Biomedical subjects

D A Stauffer

Publications and source records attributed to D A Stauffer.

4 recordsLinked to original sources

PubMed1999

Unknown identification using reference mass spectra. Quality evaluation of databases.

The high success of the "uncertified" mass spectrometry spectral collection started in 1956 demonstrated qualitatively that a partial reference mass spectrum, even one measured routinely, can be of real value. Correct matchings were still possible despite reference errors, which almost never led to close matches that were incorrect. This study shows quantitatively that the number of different compounds, not the number of peaks in a spectrum, is by far the most important determinant of database efficiency for identifying a "global" unknown. A statistical evaluation of matching performance shows that only 6, 12, and 18 peaks in a reference spectrum are 13%, 67%, and 96%, respectively, as valuable as hundreds of peaks. Also, a separately measured second spectrum of the same compound is 50% as valuable as the first. Database expansion that tripled the number of possible wrong answers only reduced the proportion of correct identifications by 5%. Corrections of a mass or abundance error in each of six reference spectra increase the database matching performance by as much as the addition of one spectrum of a new compound. A new "matching quality index" based statistically on these values indicates that the largest database is also by far the most effective for matching unknowns.

Animals↗

PubMed1994

Electrostatic potential of the acetylcholine binding sites in the nicotinic receptor probed by reactions of binding-site cysteines with charged methanethiosulfonates.

All of the potent agonists and competitive antagonists of the acetylcholine receptors are positively charged, onium compounds. Among the interactions involved in the binding of these compounds, electrostatic forces undoubtedly make an important contribution. There is evidence that the acetylcholine binding site contains both acidic and aromatic amino acids. The acidic side chains could provide long-range charge-charge interactions with acetylcholine, while the aromatic side chains could provide short-range cation-pi-electron and hydrophobic interactions. To probe the long-range electrostatic interactions in the binding site, the rate constants for the reactions of sulfhydryl-specific reagents with cysteines in the binding site have been determined as a function of ionic strength. The reagents are the positively charged methanethiosulfonate ethylammonium and methanethiosulfonate ethyltrimethylammonium, the negatively charged methanethiosulfonate ethylsulfonate, and the neutral methyl methanethiosulfonate. In addition, the rate constants of the reactions of these methanethiosulfonates with positively charged, negatively charged, and uncharged simple thiol compounds have been similarly determined. An analysis of these rate constants in terms of absolute rate theory and Debye-Hückel theory is consistent with the acetylcholine binding site containing two to three negative charges and an electrostatic potential at zero ionic strength of about -80 mV relative to bulk solution.

Acetylcholine↗

PubMed1992

Acetylcholine receptor channel structure probed in cysteine-substitution mutants.

In order to understand the structural bases of ion conduction, ion selectivity, and gating in the nicotinic acetylcholine receptor, mutagenesis and covalent modification were combined to identify the amino acid residues that line the channel. The side chains of alternate residues--Ser248, Leu250, Ser252, and Thr254--in M2, a membrane-spanning segment of the alpha subunit, are exposed in the closed channel. Thus alpha 248-254 probably forms a beta strand, and the gate is closer to the cytoplasmic end of the channel than any of these residues. On channel opening, Leu251 is also exposed. These results lead to a revised view of the closed and open channel structures.

Acetylcholine↗

PubMed1990

Acetylcholine binding by a synthetic receptor: implications for biological recognition.

The neurotransmitter acetylcholine (ACh) is bound with 50-micromolar affinity by a completely synthetic receptor (host) comprising primarily aromatic rings. The host provided an overall hydrophobic binding site, but one that could recognize the positive charge of the quaternary ammonium group of ACh through a stabilizing interaction with the electron-rich pi systems of the aromatic rings (cation-pi interaction). Similar interactions may be involved in biological recognition of ACh and other choline derivatives.

Acetylcholine↗