The four-helix bundle: An attractive fold

Eckenhoff, Roderic G.; Liu, Renyu; Johansson, Jonas; Loll, Patrick J.

doi:10.1016/j.ics.2005.06.079

Cited by 2 publications

(1 citation statement)

References 15 publications

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“…DaliLite aligns 67 residues at RMSD ¼ 2.5 Å for this protein pair. However, the generated alignment is insufficient to describe the fold of 2ES9 in sufficient detail, since only the four-helix bundle, which is a common motive (Mehl et al 2003;Eckenhoffa et al 2005), was aligned, while the fifth lateral a-helix was skipped.…”

Section: Large-scale Database Comparisonmentioning

confidence: 99%

Novel protein folds and their nonsequential structural analogs

Guerler

Knapp

2008

Protein Science

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Newly determined protein structures are classified to belong to a new fold, if the structures are sufficiently dissimilar from all other so far known protein structures. To analyze structural similarities of proteins, structure alignment tools are used. We demonstrate that the usage of nonsequential structure alignment tools, which neglect the polypeptide chain connectivity, can yield structure alignments with significant similarities between proteins of known three-dimensional structure and newly determined protein structures that possess a new fold. The recently introduced protein structure alignment tool, GANGSTA, is specialized to perform nonsequential alignments with proper assignment of the secondary structure types by focusing on helices and strands only. In the new version, GANGSTA+, the underlying algorithms were completely redesigned, yielding enhanced quality of structure alignments, offering alignment against a larger database of protein structures, and being more efficient. We applied DaliLite, TM-align, and GANGSTA+ on three protein crystal structures considered to be novel folds. Applying GANGSTA+ to these novel folds, we find proteins in the ASTRAL40 database, which possess significant structural similarities, albeit the alignments are nonsequential and in some cases involve secondary structure elements aligned in reverse orientation. A web server is available at http:// agknapp.chemie.fu-berlin.de/gplus for pairwise alignment, visualization, and database comparison.

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Section: Large-scale Database Comparisonmentioning

confidence: 99%

Novel protein folds and their nonsequential structural analogs

Guerler

Knapp

2008

Protein Science

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Characteristics and Kinetics of Iron Releasefrom the Ferritin under the EGCG reduction

Huang

Lin

et al. 2011

Biol Trace Elem Res

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The mechanism of iron release from ferritin in vivo is still unclear even though it represents a key step of the metabolism of iron in vivo. Here, both interaction intensity and binding stability between epigallocatechin gallate (EGCG) from tea and liver ferritin of Dasyatis akajei (DALF) were investigated using UV-visible, fluorescence and circular dichroism (CD) spectrometry, respectively. The results indicated that EGCG could reduce the iron within the ferritin shell directly in the absence of chemical reducers such as Na(2)S(2)O(4), but this process was strictly pH-dependent, and the rate of iron release is faster at low pH than at high pH. The kinetic study of iron release showed that this process fitted the law of zero order reaction, which differed from that of first order reaction by various chemical reducers such as Vitamin C. In addition, Both fluorescence and CD spectrometry were further used to study the reduction mechanism of iron release in vitro, showing that there was a slight conformation change of the ferritin shell during EGCG reduction because of a complex formation of DALF-EGCG. It appears that chemical reducers with large molecular sizes reduce the iron across the protein shell by the way of an electron transfer pathway (ETP). A novel pathway for iron release from DALF with EGCG reduction is suggested to explain for a reductive route of iron metabolism by biological reducers in vivo.

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The four-helix bundle: An attractive fold

Cited by 2 publications

References 15 publications

Novel protein folds and their nonsequential structural analogs

Novel protein folds and their nonsequential structural analogs

Characteristics and Kinetics of Iron Releasefrom the Ferritin under the EGCG reduction

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