Complete sequence and gene organization of the Nosema heliothidis ribosomal RNA gene region

By sequencing the entire ribosomal RNA (rRNA) gene region of Nosema heliothidis isolated from cotton bollworm (Helicoverpa armigera), we showed that its gene organization is similar to the type species, Nosema bombycis: the 5'-large subunit rRNA (2,490 bp)-internal transcribed spacer (192 bp)-small subunit rRNA (1,232 bp)-intergenic spacer (274 bp)-5S rRNA (115 bp)-3'. We constructed two phylogenetic trees, analyzed phylogenetic relationships, examined rRNA organization of microsporidia, and compared the secondary structure of small subunit rRNA with closely related microsporidia. The latter two features may provide important information for the classification and phylogenetic analysis of microsporidia.     

Database of homology-derived protein structures and the structural meaning of sequence alignment

The database of known protein three-dimensional structures can be significantly increased by the use of sequence homology, based on the following observations. (1) The database of known sequences, currently at more than 12,000 proteins, is two orders of magnitude larger than the database of known structures. (2) The currently most powerful method of predicting protein structures is model building by homology. (3) Structural homology can be inferred from the level of sequence similarity. (4) The threshold of sequence similarity sufficient for structural homology depends strongly on the length of the alignment. Here, we first quantify the relation between sequence similarity, structure similarity, and alignment length by an exhaustive survey of alignments between proteins of known structure and report a homology threshold curve as a function of alignment length. We then produce a database of homology-derived secondary structure of proteins (HSSP) by aligning to each protein of known structure all sequences deemed homologous on the basis of the threshold curve. For each known protein structure, the derived database contains the aligned sequences, secondary structure, sequence variability, and sequence profile. Tertiary structures of the aligned sequences are implied, but not modeled explicitly. The database effectively increases the number of known protein structures by a factor of five to more than 1800. The results may be useful in assessing the structural significance of matches in sequence database searches, in deriving preferences and patterns for structure prediction, in elucidating the structural role of conserved residues, and in modeling three-dimensional detail by homology.     

Information on the secondary structure improves the quality of protein sequence alignment

The most popular algorithms employed in the pairwise alignment of protein primary structures (Smith-Watermann (SW) algorithm, FASTA, BLAST, etc.) only analyze the amino acid sequence. The SW algorithm is the most accurate, yielding alignments that agree best with superimpositions of the corresponding spatial structures of proteins. However, even the SW algorithm fails to reproduce the spatial structure alignment when the sequence identity is lower than 30%. The objective of this work was to develop a new and more accurate algorithm taking the secondary structure of proteins into account. The alignments generated by this algorithm and having the maximal weight with the secondary structure considered proved to be more accurate than SW alignments. With sequences having less than 30% identity, the accuracy (i.e., the portion of reproduced positions of a reference alignment obtained by superimposing the protein spatial structures) of the new algorithm is 58 vs. 35% of the SW algorithm. The accuracy of the new algorithm is much the same with secondary structures established experimentally or predicted theoretically. Hence, the algorithm is applicable to proteins with unknown spatial structures. The program is available at ftp://194.149.64.196/STRUSWER/.     

Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities

The profile method, for detecting distantly related proteins by sequence comparison, has been extended to incorporate secondary structure information from known X-ray structures. The sequence of a known structure is aligned to sequences of other members of a given folding class. From the known structure, the secondary structure (alpha-helix, beta-strand or "other") is assigned to each position of the aligned sequences. As in the standard profile method, a position-dependent scoring table, termed a profile, is calculated from the aligned sequences. However, rather than using the standard Dayhoff mutation table in calculating the profile, we use distinct amino acid mutation tables for residues in alpha-helices, beta-strands or other secondary structures to calculate the profile. In addition, we also distinguish between internal and external residues. With this new secondary structure-based profile method, we created a profile for eight-stranded, antiparallel beta barrels of the insecticyanin folding class. It is based on the sequences of retinol-binding protein, insecticyanin and beta-lactoglobulin. Scanning the sequence database with this profile, it was possible to detect the sequence of avidin. The structure of streptavidin is known, and it appears to be distantly related to the antiparallel beta barrels. Also detected is the sequence of complement component C8, which we therefore predict to be a member of this folding class.     

Analysis of sequence requirements for protein tyrosine sulfation.

We analyzed sequences surrounding known tyrosine sulfation sites to determine the characteristics that distinguish these sites from those that do not undergo sulfation. Tests evaluated the number and position of acidic, basic, hydrophobic, and small amino acids, as well as disulfide and N-glycosylation (sugar) sites. We determined that composition-based tests that select close to 100% of known tyrosine sulfation sites reject 97% of the non-sulfated tyrosines. The acidic test, by far the most selective, eliminated 95% of the non-sulfated tyrosine residues and none of the sulfated tyrosines. Including the basic, hydrophobic, and disulfide tests increased the elimination rate to 97%. Whereas no position flanking the tyrosine residues had the same amino acid always present, imperfectly conserved amino acids found in some positions will improve the specificity of the tests.     

Walking through protein sequence space

Following the original idea of Maynard Smith on evolution of the protein sequence space, a novel tool is developed that allows the "space walk", from one sequence to its likely evolutionary relative and further on. At a given threshold of identity between consecutive steps, the walks of many steps are possible. The sequences at the ends of the walks may substantially differ from one another. In a sequence space of randomized (shuffled) sequences the walks are very short. The approach opens new perspectives for protein evolutionary studies and sequence annotation.     

Comparison of conformational characteristics in structurally similar protein pairs.

Although it is known that three-dimensional structure is well conserved during the evolutionary development of proteins, there have been few studies that consider other parameters apart from divergence of the main-chain coordinates. In this study, we align the structures of 90 pairs of homologous proteins having sequence identities ranging from 5 to 100%. Their structures are compared as a function of sequence identity, including not only consideration of C alpha coordinates but also accessibility, Ooi numbers, secondary structure, and side-chain angles. We discuss how these properties change as the sequences become less similar. This will be of practical use in homology modeling, especially for modeling very distantly related or analogous proteins. We also consider how the average size and number of insertions and deletions vary as sequences diverge. This study presents further quantitative evidence that structure is remarkably well conserved in detail, as well as at the topological level, even when the sequences do not show similarity that is significant statistically.     

同义密码子的反常蛋白质二级结构偏好性

统计分析了 119种人蛋白质和 92种大肠杆菌蛋白质的mRNA序列和蛋白质二级结构的关系 .从二肽频数出发 ,研究了同义密码子使用对蛋白质二级结构的影响 ,证明其影响在 10 %到 2 0 %的量级 .对于人和大肠杆菌 ,在 90 %置信水平上 ,4 0 0对二肽中分别有 79对和 6 0对 ,在 95 %置信水平上 ,分别有 4 5对和 36对二肽的相应密码子二联体具有不同于氨基酸的反常二级结构偏好性 ,并且这种反常不能归因于随机涨落     

Clustal W—蛋白质与核酸序列分析软件

蛋白质与核酸的序列分析在现代生物学和生物信息学中发挥着重要作用,新的算法和软件层出不穷,本文介绍一个可运行在ＰＣ机上的完全免费的多序列比较软件－ＣｌｕｓｔａｌＷ,它不但可以进行蛋白质与核酸的多序列比较,分析不同序列之间的相似性关系,还可以绘制进化树。由于其灵活的输入输出格式、方便的参数设定和选择、详尽的在线帮助以及良好的可移植性,使得ＣｌｕｓｔａｌＷ在蛋白质与核酸的序列分析中得到了广泛应用。     

Conformational characteristics of the complete sequence of group A streptococcal M6 protein

M protein is considered a virulence determinant on the streptococcal cell wall by virtue of its ability to allow the organism to resist attack by human neutrophils. The complete DNA sequence of the M6 gene from streptococcal strain D471 has allowed, for the first time, the study of the structural characteristics of the amino acid sequence of an entire M protein molecule. Predictive secondary structural analysis revealed that the majority of this fibrillar molecule exhibits strong alpha-helical potential and that, except for the ends, nonpolar residues in the central region of the molecule exhibit the 7-residue periodicity typical for coiled-coil proteins. Differences in this heptad pattern of nonpolar residues allow this central rod region to be divided into three subdomains which correlate essentially with the repeat regions A, B, and C/D in the M6 protein sequence. Alignment of the N-terminal half of the M6 sequence with PepM5, the N-terminal half of the M5 protein, revealed that 42% of the amino acids were identical. The majority of the identities were "core" nonpolar residues of the heptad periodicity which are necessary for the maintenance of the coiled coil. Thus, conservation of structure in a sequence-variable region of these molecules may be biologically significant. Results suggest that serologically different M proteins may be built according to a basic scheme: an extended central coiled-coil rod domain (which may vary in size among strains) flanked by functional end domains.     

蛋白质亚细胞定位预测中的序列编码技术

蛋白质序列的编码是亚细胞定位预测问题中的关键技术之一。该文较为详细地介绍了目前已有的蛋白质序列编码算法;并指出了序列编码中存在的一些问题及可能的发展方向。     

蛋白质结构型的定义和识别

提出紧结构域的概念,由二级结构序列中一段或几段连续的α螺旋和β折叠构成的空间紧密堆集的最大折叠体称为紧结构域.利用3种紧结构域（α域,β域和α/β域）定义球蛋白的5种结构型：α型蛋白,β型蛋白,α/β型蛋白,多域蛋白和ζ型蛋白.将1 261个代表性的蛋白质(1 022家族)进行分类,并和SCOP库的分类做了比较.进行了删去序列冗余的分析.在此基础上提出结构型的预测方案,成功率在82%～85%.     

Complete amino acid sequence of Bombyx egg-specific protein deduced from cDNA clone

Complementary (c)DNA coding for an insect yolk protein, the egg-specific protein of the silkworm Bombyx mori was cloned and the nucleotide sequence determined. The sequence covers the entire coding region of 1,677 base pairs with 5′ and 3′ noncoding regions (21 and 115 base pairs, respectively). The deduced amino acid sequence of the egg-specific protein consists of 559 amino acid residues. The NH₂-terminal 18 amino acid sequence is enriched in hydrophobic amino acids and assumed to be a signal peptide. A sequence, Asn-X-Thr, a potential N-linked glycosylation site, is found at positions 191 to 193. A serine-rich domain is localized in the region from 63 to 90, in which phosphorylation takes place. Cys His motif in 405 to 415 is analogous to a proposed metal binding sequence. Lys¹³²-Asn¹³³ and Arg²²⁸-Asp²²⁹ are probably the sites cleaved by the egg-specific protein protease that appears during embryogenesis. The derived amino acid sequence has no appreciable homology to other sequenced proteins.     

Ion pairs in non-redundant protein structures

Ion pairs contribute to several functions including the activity of catalytic triads, fusion of viral membranes, stability in thermophilic proteins and solvent-protein interactions. Furthermore, they have the ability to affect the stability of protein structures and are also a part of the forces that act to hold monomers together. This paper deals with the possible ion pair combinations and networks in 25% and 90% non-redundant protein chains. Different types of ion pairs present in various secondary structural elements are analysed. The ion pairs existing between different subunits of multisubunit protein structures are also computed and the results of various analyses are presented in detail. The protein structures used in the analysis are solved using X-ray crystallography, whose resolution is better than or equal to 1.5 A and R-factor better than or equal to 20%. This study can, therefore, be useful for analyses of many protein functions. It also provides insights into the better understanding of the architecture of protein structure.