ProSeg: a database of local structures of protein segments

Sawada, Yoshito; Honda, Shinya

doi:10.1007/s10822-008-9248-x

Cited by 4 publications

(5 citation statements)

References 23 publications

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“…The space is defined by axes that were independently determined using principal component analysis (PCA) of protein segments having representative backbone conformations. 7 As shown in Figure 3B, the MD structures converge on a certain area that overlaps with both the crystal and solution structures, indicating that the MD simulation accurately reproduces the protein's environment. The simulation time was apparently long enough to reach an equilibrium state, so a free energy surface of CLN025 was produced by calculating the potential of mean force (PMF).…”

Section: Design and Stability Of Cln025mentioning

confidence: 70%

“…These MD structures were then mapped on a DA space to visualize their distribution as shown in Figure B (see also Figure S8, Supporting Information). The space is defined by axes that were independently determined using principal component analysis (PCA) of protein segments having representative backbone conformations . As shown in Figure B, the MD structures converge on a certain area that overlaps with both the crystal and solution structures, indicating that the MD simulation accurately reproduces the protein’s environment.…”

Section: Resultsmentioning

confidence: 99%

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Crystal Structure of a Ten-Amino Acid Protein

et al. 2008

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Abstract:What is the smallest protein? This is actually not such a simple question to answer, because there is no established consensus among scientists as to the definition of a protein. We describe here a designed molecule consisting of only 10 amino acids. Despite its small size, its essential characteristics, revealed by its crystal structure, solution structure, thermal stability, free energy surface, and folding pathway network, are consistent with the properties of natural proteins. The existence of this kind of molecule deepens our understanding of proteins and impels us to define an "ideal protein" without inquiring whether the molecule actually occurs in nature.

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Section: Design and Stability Of Cln025mentioning

confidence: 70%

Section: Resultsmentioning

confidence: 99%

Crystal Structure of a Ten-Amino Acid Protein

et al. 2008

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“…constructed the BriX database encompassing more than 1000 frequent local conformations ranging from 4 to 14 residues 31. Similarly, Sawada and Honda developed a database of structural clusters taking into account fragments of 5, 9, 11, and 15 residues 32. But, in these cases, prediction methods were not developed.…”

Section: Introductionmentioning

confidence: 99%

A new prediction strategy for long local protein structures using an original description

2009

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A relevant and accurate description of three-dimensional (3D) protein structures can be achieved by characterizing recurrent local structures. In a previous study, we developed a library of 120 3D structural prototypes encompassing all known 11-residues long local protein structures and ensuring a good quality of structural approximation. A local structure prediction method was also proposed. Here, overlapping properties of local protein structures in global ones are taken into account to characterize frequent local networks. At the same time, we propose a new long local structure prediction strategy which involves the use of evolutionary information coupled with Support Vector Machines (SVMs). Our prediction is evaluated by a stringent geometrical assessment. Every local structure prediction with a Calpha RMSD less than 2.5 A from the true local structure is considered as correct. A global prediction rate of 63.1% is then reached, corresponding to an improvement of 7.7 points compared with the previous strategy. In the same way, the prediction of 88.33% of the 120 structural classes is improved with 8.65% mean gain. 85.33% of proteins have better prediction results with a 9.43% average gain. An analysis of prediction rate per local network also supports the global improvement and gives insights into the potential of our method for predicting super local structures. Moreover, a confidence index for the direct estimation of prediction quality is proposed. Finally, our method is proved to be very competitive with cutting-edge strategies encompassing three categories of local structure predictions.

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“…This propensity corresponds to the ratio of the frequency count of a certain residue type appearing at a particular position to the global frequency count of the amino acid residues. The segments and information of amino acid preferences in each structural class were classified using ProSeg: a database of local structures of protein segments http://riodb.ibase.aist.go.jp/proseg/index.html[52]. …”

Section: Methodsmentioning

confidence: 99%

Convergent evolution in structural elements of proteins investigated using cross profile analysis

2012

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BackgroundEvolutionary relations of similar segments shared by different protein folds remain controversial, even though many examples of such segments have been found. To date, several methods such as those based on the results of structure comparisons, sequence-based classifications, and sequence-based profile-profile comparisons have been applied to identify such protein segments that possess local similarities in both sequence and structure across protein folds. However, to capture more precise sequence-structure relations, no method reported to date combines structure-based profiles, and sequence-based profiles based on evolutionary information. The former are generally regarded as representing the amino acid preferences at each position of a specific conformation of protein segment. They might reflect the nature of ancient short peptide ancestors, using the results of structural classifications of protein segments.ResultsThis report describes the development and use of "Cross Profile Analysis" to compare sequence-based profiles and structure-based profiles based on amino acid occurrences at each position within a protein segment cluster. Using systematic cross profile analysis, we found structural clusters of 9-residue and 15-residue segments showing remarkably strong correlation with particular sequence profiles. These correlations reflect structural similarities among constituent segments of both sequence-based and structure-based profiles. We also report previously undetectable sequence-structure patterns that transcend protein family and fold boundaries, and present results of the conformational analysis of the deduced peptide of a segment cluster. These results suggest the existence of ancient short-peptide ancestors.ConclusionsCross profile analysis reveals the polyphyletic and convergent evolution of β-hairpin-like structures, which were verified both experimentally and computationally. The results presented here give us new insights into the evolution of short protein segments.

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ProSeg: a database of local structures of protein segments

Cited by 4 publications

References 23 publications

Crystal Structure of a Ten-Amino Acid Protein

Crystal Structure of a Ten-Amino Acid Protein

A new prediction strategy for long local protein structures using an original description

Convergent evolution in structural elements of proteins investigated using cross profile analysis

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