Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre

2008 ◽  
Vol 70 (3) ◽  
pp. 611-625 ◽  
Author(s):  
Riccardo M. Bennett‐Lovsey ◽  
Alex D. Herbert ◽  
Michael J. E. Sternberg ◽  
Lawrence A. Kelley
Keyword(s):  
Fold Recognition ◽  
Sequence Structure ◽  
Structure Space

Evidence for the Emergence of β-Trefoils by ‘Peptide Budding’ from an IgG-like β-Sandwich

2021 ◽  
Author(s):  
Liam M. Longo ◽  
Rachel Kolodny ◽  
Shawn E. McGlynn
Keyword(s):  
De Novo ◽  
General Trend ◽  
Sequence Structure ◽  
Structure Comparison ◽  
Related Sequence ◽  
Structure Space ◽  
Protein Universe ◽  
Remote Islands ◽  
Comparison Algorithms ◽  
Hallmark Feature

AbstractAs sequence and structure comparison algorithms gain sensitivity, the intrinsic interconnectedness of the protein universe has become increasingly apparent. Despite this general trend, β-trefoils have emerged as an uncommon counterexample: They are an isolated protein lineage for which few, if any, sequence or structure associations to other lineages have been identified. If β-trefoils are, in fact, remote islands in sequence-structure space, it implies that the oligomerizing peptide that founded the β-trefoil lineage itself arose de novo. To better understand β-trefoil evolution, and to probe the limits of fragment sharing across the protein universe, we identified both ‘β-trefoil bridging themes’ (evolutionarily-related sequence segments) and ‘β-trefoil-like motifs’ (structure motifs with a hallmark feature of the β-trefoil architecture) in multiple, ostensibly unrelated, protein lineages. The success of the present approach stems, in part, from considering β-trefoil sequence segments or structure motifs rather than the β-trefoil architecture as a whole, as has been done previously. The newly uncovered inter-lineage connections presented here suggest a novel hypothesis about the origins of the β-trefoil fold itself – namely, that it is a derived fold formed by ‘budding’ from an Immunoglobulin-like β-sandwich protein. These results demonstrate how the emergence of a folded domain from a peptide need not be a signature of antiquity and underpin an emerging truth: few protein lineages escape nature’s sewing table.

scholarly journals RASS: a web server for RNA alignment in the joint sequence-structure space

2014 ◽  
Vol 42 (W1) ◽  
pp. W377-W381 ◽  
Author(s):  
Gewen He ◽  
Albert Steppi ◽  
Jose Laborde ◽  
Anuj Srivastava ◽  
Peixiang Zhao ◽  
...  
Keyword(s):  
Web Server ◽  
Sequence Structure ◽  
Structure Space

scholarly journals RNA global alignment in the joint sequence–structure space using elastic shape analysis

2013 ◽  
Vol 41 (11) ◽  
pp. e114-e114 ◽  
Author(s):  
Jose Laborde ◽  
Daniel Robinson ◽  
Anuj Srivastava ◽  
Eric Klassen ◽  
Jinfeng Zhang
Keyword(s):  
Shape Analysis ◽  
Global Alignment ◽  
Sequence Structure ◽  
Structure Space ◽  
Elastic Shape Analysis

Fold recognition and accurate sequence-structure alignment of sequences directing β-sheet proteins

2006 ◽  
Vol 63 (4) ◽  
pp. 976-985 ◽  
Author(s):  
Andrew V. McDonnell ◽  
Matthew Menke ◽  
Nathan Palmer ◽  
Jonathan King ◽  
Lenore Cowen ◽  
...  
Keyword(s):  
Fold Recognition ◽  
Structure Alignment ◽  
Sequence Structure ◽  
Β Sheet

FACTORS INFLUENCING HOME BUYERS’ PURCHASE DECISIONS IN KLANG VALLEY, MALAYSIA

2020 ◽  
Vol 7 (2) ◽  
pp. 77
Author(s):  
JieSheng Mang ◽  
Rozlin Zainal ◽  
Indera Syahrul Mat Radzuan
Keyword(s):  
Purchase Decision ◽  
Purchase Decisions ◽  
Structure Space ◽  
Factors Influencing ◽  
Klang Valley ◽  
Housing Industry ◽  
House Structure ◽  
Research Studies

Focusing on Klang Valley, this research studies the outcome of house purchase factors in Malaysia. This research identifies the house purchase factors that affect home buyers’ purchase decisions. The researcher collected data using SurveyMonkey by using a questionnaire to elicit the opinions of Klang Valley residents on housing purchase factors and purchase decision. The factors were evaluated and studied to identify their influence on home buyers’ purchase decision. Findings show that home buyers’ purchase decision are influenced by house structure, space, finance, location, and neighbourhood factors. The findings have laid a foundation for the housing industry to improve.

scholarly journals A Cluster of Cuticle Protein Genes of Drosophila melanogaster at 65A: Sequence, Structure and Evolution

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1213-1224
Author(s):  
Jean-Philippe Charles ◽  
Carol Chihara ◽  
Shamim Nejad ◽  
Lynn M Riddiford
Keyword(s):  
Drosophila Melanogaster ◽  
Genomic Dna ◽  
Multiple Copy ◽  
Sequence Structure ◽  
Coding Regions ◽  
The Third ◽  
Genetic Complexity ◽  
Genes Encoding ◽  
Cuticle Protein ◽  
Cuticle Proteins

A 36-kb genomic DNA segment of the Drosophila melanogaster genome containing 12 clustered cuticle genes has been mapped and partially sequenced. The cluster maps at 65A 5-6 on the left arm of the third chromosome, in agreement with the previously determined location of a putative cluster encompassing the genes for the third instar larval cuticle proteins LCP5, LCP6 and LCP8. This cluster is the largest cuticle gene cluster discovered to date and shows a number of surprising features that explain in part the genetic complexity of the LCP5, LCP6 and LCP8 loci. The genes encoding LCP5 and LCP8 are multiple copy genes and the presence of extensive similarity in their coding regions gives the first evidence for gene conversion in cuticle genes. In addition, five genes in the cluster are intronless. Four of these five have arisen by retroposition. The other genes in the cluster have a single intron located at an unusual location for insect cuticle genes.

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