Mol. Cell. Proteomics

Chemical cross-linking in combination with mass spectrometric analysis offers the potential to obtain low-resolution structural information from proteins and protein complexes. Identification of peptides connected by a cross-link provides direct evidence for the physical interaction of amino acid side chains, information that can be used for computational modeling purposes. Despite impressive advances that were made in recent years, the number of experimentally observed cross-links still falls below the number of possible contacts of cross-linkable side chains within the span of the cross-linker. Here, we propose two complementary experimental strategies to expand cross-linking data sets. First, enrichment of cross-linked peptides by size exclusion chromatography selects cross-linked peptides based on their higher molecular mass, thereby depleting the majority of unmodified peptides present in proteolytic digests of cross-linked samples. Second, we demonstrate that the use of proteases in addition to trypsin, such as Asp-N, can additionally boost the number of observable cross-linking sites. The benefits of both SEC enrichment and multiprotease digests are demonstrated on a set of model proteins and the improved workflow is applied to the characterization of the 20S proteasome from rabbit and Schizosaccharomyces pombe

The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data

Motivation: Mass spectrometry experiments in the field of proteomics produce lists containing tens to thousands of identified proteins. With the protein information and property explorer (PIPE), the biologist can acquire functional annotations for these proteins and explore the enrichment of the list, or fraction thereof, with respect to functional classes. These protein lists may be saved for access at a later time or different location. The PIPE is interoperable with the Firegoose and the Gaggle, permitting wide-ranging data exploration and analysis. The PIPE is a rich-client web application which uses AJAX capabilities provided by the Google Web Toolkit, and server-side data storage using Hibernate. Availability: http://pipe.systemsbiology.net Contact: [email protected]

Role of interband scattering in neutron irradiated MgB2_2 thin films by Scanning Tunneling Spectroscopy measurements

A series of MgB$_2$ thin films systematically disordered by neutron irradiation have been studied by Scanning Tunneling Spectroscopy. The c-axis orientation of the films allowed a reliable determination of local density of state of the $\pi$ band. With increasing disorder, the conductance peak moves towards higher voltages and becomes lower and broader, indicating a monotonic increase of the $\pi$ gap and of the broadening parameter. These results are discussed in the frame of two-band superconductivity.Comment: The text will be submitted in Latex format, and the corresponding pdf file should take 6 pages. There are 5 figures (eps files submitted) and 1 tabl

Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes

The study of proteins and protein complexes using chemical cross-linking followed by the MS identification of the cross-linked peptides has found increasingly widespread use in recent years. Thus far, such analyses have used almost exclusively homobifunctional, amine-reactive cross-linking reagents. Here we report the development and application of an orthogonal cross-linking chemistry specific for carboxyl groups. Chemical cross-linking of acidic residues is achieved using homobifunctional dihydrazides as cross-linking reagents and a coupling chemistry at neutral pH that is compatible with the structural integrity of most protein complexes. In addition to cross-links formed through insertion of the dihydrazides with different spacer lengths, zero-length cross-link products are also obtained, thereby providing additional structural information. We demonstrate the application of the reaction and the MS identification of the resulting cross-linked peptides for the chaperonin TRiC/CCT and the 26S proteasome. The results indicate that the targeting of acidic residues for cross-linking provides distance restraints that are complementary and orthogonal to those obtained from lysine cross-linking, thereby expanding the yield of structural information that can be obtained from cross-linking studies and used in hybrid modeling approaches

Outcome of proximal esophageal cancer after definitive combined chemo-radiation: a Swiss multicenter retrospective study.

To report oncological outcomes and toxicity rates, of definitive platin-based chemoradiadiationtherapy (CRT) in the management of proximal esophageal cancer. We retrospectively reviewed the medical records of patients with cT1-4 cN0-3 cM0 cervical esophageal cancer (CEC) (defined as tumors located below the inferior border of the cricoid cartilage, down to 22 cm from the incisors) treated between 2004 and 2013 with platin-based definitive CRT in four Swiss institutions. Acute and chronic toxicities were retrospectively scored using the National Cancer Institute's Common Terminology Criteria for Adverse Events, version 4.0 (CTCAE-NCI v.4.0). Primary endpoint was loco-regional control (LRC). We also evaluated overall survival (OS) and disease-free survival (DFS) rates. The influence of patient- and treatment related features have been calculated using the Log-rank test and multivariate Cox proportional hazards model. We enrolled a total of 55 patients. Median time interval from diagnosis to CRT was 78 days (6-178 days). Median radiation dose was 56Gy (28-72Gy). Induction chemotherapy (ICHT) was delivered in 58% of patients. With a median follow up of 34 months (6-110months), actuarial 3-year LRC, DFS and OS were 52% (95% CI: 37-67%), 35% (95% CI: 22-50%) and 52% (95% CI: 37-67%), respectively. Acute toxicities (dysphagia, pain, skin-toxicity) ranged from grade 0 - 4 without significant dose-dependent differences. On univariable analyses, the only significant prognostic factor for LRC was the time interval > 78 days from diagnosis to CRT. On multivariable analysis, total radiation dose >56Gy (p <0.006) and ICHT (p < 0.004) were statistically significant positive predictive factors influencing DFS and OS. Definitive CRT is a reliable therapeutic option for proximal esophageal cancer, with acceptable treatment related toxicities. Higher doses and ICHT may improve OS and DFS and. These findings need to be confirmed in further prospective studies

Excitation Spectrum and Superexchange Pathways in the Spin Dimer VODPO_4 . 1/2 D_2O

Magnetic excitations have been investigated in the spin dimer material VODPO_4 \cdot 1/2 D_2O using inelastic neutron scattering. A dispersionless magnetic mode was observed at an energy of 7.81(4) meV. The wavevector dependence of the scattering intensityfrom this mode is consistent with the excitation of isolated V^{4+} spin dimers with a V-V separation of 4.43(7) \AA. This result is unexpected since the V-V pair previously thought to constitute themagnetic dimer has a separation of 3.09 \AA. We identify an alternative V-V pair as the likely magnetic dimer, which involves superexchange pathways through a covalently bonded PO_4 group. This surprising result casts doubt on the interpretation of (VO)_2P_2O_7 as a spin ladder.Comment: 4 pages, 4 postscript figures - identical to previous paper but figure 2 and 3 hopefully more compatible .p

Swath-ms: a new data independent acquisition LC-MS methodology for quantitative complete proteome analysis

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