Toward a MALDI in-source decay (ISD) method for top-down analysis of protein footprinting.

Irreversible protein footprinting is a mass spectrometry-based approach in which solvent-accessible sites of a protein are modified to assess high-order protein structure. Structural insights can be gained by determining the position and extents of modification. The usual approach to obtain the "footprint" is to analyze the protein through bottom-up LC-MS/MS. In this approach, the proteins are digested to yield a mixture of peptides that are then separated by LC before locating the modification sites by MS/MS. This process consumes substantial amounts of time and is difficult to accelerate for applications that require quick and high-throughput analysis. Here, we describe employing matrix-assisted laser desorption/ionization (MALDI) in-source decay (ISD) to analyze a footprinted small test protein (ubiquitin) via a top-down approach. Matrix-assisted laser desorption/ionization is easily adapted for high-throughput analysis, and top-down strategies can avoid lengthy proteolysis and LC separation. We optimized the method with model peptides and then demonstrated its feasibility on ubiquitin submitted to two types of footprinting. We found that MALDI ISD can produce a comprehensive set of fragment ions for small proteins, affording footprinting information in a fast manner and giving results that agree with the established methods, and serve as a rough measure of protein solvent accessibility. To assist in the implementation of the MALDI approach, we developed a method of processing top-down ISD data.

MALDI Peptide Mapping for Fast Analysis in Protein Footprinting.

Although protein footprinting results are commonly obtained by ESI-based LC-MS/MS, a more rapid-turnaround alternative approach is desirable to expand the scope of protein footprinting and facilitate routine analysis such as monitoring protein high order structure in quality control or checking epitope maps. Considering that MALDI is a faster procedure that can be easily adapted for high-throughput analysis, we explore here the feasibility of developing a MALDI-based analysis "portfolio" of bottom-up peptide mass mapping for footprinting. The approach was applied to several model proteins that were submitted to two footprinting strategies, FPOP and GEE labeling, and their performance was evaluated. We found adequate coverage that can be improved with automatic off-line separation and spotting, demonstrating the capability to footprint accurately protein conformational change, showing that MALDI may be useful for selected applications in protein footprinting.

Binding of red form of Orange Carotenoid Protein (OCP) to phycobilisome is not sufficient for quenching.

The Orange Carotenoid Protein (OCP) is responsible for photoprotection in many cyanobacteria. Absorption of blue light drives the conversion of the orange, inactive form (OCPO) to the red, active form (OCPR). Concomitantly, the N-terminal domain (NTD) and the C-terminal domain (CTD) of OCP separate, which ultimately leads to the formation of a quenched OCPR-PBS complex. The details of the photoactivation of OCP have been intensely researched. Binding site(s) of OCPR on the PBS core have also been proposed. However, the post-binding events of the OCPR-PBS complex remain unclear. Here, we demonstrate that PBS-bound OCPR is not sufficient as a PBS excitation energy quencher. Using site-directed mutagenesis, we generated a suite of single point mutations at OCP Leucine 51 (L51) of Synechocystis 6803. Steady-state and time-resolved fluorescence analyses demonstrated that all mutant proteins are unable to quench the PBS fluorescence, owing to either failed OCP binding to PBS, or, if bound, an OCP-PBS quenching state failed to form. The SDS-PAGE and Western blot analysis support that the L51A (Alanine) mutant binds to the PBS and therefore belongs to the second category. We hypothesize that upon binding to PBS, OCPR likely reorganizes and adopts a new conformational state (OCP3rd) different than either OCPO or OCPR to allow energy quenching, depending on the cross-talk between OCPR and its PBS core-binding counterpart.

Isolation of Amine Derivatives of (ZnSe)34 and (CdTe)34. Spectroscopic Comparisons of the (II-VI)13 and (II-VI)34 Magic-Size Nanoclusters.

The spectroscopically observed magic-size nanoclusters (ZnSe)34 and (CdTe)34 are isolated as amine derivatives. The nanoclusters [(ZnSe)34( n-octylamine)29±6(di- n-octylamine)5±4] and [(CdTe)34( n-octylamine)4±3(di- n-pentylamine)13±3] are fully characterized by combustion-based elemental analysis, UV-visible spectroscopy, IR spectroscopy, and mass spectrometry. Amine derivatives of both (ZnSe)34 and (CdTe)34 are observed to convert to the corresponding (ZnSe)13 and (CdTe)13 derivatives, indicating that the former are kinetic products and the latter thermodynamic products, under the conditions employed. This conversion process is significantly inhibited in the presence of secondary amines. The isolation of the two new nanocluster derivatives adds to a total of nine of 12 possible isolated derivatives in the (II-VI)13 and (II-VI)34 families (II = Zn, Cd; VI = S, Se, Te), allowing comparisons of their properties. The members of these two families exhibit extensive spectroscopic homologies. In both the (II-VI)13 and (II-VI)34 families, linear relationships are established between the lowest-energy nanocluster electronic transition and the band gap of the corresponding bulk semiconductor phase.