Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 A

The three-dimensional structures of an antibody to a peptide and its complex with the peptide antigen have been determined at 2.8 A resolution. The antigen is a synthetic 19-amino acid peptide homolog of the C helix of myohemerythrin (Mhr). The unliganded Fab' crystals are orthorhombic with two molecules per asymmetric unit, whereas the complex crystals are hexagonal with one molecule per asymmetric unit. The Fab' and the Fab'-peptide complex structures have been solved independently by molecular replacement methods and have crystallographic R factors of 0.197 and 0.215, respectively, with no water molecules included. The amino-terminal portion of the peptide sequence (NH2-Glu-Val-Val-Pro-His-Lys-Lys) is clearly interpretable in the electron density map of the Fab'-peptide complex and adopts a well-defined type II beta-turn in the concave antigen binding pocket. This same peptide amino acid sequence in native Mhr is alpha-helical. The peptide conformation when bound to the Fab' is inconsistent with binding of the Fab' to native Mhr, and suggests that binding of the Fab' to conformationally altered forms of the native Mhr or to apo-Mhr. Immunological mapping previously identified this sequence as the peptide epitope, and its fine specificity correlates well with the structural analysis. The binding pocket includes a large percentage of hydrophobic residues. The buried surfaces of the peptide and the antibody are complementary in shape and cover 460 A2 and 540 A2, respectively. These two structures now enable a comparison of a specific monoclonal Fab' both in its free and antigen complexed state. While no major changes in the antibody were observed when peptide was bound, there were some small but significant side chain and main chain rearrangements.     

Convergence of Ets- and notch-related structural motifs in a heteromeric DNA binding complex

Analysis of the heteromeric DNA binding protein GABP has revealed the interaction of two distinct peptide sequence motifs normally associated with proteins located in different cellular compartments. The alpha subunit of GABP contains an 85-amino acid segment related to the Ets family of DNA binding proteins. The ETS domain of GABP alpha facilitates weak binding to DNA and, together with an adjacent segment of 37 amino acids, mediates stable interaction with GABP beta. The beta subunit of GABP contains four imperfect repeats of a sequence present in several transmembrane proteins including the product of the Notch gene of Drosophila melanogaster. These amino-terminal repeats of GABP beta mediate stable interaction with GABP alpha and, when complexed with GABP alpha, directly contact DNA. These observations provide evidence for a distinct biochemical role for the 33-amino acid repeats, and suggest that they may serve as a module for the generation of specific dimerization interfaces.     

Three-dimensional solution structure of a single zinc finger DNA-binding domain

The three-dimensional solution structure of a zinc finger nucleic acid binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. Spectra of a synthetic peptide corresponding to a single zinc finger from the Xenopus protein Xfin yielded distance and dihedral angle constraints that were used to generate structures from distance geometry and restrained molecular dynamics calculations. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding.     

Cloning and Expression Profile of Deoxyhypusine Snyhtase Gene and Deoxyhypusine Hydroxylase Gene in Silkworm, Bombyx mori

Deoxyhypusine snyhtase （DHS） and deoxyhypusine hydroxylase （DOHH） are the two enzymes that catalyze the synthesis of hypusine within eukaryotic initiation factor 5A （eIF5A）. Synthesis of hypusine is essential for the function of eIF5A in eukaryotic cell proliferation and survival. Here we described the cloning and expression of two full-length cDNAs, encoding respectively DHS-like protein and DOHH-like protein from Bombyx mori by using the methods of bioinformatics, RACE, and RT-PCR technology, named as BmDHS and BmDOHH. Sequencing results indicate that they are 1 311 and 1 874 bp in length including complete open reading frame （ORF） 1 116 and 915 bp, which encode 371 amino acids （molecular weight is about 41.11 kD and isoelectric point is 5.84） and 304 amino acids （molecular weight is about 34.30 kD and isoelectric point is 4.86）, respectively. BmDHS contains only 1 exon, and BmDOHH contains 4 exons and 3 introns. The deduced amino acid sequence of BmDHS contains a deoxyhypusine synthase domain from 47 to 361 amino acid residues, and the deduced amino acid sequence of BmDOHH contains 6 E-Z type HEAT repeat domains （23-52, 54-83, 87-116, 177-206, 208-237, and 241- 270）. Compared to DHS and DOHH amino acid sequences from other species, such as Homo sapiens and Drosophila melanogaster, both silkworm DHS protein and DOHH protein have more than 55% identity. The conservative regions are very similar with each other. The phylogenetic tree analysis indicated that not only DHS but also DOHH from different species has genus-specific features. The expressions of BmDHS and BmDOHH are no tissue and stage specific in our tested samples.     

A new cofactor in a prokaryotic enzyme: tryptophan tryptophylquinone as the redox prosthetic group in methylamine dehydrogenase

Methylamine dehydrogenase (MADH), an alpha 2 beta 2 enzyme from numerous methylotrophic soil bacteria, contains a novel quinonoid redox prosthetic group that is covalently bound to its small beta subunit through two amino acyl residues. A comparison of the amino acid sequence deduced from the gene sequence of the small subunit for the enzyme from Methylobacterium extorquens AM1 with the published amino acid sequence obtained by the Edman degradation method, allowed the identification of the amino acyl constituents of the cofactor as two tryptophyl residues. This information was crucial for interpreting 1H and 13C nuclear magnetic resonance, and mass spectral data collected for the semicarbazide- and carboxymethyl-derivatized bis(tripeptidyl)-cofactor of MADH from bacterium W3A1. The cofactor is composed of two cross-linked tryptophyl residues. Although there are many possible isomers, only one is consistent with all the data: The first tryptophyl residue in the peptide sequence exists as an indole-6,7-dione, and is attached at its 4 position to the 2 position of the second, otherwise unmodified, indole side group. Contrary to earlier reports, the cofactor of MADH is not 2,7,9-tricarboxypyrroloquinoline quinone (PQQ), a derivative thereof, or pro-PQQ. This appears to be the only example of two cross-linked, modified amino acyl residues having a functional role in the active site of an enzyme, in the absence of other cofactors or metal ions.     

Synthesis of a sequence-specific DNA-cleaving peptide

A synthetic 52-residue peptide based on the sequence-specific DNA-binding domain of Hin recombinase (139-190) has been equipped with ethylenediaminetetraacetic acid (EDTA) at the amino terminus. In the presence of Fe(II), this synthetic EDTA-peptide cleaves DNA at Hin recombination sites. The cleavage data reveal that the amino terminus of Hin(139-190) is bound in the minor groove of DNA near the symmetry axis of Hin recombination sites. This work demonstrates the construction of a hybrid peptide combining two functional domains: sequence-specific DNA binding and DNA cleavage.     

金花茶多糖的凝集反应特性初探

采用比色法分析比较了金花茶多糖与蓖麻凝集素、伴刀豆凝集素等凝集素的凝集反应特性.结果显示,不同凝集素均能与金花茶多糖发生凝集反应,但凝集反应程度有明显差异.特异结合糖残基为半乳糖的蓖麻凝集素与金花茶多糖的凝集反应效果最显著,而特异结合糖残基同样为半乳糖或其衍生物的海红豆凝集素、欧卫矛凝集素、怀槐凝集素和花生凝集素的凝集反应程度则比较弱.当金花茶多糖浓度上升至6.59 mg/mL时,蓖麻凝集素的凝集反应是其他凝集素的6～10倍.另一方面,特异结合糖残基为甘露糖的伴刀豆凝集素与金花茶多糖虽然有类似的凝集反应特征,但是其凝集反应程度明显弱于蓖麻凝集素.从以上结果推测,凝集素的分子形态对金花茶多糖的凝集反应有显著影响.     

Amino Acid Composition of Hemerythrin in Relation to Subunit Structure

Determination of the amino acid composition of coelomic hemerythrin from Golfingia gouldii shows 3 arginine residues and 10 to 11 lysine residues per protein subunit of 13,500 molecular weight. On this basis, the 28 to 30 major peptide spots revealed by electrophoresis and chromatography of tryptic hydrolysates would indicate two kinds of subunit. However, similar evidence from chymotryptic hydrolyses is not unequivocal, since the number of peptide spots is also compatible with an assumption of only one kind of chain. In addition to indicating the possible existence of two types of subunit, the peptide maps of enzymic digests of hemerythrin from individual animals shows at least one and perhaps more differences in peptide composition.     

α?芋螺毒素LvIA第11位氨基酸的新突变体合成及其靶点活性

为了进一步探究第11位氨基酸的性质对LvIA靶点结合活性的影响，设计了LvIA的2个新型突变体[D11R]LvIA和[D11H]LvIA，即用2个碱性氨基酸?精氨酸（R）和组氨酸（H）分别替换原来的酸性氨基酸D。先人工合成了这2个新突变体的线性肽，然后采用2步氧化法进行折叠，以获得在第1位和第3位半胱氨酸（Cys 1～3）、第2位和第4位半胱氨酸（Cys 2～4）之间定点连接形成二硫键。经高效液相色谱分离纯化和质谱鉴定，合成了含有Cys(1～3, 2～4)二硫键连接方式的多肽，其分子质量正确，纯度在95%以上。利用双电极电压钳电生理学技术对这2种突变体与α3β2 nAChR的结合活性进行了检测。结果发现，当该位点的氨基酸性质由酸性转换为碱性后，对LvIA的活性影响巨大，直接导致对α3β2 nAChR的阻断活性丧失。[D11R]LvIA和[D11H]LvIA的活性与野生型LvIA相比分别降低了574.38%和408.62%。由此表明，第11位氨基酸的酸碱性对LvIA的活性至关重要。     

猪OLR1基因克隆及生物信息学分析

设计猪氧化低密度脂蛋白受体1(OLR1)基因编码区全长引物,从猪脂肪组织中扩增OLR1基因编码区全长序列,对其蛋白质序列进行比对分析,预测蛋白质信号肽位点及结构域并研究该基因密码子使用偏好性。结果表明:猪OLR1基因编码区全长为825 bp,共编码273个氨基酸,猪OLR1基因与牛同源性最高(84%),其次是人(79%)、大鼠(51%)和小鼠(27%)。猪OLR1蛋白38~60位氨基酸为信号肽所在位置,144~256位氨基酸正是C型凝集素家族共有结构域;OLR1基因密码子A U含量(61.2%)远高于G C含量(38.8%),而且偏向使用A/U结尾的密码子(占76.53%),这可能影响到OLR1基因的表达水平。     

Structure of a peptide inhibitor bound to the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase

The structure of a 20-amino acid peptide inhibitor bound to the catalytic subunit of cyclic AMP-dependent protein kinase, and its interactions with the enzyme, are described. The x-ray crystal structure of the complex is the basis of the analysis. The peptide inhibitor, derived from a naturally occurring heat-stable protein kinase inhibitor, contains an amphipathic helix that is followed by a turn and an extended conformation. The extended region occupies the cleft between the two lobes of the enzyme and contains a five-residue consensus recognition sequence common to all substrates and peptide inhibitors of the catalytic subunit. The helical portion of the peptide binds to a hydrophobic groove and conveys high affinity binding. Loops from both domains converge at the active site and contribute to a network of conserved residues at the sites of magnesium adenosine triphosphate binding and catalysis. Amino acids associated with peptide recognition, nonconserved, extend over a large surface area.     

Stimulation of gonadotropin release by a non-GnRH peptide sequence of the GnRH precursor

The human gonadotropin-releasing hormone (GnRH) precursor comprises the GnRH sequence followed by an extension of 59 amino acids. Basic amino acid residues in the carboxyl terminal extension may represent sites of processing to biologically active peptides. A synthetic peptide comprising the first 13 amino acids (H X Asp-Ala-Glu-Asn-Leu-Ile-Asp-Ser-Phe-Gln-Glu-Ile-Val X OH) of the 59-amino acid peptide was found to stimulate the release of gonadotropic hormones from human and baboon anterior pituitary cells in culture. The peptide did not affect thyrotropin or prolactin secretion. A GnRH antagonist did not inhibit gonadotropin stimulation by the peptide, and the peptide did not compete with GnRH for GnRH pituitary receptors, indicating that the action of the peptide is independent of the GnRH receptor. The GnRH precursor contains two distinct peptide sequences capable of stimulating gonadotropin release from human and baboon pituitary cells.     

大菱鲆hepcidin抗菌肽基因的克隆及在大肠杆菌中的高效表达

通过同源克隆结合RACE的方法从大菱鲆(Scophthal mus maximus)肝脏中克隆了大菱鲆hepcidin抗菌肽基因全长cDNA(GenBank accession number AY994074)。大菱鲆hepcidin基因cDNA全长778bp,包含有1个273bp的开放阅读框,编码1个长90氨基酸的前体肽。将大菱鲆hepcidin抗菌肽基因的成熟肽序列重组至原核表达载体pGEX-4T-1中,用IPTG诱导后,SDS-PAGE电泳显示在29ku处有特异性蛋白条带出现,表达的融合蛋白主要以包涵体形式存在,融合蛋白约占总蛋白的26%。Western-blotting分析发现表达的融合蛋白可以特异性地与GST抗体相识别。这些结果表明大菱鲆hepcidin抗菌肽基因成功实现了原核表达。     

Design and synthesis of a peptide having chymotrypsin-like esterase activity

A peptide having enzyme-like catalytic activity has been designed and synthesized. Computer modeling was used to design a bundle of four short parallel amphipathic helical peptides bearing the serine protease catalytic site residues serine, histidine, and aspartic acid at the amino end of the bundle in the same spatial arrangement as in chymotrypsin (ChTr). The necessary "oxyanion hole" and substrate binding pocket for acetyltyrosine ethyl ester, a classical ChTr substrate, were included in the design. The four chains were linked covalently at their carboxyl ends. The peptide has affinity for ChTr ester substrates similar to that of ChTr and hydrolyzes them at rates approximately 0.01 that of ChTr; total turnovers greater than 100 have been observed. The peptide is inhibited by ChTr specific inhibitors and is inactive toward benzoyl arginine ethyl ester, a trypsin substrate. The peptide is inactivated by heating above 60 degrees C, but recovers full catalytic activity upon cooling and lyophilization from acetic acid.     

Hydroxamic acids in nature

The hydroxamic acid bond occurs in products from fungi, yeast, bacteria, and plants. The -CON(OH)-bond arises by oxidation of a free or bound amino group in a unit structure which is often closely related to conventional amino acids. Products are known with one, two, or three hydroxamic acid groups per molecule. The chemistry of the ferrichrome type compounds, which are ferric trihydroxamate-containing peptides, has been worked out in detail and includes a complete crystallographic analysis of the ferrichrome A molecule. The trihydroxamates form potent complexes with ferric ion, called siderochromes, and these are believed to play a role in the metabolism of the metal ion in microorganisms. The actual physiological activity observed ranges from that of growth factor, antibiotic, antibiotic antagonist, tumor inhibitor or cell-division factor. The precise molecular mechanism whereby these substances exert their potent beological activity remains to be elucidated.     

Identification of a neuropeptide hormone that regulates sex pheromone production in female moths

A pheromone biosynthesis activating neuropeptide (PBAN) hormone that controls sex pheromone production in female moths was identified from the brain-subesophageal ganglion complexes of the adult corn earworm, Heliothis zea. PBAN has 33 amino acid residues and a molecular weight of 3900. Its amino acid sequence has no significant homology with any of the fully characterized peptide hormones. The synthetic peptide, at a dose of between 2 and 4 picomoles, induced production of a normal quantity of sex pheromone in ligated H. zea females. The peptide also induced pheromone production in six other species of moths, thus indicating that this or similar peptides may be responsible for the regulation of pheromone production in moths.     

Mechanisms of antibody binding to a protein

The mechanisms of antibody binding to a protein were studied by an analysis of specific amino acid residues critical to nine antigenic sites on myohemerythrin. Rabbit antisera to the whole protein were assayed for binding to more than 1500 distinct peptide analogs differing from the protein sequence by single amino acid replacements. The results, combined with information from the three-dimensional crystallographic structure, were used to evaluate probable mechanisms of antibody binding at individual sites. The data from all sites examined indicate that initial binding to solvent-exposed amino acid residues may promote local side-chain displacements and thereby allow the participation of other, previously buried, residues.