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41.
Parthasarathy Manavalan Alan E. Smith John M. McPherson 《Journal of Protein Chemistry》1993,12(3):279-290
A sequence comparison of the two membrane-associated (MA) domains of the cystic fibrosis transmembrane conductance regulator (CFTR), multidrug resistance transporter (MDR), and -factor pheromone export system (STE6) proteins, each of which are believed to contain a total of 12 transmembrane (TM) segments, reveals significant amino acid homology and length conservation in the loop regions that connect individual TM sequences. Similar structural homology is observed between these proteins, hemolysin B (HLYB) and the major histocompatibility-linked peptide transporter, HAM1, the latter two which contain a single MA domain composed of six TM segments. In addition, there are specific sequences that are conserved within the TM segments of the five different membrane proteins. This observation suggests that the folding topologies of the MA domains of MDR, STE6, and CFTR in the plasma membrane are likely to be very similar. The sequence analysis also reveals that there are three characteristic motifs (a pair of aromatic residues, LTLXXXXXXP and GXXL) that are conserved in MDR, STE6, HLYB, HAM1, but not in CFTR. We propose that although CFTR may be evolutionarily related to these other membrane proteins, it belongs to a separate subclass. 相似文献
42.
在地衣芽孢杆菌NCIB 6816菌株碱性蛋白酶基因已知序列的基础上,通过设计合适的引物,利用PCR(Polymerase Chain Reaction)技术从地衣芽孢杆菌2709菌株的柒色体DNA中扩增了2709碱性蛋白酶的编码序列。对两个克隆的PCR片段的全序列分析结果显示,2709碱性蛋白酶的编码序列同相应的NCIB 6816序列相比有3%左右的碱基组成差异。由此推定的2709碱性蛋白酶的氨基酸序列肯定了2709碱性蛋白酶属典型的subtilisin Carlsberg类,同时还表明来源于不同地衣芽孢杆菌菌株的subtilisin Carlsberg存在着若干氨基酸组成上的差异。 相似文献
43.
44.
Comparison of conformational characteristics in structurally similar protein pairs. 总被引:17,自引:7,他引:10 下载免费PDF全文
T. P. Flores C. A. Orengo D. S. Moss J. M. Thornton 《Protein science : a publication of the Protein Society》1993,2(11):1811-1826
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. 相似文献
45.
Manuel B. Aguilar Daniel Soyez Rocco Falchetto David Arnott Jeffrey Shabanowitz Donald F. Hunt Alberto Huberman 《Peptides》1995,16(8):1375-1383
The primary structure of the neurohormone crustacean hyperglycemic hormone (CHH-II) was determined by means of enzymatic digestions, manual Edman degradation, and mass spectrometry. CHH-II is a 72 residue peptide (molecular mass 8388 Da), with six cysteines forming three disulfide bridges that connect residues 7–43, 23–39, and 26–52. The peptide has blocked N- and C-termini, and lacks tryptophan, histidine, and methionine. The CHH-I and CHH-II of Procambarus bouvieri have identical sequences and elicit levels of hyperglycemia that are not distinguishable. The difference between the two isomorphs consists in a posttranslational modification of a l-Phe in CHH-I to a d-Phe in CHH-II at the third position from the N-terminus. 相似文献
46.
The possible B-cell epitopes of the outer membrane porin OmpC ofSalmonella typhi have been identified, using the primary structure of the protein, by means of multiple sequence alignment and the known molecular
structure of two other porins. From the analysis, 8 regions were identified as immunodominant and these were ranked based
on antigenic index and the ratio of the number of nonconserved residues to the fragment length. Model building of the top
two ranked regions show the tendency to form loop structures supporting the possibility of these being candidate epitopes. 相似文献
47.
The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment 总被引:20,自引:0,他引:20
The size distributions of deletions, insertions, and indels (i.e., insertions or deletions) were studied, using 78 human processed pseudogenes and other published data sets. The following results were obtained: (1) Deletions occur more frequently than do insertions in sequence evolution; none of the pseudogenes studied shows significantly more insertions than deletions. (2) Empirically, the size distributions of deletions, insertions, and indels can be described well by a power law, i.e., f
k
= Ck
–b
, where f
k
is the frequency of deletion, insertion, or indel with gap length k, b is the power parameter, and C is the normalization factor. (3) The estimates of b for deletions and insertions from the same data set are approximately equal to each other, indicating that the size distributions for deletions and insertions are approximately identical. (4) The variation in the estimates of b among various data sets is small, indicating that the effect of local structure exists but only plays a secondary role in the size distribution of deletions and insertions. (5) The linear gap penalty, which is most commonly used in sequence alignment, is not supported by our analysis; rather, the power law for the size distribution of indels suggests that an appropriate gap penalty is w
k
= a + b ln k, where a is the gap creation cost and blnk is the gap extension cost. (6) The higher frequency of deletion over insertion suggests that the gap creation cost of insertion (a
i
) should be larger than that of deletion (a
d
); that is, a
i
– a
d
= In R, where R is the frequency ratio of deletions to insertions.
Correspondence to: W.-H. Li 相似文献
48.
R. J. Siezen J. A. Leunissen 《Protein science : a publication of the Protein Society》1997,6(3):501-523
Subtilases are members of the clan (or superfamily) of subtilisin-like serine proteases. Over 200 subtilases are presently known, more than 170 of which with their complete amino acid sequence. In this update of our previous overview (Siezen RJ, de Vos WM, Leunissen JAM, Dijkstra BW, 1991, Protein Eng 4:719-731), details of more than 100 new subtilases discovered in the past five years are summarized, and amino acid sequences of their catalytic domains are compared in a multiple sequence alignment. Based on sequence homology, a subdivision into six families is proposed. Highly conserved residues of the catalytic domain are identified, as are large or unusual deletions and insertions. Predictions have been updated for Ca(2+)-binding sites, disulfide bonds, and substrate specificity, based on both sequence alignment and three-dimensional homology modeling. 相似文献
49.
D. Casane S. Boissinot B.H.-J. Chang L.C. Shimmin W.-H. Li 《Journal of molecular evolution》1997,45(3):216-226
We sequenced three argininosuccinate-synthetase-processed pseudogenes (ΨAS-A1, ΨAS-A3, ΨAS-3) and their noncoding flanking
sequences in human, orangutan, baboon, and colobus. Our data showed that these pseudogenes were incorporated into the genome
of the Old World monkeys after the divergence of the Old World and New World monkey lineages. These pseudogene flanking regions
show variable mutation rates and patterns. The variation in the G/C to A/T mutation rate (u) can account for the unequal GC contents at equilibrium: 34.9, 36.9, and 41.7% in the pseudogene ΨAS-A1, ΨAS-A3, and ΨAS-3
flanking regions, respectively. The A/T to G/C mutation rate (v) seems stable and the u/v ratios equal 1.9, 1.7, and 1.4 in the flanking regions of ΨAS-A1, ΨAS-A3, and ΨAS-3, respectively. These ``regional' variations
of the mutation rate affect the evolution of the pseudogenes, too. The ratio u/v being greater than 1.0 in each case, the overall mutation rate in the GC-rich pseudogenes is, as expected, higher than in
their GC-poor flanking regions. Moreover, a ``sequence effect' has been found. In the three cases examined u and v are higher (at least 20%) in the pseudogene than in its flanking region—i.e., the pseudogene appears as mutation ``hot'
spots embedded in ``cold' regions. This observation could be partly linked to the fact that the pseudogene flanking regions
are long-standing unconstrained DNA sequences, whereas the pseudogenes were relieved of selection on their coding functions
only around 30–40 million years ago. We suspect that relatively more mutable sites maintained unchanged during the evolution
of the argininosuccinate gene are able to change in the pseudogenes, such sites being eliminated or rare in the flanking regions
which have been void of strong selective constraints over a much longer period. Our results shed light on (1) the multiplicity
of factors that tune the spontaneous mutation rate and (2) the impact of the genomic position of a sequence on its evolution.
Received: 10 February 1997 / Accepted: 21 April 1997 相似文献
50.
Maria Manuela M. Caniça Chang Y. Lu Rajagopal Krishnamoorthy Gérard C. Paul 《Journal of molecular evolution》1997,44(1):57-65
The molecular diversity of inhibitor-resistant TEM (IRT) enzymes was explored using a strategy which involved DNA amplification
by polymerase chain reaction (PCR), analysis of restriction fragment length polymorphism (RFLP), and direct nucleotide sequencing.
The study of plasmid-borne genes from 27 strains, resistant to amoxicillin and β-lactamase-inhibitor combinations, identified
mutations resulting in amino acid change at positions 69, 244, 275, and 276 known to be associated with the IRT phenotype
and a mutation at nucleotide position 162 in the promoter region. These mutations were found to lie on two different gene
sequences, described here as ``TEM-1B like' and ``TEM-2 like' restriction linkage groups. Further analysis, of nucleotide
sequences of promoter and coding regions of the β-lactamases, confirmed that a given mutation causing IRT phenotype could
be associated with two different gene sequence frameworks and two different causal mutations could lie on identical gene sequence
framework. These data argue in favor of convergent phenotypic evolution of IRT enzymes under the selective pressure imposed
by the intensive clinical use of β-lactam–β-lactamase inhibitor combinations.
Received: 18 March 1996 / Accepted: 15 July 1996 相似文献