Access of hydrogen-radicals to the peptide-backbone as a measure for estimating the flexibility of proteins using matrix-assisted laser desorption/ionization mass spectrometry.

A factor for estimating the flexibility of proteins is described that uses a cleavage method of "in-source decay (ISD)" coupled with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). The MALDI-ISD spectra of bovine serum albumin (BSA), myoglobin and thioredoxin show discontinuous intense ion peaks originating from one-side preferential cleavage at the N-Cα bond of Xxx-Asp, Xxx-Asn, Xxx-Cys and Gly-Xxx residues. Consistent with these observations, Asp, Asn and Gly residues are also identified by other flexibility measures such as B-factor, turn preference, protection and fluorescence decay factors, while Asp, Asn, Cys and Gly residues are identified by turn preference factor based on X-ray crystallography. The results suggest that protein molecules embedded in/on MALDI matrix crystals partly maintain α-helix and that the reason some of the residues are more susceptible to ISD (Asp, Asn, Cys and Gly) and others less so (Ile and Val) is because of accessibility of the peptide backbone to hydrogen-radicals from matrix molecules. The hydrogen-radical accessibility in MALDI-ISD could therefore be adopted as a factor for measuring protein flexibility.

Photochemical Reactions of Aminonaphthols Caused by Laser Desorption/Ionization.

The formation of monomeric and dimeric ions of seven different aminonaphthols (ANLs) has been studied by using laser desorption/ionization (LDI) with a nitrogen laser. The positive-ion data of all the ANLs merely showed molecular ion M(·+) without protonated molecule [M+H](+), while 1-amino-2-naphthol (1,2-ANL) and 2-amino-1-naphthol (2,1-ANL) showed an intense dimeric ion [2 M-2H2O+H](+). The negative-ion data showed deprotonated molecule [M-H](-) in common, while the spectra of 1,2-ANL, 2,1-ANL and 8-amino-2-naphthol (8,2-ANL) accompanied an intense peak corresponding to negative molecular ion M(·-) and the 8,2-ANL and 4-amino-1-naphthol (4,1-ANL) accompanied dehydrogenated anion [M-2H](·-). The formation of monomeric ions was discussed from the standpoints of thermochemical properties such as ionization energy, gas-phase acidity, electron affinity, and bond dissociation energy. The formation of dimeric ions [2 M-2H2O+H](+) observed in the 1,2-ANL and 2,1-ANL could be explained by the radical combination in the amino groups. An isomer 5-amino-1-naphthol (1-ANL) did not give any dimeric ions in the both positive- and negative-ion spectra. The influence of laser fluence upon the appearance of the monomeric ions such as M(·+), [M+H](+), [M-H](-) and [M-2H](·-) of the 5,1-ANL has been examined.