In-depth MS-based proteomics has necessitated fractionation of either proteins or peptides or both, often requiring considerable analysis time. Here we employ long liquid chromatography runs with high resolution coupled to an instrument with fast sequencing speed to investigate how much of the proteome is directly accessible to liquid chromatography-tandem MS characterization without any prefractionation steps. Triplicate single-run analyses identified 2990 yeast proteins, 68% of the total measured in a comprehensive yeast proteome. Among them, we covered the enzymes of the glycolysis and gluconeogenesis pathway targeted in a recent multiple reaction monitoring study. In a mammalian cell line, we identified 5376 proteins in a triplicate run, including representatives of 173 out of 200 KEGG metabolic and signaling pathways. Remarkably, the majority of proteins could be detected in the samples at sub-femtomole amounts and many in the low attomole range, in agreement with absolute abundance estimation done in previous works (Picotti et al. Cell, 138, 795–806, 2009). Our results imply an unexpectedly large dynamic range of the MS signal and sensitivity for liquid chromatography-tandem MS alone. With further development, single-run analysis has the potential to radically simplify many proteomic studies while maintaining a systems-wide view of the proteome.

Diproline segments have been advanced as templates for nucleation of folded structure in designed peptides. The conformational space available to homochiral and heterochiral diproline segments has been probed by crystallographic and NMR studies on model peptides containing L-Pro-L-Pro and D-Pro-L-Pro units. Four distinct classes of model peptides have been investigated: a) isolated D-Pro-L-Pro segments which form type II' beta-turn; b) D-Pro-L-Pro-L-Xxx sequences which form type II'-I (betaII'-I, consecutive beta-turns) turns; c) D-Pro-L-Pro-D-Xxx sequences; d) L-Pro-L-Pro-L-Xxx sequences. A total of 17 peptide crystal structures containing diproline segments are reported. Peptides of the type Piv-D-Pro-L-Pro-L-Xxx-NHMe are conformationally homogeneous, adopting consecutive beta-turn conformations. Peptides in the series Piv-D-Pro-L-Pro-D-Xxx-NHMe and Piv-L-Pro-L-Pro-L-Xxx-NHMe, display a heterogeneity of structures in crystals. A type VIa beta-turn conformation is characterized in Piv-L-Pro-L-Pro-L-Phe-OMe (18), while an example of a 5-->1 hydrogen bonded alpha-turn is observed in crystals of Piv-D-Pro-L-Pro-D-Ala-NHMe (11). An analysis of pyrrolidine conformations suggests a preferred proline puckering geometry is favored only in the case of heterochiral diproline segments. Solution NMR studies, reveal a strong conformational influence of the C-terminal Xxx residues on the structures of diproline segments. In L-Pro-L-Pro-L-Xxx sequences, the Xxx residues strongly determine the population of Pro-Pro cis conformers, with an overwhelming population of the trans form in L-Xxx=L-Ala (19).

A one-dimensional water wire has been characterized by X-ray diffraction in single crystals of the tripeptide Ac-Phe-Pro-Trp-OMe. Crystals in the hexagonal space group P6(5) reveal a central hydrophobic channel lined by aromatic residues which entraps an approximately linear array of hydrogen bonded water molecules. The absence of any significant van der Waals contact with the channel walls suggests that the dominant interaction between the "water wire" and "peptide nanotube" is electrostatic in origin. An energy difference of 16 kJ mol(-1) is estimated for the distinct orientations of the water wire dipole with respect to the macrodipole of the peptide nanotube. The structural model suggests that Grotthuss type proton conduction may, through constricted hydrophobic channels, be facilitated by concerted, rotational reorientation of water molecules.

Background: Heart disease is the leading cause of tobacco‐related death in smokers and of deaths due to secondhand smoke (SHS) exposure in nonsmokers. This study centers on the development and evaluation of an evidence‐based model curriculum for improving clinical attention to tobacco use and SHS exposure in cardiology. Hypothesis: We hypothesized that the curriculum would be associated with improvements in clinician tobacco‐related knowledge, attitudes, confidence, and counseling behaviors from pre‐to post‐training and at the 3‐month follow‐up. Methods: The 1‐hour Cardiology Rx for Change curriculum was evaluated with 22 cardiology fellows and 77 medical residents with consistent training effects observed between the 2 groups. Results: Trainees' tobacco treatment knowledge increased significantly from pre‐ to post‐training (t[81] = 6.51, P<0.001), and perceived barriers to providing cessation treatment decreased significantly (t[81] = −3.97, P<0.001). The changes, however, were not sustained at the 3‐month follow‐up, suggesting the need for booster training efforts. From pretraining to 3‐month follow‐up, the training was associated with significant sustained gains in clinician confidence for treating tobacco dependence (t[61] = 3.69, P = 0.001) and with improvements in clinicians assessing patients' readiness to quit smoking (from 61% to 79%, t[59] = 3.69,P<0.001) and providing assistance with quitting (from 47% to 59%, t[59] = 2.12, P = 0.038). Asking patients about tobacco use, advising cessation, and arranging follow‐up also increased over time, but not significantly. All participants (100%) recommended the curriculum for dissemination to other training programs. Conclusions: Available online via http://rxforchange.ucsf.edu, Cardiology Rx for Change offers a packaged training tool for improving treatment of tobacco use and SHS exposure in cardiology care. © 2011 Wiley Periodicals, Inc. This work was supported by the Flight Attendant Medical Research Institute (FAMRI) William Cahan Distinguished Professor Award (PI: W. Grossman), and the State of California Tobacco‐Related Disease Research Program (# 17RT‐0077, PI: J.J. Prochaska). The authors have no other funding, financial relationships, or conflicts of interest to disclose.