scholarly journals Probing the “Dark Matter” of Protein Fold Space

Structure ◽  
2009 ◽  
Vol 17 (9) ◽  
pp. 1244-1252 ◽  
Author(s):  
William R. Taylor ◽  
Vijayalakshmi Chelliah ◽  
Siv Midtun Hollup ◽  
James T. MacDonald ◽  
Inge Jonassen
Biomolecules ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 193 ◽  
Author(s):  
William R. Taylor

The model of protein folding proposed by Ptitsyn and colleagues involves the accretion of secondary structures around a nucleus. As developed by Efimov, this model also provides a useful way to view the relationships among structures. Although somewhat eclipsed by later databases based on the pairwise comparison of structures, Efimov’s approach provides a guide for the more automatic comparison of proteins based on an encoding of their topology as a string. Being restricted to layers of secondary structures based on beta sheets, this too has limitations which are partly overcome by moving to a more generalised secondary structure lattice that can encompass both open and closed (barrel) sheets as well as helical packing of the type encoded by Murzin and Finkelstein on small polyhedra. Regular (crystalline) lattices, such as close-packed hexagonals, were found to be too limited so pseudo-latticses were investigated including those found in quasicrystals and the Bernal tetrahedron-based lattice that he used to represent liquid water. The Bernal lattice was considered best and used to generate model protein structures. These were much more numerous than those seen in Nature, posing the open question of why this might be.


Author(s):  
Michael T. Zimmermann ◽  
Fadi Towfic ◽  
Robert L. Jernigan ◽  
Andrzej Kloczkowski

2003 ◽  
Vol 330 (4) ◽  
pp. 839-850 ◽  
Author(s):  
Adrian P Cootes ◽  
Stephen H Muggleton ◽  
Michael J.E Sternberg

2016 ◽  
Vol 113 (9) ◽  
pp. 2436-2441 ◽  
Author(s):  
Jennifer R. Brum ◽  
J. Cesar Ignacio-Espinoza ◽  
Eun-Hae Kim ◽  
Gareth Trubl ◽  
Robert M. Jones ◽  
...  

Viruses are ecologically important, yet environmental virology is limited by dominance of unannotated genomic sequences representing taxonomic and functional “viral dark matter.” Although recent analytical advances are rapidly improving taxonomic annotations, identifying functional dark matter remains problematic. Here, we apply paired metaproteomics and dsDNA-targeted metagenomics to identify 1,875 virion-associated proteins from the ocean. Over one-half of these proteins were newly functionally annotated and represent abundant and widespread viral metagenome-derived protein clusters (PCs). One primarily unannotated PC dominated the dataset, but structural modeling and genomic context identified this PC as a previously unidentified capsid protein from multiple uncultivated tailed virus families. Furthermore, four of the five most abundant PCs in the metaproteome represent capsid proteins containing the HK97-like protein fold previously found in many viruses that infect all three domains of life. The dominance of these proteins within our dataset, as well as their global distribution throughout the world’s oceans and seas, supports prior hypotheses that this HK97-like protein fold is the most abundant biological structure on Earth. Together, these culture-independent analyses improve virion-associated protein annotations, facilitate the investigation of proteins within natural viral communities, and offer a high-throughput means of illuminating functional viral dark matter.


2008 ◽  
Vol 375 (4) ◽  
pp. 920-933 ◽  
Author(s):  
Peter Minary ◽  
Michael Levitt

2003 ◽  
Vol 100 (5) ◽  
pp. 2386-2390 ◽  
Author(s):  
J. Hou ◽  
G. E. Sims ◽  
C. Zhang ◽  
S.-H. Kim

2005 ◽  
Vol 6 (2-3) ◽  
pp. 63-70 ◽  
Author(s):  
Sung-Hou Kim ◽  
Dong Hae Shin ◽  
Jinyu Liu ◽  
Vaheh Oganesyan ◽  
Shengfeng Chen ◽  
...  

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