Improved sensitivity proteomics by postharvest alkylation and radioactive labelling of proteins

We describe approaches to improve the detection of proteins by postharvest alkylation and subsequent radioactive labeling with either [3H]iodoacetamide or 125I. Database protein sequence analysis suggested that cysteine is not suitable for detection of the entire proteome, but that cysteine alkylating reagents can increase the number of proteins able to be detected by iodination chemistry. Proteins were alkylated with beta-(4-hydroxyphenyl)ethyl iodoacetamide, or with 1,5-l-AEDANS (the Hudson Weber reagent). Subsequent iodination using the Iodo-Gen system was found to be most efficient. The enhanced sensitivity obtainable by using these approaches is expected to be sufficient for visualization of the lowest copy number proteins from human cells, such as from clinical samples. However, we argue that significantly improved methods of protein separation will be necessary to resolve the large number of proteins expected to be detectable with this sensitivity.     

Rydberg-London potential for diatomic molecules and unbonded atom pairs

We propose and test a pair potential that is accurate at all relevant distances and simple enough for use in large-scale computer simulations. A combination of the Rydberg potential from spectroscopy and the London inverse-sixth-power energy, the proposed form fits spectroscopically determined potentials better than the Morse, Varnshi, and Hulburt-Hirschfelder potentials and much better than the Lennard-Jones and harmonic potentials. At long distances, it goes smoothly to the London force appropriate for gases and preserves van der Waals's "continuity of the gas and liquid states," which is routinely violated by coefficients assigned to the Lennard-Jones 6-12 form.     

Building unit and topological evolution in the hydrothermal DABCO-U-F system

Compounds NDUF-1 ([C(6)H(14)N(2)](UO(2))(2)F(6); P2(1)/c, a = 6.9797(15) A, b = 8.3767(15) A, c = 23.760(5) A, beta = 91.068(4) degrees, V = 1388.9(5) A(3), Z = 4), NDUF-2 ([C(6)H(14)N(2)](2)(UO(2))(2)F(5)UF(7).H(2)O), NDUF-3 ((NH(4))(7)U(6)F(31); R3, a = 15.4106(8) A, c = 10.8142(8) A, V = 2224.1(2) A(3), Z = 3), and NDUF-4 ([NH(4)]U(3)F(13)) have been synthesized hydrothermally from fixed composition reactant mixtures over variable time periods [DABCO (C(6)H(12)N(2)), UO(2)(NO(3))(2).6H(2)O, HF, and H(2)O; 2-14 days]. Observed is a systematic evolution of the structural building units within these materials from the UO(2)F(5) pentagonal bipyramid in NDUF-1 and -2 to the UF(8) trigonal prism in NDUF-2 and finally to the UF(9) polyhedron in NDUF-3 and -4 as a function of reaction time. Coupled to this coordination change is a reduction of U(VI) to U(IV) as well as a breakdown of the organic structure-directing agent from DABCO to NH(4)(+). These processes contribute to a structural transition from layered topologies (NDUF-1) to chain (NDUF-2), back to layered (NDUF-3), and ultimately to framework (NDUF-4) connectivities. The synthesis conditions, crystal structures, and possible transformation mechanisms within this system are presented.     

Isoelectric focusing in long immobilized pH gradient gels to improve protein separation in proteomic analysis.

The number of protein spots detected on two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) gels increases as the gel size increases. The largest commercially available systems resolve a few thousand spots, being only a fraction of the total proteome. We have developed an extremely long isoelectric focusing (IEF) system aimed at more complete protein profiling. The system is especially well suited to sensitive detection methods, such as radioactive detection. The major constraint preventing progress in this area has been the inability to create an even density gradient during the immobilized pH gradient (IPG) casting process. We demonstrate for the first time that this constraint can be effectively overcome, to enable greatly increased IEF separating power with all the advantages of IPG technology,     

Extended particles and solitons

A variational method is introduced for approximating the eigenstates of the Hamiltonian in relativistic quantum field theory. The method has three ingredients: the coherent states, the solutions of the corresponding classical field theory, and the generator-coordinate technique of nuclear physics. It provides a quantum-mechanical interpretation for solitons, some of which resemble extended particles.