Bioorthogonal organic chemistry in living cells: novel strategies for labeling biomolecules

The chemical labeling of biomolecules continues to be an important tool for the study of their function and cellular fate. Attention is increasingly focused on labeling of biomolecules in living cells, since cell lysis introduces many artefacts. In addition, with the advances in biocompatible synthetic organic chemistry, a whole new field of opportunity has opened up, affording high diversity in the nature of the label as well as a choice of ligation reactions. In recent years, several different two-step labeling strategies have emerged. These rely on the introduction of a bioorthogonal attachment site into a biomolecule, then ligation of a reporter molecule to this site using bioorthogonal organic chemistry. This Perspective focuses on these techniques, their implications and future directions.     

Long range transport of biomass aerosol to Greenland: Multi-spectroscopic investigation of particles deposited in the snow

Summary Results are given from the NIST component of a pilot (“winter-over”) study of seasonal patterns of natural and anthropogenic species in air and snow transported to Summit, Greenland. Central to this research is the quantitative apportionment of fossil and biomass particulate carbon, based on advanced (micromolar) ¹⁴C accelerator mass spectrometry (AMS) applied to remote snow samples containing as little as 9 µg C/kg. The measurements were made practicable through stringent attention to the nature and sources of the isotopic-chemical blank, resulting in a blank reduction from »5 µg C to <0.5 µg C. An important result of this work is the first evidence of a seasonal pattern in biomass-C particles in Greenland snow. Although ¹⁴C AMS data serve to resolve fossil and biomass carbon quantitatively, a deeper understanding of the aerosol sources and character demands a multidisciplinary approach. This is illustrated with “multi-spectrometric” macro- and micro-analytical data for two cases involving substantial incursions of biomass aerosol to the Summit, Greenland snow.     

CCR5 antagonists: 3-(pyrrolidin-1-yl)propionic acid analogues with potent anti-HIV activity

[reaction: see text] A novel approach to alpha,alpha-disubstituted-beta-amino acids (beta(2,2)-amino acids) was employed in the synthesis of a series of 3-(pyrrolidin-1-yl)propionic acids possessing high affinity for the CCR5 receptor and potent anti-HIV activity. The rat pharmacokinetics for these new analogues featured higher bioavailabilities and lower rates of clearance as compared to cyclopentane 1.     

Comparison of (π− d→nn withdσ(π+ d→pp) to test charge symmetry in the Δ-region

First results on ^– d are reported. The measurements were made using 8 specially designed neutron counters, which were carefully calibratedin situ. The differential cross sections atT =142, 180, 217, and 254 MeV were obtained at four angles between 0° and 90°, they are compared to ⁺ d pp data measured at the same energies and angles with the same setup. At every beam energy, the shape of the angular distributions of ^– d nn and ⁺ d pp is the same to ±2%. The absolute cross sections differ by 1 to 10%. The error in this comparison is ±4% implying a small violation of charge symmetry.Dedicated to Prof. I. laus on the occasion of his 60th birthdayDeceased     

A model for making project funding decisions at the National Cancer Institute

This paper describes the development of a model for making project funding decisions at The National Cancer Institute (NCI). The American Stop Smoking Intervention Study (ASSIST) is a multiple-year, multiple-site demonstration project, aimed at reducing smoking prevalence. The initial request for ASSIST proposals was answered by about twice as many states as could be funded. Scientific peer review of the proposals was the primary criterion used for funding decisions. However, a modified Delphi process made explicit several criteria of secondary importance. A structured questionnaire identified the relative importance of these secondary criteria, some of which we incorporated into a composite preference function. We modeled the proposal funding decision as a zero-one program, and adjusted the preference function and available budget parametrically to generate many suitable outcomes. The actual funding decision, identified by our model, offers significant advantages over manually generated solutions found by experts at NCI.     

Cyclic Heptapeptides Axinastatin 2, 3, and 4: Conformational analysis and evaluation of the biological potential

The conformational analysis of naturally occurring cytostatic cyclic heptapeptides axinastatin 2, 3, and 4 was carried out by two-dimensional NMR spectroscopy in combination with distance-geometry (DG) and molecular-dynamics (MD) calculations in explicit solvents. The synthesized secondary metabolites were examined in (D₆)DMSO. Axinastatin 2 was also investigated in CD₃OH. In all structures, Pro² is in the i + 1 position of a βI turn and Pro⁶ occupies the i + 2 position of a βVIa turn about the cis amide bond between residue 5 and Pro^6. In all peptides, a bifurcated H-bond occurs between residue 4 CO and the amide protons of residue 1 and 7. For axinastatin 2 and 3, an Asn I_g turn was found about Asn¹ and Pro^2. We compared these structures with conformations of cyclic heptapeptides obtained by X-ray and NMR studies. A β-bulge motif with two β turns and one bifurcated H-bond is found as the dominating backbone conformation of cyclic all-L-heptapeptides. Axinastatin 2, 3, and 4 can be characterized by six trans and one cis amide bond resulting in a β/βVI(a)-turn motif, a conformation found for many cyclic heptapeptides. Detailed biological tests of the synthetic compounds in different human cancer cell lines indicates these axinastatins to be inactive or of low activity.     

Curve encirclement and protein structure

A method of measuring the extent to which space curves encircle one another is introduced. The method provides a family of sets which characterize encircling curves, allowing curve pairs that engage (and also single curves that self-engage) to be distinguished. The method is applied to the backbone chains of protein molecules.