OLIGAMI: OLIGomer Architecture and Molecular Interface

Fujiwara, Kazuo; Ikeguchi, Masamichi

doi:10.2174/1875036200802010050

Cited by 5 publications

(4 citation statements)

References 19 publications

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“…To facilitate the analysis, we wanted to extract monomeric or homo-oligomeric and single-domain proteins from PDB. This has been accomplished in OLIGAMI ( http://protein.t.soka.ac.jp/oligami/ ) [ 4 ] which is database combined SCOP database (Structural Classification of Proteins) [ 2 ] and oligomeric information. From these coordinates, a non-redundant subset of PDB entries (in which no pair of structures had >60% sequence identity) was created for each fold of the four main SCOP classes of proteins: “all-α”, “all-β”, “α/β”, and “α + β”.…”

Section: Methodsmentioning

confidence: 99%

“…Remaining folds are assigned to "Multi-domain", "Membrane and cell surface" or "Small" proteins classes. In 2009, we developed a quaternary structural database for proteins, OLIGAMI [ 4 ] in which the oligomer information was added to the SCOP classification [ 2 ], to allow an exhaustive survey of tertiary or quaternary structures of proteins.…”

Section: Introductionmentioning

confidence: 99%

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Dependence of alpha-helical and beta-sheet amino acid propensities on the overall protein fold type

2012

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BackgroundA large number of studies have been carried out to obtain amino acid propensities for α-helices and β-sheets. The obtained propensities for α-helices are consistent with each other, and the pair-wise correlation coefficient is frequently high. On the other hand, the β-sheet propensities obtained by several studies differed significantly, indicating that the context significantly affects β-sheet propensity.ResultsWe calculated amino acid propensities for α-helices and β-sheets for 39 and 24 protein folds, respectively, and addressed whether they correlate with the fold. The propensities were also calculated for exposed and buried sites, respectively. Results showed that α-helix propensities do not differ significantly by fold, but β-sheet propensities are diverse and depend on the fold. The propensities calculated for exposed sites and buried sites are similar for α-helix, but such is not the case for the β-sheet propensities. We also found some fold dependence on amino acid frequency in β-strands. Folds with a high Ser, Thr and Asn content at exposed sites in β-strands tend to have a low Leu, Ile, Glu, Lys and Arg content (correlation coefficient = −0.90) and to have flat β-sheets. At buried sites in β-strands, the content of Tyr, Trp, Gln and Ser correlates negatively with the content of Val, Ile and Leu (correlation coefficient = −0.93). "All-β" proteins tend to have a higher content of Tyr, Trp, Gln and Ser, whereas "α/β" proteins tend to have a higher content of Val, Ile and Leu.ConclusionsThe α-helix propensities are similar for all folds and for exposed and buried residues. However, β-sheet propensities calculated for exposed residues differ from those for buried residues, indicating that the exposed-residue fraction is one of the major factors governing amino acid composition in β-strands. Furthermore, the correlations we detected suggest that amino acid composition is related to folding properties such as the twist of a β-strand or association between two β sheets.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Dependence of alpha-helical and beta-sheet amino acid propensities on the overall protein fold type

2012

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“…This behavior is similar to that observed for mammalian ferritins. − In the 24-meric crystal structure, each subunit made contact with five neighbors (Figure S1). Assuming that a pair of subunits in contact within the 24-mer keeps their contact in the acid-dissociated state, five dimeric structures are possible (AC, AD, AF, AO, and AX; the letters identifying the subunits are based on the OLIGAMI database). Of these five dimers, AC and AX have the same shape, and AD and AO do also.…”

Section: Resultsmentioning

confidence: 99%

A Physicochemical and Mutational Analysis of Intersubunit Interactions of Escherichia coli Ferritin A

Ohtomo

Sato

et al. 2015

Biochemistry

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Ferritin A from Escherichia coli (EcFtnA) is 24-meric protein, which forms spherical cagelike structures called nanocages. The nanocage structure is stabilized by the interface around 4-, 3-, and 2-fold symmetric axes. The subunit structure of EcFtnA comprises a four-helix bundle (helices A-D) and an additional helix E, which forms a 4-fold axis. In this study, we examined the contribution of the interface around three symmetric axes. pH-induced dissociation experiments monitored by analytical ultracentrifugation and small-angle X-ray scattering showed that the dimer related by 2-fold symmetry is the most stable unit. Mutations located near the 3-fold axis revealed that the contribution of each interaction was small. A mutant lacking helix E at the 4-fold axis formed a nanocage, suggesting that helix E is not essential for nanocage formation. Further truncation of the C-terminus of helix D abrogated the formation of the nanocage, suggesting that a few residues located at the C-terminus of helix D are critical for this process. These properties are similar to those known for mammalian ferritins and seem to be common principles for nanocage formation. The difference between EcFtnA and mammalian ferritins was that helix E-truncated EcFtnA maintained an iron-incorporating ability, whereas mammalian mutants lost it.

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“…The quaternary structure is intimately related to protein functions with a huge diversity in nature. An analysis of the quaternary arrangements of the Protein Data Bank (PDB) entries ( ) classified by the OLIGAMI database 1 reveals that approximately 47% of the catalogued proteins are monomeric and that most of the remaining form low copy number oligomers, mainly dimers (30.9%), trimers (4.6%), tetramers (8.7%) and hexamers (2.9%). In some special cases proteins form bigger complexes of, for example, 10, 12, 24 or 60 subunits.…”

Section: Introductionmentioning

confidence: 99%