Prediction of the location and type of β‐turns in proteins using neural networks

Shepherd, Adrian J.; Gorse, Denise; Thornton, Janet M.

doi:10.1110/ps.8.5.1045

Cited by 114 publications

(159 citation statements)

References 20 publications

Supporting

Mentioning

149

Contrasting

Unclassified

Order By: Relevance

“…Transmembrane regions and betaturns in an ORF were predicted by TMPRED at http://www.ch.embnet. org/software/TMPRED_form.html and BTPRED (Shepherd et al, 1999), respectively. Tandem Repeats Finder (Benson, 1999) Recombinant pUC19 (NEB) plasmids harbouring wC2 DNA inserts were grown at 37 uC in LB (Invitrogen) supplemented with 100 mg ampicillin ml 21 (ICN Biomedicals), 62 ng X-Gal ml 21 (Bio-Rad) and 0.625 mM IPTG (Sigma).…”

Section: Methodsmentioning

confidence: 99%

The complete genome sequence of Clostridium difficile phage ϕC2 and comparisons to ϕCD119 and inducible prophages of CD630

et al. 2007

View full text Add to dashboard Cite

The complete genome sequence of Clostridium difficile phage wC2 and comparisons to wCD119 and inducible prophages of CD630 The complete genomic sequence of a previously characterized temperate phage of Clostridium difficile, wC2, is reported. The genome is 56 538 bp and organized into 84 putative ORFs in six functional modules. The head and tail structural proteins showed similarities to that of C. difficile phage wCD119 and Streptococcus pneumoniae phage EJ-1, respectively. Homologues of structural and replication proteins were found in prophages 1 and 2 of the sequenced C. difficile CD630 genome. A putative holin appears unique to the C. difficile phages and was functional when expressed in Escherichia coli. Nucleotide sequence comparisons of wC2 to wCD119 and the CD630 prophage sequences showed relatedness between wC2 and the prophages, but less so to wCD119. wC2 integrated into a gene encoding a putative transcriptional regulator of the gntR family. wC2, wCD119 and CD630 prophage 1 genomes had a Cdu1-attP-integrase arrangement, suggesting that the pathogenicity locus (PaLoc) of C. difficile, flanked by cdu1, has phage origins. The attP sequences of wC2, wCD119 and CD630 prophages were dissimilar. wC2-related sequences were found in 84 % of 37 clinical C. difficile isolates and typed reference strains. INTRODUCTIONClostridium difficile has emerged as an important intestinal pathogen since the 1970s, continuing to plague hospital settings worldwide and causing recent epidemics in the USA and Canada (Loo et al., 2005;Warny et al., 2005). The major virulence factors of C. difficile are toxins A and B encoded by tcdA and tcdB respectively, which are located on a 19 kb genomic region termed the pathogenicity locus (PaLoc) (Braun et al., 1996;Hammond & Johnson, 1995). The toxins are positively regulated by TcdR (Mani & Dupuy, 2001;Rupnik et al., 2005) and are negatively regulated by TcdC (Hundsberger et al., 1997;Matamouros et al., 2006); they are encoded by tcdR and tcdC respectively, also on the PaLoc. Another toxin-associated gene, tcdE, appears phage related but its function is unknown (Tan et al., 2001). C. difficile acquires antibiotic resistance and virulence genes through plasmids and transposons (Bruggemann, 2005) shown to significantly contribute to genome plasticity (Sebaihia et al., 2006). It is possible that phages also contribute to variance in virulence-associated genes (Lemee et al., 2005) and to the emergence of outbreak strains . However, the prevalence of phage genes within C. difficile genomes is not known. In comparison to phages of Escherichia coli, Staphylococcus aureus and Lactobacillus species, the study of clostridial phages is in its infancy. Only one phage specific for C. difficile, temperate phage wCD119, has been sequenced , while two putative prophage sequences were detected in the recently sequenced genome of C. difficile CD630 (Sebaihia et al., 2006).

show abstract

Section: Methodsmentioning

confidence: 99%

The complete genome sequence of Clostridium difficile phage ϕC2 and comparisons to ϕCD119 and inducible prophages of CD630

et al. 2007

View full text Add to dashboard Cite

show abstract

“…BC021477) was cloned into the pET28a expression vector that contains an N-terminal 6ϫ His-tag. After extensive unsuccessful crystallization trials, surface-site mutations (K141A and K142A) were made within the same construct to enhance crystallization (10)(11)(12)(13). Mutations were introduced with the QuikChange Site-Directed Mutagenesis kit (Stratagene).…”

Section: Methodsmentioning

confidence: 99%

Structure and activity of the axon guidance protein MICAL

Nadella

Bianchet

Gabelli

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

132

View full text Add to dashboard Cite

During development, neurons are guided to their targets by shortand long-range attractive and repulsive cues. MICAL, a large multidomain protein, is required for the combined action of semaphorins and plexins in axon guidance. Here, we present the structure of the N-terminal region of MICAL (MICAL fd) determined by x-ray diffraction to 2.0 Å resolution. The structure shows that MICAL fd is an FAD-containing module structurally similar to aromatic hydroxylases and amine oxidases. In addition, we present biochemical data that show that MICAL fd is a flavoenzyme that in the presence of NADPH reduces molecular oxygen to H 2O2 (Km,NAPDH ‫؍‬ 222 M; kcat ‫؍‬ 77 sec ؊1 ), a molecule with known signaling properties. We propose that the H 2O2 produced by this reaction may be one of the signaling molecules involved in axon guidance by MICAL.hydrogen peroxide ͉ hydroxylase ͉ monooxygenase ͉ x-ray diffraction

show abstract

“…The network output was either 1 (a positive ␤ hairpin prediction) or 0. The network was trained following the procedure described in Shepherd et al (40) presenting the network with a number of inputs, together with their associated target outputs. For nonhairpins, the network was presented with all of the scores resulting from threading the query sequence onto all of the same-sized database hairpins.…”

Section: Methodsmentioning

confidence: 99%

“…In addition, after training, the performance in the test case was not used to alter the training procedure. The network weights were optimized by using scaled conjugate gradients with 50 iterations (40). The results cited in the present work were obtained by using a 5-fold crossvalidation procedure.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Toward predicting protein topology: An approach to identifying β hairpins

Cruz

Hutchinson

Shepherd

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

Although secondary structure prediction methods have recently improved, progress from secondary to tertiary structure prediction has been limited. A promising but largely unexplored route to this goal is to predict structure motifs from secondary structure knowledge. Here we present a novel method for the recognition of ␤ hairpins that combines secondary structure predictions and threading methods by using a database search and a neural network approach. The method successfully predicts 48 and 77%, respectively, of all of hairpin and nonhairpin ␤-coil-␤ motifs in a protein database. We find that the main contributors to motif recognition are predicted accessibility and turn propensities.

show abstract

Prediction of the location and type of β‐turns in proteins using neural networks

Cited by 114 publications

References 20 publications

The complete genome sequence of Clostridium difficile phage ϕC2 and comparisons to ϕCD119 and inducible prophages of CD630

The complete genome sequence of Clostridium difficile phage ϕC2 and comparisons to ϕCD119 and inducible prophages of CD630

Structure and activity of the axon guidance protein MICAL

Toward predicting protein topology: An approach to identifying β hairpins

Contact Info

Product

Resources

About