The predicted structure of immunoglobulin D1.3 and its comparison with the crystal structure

Predictions of the structures of the antigen-binding domains of an antibody, recorded before its experimental structure determination and tested subsequently, were based on comparative analysis of known antibody structures or on conformational energy calculations. The framework, the relative positions of the hypervariable regions, and the folds of four of the hypervariable loops were predicted correctly. This portion includes all residues in contact with the antigen, in this case hen egg white lysozyme, implying that the main chain conformation of the antibody combining site does not change upon ligation. The conformations of three residues in each of the other two hypervariable loops are different in the predicted models and the experimental structure.     

Inhibition of self-binding antibodies (autobodies) by a VH-derived peptide

The self-binding properties of a dominant idiotypic antibody (T15) and a minor idiotypic antibody (M603), both specific for phosphorylcholine, were examined as models of self-binding antibodies (autobodies). Observed differences in the self-binding affinity of T15 and M603 relate to variable sequence differences in their respective heavy and light chains. A molecular recognition theory based on the translation of coding and noncoding DNA strands was used to identify complementary amino acid sequences responsible for self-binding. The second hypervariable region of the heavy chain domain, extending into the third framework region, was predicted as the primary self-binding locus. Among peptides synthesized with different variable heavy and light chain regions, a 24-residue peptide spanning the second hypervariable and third framework regions of the heavy chain of T15 was nearly as effective as phosphorycholine in inhibiting the self-binding complexes.     

Antibody active sites and immunoglobulin molecules

In order to obtain detailed information about the relationship between structure and function in antibody molecules, a method called affinity labeling has been devised to attach chemical labels specifically to amino acid residues in the active sites of antibody molecules. With antibodies to three different haptens, highly specific labeling of the active sites has been achieved. Tyrosine residues on both heavy and light polypeptide chains have been labeled in a molar ratio close to 2:1, and labels on the two chains are equally specific to the active sites. Peptide fragmentation studies of the labeled chains of one antibody system have shown that: (i) within 25 amino acid residues of the labeled tyrosine on either chain, substantial chemical heterogeneity exists among different antibody molecules of the same specificity; and (ii) the labeled peptide fragments from both chains are very similar in physicochemical characteristics, including average size, heterogeneity, and unusual hydrophobicity. These experimental results have led us to the view that a particular region of the heavy chain and a particular region of the light chain are utilized to construct the active sites of the three different antibodies, differences in specificity arising from chemical perturbations in these two regions. Correlated structural studies of affinity-labeled antibodies and of the homogeneous light chains (Bence Jones proteins) and heavy chains produced in multiple myeloma may permit the identification of these special active-site regions. The view that active sites of different specificity are chemical perturbations of a particular region of the antibody molecule has a possible close analogue in enzyme systems, particularly among the esterases. The marked chemical similarities we have observed between the active site regions of heavy and light chains indicate to us that chemical homologies, but not identities, exist between the chains. This is reinforced by recently obtained amino acid sequence data which reveal homologies between the two chains near their carboxyl-terminals. These results indicate that the structural genes which code for the synthesis of heavy and light chains are related, presumably having arisen from some common ancestral gene during evolution. This conclusion strongly suggests that both heavy and light chains determine antibody specificity, and has important implications for the still-unknow mechanisms of antibody biosynthesis.     

鸡传染性法氏囊病病毒河南分离株HeYD VP2基因高变区基因克隆及序列分析

为初步确定新分离的鸡传染性法氏囊病毒(IBDV)河南株HeYD的毒力,根据GenBank数据库中已报道的IBDV基因组序列,设计合成了1对VP2基因高变区特异性引物,应用RT-PCR方法对分离自河南省某发病鸡场的IBDV野毒株HeYD的VP2基因高变区进行了基因克隆及序列分析,并与其他参考毒株高变区进行了序列比对,序列...     

Three-dimensional structure of an antigen-antibody complex at 2.8 A resolution

The 2.8 A resolution three-dimensional structure of a complex between an antigen (lysozyme) and the Fab fragment from a monoclonal antibody against lysozyme has been determined and refined by x-ray crystallographic techniques. No conformational changes can be observed in the tertiary structure of lysozyme compared with that determined in native crystalline forms. The quaternary structure of Fab is that of an extended conformation. The antibody combining site is a rather flat surface with protuberances and depressions formed by its amino acid side chains. The antigen-antibody interface is tightly packed, with 16 lysozyme and 17 antibody residues making close contacts. The antigen contacting residues belong to two stretches of the lysozyme polypeptide chain: residues 18 to 27 and 116 to 129. All the complementarity-determining regions and two residues outside hypervariable positions of the antibody make contact with the antigen. Most of these contacts (10 residues out of 17) are made by the heavy chain, and in particular by its third complementarity-determining region. Antigen variability and antibody specificity and affinity are discussed on the basis of the determined structure.     

中国柑橘黄龙病病原菌两个原噬菌体超变异基因遗传多样性

【目的】通过原噬菌体区域高度变异的基因位点研究柑橘黄龙病病原菌亚洲种（‘Candidatus Liberibacter asiaticus’）的种群分化,探讨病原菌种群遗传多样性水平和遗传结构。【方法】基于2种原噬菌体类型（SC1和SC2）对应的超变异基因区域设计2对引物（Lap-TJ-F/Lap-TJ-R1和Lap-TJ-F/Lap-TJ-R2）,对中国不同柑橘产区的224个‘Ca. L. asiaticus’株系进行PCR检测和序列分析。【结果】PCR扩增的条带类型呈多态性,具有4种条带类型（SC1-1、SC1-2、SC2-1和SC2-2）,西南地区以SC1-1型为主,广东、广西地区以SC2-1型为主,福建、江西、浙江地区没有明显优势的扩增型。分析SC1-1和SC1-2对应序列表明,其差异系由于132 bp的卫星序列和24 bp的小卫星序列2种串联重复序列数不同引起,而SC2-1和SC2-2的差异系由原噬菌体内部基因重排引起。【结论】中国不同地理来源病原菌株系在原噬菌体区域具有较丰富的多态性,对该基因区域研究将有助于揭示中国‘Ca. L. asiaticus’种群的遗传多样性。     

中国不同地区烟草寄生疫霉(Phytophthora parasitica var. nicotianae)菌株的随即多态性DNA扩增分析

来自中国云南、辽宁、山东3省的烟草寄生疫霉（Phytophthora parasitica var.nicotianae)菌株的致病性已被划分为3种致病类型组，即强致病性组、中致病性组和弱致性组。上述省是中国的烟草主产区，选自云南省的15个烟草寄生疫霉菌株、山东省的13个烟草寄生霉菌株和辽宁省的20个烟草寄生疫霉菌株，选择3个烟草栽培品种在温室内进行接种试验测定不同菌株的致病性分化。提取受试菌株的DNA，利用PCR技术对受试苗菌株的模板DNA进行随机多态性扩增分析，对扩增DNA片段谱带借助于UPGMA分析法构建遗传树，结果表明，受试菌株被划分为4个遗传聚类组，每个遗传聚类组内包括不同的烟草寄生疫霉致病性菌株，而且来自于不同烟区相同的致病性菌株和每种致病性的不同菌株皆不属于同一个遗传聚类组内。结果表明RAPD－PCR的遗传标记分析结果与不同致病性组的划分未有明显的区别。因此，随机多态性DNA图谱的相同与不同不能当作区分来自不同烟区的烟草寄生疫霉的致病性分化的分子检测的工具。     

Structure of a gammadelta T cell receptor in complex with the nonclassical MHC T22

Gammadelta T cell receptors (TCRs), alphabeta TCRs, and antibodies are the three lineages of somatically recombined antigen receptors. The structural basis for ligand recognition is well defined for alphabeta TCR and antibodies but is lacking for gammadelta TCRs. We present the 3.4 A structure of the murine gammadelta TCR G8 bound to its major histocompatibility complex (MHC) class Ib ligand, T22. G8 predominantly uses germline-encoded residues of its delta chain complementarity-determining region 3 (CDR3) loop to bind T22 in an orientation substantially different from that seen in alphabeta TCR/peptide-MHC. That junctionally encoded G8 residues play an ancillary role in binding suggests a fusion of innate and adaptive recognition strategies.     

甘蔗花叶病毒(SCMV)种群结构分析

针对已公布的18个甘蔗花叶病毒(SCMV)全基因组序列,利用MEGA 5.1分析了其11个蛋白(P1、HC-Pro、P3、6K1、CI、6K2、VPg、NIa-Pro、Nib、CP-C和多聚蛋白)编码基因所受的选择压,并结合其编码蛋白的功能,预测了部分基因在SCMV进化过程中的角色和变异位点.结果显示:P1和CP-N端的变异性程度较大,P1蛋白多样性最高;CP-C端变异性和多样性均较低;PIPO受到的选择压最小,但多样性最低,可能是由于PIPO与P3共用一段编码序列.来源于甘蔗的SCMV多聚蛋白的第2 853、2 897和2 904个氨基酸位点(在CP中部)分别为T、R和E,而来源于玉米的SCMV多聚蛋白对应的氨基酸位点分别为S、K和D,表明这3个位点具有寄主依赖性.     

檀香咖啡豹蠹蛾虫害的树干区域分类研究

目的檀香是一种典型的珍贵树种,但不易成活且常遭受病虫害的干扰。本研究针对受咖啡豹蠹蛾危害的檀香,为提高受害檀香树干区域的分类效果,根据不同区域在颜色和纹理方面的特点,提出了一种复杂背景下受咖啡豹蠹蛾危害的檀香树干区域分类方法。方法(1) 本文首先结合高斯高通滤波、Otsu法、2G-R-B因子以及形态学运算,将树干从复杂背景中提取出来,再通过L*a*b*系统中的L*通道和a*通道将树干分割为健康区域、虫害区域和排泄物区域。(2)提出“多纹理”并使用“相对颜色”特征变换方法以提取图像特征。(3)提出BP神经网络和RBF-SVM相结合的方法对区域进行识别。结果(1) 本文提出的图像分割算法有效地将受虫害危害的檀香从背景中提取出来,并成功分割为健康区域、虫害区域和排泄物区域。(2)与传统PCA处理相比,使用“多纹理”和“相对颜色特征”得到的分类精度有所提高。其中,“多纹理”特征通过差异扩大的方法构建出的图像特征,明显增加了类间方差;“相对颜色特征”则减小了光照对样本的影响,从而减小了类内方差。(3)通过将RBF-SVM与BP神经网络方法相结合,对比发现,使用一种方法进行三分类的精度较低,分别为74.44%和81.11%;两次二分类后提高了精度,分别为87.77%和85.56%;而两种方法相结合的方式所得到的分类精度最高,总体可达91.11%。结论本文通过数字图像对受咖啡豹蠹蛾危害的檀香树干区域进行分类,为该虫害的早期识别以及受损率计算提供了方法,可以有效地减小檀香生长所受危害,提高心材质量,也为数字图像技术在林业中的应用提供了参考。      

四川小麦地方品种AS1643中α/β醇溶蛋白基因

用PCR方法从四川小麦地方品种AS1643中克隆到3个α/β-醇溶蛋白基因，即Gli-AS1643-1（GenBank No.DQ166376）、Gli-AS1643-2（GenBank No.DQ166377）和Gli-AS1643-3（GenBank No.DQ166378）。其中，Gli-AS1643-1和Gli-AS1643-2的编码区长度分别为873bp和852bp，可编码270和263个氨基酸残基的成熟蛋白。Gli-AS1643-3由于在编码区内有一个提前终止密码子，为不可编码成熟蛋白的假基因。序列比较显示Gli-AS1643-1、Gli-AS1643-2和 Gli-AS1643-3分别与GenBank中的α/β-醇溶蛋白基因具有较高的一致性，且序列结构非常相似。它们的N-端氨基酸序列与各种α-、β-、γ-和α/β-醇溶蛋白的基本一致，但与ω-醇溶蛋白和低分子量谷蛋白亚基的明显不同。N-端12肽串联重复紧密相关的5个脯氨酸框和类似于微卫星序列编码的2个多聚谷氨酰胺区域。在Gli-AS1643-2的N-端存在腹泻疾病活性序列，C-端含有12型腺病毒感染序列。Gli-AS1643-1、Gli-AS1643-2和Gli-AS1643-3各由6个保守的半胱氨酸残基形成3个分子内二硫键。     

Erratum

In the report "Broadly neutralizing antibodies elicited by the hypervariable neutralizing determinant of HIV-1" by K. Javaherian et al. (14 Dec., p. 1590), the headings for tables 4 and 5 on page 1592 were incorrectly interchanged.     

Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins

Ras proteins participate as a molecular switch in the early steps of the signal transduction pathway that is associated with cell growth and differentiation. When the protein is in its GTP complexed form it is active in signal transduction, whereas it is inactive in its GDP complexed form. A comparison of eight three-dimensional structures of ras proteins in four different crystal lattices, five with a nonhydrolyzable GTP analog and three with GDP, reveals that the "on" and "off" states of the switch are distinguished by conformational differences that span a length of more than 40 A, and are induced by the gamma-phosphate. The most significant differences are localized in two regions: residues 30 to 38 (the switch I region) in the second loop and residues 60 to 76 (the switch II region) consisting of the fourth loop and the short alpha-helix that follows the loop. Both regions are highly exposed and form a continuous strip on the molecular surface most likely to be the recognition sites for the effector and receptor molecule(or molecules). The conformational differences also provide a structural basis for understanding the biological and biochemical changes of the proteins due to oncogenic mutations, autophosphorylation, and GTP hydrolysis, and for understanding the interactions with other proteins.     

Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution

The structure of a complex between a peptide inhibitor with the sequence N-acetyl-Thr-Ile-Nle-psi[CH2-NH]-Nle-Gln-Arg.amide (Nle, norleucine) with chemically synthesized HIV-1 (human immunodeficiency virus 1) protease was determined at 2.3 A resolution (R factor of 0.176). Despite the symmetric nature of the unliganded enzyme, the asymmetric inhibitor lies in a single orientation and makes extensive interactions at the interface between the two subunits of the homodimeric protein. Compared with the unliganded enzyme, the protein molecule underwent substantial changes, particularly in an extended region corresponding to the "flaps" (residues 35 to 57 in each chain), where backbone movements as large as 7 A are observed.     

偶蹄动物朊蛋白基因变异性和其系统发生关系分析

【目的】为明了偶蹄动物PrP基因的结构特征及其变异与结构、功能和朊粒病传染种间屏障的关系以及系统发生关系;【方法】利用DNAstar和Clustalx程序及treev32软件进行了22种偶蹄动物的43个完整PrP基因序列的同源性分析、多重排比和进化树构建;【结果】不同种属偶蹄动物的PrP基因完整ORF大小有所差异,范围为768～795 bp,可编码255～264个氨基酸的朊蛋白。核苷酸和氨基酸序列的同源性,偶蹄动物间≥88.6%和≥93.3%,反刍动物间≥95.4%和≥96.5%。共发现40个点突变和2个突变区。在N-端柔韧无序"尾"区(25～135)以八肽重复缺失为主,球形结构域区(136～241)以点突变为主,点突变主要簇聚在S1 -折叠前的柔韧无规卷曲区的C-端部分和HC -螺旋内。氨基酸104～135区和球形结构域区存在有8个高突变位点。已知PrP肽基元和功能位点如芳烃回文序列基元、2个N-连接糖基化位点、2个苏氨酸磷酸化位点、1个酪氨酸硫化位点、形成二硫键的2个半胱氨酸以及GPI锚锚着点丝氨酸为偶蹄动物所共有,各种间变异体的各结构模式非常一致。进化关系分析,可将偶蹄动物PrP基因区分为3大类,反刍动物PrP基因分为3小类。令人意外的是,2个双峰驼PrP基因的进化关系与牛属动物基因同源。【结论】偶蹄动物的PrP基因是一个保守基因,氨基酸104～135区和球形结构域区内的8个高突变位点可能是影响分子间相互作用、形成朊粒病传染种间屏障的主要位点,物种间各氨基酸变异并不影响PrP的主要结构和功能。     

Receptor and antibody epitopes in human growth hormone identified by homolog-scanning mutagenesis

A strategy, termed homolog-scanning mutagenesis, was used to identify the epitopes on human growth hormone (hGH) for binding to its cloned liver receptor and eight different monoclonal antibodies (Mab's). Segments of sequences (7 to 30 residues long) that were derived from homologous hormones known not to bind to the hGH receptor or Mab's, were systematically substituted throughout the hGH gene to produce a set of 17 chimeric hormones. Each Mab or receptor was categorized by a particular subset of mutant hormones was categorized by a particular subset of mutant hormones that disrupted binding. Each subset of the disruptive mutations mapped within close proximity on a three-dimensional model of hGH, even though the residues changed within each subset were usually distant in the primary sequence. The mapping analysis correctly predicted those Mab's which could or could not block binding of the receptor to hGH and further suggested (along with other data) that the folding of these chimeric hormones is like that of HGH. By this analysis, three discontinuous polypeptide determinants in hGH--the loop between residues 54 and 74, the central portion of helix 4 to the carboxyl terminus, and to a lesser extent the amino-terminal region of helix 1--modulate binding to the liver receptor. Homolog-scanning mutagenesis should be of general use in identifying sequences that cause functional variation among homologous proteins.     

Expression in Escherichia coli of open reading frame gene segments of HTLV-III

Human T-cell lymphotropic virus type III (HTLV-III), the causative agent of the acquired immune deficiency syndrome (AIDS), was recently isolated and its genomic structure analyzed by DNA cloning methods. In the studies reported here a combined cloning and expression system was used to identify HTLV-III encoded peptides that react immunologically with antibodies in sera from AIDS patients. Cloned HTLV-III DNA was sheared into approximately 500-base-pair fragments and inserted into an "open reading frame" expression vector, pMR100. The inserted DNA was expressed in Escherichia coli transformants as a polypeptide fused to the lambda CI protein at its amino terminus and to beta-galactosidase at its carboxyl terminus. Sera from AIDS patients containing antibodies to HTLV-III were then used to screen for immunoreactive fusion proteins. Twenty clones, each specifying a fusion protein strongly reactive with AIDS serum, were identified. DNA sequence analysis indicated that the HTLV-III fragments were derived from the open reading frame DNA segments corresponding to the gag and pol gene coding regions and also the large open reading frame region (env-lor) located near the 3' end of the viral genome.     

基于农业分区的陕西省现代农业发展水平评价

现代农业除了具有高投入、高产出及生态效益等基本特征之外,还需要充分立足区域自然资源禀赋的特征。选取陕西省为实证研究对象,围绕现代农业基本特征,从农业投入水平等7个一级指标和有效灌溉率等23个二级指标,构建了陕西省现代农业发展水平评价基本指标体系。立足陕西省三大农业自然分区及其农业资源禀赋特征,采用层次分析法,分别对陕北、关中和陕南现代农业发展指标赋权,体现区域农业发展特色,并在一定程度上实现了不同区域评估结果的可比性与兼容性。运用综合评价法,评估陕西三大区域现代农业水平。结果表明,陕西省处于现代农业初步实现阶段;三大区域现代农业发展水平呈现倒"U"型;同一区域内部现代农业发展水平不均衡。最后,分别从陕西省和区域角度提出政策涵义。     

Conserved residues make similar contacts in two repressor-operator complexes

Comparison of a lambda repressor-operator complex and a 434 repressor-operator complex reveals that three conserved residues in the helix-turn-helix (HTH) region make similar contacts in each of the crystallographically determined structures. These conserved residues and their interactions with phosphodiester oxygens help establish a frame of reference within which other HTH residues make contacts that are critical for site-specific recognition. Such "positioning contacts" may be important conserved features within families of HTH proteins. In contrast, the structural comparisons appear to rule out any simple "recognition code" at the level of detailed side chain-base pair interactions.