protein (MP) gene was replaced by the ToMV MP gene, showed T/OMP caused necrotic lesions that were similar in size to those of ToMV in tobacco plants containing the N gene. The coat protein and MP of the three viruses accumulated in planta with similar levels, and the replication level of TMV and T/OMP in protoplasts also had no difference. Comparison of the activities of defense-related enzymes (PAL, POD and PPO) induced by the three viruses also showed that the variability of enzyme activity induced by T/OMP was similar to that induced by TMV, but different from that induced by ToMV. The results indicate that the size difference of necrotic lesions induced by TMV and ToMV in tobacco plants containing the N gene results from the functional difference of their MP genes.     

N-(4-{[4-(1H-Benzoimidazol-2-yl)-arylamino]-methyl}-phenyl)-benzamide derivatives as small molecule heparanase inhibitors

A novel class of N-(4-{[4-(1H-benzoimidazol-2-yl)-arylamino]-methyl}-phenyl)-benzamides are described as inhibitors of the endo-beta-glucuronidase heparanase. Among them are N-(4-{[4-(1H-benzoimidazol-2-yl)-phenylamino]-methyl}-phenyl)-3-bromo-4-methoxy-benzamide (15h), and N-(4-{[5-(1H-benzoimidazol-2-yl)-pyridin-2-ylamino]-methyl}- phenyl)-3-bromo-4-methoxy-benzamide (23) which displayed good heparanase inhibitory activity (IC(50) 0.23-0.29 microM), with the latter showing oral exposure in mice.