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Recent Research Papers of Note: Oct 1, 2009


Journal: Protein and Peptide Letters, Nov. 10 [Epub ahead of print]
Title: Evaluation of protein phosphorylation site predictors
Authors: S Que; Y Wang; P Chen; Y Tang; Z Zhang; H He

Authors selected six recently published methods of phosphorylation site prediction methods to evaluate their performance: Disphos; NetPhosK; PPSP; KinasePhos; Scansite; and PredPhospho. They compiled three testing datasets containing experimentally verified phosphorylation sites for mammalian, Arabidopsis, and rice proteins. They then present the performance of the methods on the three independent datasets. "Rather than quantitatively ranking the performance of these methods, we focused on providing an understanding of the overall performance of the predictors," the authors said in the abstract.

Journal: Nature Biotechnology, Sept. 20 [Epub ahead of print]
Title: A proteomics approach to discovering natural products and their biosynthetic pathways
Authors: SB Bumpus; BS Evans; PM Thomas; I Ntai; NL Kelleher

According to the abstract, many natural products with antibiotic, anticancer, and antifungal properties are synthesized by nonribosomal peptide synthetases and polyketide synthases. Genomic sequencing has shed light on the diversity of these enzymes but identifying new products and their biosynthetic pathways remain difficult. "By taking advantage of the size of these enzymes (often >2,000 amino acids) and unique marker ions derived from their common phosphopantetheinyl cofactor, we adapted mass spectrometry-based proteomics to selectively detect NRPS and PKS gene clusters in microbial proteomes without requiring genome sequence information," the authors said in the abstract. They detected known NRPS systems in members of the genera Bacillus and Streptomyces and screened 22 environmental isolates to reveal production of unknown natural products from the nybrid NRPS PKS zwittermicin A biosynthetic gene cluster. They also discovered an NRPS cluster that generates a seven-residue lipopeptide.

Journal: Archives of Physiology and Biochemistry, Sept. 18 [Epub ahead of print]
Title: Enhancing mass spectrometry-based serum profiling by a combination of free flow electrophoresis and ClinProt
Authors: S Hartwig; J Kotzka; H Muller-Wieland; J Eckel; S Lehr

Presented is a 2D fractionation approach that combines liquid-based isoelectric focusing and affinity chromatography. In the first dimension, the authors fractionated serum specimen according to the isoelectric point of protein components by free-flow electrophoresis. Fractions were then separated in the second dimension by ClinProt. Protein profiling was done by MALDI-TOF analysis. Compared to using the ClinProt approach alone, the authors said their approach enhanced detectable protein mass signals by a factor of 15 with high reproducibility.

Journal: Electrophoresis, Sept. 18 [Epub ahead of print]
Title: Improvement of gel-separated protein identification by DMF-assisted digestion and peptide recovery after electroblotting
Authors: Y Lin; Y Li; Y Liu; W Han; Q He; J Li; P Chen; X Wang; L Liang

Presented is a method for efficient protein digestion and tryptic peptide recovery. The method comprises electroblotting gel-separated proteins onto a PVDF membrane, excising the PVDF bands containing proteins of interest, and dissolving the bands with pure DMF. "This protocol allowed more efficient digestion and peptide recovery, thereby increasing the sequence coverage and the confidence of protein identification," the authors said in the abstract.

Journal: Cornea, Sept. 16 [Epub ahead of print]
Title: Mass spectrometry-based proteomic analyses in contact lens-related dry eye
Authors: JJ Nichols; KB Green-Church

To identify potential protein biomarkers associated with dry eye in contact lens wearers, 21 subjects were enrolled in a study. Several proteins were identified as potential biomarkers of dry eye disease.

Journal: Nature Methods, Sept. 13 [Epub ahead of print]
Title: Proteomics strategy for quantitative protein interaction profiling in cell extracts
Authors: K Sharma; C Weber; M Bairlein; Z Greff; G Keri; J Cox; JV Olsen; H Daub

Authors report a strategy to identify and quantify cellular target protein interactions with externally introduced ligands. They determined "dissociation constants for target proteins interacting with the ligand of interest by combining quantitative mass spectrometry with a defined set of affinity purification experiments," according to the abstract. They also demonstrate the general utility of their method.

Journal: Proteomics, Sept. 11 [Epub ahead of print]
Title: Development of a new method for absolute protein quantification on 2D gels.
Authors: P Baudouin-Cornu; G Lagniel; S Chedin; J Labarre

Authors propose a method for absolute quantification based on radioactive labeling with an S35 compound and 2D PAGE. Using yeast, they grew cells for more than four generation in the presence of a "unique" sulfur source labeled at a defined specific radioactivity, "ensuring that more than 90 percent of the proteins are labeled at the same specific radioactivity as the sulfur source," according to the abstract. After separation of the S35-labeled proteins on 2D gels, each protein is counted. The amount of each protein in the gel is calculated, and the amount of each protein for each cell is deduced. The method is limited to soluble and abundant proteins visible on 2D gels.

Journal: Protein Expression and Purification, Sept. 10 [Epub ahead of print]
Title: Over-producing soluble protein complex and validating protein-protein interaction through a new bacterial co-expression system
Authors: J Zeng; L Zhang; Y Li; Y Wang; M Wang; X Duan; ZG He

Authors have developed a novel co-expression vector, pHEX, which they say is compatible with and can be partnered with many commericial E. coli vectors. pHEX, would be especially useful in protein-protein interactions of toxic or hydrophobic proteins, which likely would need a "critical" partner protein to ensure their proper folding and stability. pHEX contains the p15A origin of replication and a T7 promoter, "which can over-produce a His-tagged recombinant protein," according to the abstract. The new co-expression system was demonstrated to efficiently co-produce and co-purify heterodimeric protein complexes, the authors said.

Journal: Cytometry A, Sept. 8 [Epub ahead of print]
Title: Approaching clinical proteomics: Current state and future fields of application in cellular proteomics
Authors: R Apweiler; C Aslanidis; T Deufel; A Gerstner; J Hansen, et al.
Recent advances and application "that fulfill the criteria for clinical proteomics" is discussed with a focus on cellular proteomics, or cytoproteomics, "as related to preanalyical and analytical standardization and to quality control measures required for effective implementation of … technologies and analytes into routine laboratory testing to generate novel actionable health information," according to the abstract.

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.