Current status of membrane protein structure classification

Neumann, Sindy; Fuchs, Angelika; Frishman, Dmitrij

doi:10.1002/prot.22692

Cited by 24 publications

(22 citation statements)

References 59 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…3). A bundle formed of 4 alpha-helices represents one of the widespread protein folds; this is one of few folds which are found both in water-soluble and in membrane proteins [93]. Binding of two hemes has been shown to stabilize the fold [94]; it has been shown that of the half of the de novo four-helical proteins from designed combinatorial libraries could bind the heme [95].…”

Section: Evolution Of the Cytochrome Bc Complexes: From Membrane-amentioning

confidence: 99%

Evolution of cytochrome bc complexes: From membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates

Dibrova

Cherepanov

Galperin

et al. 2013

Biochimica et Biophysica Acta (BBA) - Bioenergetics

View full text Add to dashboard Cite

This review traces the evolution of the cytochrome bc complexes from their early spread among prokaryotic lineages and up to the mitochondrial cytochrome bc1 complex (complex III) and its role in apoptosis. The results of phylogenomic analysis suggest that the bacterial cytochrome b6f-type complexes with short cytochromes b were the ancient form that preceded in evolution the cytochrome bc1-type complexes with long cytochromes b. The common ancestor of the b6f-type and the bc1-type complexes probably resembled the b6f-type complexes found in Heliobacteriaceae and in some Planctomycetes. Lateral transfers of cytochrome bc operons could account for the several instances of acquisition of different types of bacterial cytochrome bc complexes by archaea. The gradual oxygenation of the atmosphere could be the key evolutionary factor that has driven further divergence and spread of the cytochrome bc complexes. On one hand, oxygen could be used as a very efficient terminal electron acceptor. On the other hand, auto-oxidation of the components of the bc complex results in the generation of reactive oxygen species (ROS), which necessitated diverse adaptations of the b6f-type and bc1-type complexes, as well as other, functionally coupled proteins. A detailed scenario of the gradual involvement of the cardiolipin-containing mitochondrial cytochrome bc1 complex into the intrinsic apoptotic pathway is proposed, where the functioning of the complex as an apoptotic trigger is viewed as a way to accelerate the elimination of the cells with irreparably damaged, ROS-producing mitochondria.

show abstract

Section: Evolution Of the Cytochrome Bc Complexes: From Membrane-amentioning

confidence: 99%

Evolution of cytochrome bc complexes: From membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates

Dibrova

Cherepanov

Galperin

et al. 2013

Biochimica et Biophysica Acta (BBA) - Bioenergetics

View full text Add to dashboard Cite

show abstract

“…Unlike most globular proteins, most membrane protein structures can be classified, independent of evolutionary relationships, into two main groups, “all-alpha” and “all-beta”, based on structural characteristics alone [51], [52]. One dominant characteristic is the requirement for stability within the nonpolar interior of the membrane, and this is reflected in recurring patterns of defined length hydrophobic segments, imposed by the physical constraints of alpha-helical or beta-strand secondary structure elements.…”

Section: Resultsmentioning

confidence: 99%

A Horizontal Alignment Tool for Numerical Trend Discovery in Sequence Data: Application to Protein Hydropathy

2013

View full text Add to dashboard Cite

An algorithm is presented that returns the optimal pairwise gapped alignment of two sets of signed numerical sequence values. One distinguishing feature of this algorithm is a flexible comparison engine (based on both relative shape and absolute similarity measures) that does not rely on explicit gap penalties. Additionally, an empirical probability model is developed to estimate the significance of the returned alignment with respect to randomized data. The algorithm's utility for biological hypothesis formulation is demonstrated with test cases including database search and pairwise alignment of protein hydropathy. However, the algorithm and probability model could possibly be extended to accommodate other diverse types of protein or nucleic acid data, including positional thermodynamic stability and mRNA translation efficiency. The algorithm requires only numerical values as input and will readily compare data other than protein hydropathy. The tool is therefore expected to complement, rather than replace, existing sequence and structure based tools and may inform medical discovery, as exemplified by proposed similarity between a chlamydial ORFan protein and bacterial colicin pore-forming domain. The source code, documentation, and a basic web-server application are available.

show abstract

“…SCOP [11] and/or CATH [12] annotations could be obtained for 54 chains although only 24 chains had a classification in both databases. In accordance with the current approach adopted both by SCOP and CATH for transmembrane proteins [13], all proteins were treated as single domain proteins.…”

Section: Methodsmentioning

confidence: 99%

“…However, our comparative analysis of the structural classification of α-helical membrane proteins in these databases has shown that the fold definition initially developed for globular proteins is applicable to membrane proteins only to a limited degree [13]. We therefore suggested revising the fold definition for membrane proteins by incorporating more fine-grained structural features such as helix-helix interactions.…”

Section: Introductionmentioning

confidence: 99%

Classification of α-Helical Membrane Proteins Using Predicted Helix Architectures

et al. 2013

Self Cite

View full text Add to dashboard Cite

Despite significant methodological advances in protein structure determination high-resolution structures of membrane proteins are still rare, leaving sequence-based predictions as the only option for exploring the structural variability of membrane proteins at large scale. Here, a new structural classification approach for α-helical membrane proteins is introduced based on the similarity of predicted helix interaction patterns. Its application to proteins with known 3D structure showed that it is able to reliably detect structurally similar proteins even in the absence of any sequence similarity, reproducing the SCOP and CATH classifications with a sensitivity of 65% at a specificity of 90%. We applied the new approach to enhance our comprehensive structural classification of α-helical membrane proteins (CAMPS), which is primarily based on sequence and topology similarity, in order to find protein clusters that describe the same fold in the absence of sequence similarity. The total of 151 helix architectures were delineated for proteins with more than four transmembrane segments. Interestingly, we observed that proteins with 8 and more transmembrane helices correspond to fewer different architectures than proteins with up to 7 helices, suggesting that in large membrane proteins the evolutionary tendency to re-use already available folds is more pronounced.

show abstract

Current status of membrane protein structure classification

Cited by 24 publications

References 59 publications

Evolution of cytochrome bc complexes: From membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates

Evolution of cytochrome bc complexes: From membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates

A Horizontal Alignment Tool for Numerical Trend Discovery in Sequence Data: Application to Protein Hydropathy

Classification of α-Helical Membrane Proteins Using Predicted Helix Architectures

Contact Info

Product

Resources

About