Cascaded multiple classifiers for secondary structure prediction

Ouali, Mohammed Assam; King, Ross D.

doi:10.1110/ps.9.6.1162

Cited by 322 publications

(217 citation statements)

References 64 publications

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“…The sequence of EnvZ per from E. coli was aligned against the corresponding sequences from other γ -proteobacteria ( Figure 1B). PHD (Profile network from HeiDelberg) secondary structure prediction [23] (Figure 1B) estimates this region of EnvZ to consist of 45 % α-helices and 22 % β-sheets. ClustalW multiple sequence alignment revealed a low (16 %) overall sequence identity in EnvZ per between the different γ -proteobacterial species.…”

Section: Structural Characterizationmentioning

confidence: 99%

Structural characterization of Escherichia coli sensor histidine kinase EnvZ: the periplasmic C-terminal core domain is critical for homodimerization

Khorchid

Inouye

Ikura

2004

Biochemical Journal

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Escherichia coli EnvZ is a membrane sensor histidine kinase that plays a pivotal role in cell adaptation to changes in extracellular osmolarity. Although the cytoplasmic histidine kinase domain of EnvZ has been extensively studied, both biochemically and structurally, little is known about the structure of its periplasmic domain, which has been implicated in the mechanism underlying its osmosensing function. In the present study, we report the biochemical and biophysical characterization of the periplasmic region of EnvZ (Ala 38 -Arg 162 ). This region was found to form a dimer in solution, and to consist of two well-defined domains: an N-terminal α-helical domain and a C-terminal core domain (Glu 83 -Arg 162 ) containing both α-helical and β-sheet secondary structures. Our pull-down assays and analytical ultracentrifugation analysis revealed that dimerization of the periplasmic region is highly sensitive to the presence of CHAPS, but relatively insensitive to salt concentration, thus suggesting the significance of hydrophobic interactions between the homodimeric subunits. Periplasmic homodimerization is mediated predominantly by the C-terminal core domain, while a regulatory function may be attributed mainly to the N-terminal α-helical domain, whose mutations have been shown previously to produce a high-osmolarity phenotype.

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Section: Structural Characterizationmentioning

confidence: 99%

Structural characterization of Escherichia coli sensor histidine kinase EnvZ: the periplasmic C-terminal core domain is critical for homodimerization

Khorchid

Inouye

Ikura

2004

Biochemical Journal

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“…Analyzed predictors include the systems Jufo [18], Prof [20], Porter [21], Psipred [17], Nn-predict [14], HMMSTR/Rosetta [4], SAM [13], Gor IV [8], Hnn [9].…”

Section: Resultsmentioning

confidence: 99%

“…In this section we present the experimental framework we adopted to compare the performance of nine secondary structure prediction tools, that are: Jufo [18], Prof [20], Porter [21], Psipred [17], Nn-predict [14], all exploiting neural network-based approaches; HMMSTR/Rosetta [4], based on an ab initio method; SAM [13], based on linear hidden Markov models; Gor IV [8], using frequency analysis of amino acid conformational states; Hnn [9], based on a hierarchical and modular approach.…”

Section: Experiments On Protein Predictionmentioning

confidence: 99%

Experimental Evaluation of Protein Secondary Structure Predictors

Miceli¹,

Palopoli²,

Rombo³

et al. 2009

Lecture Notes in Computer Science

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Abstract. Understanding protein biological function is a key issue in modern biology, which is largely determined by its 3D shape. Protein 3D shape, in its turn, is functionally implied by its amino acid sequence. Since the direct inspection of such 3D structures is rather expensive and time consuming, a number of software techniques have been developed in the last few years that predict a spatial model, either of the secondary or of the tertiary form, for a given target protein starting from its amino acid sequence.This paper offers a comparison of several available automatic secondary structure prediction tools. The comparison is of the experimental kind, where two relevant sets of proteins, a non-redundant one including 100 elements, and a 180-protein set taken from the CASP 6 contest, were used as test cases. Comparisons have been based on evaluating standard quality measures, such as the Q3 and SOV.

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“…The stability of the tree was estimated using bootstrap analysis from 1000 pseudo-replications of the sequence alignment. For the C-terminal domains of CjDsbI and HpDsbI, secondary structure prediction was carried out using programs PSI-PRED (Jones, 1999), SAM-T02 (Karplus et al, 2003) and PROF (Ouali & King, 2000). Table 2.…”

Section: Methodsmentioning

confidence: 99%

Characterization of new DsbB-like thiol-oxidoreductases of Campylobacter jejuni and Helicobacter pylori and classification of the DsbB family based on phylogenomic, structural and functional criteria

et al. 2005

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In Gram-negative bacterial cells, disulfide bond formation occurs in the oxidative environment of the periplasm and is catalysed by Dsb (disulfide bond) proteins found in the periplasm and in the inner membrane. In this report the identification of a new subfamily of disulfide oxidoreductases encoded by a gene denoted dsbI, and functional characterization of DsbI proteins from Campylobacter jejuni and Helicobacter pylori, as well as DsbB from C. jejuni, are described. The N-terminal domain of DsbI is related to DsbB proteins and comprises five predicted transmembrane segments, while the C-terminal domain is predicted to locate to the periplasm and to fold into a b-propeller structure. The dsbI gene is co-transcribed with a small ORF designated dba (dsbI-accessory). Based on a series of deletion and complementation experiments it is proposed that DsbB can complement the lack of DsbI but not the converse. In the presence of DsbB, the activity of DsbI was undetectable, hence it probably acts only on a subset of possible substrates of DsbB. To reconstruct the principal events in the evolution of DsbB and DsbI proteins, sequences of all their homologues identifiable in databases were analysed. In the course of this study, previously undetected variations on the common thiol-oxidoreductase theme were identified, such as development of an additional transmembrane helix and loss or migration of the second pair of Cys residues between two distinct periplasmic loops. In conjunction with the experimental characterization of two members of the DsbI lineage, this analysis has resulted in the first comprehensive classification of the DsbB/DsbI family based on structural, functional and evolutionary criteria.

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Cascaded multiple classifiers for secondary structure prediction

Cited by 322 publications

References 64 publications

Structural characterization of Escherichia coli sensor histidine kinase EnvZ: the periplasmic C-terminal core domain is critical for homodimerization

Structural characterization of Escherichia coli sensor histidine kinase EnvZ: the periplasmic C-terminal core domain is critical for homodimerization

Experimental Evaluation of Protein Secondary Structure Predictors

Characterization of new DsbB-like thiol-oxidoreductases of Campylobacter jejuni and Helicobacter pylori and classification of the DsbB family based on phylogenomic, structural and functional criteria

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