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Protein fluorescence quenching by small molecules: Protein penetration versus solvent exposure
Author(s) -
Calhoun Dorothy B.,
Vanderkooi Jane M.,
Holtom Gary R.,
Englander S. Walter
Publication year - 1986
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340010202
Subject(s) - quenching (fluorescence) , tryptophan , chemistry , fluorescence , nanosecond , solvent , photochemistry , acrylamide , molecule , biophysics , crystallography , biochemistry , organic chemistry , quantum mechanics , optics , copolymer , biology , polymer , laser , physics , amino acid
Experiments were done to test the thesis that acrylamide and similar small molecules can penetrate into proteins on a nanosecond time scale. The approach taken was to measure the pattern of fluorescence quenching exhibited by quenching molecules differing in molecular character (size, polarity, charge) when these are directed against protein tryptophans that cover the whole range of tryptophan accesibility. If quenching involves protein penetration and internal quencher migration, one expects that larger quenchers and more polar quenchers should display lesser quenching. In fact, no significant dependence on quencher character was found. For proteins that display measurable quenching, the disparate quenchers studied display very similar quenching rate constants when directed against any particular protein tryptophan. For several proteins having tryptophans known to be buried, no quenching occurs. These results are not consistent with the view that the kinds of small molecules studied can quite generally penetrate into and diffuse about within proteins at near‐diffusion‐limited rates. Rather the results suggest that when quenching is observed, the pathway involves encounters with tryptophans that are partially exposed at the protein surface. Available crystallographic results support this conclusion.