Donut-Shaped Fingerprint In Homologous Polypeptide Relationships-A Topological Feature Related To Pathogenic Structural Changes In Conformational Disease

Features of homologous relationship of proteins can provide us a general picture of protein universe, assist protein design and analysis, and further our comprehension of the evolution of organisms. Here we carried Out a Study of the evolution Of protein molecules by investigating homologous relationships among residue segments. The motive was to identify detailed topological features of homologous relationships for short residue segments in the whole protein universe. Based on the data of a large number of non-redundant Proteins, the universe of non-membrane polypeptide was analyzed by considering both residue mutations and structural conservation. By connecting homologous segments with edges, we obtained a homologous relationship network of the whole universe of short residue segments, which we named the graph of polypeptide relationships (GPR). Since the network is extremely complicated for topological transitions, to obtain an in-depth understanding, only subgraphs composed of vital nodes of the GPR were analyzed. Such analysis of vital subgraphs of the GPR revealed a donut-shaped fingerprint. Utilization of this topological feature revealed the switch sites (where the beginning of exposure Of previously hidden "hot spots" of fibril-forming happens, in consequence a further opportunity for protein aggregation is Provided; 188-202) of the conformational conversion of the normal alpha-helix-rich prion protein PrPC to the beta-sheet-rich PrPSc that is thought to be responsible for a group of fatal neurodegenerative diseases, transmissible spongiform encephalopathies. Efforts in analyzing other proteins related to various conformational diseases are also introduced. (C) 2009 Elsevier Ltd. All rights reserved.

Accelerated evolution of the pituitary adenylate cyclase-activating polypeptide precursor gene during human origin

Pituitary adenylate cyclase-activating polypeptide (PACAP) is a neuropeptide abundantly expressed in the central nervous system and involved in regulating neurogenesis and neuronal signal transduction. The amino acid sequence of PACAP is extremely conserved across vertebrate species, indicating a strong functional constraint during the course of evolution. However, through comparative sequence analysis, we demonstrated that the PACAP precursor gene underwent an accelerated evolution in the human lineage since the divergence from chimpanzees, and the amino acid substitution rate in humans is at least seven times faster than that in other mammal species resulting from strong Darwinian positive selection. Eleven human-specific amino acid changes were identified in the PACAP precursors, which are conserved from murine to African apes. Protein structural analysis suggested that a putative novel Deuropeptide might have originated during human evolution and functioned in the human brain. Our data suggested that the PACAP precursor gene underwent adaptive changes during human origin and may have contributed to the formation of human cognition.

Pituitary adenylate cyclase-activating polypeptide

Pituitary adenylate cyclase-activating polypeptide (PACAP) which belongs to the secretin/glucagon/ VIP family has been originally isolated from the sheep hypothalamus on the basis of its ability to stimulate cAMP formation in culture rat anterior pituitary cells. Post-translational processing of the PACAP precursor generates two biologically active molecular forms, PACAP-38 and PACAP-27. The primary structure of PACAP has been remarkably conserved during evolution. The sequence of PACAP-27 exhibits substantial similarities with those of vasoactive intestinal polypeptide (VIP), glucagon and secretin. The gene encoding the PACAP precursor is widely expressed in brain and various peripheral organs, notably in endocrine glands, gastro-intestinal, urogenital tracts and respiratory system. In vivo, and in vitro studies have shown that PACAP exhibits multiple activities especially a trophic activity during ontogenesis, notably in the adrenal medulla and the central nervous system. The biological effects of PACAP are mediated through three distinct receptor subtypes which exhibit differential affinities for PACAP and VIP. The PAC1 receptor, which shows high selectivity for PACAP, is coupled to several transduction systems. In contrast, VPAC1 and VPAC2, which bind with the same affinity for PACAP and VIP, are mainly coupled to the adenylyl cyclase pathway. In conclusion, PACAP is neuropeptide, and it functions as a hypothalamic hormone, neurohormone, neuromodulator, vasodilator, neurotransmitter or trophic factor in the brain and the various organs.

Additional angles to calculate the deformation of RNA helices induced by bulge loops

Bulges are common features of folded RNA structures. The RNA axial kinking caused by bulges has been confirmed by many experiments. Usually, a kinking angle zeta and a bending angle theta are used to describe the kinking and twisting of RNA molecules containing bulges. Here, we present two additional angles (twist angle zeta(1), twist angle zeta(2)) to describe the deformation of RNA helices induced by bulge loops because only two angles (a kinking angle zeta and a bending angle theta) are not enough to define the deformation of RNA induced by bulges. (C) 2002 Elsevier Science B.V. All rights reserved.

Identification of a putative oocyte-specific small nuclear ribonucleoprotein polypeptide C in gibel carp

Previous studies have demonstrated that germinal vesicle of amphibian oocyte contains small nuclear ribonucleoprotein polypeptide C (SNRPC). In this study, a putative member of SNRPC was identified from Carassius auratus gibelio oocyte cDNA library. Its full-length cDNA has an open reading frame of 201 nt for encoding a peptide of 66 an, a short 5'-UTR of 19 nt and a long 3'-UTR of 347 nt including a polyadenylation signal and poly- (A) tail, and the deduced amino acid sequence has 47% identity with the C-terminal of the zebrafish small nuclear ribonucleoprotein polypeptide C. Western blot analysis revealed its oocyte-specific expression. Immunofluorescence localization indicated that its gene product localized to numerous nucleoli within the oocytes and showed dynamic changes with the nucleoli during oocyte maturation. RT-PCR and Western blot analysis further revealed its constant presence in the oocytes and in the embryos until hatching. The data suggested that the newly identified CagOSNRPC might be a nucleolar protein. (c) 2006 Elsevier Inc. All rights reserved.

Self-assembly of a hydrophobic polypeptide containing a short hydrophilic middle segment: Vesicles to large compound micelles

This report describes a facile route to prepare the vesicles and large compound micelles (LCMs) from a series of poly(epsilon-benzyloxycarbonyl L-lysine)-block-poly[diethylene glycol bis(3-amino propyl) ether]-block-poly(epsilon-benzyloxycarbonyl L-lySine) (PZLL-DGBE-PZLL) in their water solution, depending on molecular weight of the polypeptides. A pyrene probe is used to demonstrate the aggregate formation of PZLL-DGBE-PZLL in solution, and also to measure their critical micelle concentration as a function of molecular weight of the polymer.

Synthesis and self-assembly of a novel Y-shaped copolymer with a helical polypeptide arm

novel biodegradable Y-shaped copolymer, poly(L-lactide)(2)-b-poly(gamma-benzyl-L-glutamic acid) (PLLA(2)-b-PBLG), was synthesized by the ring-opening polymerization (ROP) of N-carboxyanhydride of gamma-benzyl-L-glutamate (BLG-NCA) with centrally amino-functionalized poly(L-lactide), PLLA(2)-NH2, as a macroinitiator in a convenient way. The Y-shaped copolymer and its precursors were characterized by H-1 NMR, FT-IR, GPC, WAXD and DSC measurements. The self-assembly of the PLLA(2)-b-PBLG copolymer in toluene and benzyl alcohol was examined. It was found that the self-assembly of the copolymer was dependent on solvent and on relative length of the PBLG block. For a copolymer with PLLA blocks of 26 in total degree of polymerization (DP), if the PBLG block was long enough (e.g., DP = 54 or more), the copolymer/toluene solution became a transparent gel at room temperature. In benzyl alcohol Solution, only PLLA(2)-b-PBLG containing ca. 190 BLG residues could form a gel: those with shorter PBLG blocks (e.g., DP = 54) became nano-scale fibrous aggregates and these aggregates were dispersed in benzyl alcohol homogeneously.

Purification, sequencing and biological activity of polypeptide from velvet antler

The velvet antler polypeptide CNT14 was extracted and purified by gel filtration, ion exchange chromatography and RP C, which showed a single peak in HPLC chromatography and a single band in SDS-PAGE. The molecular weight measured by MALDI/TOF/MS spectrum was 1479. 9028. The polypeptide consisted mostly of Glu, Leu, Val, Pro. The amino acid sequence of the polypeptide was detected with ESI-MS/ MS, and the sequence was E-P-T-V-L-D-E-V-C-L-A-H-G-P. The experiments of biological activity of polypeptide CNT14 in vivo were carried out, and the results show that CNT14 has stimulant effects on the growth of rat HT22 cells. Then we produced the polypeptide CNT14 according the amino acid sequence by solid phase synthesis, confirmed the sequence of the polypeptide to be consistent with the amino acid sequence of polypeptide CNT14 which was separated from the velvet antler.

Self-assembly of polypeptide-containing ABC-type triblock copolymers in aqueous solution and its pH dependence

Self-assembling of novel biodegradable ABC-type triblock copolymer poly(ethylene glycol)-poly(L-lactide)-poly(L-glutamic acid) (PEG-PLLA-PLGA) is studied. In aqueous media, it self-assembles into a spherical micelle with the hydrophobic PLLA segment in the core and the two hydrophilic segments PEG and PLGA in the shell. With the lengths of PEG and PLLA blocks fixed, the diameter of the micelles depends on the length of the PLGA block and on the volume ratio of H2O/dimethylformamide (DMF) in the media. When the PLGA block is long enough, morphology of the self-assembly is pH-dependent. It assembles into the spherical micelle in aqueous media at pH 4.5 and into the connected rod at or below pH 3.2. The critical micelle concentration (cmc) of the copolymer changes accordingly with decreasing solution pH. Both aggregation states can convert to each other at the proper pH value. This reversibility is ascribed to the dissociation and neutralization of the COOH groups in the LGA residues. When the PLGA block is short compared to the PEG or PLLA block, it assembles only into the spherical micelle at various pH values.

Polypeptide modification of multiwalled carbon nanotubes by a graft-from approach

Covalent surface functionalization of carbon nanotubes with polypeptides is promising for possible medical applications. This work presents a graft-from approach to perform the polypeptide modification of multiwalled carbon nanotubes (MWTNs). The raw MWNTs are first amine-functionalized. The amine-functionalized MWNTs are then used as the initiator to initiate the ring-opening polymerization of gamma-benzyl-L-glutamate N-carboxyanhydride (BLG- NCA), to results in the polypeptide-grafted MWNTs. FT-IR, XPS, and TGA data demonstrate that the functionalization is successful. The TEM images of the products show that the thickness of the polypeptide shell of the PBLG-MWNT is about 4.5-22 nm. Using the facile route developed here, carbon nanotubes functionalized with other types of polypeptides can be easily fabricated using the corresponding NCAs.

A novel polypeptide from shark cartilage with potent anti-angiogenic activity

Using guanidine-HCl extraction, acetone precipitation, ultra-filtration and chromatography, a novel polypeptide with potent anti-angiogenic activity was purified from cartilage of the shark, Prionace glauca. N-terminal amino acid sequence analysis and SDS-PAGE revealed that the substance is a novel polypeptide with MW 15500 (PG155). The anti-angiogenic effects of PG155 were evaluated using zebrafish embryos model in vivo. Treatment of the embryos with 20 mu g/ml PG155 resulted in a significant reduction in the growth of subintestinal vessels (SIVs). A higher dose resulted in almost complete inhibition of SIV growth, as observed by endogenous alkaline phosphatase (EAP) staining assay. An in vitro transwell experiment revealed that the polypeptide inhibited vascular endothelial growth factor (VEGF) induced migration and tubulogenesis of human umbilical vein endothelial cells (HUVECs). Exposure of HUVECs in 20 mu g/ml PG155 significantly decreased the density of migrated cells. Almost complete inhibition of cell migration was found when HUVECs were treated with 40-80 mu g/ml PG155. PG155 (20 mu g/ml) markedly inhibited the tube formation of HUVECs and a dose-dependent effect was also found when treatment of HUVECs with PG155 at the concentration from 20 to 160 mu g/ml.

Direct observation of adsorption sites of protein impurities and their effects on step advancement of protein crystals

We measured noninvasively step velocities of elementary two-dimensional (2D) islands on {110} faces of tetragonal lysozyme crystals, under various supersaturations, by laser confocal microscopy combined with differential interference contrast microscopy. We studied the correlation between the effects of protein impurities on the growth of elementary steps and their adsorption sites on a crystal surface, using three kinds of proteins: fluorescent-labeled lysozyme (F-lysozyme), covalently bonded dimers of lysozyme (dimer), and a 18 kDa polypeptide (18 kDa). These three protein impurities suppressed the advancement of the steps. However, they exhibited different supersaturation dependencies of the suppression of the step velocities. To clarify the cause of this difference, we observed in situ the adsorption sites of individual molecules of F-lysozyme and fluorescent-labeled dimer (F-dimer) on the crystal surface by single-molecule visualization. We found that F-lysozyme adsorbed preferentially on steps (i.e., kinks), whereas F-dimer adsorbed randomly on terraces. Taking into account the different adsorption sites of F-lysozyme and F-dimer, we could successfully explain the different effects of the impurities on the step velocities. These observations strongly suggest that 18 kDa also adsorbs randomly on terraces. Seikagaku lysozyme exhibited a complex effect that could not alone be explained by the two major impurities (dimer and 18 kDa) present in Seikagaku lysozyme, indicating that trace amounts of other impurities significantly affect the step advancement.

白杄花粉管微丝骨架介导信号传导的蛋白质组学研究

在高等植物有性生殖过程中，花粉管作为运输精子到胚珠的载体，它的生长具有高度极性化，并且要依赖于微丝。由于花粉管本身所具的特性，它已经成为研究细胞相互识别、胞内和胞外信号的模式系统。本文为了研究微丝在白杄（Picea meyeri Rehd. et Wils.）花粉管生长中的作用，我们应用不同浓度的微丝聚合抑制剂Latrunculin B (LATB) 处理花粉管，并通过激光共聚焦显微镜观察微丝聚合状态的动态变化。结果发现，在低浓度下的LATB能使花粉管中的微丝严重解聚，且抑制其顶端生长。 我们进一步利用蛋白质组学的手段，分析了白杄花粉管微丝解聚后蛋白质的表达图谱。通过双向电泳分离出500个左右考马斯亮兰染色的蛋白质斑点，经过软件分析发现，其中大部分蛋白质的表达量未发生变化，而只有110个蛋白斑点有较大变化。将这些蛋白斑点从胶上切下酶解后用于质谱鉴定，最终鉴定出35个蛋白，其中有18个为上调蛋白，17个下调蛋白。根据其主要功能，通常可分为碳水化合物代谢、胁迫反应、信号和细胞扩展等几类。我们发现由于微丝解聚引起的能量代谢水平降低，可能与依赖于信号传导的微丝重组过程相关。此外，当LATB浓度增加到50 nM时，与细胞壁多糖合成相关的两个蛋白，如reversibly glycosylated polypeptide和type IIIa membrane protein cp-wap13几乎不表达，这说明当微丝聚合完全被抑制后，依赖于微丝的分泌系统也受到影响，从而引起相应蛋白质变化，最终导致细胞壁成分合成的减少。细胞骨架蛋白actin的下调，进一步说明微丝在花粉管生长过程中起着提供或支持的一种机制，也就是能调节信号介导的花粉管生长，并使其在特定的时期到达特定的部位，从而完成植物的受精作用。