Computer Literacy and the Art Program

Hubbard, Guy

doi:10.2307/3192838

Cited by 11 publications

(7 citation statements)

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“…For example, the strongest protections seen in D1 include helix b and the regions surrounding ζ and EBS1. Using the NACCESS program (Hubbard and Thornton, 1993), solvent‐inaccessible regions of the model were calculated and compared with the protection data (not shown). Remarkably, there was overlap between almost every inaccessible region in the model and regions identified in the protection studies (within the experimental error of 1–2 nt).…”

Section: Resultsmentioning

confidence: 99%

Visualizing the solvent-inaccessible core of a group II intron ribozyme

Swisher

Duarte

et al. 2001

The EMBO Journal

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Group II introns are well recognized for their remarkable catalytic capabilities, but little is known about their three-dimensional structures. In order to obtain a global view of an active enzyme, hydroxyl radical cleavage was used to de®ne the solvent accessibility along the backbone of a ribozyme derived from group II intron ai5g. These studies show that a highly homogeneous ribozyme population folds into a catalytically compact structure with an extensively internalized catalytic core. In parallel, a model of the intron core was built based on known tertiary contacts. Although constructed independently of the footprinting data, the model implicates the same elements for involvement in the catalytic core of the intron.

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Section: Resultsmentioning

confidence: 99%

Visualizing the solvent-inaccessible core of a group II intron ribozyme

Swisher

Duarte

et al. 2001

The EMBO Journal

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“…There were 22 residues in OV region (178 atoms) (in our initial multiple sequence alignment of the sequences in Ubiquitin cluster there were five receptor sequences where Lys63 was mutated to Arg resulting in a gap; however, in the present set of nine heterodimers Lys63 is not mutated and included in the interfaces in most of the cases, therefore we defined this residue as part of the OV region) and 36 residues in Non‐OV region (286 atoms). The rest of the residues (14 in number, corresponds to 110 atoms) were defined to be in the noninterface part of the Ubiquitin, of which 6 residues (48 atoms) were in surface 54…”

Section: Methodsmentioning

confidence: 99%

Counterbalance of ligand‐ and self‐coupled motions characterizes multispecificity of ubiquitin

2012

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Date hub proteins are a type of proteins that show multispecificity in a time-dependent manner. To understand dynamic aspects of such multispecificity we studied Ubiquitin as a typical example of a date hub protein. Here we analyzed 9 biologically relevant Ubiquitin-protein (ligand) heterodimer structures by using normal mode analysis based on an elastic network model. Our result showed that the self-coupled motion of Ubiquitin in the complex, rather than its ligandcoupled motion, is similar to the motion of Ubiquitin in the unbound condition. The ligand-coupled motions are correlated to the conformational change between the unbound and bound conditions of Ubiquitin. Moreover, ligand-coupled motions favor the formation of the bound states, due to its in-phase movements of the contacting atoms at the interface. The self-coupled motions at the interface indicated loss of conformational entropy due to binding. Therefore, such motions disfavor the formation of the bound state. We observed that the ligand-coupled motions are embedded in the motions of unbound Ubiquitin. In conclusion, multispecificity of Ubiquitin can be characterized by an intricate balance of the ligand-and self-coupled motions, both of which are embedded in the motions of the unbound form.

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“…In all, 11 amino‐acid residues in p47 UBA and 12 in ubiquitin were identified to have weighted chemical shift changes significantly greater than the average; 0.07 ppm in ubiquitin and 0.09 ppm in p47 UBA were chosen as suitable cutoff values. After filtering for a relative solvent accessibility greater than 50%, as calculated using the program Naccess (Hubbard and Thornton, 1993), eight residues in p47 UBA (Q6, V15, G17, Q35, A39, S40, Y42 and D44) and eight for ubiquitin (K6, K11, A46, K48, Q49, H68, R72 and R74) were identified as active residues. Residues juxtaposed to these, which have a relative solvent accessibility greater than 50%, were termed passive residues.…”

Section: Methodsmentioning

confidence: 99%

Structure, dynamics and interactions of p47, a major adaptor of the AAA ATPase, p97

Yuan

Simpson

Mckeown

et al. 2004

EMBO J

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p47 is a major adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is in regulation of membrane fusion events. Mono-ubiquitin recognition by p47 has also been shown to be crucial in the p97-p47-mediated Golgi membrane fusion events. Here, we describe the high-resolution solution structures of the N-terminal UBA domain and the central domain (SEP) from p47. The p47 UBA domain has the characteristic three-helix bundle fold and forms a highly stable complex with ubiquitin. We report the interaction surfaces of the two proteins and present a structure for the p47 UBA-ubiquitin complex. The p47 SEP domain adopts a novel fold with a betabetabetaalphaalphabeta secondary structure arrangement, where beta4 pairs in a parallel fashion to beta1. Based on biophysical studies, we demonstrate a clear propensity for the self-association of p47. Furthermore, p97 N binding abolishes p47 self-association, revealing the potential interaction surfaces for recognition of other domains within p97 or the substrate.

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Computer Literacy and the Art Program

Cited by 11 publications

References 0 publications

Visualizing the solvent-inaccessible core of a group II intron ribozyme

Visualizing the solvent-inaccessible core of a group II intron ribozyme

Counterbalance of ligand‐ and self‐coupled motions characterizes multispecificity of ubiquitin

Structure, dynamics and interactions of p47, a major adaptor of the AAA ATPase, p97

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