Mapping Putative Contact Sites Between Subunits in a Bacterial ATP-binding Cassette (ABC) Transporter by Synthetic Peptide Libraries

Blüschke, Bettina; Eckey, Viola; Kunert, Britta; Berendt, Susanne; Landmesser, Heidi; Portwich, Michael; Volkmer, Rudolf; Schneider, Erwin

doi:10.1016/j.jmb.2007.03.043

Cited by 8 publications

(5 citation statements)

References 51 publications

(78 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Interaction between the subunits of the transporters have been mapped to the so called EAA domain of about 20 amino acids located in the second to last trans-membrane domain of the permeases and to the Q-loop of the ATPases [110], [111]. Alignment of the MalG-like permeases revealed a conserved sequence motif of three amino acids within the EAA domain.…”

Section: Resultsmentioning

confidence: 99%

“…Since the ATP binding proteins, MalK and MsmK of the orthologue transporters in S. mutans , were demonstrated being functionally interchangeable [109], we looked for a molecular signature of such an exclusive interaction. Alignment of the region of interaction of the permeases (EAA motif) to the ATP-binding proteins showed a possible three amino acid consensus preceding the EAA domain of the MalG-like permeases [110], [111]. The amino acid triplet SLD (Figure 6B), which was found in the SP1895-6-7 and SP2108-9-10, and in MsmG and MalG of S. mutans , also shows high similarity to the MalG protein of E. coli , but is not found in the other pneumococcal CUT1 permeases (Figure 6B).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

A Functional Genomics Approach to Establish the Complement of Carbohydrate Transporters in Streptococcus pneumoniae

et al. 2012

View full text Add to dashboard Cite

The aerotolerant anaerobe Streptococcus pneumoniae is part of the normal nasopharyngeal microbiota of humans and one of the most important invasive pathogens. A genomic survey allowed establishing the occurrence of twenty-one phosphotransferase systems, seven carbohydrate uptake ABC transporters, one sodium∶solute symporter and a permease, underlining an exceptionally high capacity for uptake of carbohydrate substrates. Despite high genomic variability, combined phenotypic and genomic analysis of twenty sequenced strains did assign the substrate specificity only to two uptake systems. Systematic analysis of mutants for most carbohydrate transporters enabled us to assign a phenotype and substrate specificity to twenty-three transport systems. For five putative transporters for galactose, pentoses, ribonucleosides and sulphated glycans activity was inferred, but not experimentally confirmed and only one transport system remains with an unknown substrate and lack of any functional annotation. Using a metabolic approach, 80% of the thirty-two fermentable carbon substrates were assigned to the corresponding transporter. The complexity and robustness of sugar uptake is underlined by the finding that many transporters have multiple substrates, and many sugars are transported by more than one system. The present work permits to draw a functional map of the complete arsenal of carbohydrate utilisation proteins of pneumococci, allows re-annotation of genomic data and might serve as a reference for related species. These data provide tools for specific investigation of the roles of the different carbon substrates on pneumococcal physiology in the host during carriage and invasive infection.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

A Functional Genomics Approach to Establish the Complement of Carbohydrate Transporters in Streptococcus pneumoniae

et al. 2012

View full text Add to dashboard Cite

show abstract

“…Further, the peptide array membrane can be regenerated after the cell binding assay, allowing repetitive use of the same peptide array. The peptide arrays on cellulose membranes show remarkable affinity toward different binding moieties and have been used mainly for studying peptide−protein and peptide−antibody interactions. − Okochi et al studied the direct interaction of peptides on cellulose membrane with cells . However, the authors punched individual peptide spots into the 96-well plates followed by cell adhesion and cell labeling.…”

Section: Resultsmentioning

confidence: 99%

Peptide Arrays for Screening Cancer Specific Peptides

et al. 2010

View full text Add to dashboard Cite

In this paper, we describe a novel method to screen peptides for specific recognition by cancer cells. Seventy peptides were synthesized on a cellulose membrane in an array format, and a direct method to study the peptide-whole cell interaction was developed. The relative binding affinity of the cells for different peptides with respect to a lead 12-mer p160 peptide, identified by phage display, was evaluated using the CyQUANT fluorescence of the bound cells. Screening allowed identification of at least five new peptides that displayed higher affinity (up to 3-fold) for MDA-MB-435 and MCF-7 human cancer cells compared to the p160 peptide. These peptides showed very little binding to the control (noncancerous) human umbilical vein endothelial cells (HUVECs). Three of these peptides were synthesized separately and labeled with fluorescein isothiocyanate (FITC) to study their uptake and interaction with the cancer and control cells using confocal laser scanning microscopy and flow cytometry. The results confirmed the high and specific affinity of an 11-mer peptide 11 (RGDPAYQGRFL) and a 10-mer peptide 18 (WXEAAYQRFL) for the cancer cells versus HUVECs. Peptide 11 binds different receptors on target cancer cells as its sequence contains multiple recognition motifs, whereas peptide 18 binds mainly to the putative p160 receptor. The peptide array-whole cell binding assay reported here is a complementary method to phage display for further screening and optimization of cancer targeting peptides for cancer therapy and diagnosis.

show abstract

“…26, 32 These lengths are sufficient for antibody–protein interactions because linear epitopes do not exceed this range 81. In contrast, pepscans comprising overlapping peptides of up to 20‐mers in length have been synthesised to elucidate the binding sites of Pex,82–84 Tat62, 85 and maltose importer proteins 86. 87 Besides peptide length, the number of overlapping amino acids between the consecutive peptides defines a peptide scan.…”

Section: Fundamental Spot Technologymentioning

confidence: 99%

Optimal delineation of PCG sounds via false‐alarm bounded segmentation of a wavelet‐based principal components analyzed metric

Homaeinezhad

Atyabi

Deneshvar

et al. 2011

Numer Methods Biomed Eng

View full text Add to dashboard Cite

SUMMARYThe aim of this study is to describe a new false-alarm probability (FAP) bounded unified framework for segmentation of the phonocardiogram (PCG) signal sounds registered by an electronic stethoscope board. To meet this end, first the original PCG signal is pre-processed by application of an appropriate bandpass finite-duration impulse response (FIR) filter and then by implementation of à trous discrete wavelet transform (DWT) to the filtered signal for extracting several dyadic scales. Then, after choosing a proper scale, a fixed sample size sliding window is moved on the selected scale and in each slide, six feature vectors namely summation of the nonlinearly amplified Hilbert transform, summation of absolute first order differentiation, summation of absolute second-order differentiation, curve length, area and variance of the excerpted segment are calculated. Then, all feature trends are normalized and utilized to construct a newly proposed principal components analyzed geometric index (PCAGI) (to be used as the segmentation decision statistic (DS)) by application of a linear orthonormal projection. Next, using an adaptive smoothing filter (ASF), the obtained metric is modulated and freed from the fast fluctuations occurring in the vicinity of events onset and offset locations which consequently results in enhancement of edge detection accuracy. Later, histogram parameters of the filtered DS metric are used for the regulation of the -level Neyman-Pearson classifier for FAP-bounded delineation of the PCG events. To assess the performance quality of the proposed PCG segmentation algorithm, the method was applied to all 85 records of Nursing Student Heart Sounds database including stenosis, insufficiency, regurgitation, gallop, septal defect, sound split, rumble, murmur, clicks, friction rub and snap disorders with different sampling frequencies. The method was also applied to the records obtained from an electronic stethoscope board designed for fulfillment of this study in the presence of high-level power-line noise and external disturbing sounds and as a result, no false positive or false negative errors were detected. High robustness against measurement noises of the electronic stethoscopes, acceptable detection-segmentation accuracy of PCG events in the presence of severe heart valvular and arrhythmic dysfunctions within a tolerable computational burden (processing time) and having no parameter dependency on the acquisition sampling frequency can be mentioned as important merits and capabilities of the proposed PCAGI-based PCG events detection-segmentation algorithm.

show abstract

Mapping Putative Contact Sites Between Subunits in a Bacterial ATP-binding Cassette (ABC) Transporter by Synthetic Peptide Libraries

Cited by 8 publications

References 51 publications

A Functional Genomics Approach to Establish the Complement of Carbohydrate Transporters in Streptococcus pneumoniae

A Functional Genomics Approach to Establish the Complement of Carbohydrate Transporters in Streptococcus pneumoniae

Peptide Arrays for Screening Cancer Specific Peptides

Optimal delineation of PCG sounds via false‐alarm bounded segmentation of a wavelet‐based principal components analyzed metric

Contact Info

Product

Resources

About