scholarly journals On the Origin of Protein Superfamilies and Superfolds

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Abram Magner ◽  
Wojciech Szpankowski ◽  
Daisuke Kihara
Keyword(s):  
Protein Superfamilies

scholarly journals Comparison of DNA binding across protein superfamilies

2009 ◽  
Vol 78 (1) ◽  
pp. 52-62 ◽  
Author(s):  
Bruno Contreras-Moreira ◽  
Javier Sancho ◽  
Vladimir Espinosa Angarica
Keyword(s):  
Dna Binding ◽  
Protein Superfamilies

Structural Variations in Protein Superfamilies: Actin and Tubulin

2009 ◽  
Vol 42 (1) ◽  
pp. 49-60 ◽  
Author(s):  
Richard H. Wade ◽  
Isabel Garcia-Saez ◽  
Frank Kozielski
Keyword(s):  
Structural Variations ◽  
Protein Superfamilies

Inventory and analysis of ATP-binding cassette (ABC) systems inBrugia malayi

Parasitology ◽  
2010 ◽  
Vol 137 (8) ◽  
pp. 1195-1212 ◽  
Author(s):  
B. F. ARDELLI ◽  
L. E. STITT ◽  
J. B. TOMPKINS
Keyword(s):  
Drug Resistance ◽  
Dna Repair ◽  
Abc Transporters ◽  
Atp Binding ◽  
Switch Region ◽  
Linker Region ◽  
Protein Superfamilies ◽  
Binding Domains ◽  
Reverse Transcription Pcr ◽  
Signature Sequence

SUMMARYABC systems are one of the largest described protein superfamilies. These systems have a domain organization that may contain 1 or more transmembrane domains (ABC_TM1F) and 1 or 2 ATP-binding domains (ABC_2). The functions (e.g., import, export and DNA repair) of these proteins distinguish the 3 classes of ABC systems. Mining and PCR-based cloning were used to identify 33 putative ABC systems from theBrugia malayigenome. There were 31 class 2 genes, commonly called ABC transporters, and 2 class 3 genes. The ABC transporters were divided into subfamilies. Three belonged to subfamily A, 16 to subfamily B, 5 to subfamily C, 1 to subfamily E and 3 to subfamilies F and G, respectively. None were placed in subfamilies D and H. Similar to other ABC systems, the ABC_2 domain ofB. malayigenes was conserved and contained the Walker A and B motifs, the signature sequence/linker region and the switch region with the conserved histidine. The ABC_TM1F domain was less conserved. The relative abundance of ABC systems was quantified using real-time reverse transcription PCR and was significantly higher in female adults ofB. malayithan in males and microfilaria, particularly those in subfamilies B and C, which are associated with drug resistance.

scholarly journals Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies

2013 ◽  
Vol 9 (11) ◽  
pp. e1003325 ◽  
Author(s):  
Hannah Edwards ◽  
Sanne Abeln ◽  
Charlotte M. Deane
Keyword(s):  
New Born ◽  
Protein Superfamilies

scholarly journals Alternating dynamics of oriC, SMC and MksBEF in segregation of Pseudomonas aeruginosa chromosome

2020 ◽  
Author(s):  
Hang Zhao ◽  
Bijit Bhowmik ◽  
Valentin V. Rybenkov
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Cell Division ◽  
Chromosome Replication ◽  
Major Protein ◽  
Dual Roles ◽  
Localization Pattern ◽  
Protein Superfamilies ◽  
Organizing Center ◽  
Synthetically Lethal ◽  
Structural Entity

AbstractCondensins are essential for global chromosome organization in diverse bacteria. Atypically, Pseudomonas aeruginosa encodes condensins from two superfamilies, SMC-ScpAB and MksBEF. We report that the two proteins play specialized roles in chromosome packing and segregation and are synthetically lethal with ParB. Inactivation of SMC or MksB asymmetrically affected global chromosome layout, its timing of segregation and sometimes triggered a chromosomal inversion. Localization pattern was also unique to each protein. SMC clusters colocalized with oriC throughout cell cycle except shortly after origin duplication, whereas MksB clusters emerged at cell quarters shortly prior to oriC duplication and stayed there even after cell division. Relocation of the proteins was abrupt and coordinated with oriC dynamic. These data reveal that the two condensins asymmetrically play dual roles in chromosome maintenance by organizing it and mediating its segregation. Furthermore, the choreography of condensins and oriC relocations suggest an elegant mechanism for the birth and maturation of chromosomes.ImportanceMechanisms that define the chromosome as a structural entity remain unknown. A key element in this process are condensins, which globally organize chromosomes and contribute to their segregation. This study characterized condensin and chromosome dynamics in Pseudomonas aeruginosa, which harbors condensins from two major protein superfamilies, SMC and MksBEF. The study revealed that both proteins asymmetrically play a dual role in chromosome maintenance by spatially organizing the chromosomes and guiding their segregation but can substitute for each other in some activities. The timing of chromosome, SMC and MksBEF relocation was highly ordered and interdependent revealing causative relationships in the process. Moreover, MksBEF was found to produce clusters at the site of chromosome replication that survived cell division and remained in place until chromosome replication was complete. Overall, these data delineate the functions of condensins from the SMC MksBEF superfamilies, reveal the existence of a chromosome organizing center and suggest a mechanism that might explain the biogenesis of chromosomes.

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