TITLE

Fold classification based on secondary structure -- how much is gained by including loop topology?

PUB. DATE
January 2006
SOURCE
BMC Structural Biology;2006, Vol. 6, p3
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
No abstract available.
ACCESSION #
43714651

 

Related Articles

  • McGenus: a Monte Carlo algorithm to predict RNA secondary structures with pseudoknots. Bon, Michaël; Micheletti, Cristian; Orland, Henri // Nucleic Acids Research;Feb2013, Vol. 41 Issue 3, p1895 

    We present McGenus, an algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. McGenus can treat sequences of up to 1000 bases and performs an advanced stochastic search of their minimum free...

  • Multiple folding pathways of proteins with shallow knots and co-translational folding. Chwastyk, Mateusz; Cieplak, Marek // Journal of Chemical Physics;7/28/2015, Vol. 143 Issue 4, p1 

    We study the folding process in the shallowly knotted protein MJ0366 within two variants of a structure-based model. We observe that the resulting topological pathways are much richer than identified in previous studies. In addition to the single knot-loop events, we find novel, and dominant,...

  • The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom Gō model of fragment B of Staphylococcal protein A. Linhananta, Apichart; Zhou, Yaoqi // Journal of Chemical Physics;11/15/2002, Vol. 117 Issue 19, p8983 

    Protein topology, which refers to the arrangement of secondary structures of proteins, has been extensively investigated to examine its role in protein folding. However, recent studies show that topology alone cannot account for the variation of folding behaviors observed in some proteins of the...

  • Protein folds and protein folding. Schaeffer, R. Dustin; Daggett, Valerie // PEDS: Protein Engineering, Design & Selection;Jan2011, Vol. 24 Issue 1/2, p11 

    The classification of protein folds is necessarily based on the structural elements that distinguish domains. Classification of protein domains consists of two problems: the partition of structures into domains and the classification of domains into sets of similar structures (or folds)....

  • Principles for designing ideal protein structures. Koga, Nobuyasu; Tatsumi-Koga, Rie; Liu, Gaohua; Xiao, Rong; Acton, Thomas B.; Montelione, Gaetano T.; Baker, David // Nature;11/8/2012, Vol. 491 Issue 7423, p222 

    Unlike random heteropolymers, natural proteins fold into unique ordered structures. Understanding how these are encoded in amino-acid sequences is complicated by energetically unfavourable non-ideal features-for example kinked ?-helices, bulged ?-strands, strained loops and buried polar...

  • Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale. Islam, Barira; Sgobba, Miriam; Laughton, Charlie; Orozco, Modesto; Sponer, Jiri; Neidle, Stephen; Haider, Shozeb // Nucleic Acids Research;Feb2013, Vol. 41 Issue 4, p2723 

    The human telomeric DNA sequence with four repeats can fold into a parallel-stranded propeller-type topology. NMR structures solved under molecular crowding experiments correlate with the crystal structures found with crystal-packing interactions that are effectively equivalent to molecular...

  • A novel approach to represent and compare RNA secondary structures. Mattei, Eugenio; Ausiello, Gabriele; Ferrè, Fabrizio; Helmer-Citterich, Manuela // Nucleic Acids Research;Jun2014, Vol. 42 Issue 10, p6146 

    Structural information is crucial in ribonucleic acid (RNA) analysis and functional annotation; nevertheless, how to include such structural data is still a debated problem. Dot-bracket notation is the most common and simple representation for RNA secondary structures but its simplicity leads...

  • Flexibility and structural conservation in a c-KIT G-quadruplex. Wei, Dengguo; Husby, Jarmila; Neidle, Stephen // Nucleic Acids Research;Jan2015, Vol. 43 Issue 1, p629 

    A quadruplex sequence from the promoter region of the c-KIT gene forms a stable quadruplex, as characterized by crystallographic and NMR methods. Two new crystal structures are reported here, together with molecular dynamics simulation studies on these quadruplex crystal structures and an NMR...

  • Helix Capping in RNA Structure. Lee, Jung C.; Gutell, Robin R. // PLoS ONE;Apr2014, Vol. 9 Issue 4, p1 

    Helices are an essential element in defining the three-dimensional architecture of structured RNAs. While internal basepairs in a canonical helix stack on both sides, the ends of the helix stack on only one side and are exposed to the loop side, thus susceptible to fraying unless they are...

  • Extended molecular dynamics of a c-kit promoter quadruplex. Islam, Barira; Stadlbauer, Petr; Krepl, Miroslav; Koca, Jaroslav; Neidle, Stephen; Haider, Shozeb; Sponer, Jiri // Nucleic Acids Research;10/15/2015, Vol. 43 Issue 18, p8673 

    The 22-mer c-kit promoter sequence folds into a parallel-stranded quadruplex with a unique structure, which has been elucidated by crystallographic and NMR methods and shows a high degree of structural conservation. We have carried out a series of extended (up to 10 μs long, ~50 μs in...

Share

Read the Article

Courtesy of VIRGINIA BEACH PUBLIC LIBRARY AND SYSTEM

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics