Four-helix bundle topology re-engineered: monomeric Rop protein variants with different loop arrangements

Kresse, H.; Czubayko, Martin; Nyakatura, Gerald; Vriend, Gerrit; Sander, Chris; Bloecker, Helmut

doi:10.1093/protein/14.11.897

Cited by 19 publications

(17 citation statements)

References 30 publications

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“…To the best of our knowledge, only one case of reverse alignment is well known, the α -helix bundle with several helices, where one or many of the helices can be aligned in the opposite direction. The α -helix bundles have been studied experimentally and successful attempts on redesigning the four-helix bundle to have inverted helices have been reported [ 45 , 46 ]. Such successful redesign of α -helix bundle can be theoretically extended to other protein folds with the cases of reverse alignments observed in this study.…”

Section: Discussionmentioning

confidence: 99%

A comprehensive analysis of non-sequential alignments between all protein structures

Abyzov

Ilyin

2007

BMC Struct Biol

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BackgroundThe majority of relations between proteins can be represented as a conventional sequential alignment. Nevertheless, unusual non-sequential alignments with different connectivity of the aligned fragments in compared proteins have been reported by many researchers. It is interesting to understand those non-sequential alignments; are they unique, sporadic cases or they occur frequently; do they belong to a few specific folds or spread among many different folds, as a common feature of protein structure. We present here a comprehensive large-scale study of non-sequential alignments between available protein structures in Protein Data Bank.ResultsThe study has been conducted on a non-redundant set of 8,865 protein structures aligned with the aid of the TOPOFIT method. It has been estimated that between 17.4% and 35.2% of all alignments are non-sequential depending on variations in the parameters. Analysis of the data revealed that non-sequential relations between proteins do occur systematically and in large quantities. Various sizes and numbers of non-sequential fragments have been observed with all possible complexities of fragment rearrangements found for alignments consisting of up to 12 fragments. It has been found that non-sequential alignments are not limited to proteins of any particular fold and are present in more than two hundred of them. Moreover, many of them are found between proteins with different fold assignments. It has been shown that protein structure symmetry does not explain non-sequential alignments. Therefore, compelling evidences have been provided that non-sequential alignments between proteins are systematic and widespread across the protein universe.ConclusionThe phenomenon of the widespread occurrence of non-sequential alignments between proteins might represent a missing rule of protein structure organization. More detailed study of this phenomenon will enhance our understanding of protein stability, folding, and evolution.

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Section: Discussionmentioning

confidence: 99%

A comprehensive analysis of non-sequential alignments between all protein structures

Abyzov

Ilyin

2007

BMC Struct Biol

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“…Theory and experiment indicate that such loophelix interactions appreciably affect stability in natural and engineered four-helix bundles. [31][32][33][34][35] Thus, it is not surprising that loop residue conformation can couple to helical sliding. Mutations, insertions and deletions within inter-helical loops can be expected to generate more drastic effects.…”

Section: Discussionmentioning

confidence: 99%

Helical Shifts Generate Two Distinct Conformers in the Atomic Resolution Structure of the CheA Phosphotransferase Domain from Thermotoga maritima

Quezada¹,

Grădinaru²,

Simon³

et al. 2004

Journal of Molecular Biology

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“…The two monomers pack together as a fully antiparallel four helixbundle. The bend region of Rop has attracted considerable interest as a parallel molecular spring due to its stability and elasticity properties [23]. In the simulation, we constrain both ends of two α-helices of the molecule to move only along the z axis for stretching simulations and fix the short turn ( Fig.12).…”

Section: Simulation Of a Bio-nanorobotic Parallel Platformmentioning

confidence: 99%

Prototyping bio-nanorobots using molecular dynamics simulation and virtual reality

Hamdi

Ferreira

Sharma

et al. 2008

Microelectronics Journal

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Four-helix bundle topology re-engineered: monomeric Rop protein variants with different loop arrangements

Cited by 19 publications

References 30 publications

A comprehensive analysis of non-sequential alignments between all protein structures

A comprehensive analysis of non-sequential alignments between all protein structures

Helical Shifts Generate Two Distinct Conformers in the Atomic Resolution Structure of the CheA Phosphotransferase Domain from Thermotoga maritima

Prototyping bio-nanorobots using molecular dynamics simulation and virtual reality

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