scholarly journals Phylogeny of the Serpin Superfamily: Implications of Patterns of Amino Acid Conservation for Structure and Function

2000 ◽  
Vol 10 (12) ◽  
pp. 1845-1864
Author(s):  
James A. Irving ◽  
Robert N. Pike ◽  
Arthur M. Lesk ◽  
James C. Whisstock
Keyword(s):  
Sequence Data ◽  
Initial Point ◽  
Structure And Function ◽  
Conserved Residues ◽  
Consensus Analysis ◽  
The Family ◽  
Protein Sequence Data ◽  
And Function ◽  
Conserved Amino Acids ◽  
Genome Projects

We present a comprehensive alignment and phylogenetic analysis of the serpins, a superfamily of proteins with known members in higher animals, nematodes, insects, plants, and viruses. We analyze, compare, and classify 219 proteins representative of eight major and eight minor subfamilies, using a novel technique of consensus analysis. Patterns of sequence conservation characterize the family as a whole, with a clear relationship to the mechanism of function. Variations of these patterns within phylogenetically distinct groups can be correlated with the divergence of structure and function. The goals of this work are to provide a carefully curated alignment of serpin sequences, to describe patterns of conservation and divergence, and to derive a phylogenetic tree expressing the relationships among the members of this family. We extend earlier studies by Huber and Carrell as well as by Marshall, after whose publication the serpin family has grown functionally, taxonomically, and structurally. We used gene and protein sequence data, crystal structures, and chromosomal location where available. The results illuminate structure–function relationships in serpins, suggesting roles for conserved residues in the mechanism of conformational change. The phylogeny provides a rational evolutionary framework to classify serpins and enables identification of conserved amino acids. Patterns of conservation also provide an initial point of comparison for genes identified by the various genome projects. New homologs emerging from sequencing projects can either take their place within the current classification or, if necessary, extend it.

scholarly journals Tracing Evolution Through Protein Structures: Nature Captured in a Few Thousand Folds

2021 ◽  
Vol 8 ◽  
Author(s):  
Nicola Bordin ◽  
Ian Sillitoe ◽  
Jonathan G. Lees ◽  
Christine Orengo
Keyword(s):  
Protein Structure ◽  
Function Space ◽  
Sequence Data ◽  
Protein Structures ◽  
Structure And Function ◽  
Structure Evolution ◽  
Structural Classification ◽  
Protein Sequence Data ◽  
History Of ◽  
And Function

This article is dedicated to the memory of Cyrus Chothia, who was a leading light in the world of protein structure evolution. His elegant analyses of protein families and their mechanisms of structural and functional evolution provided important evolutionary and biological insights and firmly established the value of structural perspectives. He was a mentor and supervisor to many other leading scientists who continued his quest to characterise structure and function space. He was also a generous and supportive colleague to those applying different approaches. In this article we review some of his accomplishments and the history of protein structure classifications, particularly SCOP and CATH. We also highlight some of the evolutionary insights these two classifications have brought. Finally, we discuss how the expansion and integration of protein sequence data into these structural families helps reveal the dark matter of function space and can inform the emergence of novel functions in Metazoa. Since we cover 25 years of structural classification, it has not been feasible to review all structure based evolutionary studies and hence we focus mainly on those undertaken by the SCOP and CATH groups and their collaborators.

scholarly journals Exotoxins of Staphylococcus aureus

2000 ◽  
Vol 13 (1) ◽  
pp. 16-34 ◽  
Author(s):  
Martin M. Dinges ◽  
Paul M. Orwin ◽  
Patrick M. Schlievert
Keyword(s):  
Staphylococcus Aureus ◽  
Toxic Shock Syndrome ◽  
Molecular Basis ◽  
Molecular Mechanisms ◽  
Food Poisoning ◽  
Structure And Function ◽  
Toxic Shock ◽  
The Family ◽  
Toxic Shock Syndrome Toxin ◽  
And Function

SUMMARY This article reviews the literature regarding the structure and function of two types of exotoxins expressed by Staphylococcus aureus, pyrogenic toxin superantigens (PTSAgs) and hemolysins. The molecular basis of PTSAg toxicity is presented in the context of two diseases known to be caused by these exotoxins: toxic shock syndrome and staphylococcal food poisoning. The family of staphylococcal PTSAgs presently includes toxic shock syndrome toxin-1 (TSST-1) and most of the staphylococcal enterotoxins (SEs) (SEA, SEB, SEC, SED, SEE, SEG, and SEH). As the name implies, the PTSAgs are multifunctional proteins that invariably exhibit lethal activity, pyrogenicity, superantigenicity, and the capacity to induce lethal hypersensitivity to endotoxin. Other properties exhibited by one or more staphylococcal PTSAgs include emetic activity (SEs) and penetration across mucosal barriers (TSST-1). A detailed review of the molecular mechanisms underlying the toxicity of the staphylococcal hemolysins is also presented.

scholarly journals Primary structure of OXA-3 and phylogeny of oxacillin-hydrolyzing class D beta-lactamases.

1995 ◽  
Vol 39 (4) ◽  
pp. 887-893 ◽  
Author(s):  
F Sanschagrin ◽  
F Couture ◽  
R C Levesque
Keyword(s):  
Amino Acids ◽  
Structure And Function ◽  
Amino Acid Sequences ◽  
Specific Class ◽  
Conserved Motifs ◽  
Beta Lactamases ◽  
Class A ◽  
Class D ◽  
And Function ◽  
Conserved Amino Acids

We determined the nucleotide sequence of the blaOXA-3(pMG25) gene from Pseudomonas aeruginosa. The bla structural gene encoded a protein of 275 amino acids representing one monomer of 31,879 Da for the OXA-3 enzyme. Comparisons between the OXA-3 nucleotide and amino acid sequences and those of class A, B, C, and D beta-lactamases were performed. An alignment of the eight known class D beta-lactamases including OXA-3 demonstrated the presence of conserved amino acids. In addition, conserved motifs composed of identical amino acids typical of penicillin-recognizing proteins and specific class D motifs were identified. These conserved motifs were considered for possible roles in the structure and function of oxacillinases. On the basis of the alignment and identity scores, a dendrogram was constructed. The phylogenetic data obtained revealed five groups of class D beta-lactamases with large evolutionary distances between each group.

— Zur Morphologie und Funktion des — Helodiden-Aedoeagus (Col.)1

1972 ◽  
Vol 3 (2) ◽  
pp. 81-119 ◽  
Author(s):  
Tord Nyholm
Keyword(s):  
Distal Part ◽  
Comparative Morphology ◽  
Structure And Function ◽  
The Other ◽  
Gradual Change ◽  
Median Lobe ◽  
Initial Form ◽  
The Family ◽  
Different Types ◽  
And Function

AbstractThe structure and function of the aedeagus were investigated in 9 genera of the family Helodidae, most thoroughly in Helodes and Cyphon. On the basis of this investigation, the different types of tegmen and penis represented within the family are described. The tegmen of the Helodidae, which is either entirely devoid of a sclerotized "basal piece" or possesses only rudiments of such, may be divided into three main types; in addition there are a few quite aberrant cases. The penis (median lobe), more interesting from the standpoint of comparative morphology, is extremely diversified. A separation between two main types could however be maintained: one represented by genus Helodes alone, the other by all remaining genera. The Helodes type is more primitive, though at the same time rather specialized in certain details. The second penis type is still more specialized. Its main characteristic is a separate triangular sclerite (a "trigonium") situated ventrally in the distal part of penis. In certain genera it is cleft medially into a pair of moveable appendages ("prosthemata"). A splitting of the penis apex into two lobes ("parameroids") occurs in most species of Helodes, but also among the majority of remaining genera. The evolution of the penis from a supposed primitive initial form towards the Helodes type on one side and the highly specialized type represented by certain species of Cyphon on the other, is outlined and discussed. The importance of a gradual change of the copulatory method for this evolution is particularly stressed. The morphology of the aedeagus as basis for the systematics of the Helodidae is briefly treated. The investigation was also extended to cover representatives of other families, generally regarded as related to the Helodidae. Most of them possess an aedeagus of a rather primitive trilobed type. Deviating from this pattern are the Dascillidae, with the penis completely cleft into one dorsal and one ventral sclerite, and also the Psephenidae. In this family, the penis is supplied with a separate sclerite, apparently homologous with the "trigonium" of the Helodidae and with a similar evolution.

Post-conflict initiatives and the exclusion of conflict-affected young people in northern Uganda

2021 ◽  
Vol 59 (1) ◽  
pp. 21-39
Author(s):  
Alina Dixon
Keyword(s):  
Young People ◽  
Family System ◽  
Social Systems ◽  
Structure And Function ◽  
Northern Uganda ◽  
Social Environments ◽  
Post Conflict ◽  
The Family ◽  
And Function

ABSTRACTYoung people are among the most severely impacted by conflict and as such many post-conflict initiatives are aimed at assisting them. Yet the impacts of these initiatives on young people's ability to successfully overcome the adversity they faced during conflict are not fully understood. This paper attempts to examine these impacts by conceptualising post-conflict initiatives as enmeshed within young people's social environments. It argues that post-conflict initiatives are intimately connected to broader processes of exclusion from social systems such as the family. While these systems had previously served to protect young people against adversity, conflict and post-conflict initiatives have disrupted their ability to continue this mission. In particular, the structure and function of the family system are examined to demonstrate the types of disruptions that have taken place that have ultimately negatively impacted the landscape in which young people develop.

scholarly journals Unravelling the diversity Behind the Ophiocordyceps Unilateralis Complex: Three new species of zombie-ant fungi from the Brazilian Amazon

2014 ◽  
Author(s):  
João P. M. Araújo ◽  
Harry C. Evans ◽  
David M. Geiser ◽  
William P. Mackay ◽  
David P. Hughes
Keyword(s):  
Sequence Data ◽  
Brazilian Amazon ◽  
Closely Related Species ◽  
Form And Function ◽  
The Family ◽  
Three New Species ◽  
Specific Species ◽  
And Function ◽  
Amazonian Region ◽  
Ophiocordyceps Unilateralis

AbstractIn tropical forests, one of the most common relationships between parasites and insects is that between the fungus Ophiocordyceps (Ophiocordycipitaceae, Hypocreales, Ascomycota) and ants, especially within the tribe Camponotini. Here, we describe three new and host-specific species of the genus Ophiocordyceps on Camponotus ants from the central Amazonian region of Brazil, which can readily be separated using morphological traits, in particular, ascospore form and function. In addition, we use sequence data to infer phylogenetic relationships between these taxa and closely related species within the Ophiocordyceps unilateralis complex, as well as with other members of the family Ophiocordycipitaceae.

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