2009
DOI: 10.1016/j.bpj.2009.06.020
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An Energetic Representation of Protein Architecture that Is Independent of Primary and Secondary Structure

Abstract: Protein fold classification often assumes that similarity in primary, secondary, or tertiary structure signifies a common evolutionary origin. However, when similarity is not obvious, it is sometimes difficult to conclude that particular proteins are completely unrelated. Clearly, a set of organizing principles that is independent of traditional classification could be valuable in linking different structural motifs and identifying common ancestry from seemingly disparate folds. Here, a four-dimensional ensemb… Show more

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Cited by 5 publications
(11 citation statements)
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“…Figure 6 shows three instances of homologous pairs exhibiting conserved local stability despite secondary structure variation. This phenomenon has been previously identified as a possible thermodynamic mechanism for evolutionary fold change [9] , and the examples seen here, occurring in a variety of secondary structural contexts, suggest its generality.…”
Section: Resultssupporting
confidence: 63%
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“…Figure 6 shows three instances of homologous pairs exhibiting conserved local stability despite secondary structure variation. This phenomenon has been previously identified as a possible thermodynamic mechanism for evolutionary fold change [9] , and the examples seen here, occurring in a variety of secondary structural contexts, suggest its generality.…”
Section: Resultssupporting
confidence: 63%
“…First, in an effort to ensure that the overlap regions were not enriched with residue positions that occupied a particular region of thermodynamic parameter space, we performed principal components analysis (PCA) on the thermodynamic parameter space of the sequence segments that had the highest frequency of occurrence (top 10%) in the overlap regions and compared the eigenvalues to those obtained for the overall dataset, as well as for the datasets corresponding to the regions of no overlap [9] . The results ( Text S1 , Figure S2 ) revealed no bias in the overlap region, indicating that the high correlations were not driven by sequences enriched in a certain type of energetic environment.…”
Section: Resultsmentioning
confidence: 99%
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“…8) [39,40]. Interesting exceptions to this trend were noted that suggested a thermodynamic mechanism for localized evolutionary fold change—regions of homologous proteins could change structure from alpha helix to beta sheet and still preserve the ancestral energetic characteristics[39,79]. …”
Section: Evolutionary Conservation Of Spontaneous Fluctuationsmentioning
confidence: 99%
“…This energetic representation of proteins alone has formed the basis of an effective fold recognition algorithm, whereby sequences could be matched with their respective folds, even if the secondary structure information of the fold was not present in the training set . This last result, that the energetic information of entirely alpha‐helical proteins permitted recognition of entirely beta sheet proteins, compellingly established the universality of this energetic representation with regard to protein structure classification …”
Section: Resultsmentioning
confidence: 96%