Molecular mechanics analysis of Tet repressor TRP-43 fluorescence

Antonini, P. Silvi; Hillen, Wolfgang; Ettner, Norbert; Hinrichs, W.; Fantucci, Piercarlo; Doglia, Silvia Maria; Bousquet, Jean-Francois; Chabbert, Marie

doi:10.1016/s0006-3495(97)78826-x

Cited by 23 publications

(29 citation statements)

References 59 publications

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“…Because of the difficulty in calculating with sufficient accuracy the relevant energy differences from structures, observed shape differences could be completely without consequence, or they could dictate mechanism of action. Similar reservations can be made with respect to several solution‐based studies that are consistent with a change in the relative positioning of the DNA binding domains between the DNA‐bound and inducer‐bound states of TetR,20–22 or tryptophan fluorescence changes indicative of a change in the structure of the DNA binding domain 23. Another experimental study24 suggests that the tetracycline binding pocket and the DNA binding domain are in communication with each other, but does not directly address the resolution of intrinsic versus extrinsic mechanisms.…”

Section: Discussionmentioning

confidence: 70%

Opposite allosteric mechanisms in TetR and CAP

2009

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Regulation of the DNA binding affinity of an oligomeric protein can be considered to consist of an intrinsic component, in which the affinity of an individual DNA-binding domain is modulated in response to effector binding, and an extrinsic component, in which the relative position of the protein's two DNA-binding domains are altered so that they can or cannot contact both half-site operators simultaneously. We demonstrated directly that the TetR repressor utilizes an extrinsic mechanism and CAP, the catabolite activator protein, utilizes an intrinsic mechanism.

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Section: Discussionmentioning

confidence: 70%

Opposite allosteric mechanisms in TetR and CAP

2009

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“…Hudson (1999) proposed a model that involves reversible ionization of the excited tryptophan residue due to collisional transfer of an electron to a neighboring residue. Other groups have also suggested the involvement of an electron transfer process as the principal quenching mechanism in proteins and peptides (Antonini et al, 1997;Chen and Barkley et al, 1998;Ababou et al, 2001). In the absence of quenching side chains, the carbonyl group of the peptide itself is thought to be the responsible quencher (Ricci and Nesta, 1976;Chen et al, 1998;Sillen et al, 2000;Adams et al, 2002).…”

Section: Fluorescence Lifetimesmentioning

confidence: 99%

Tryptophan Properties in Fluorescence and Functional Stability of Plasminogen Activator Inhibitor 1

Verheyden

Sillen

Gils

et al. 2003

Biophysical Journal

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Plasminogen activator inhibitor 1 harbors four tryptophan residues at positions 86, 139, 175, and 262. To investigate the contribution of each tryptophan residue to the total fluorescence and to reveal the mutual interactions of the tryptophan residues and interactions with the other amino acids, 15 mutants in which tryptophan residues have been replaced by phenylalanines were constructed, purified, and characterized. Conformational distribution analysis revealed that the tryptophan mutants have a similar conformational distribution pattern as wild-type plasminogen activator inhibitor 1. Mutants in which tryptophan residue 175 was replaced by a phenylalanine displayed an increased functional half-life of the active conformation, whereas the functional half-life of mutants in which tryptophan residue 262 was replaced by a phenylalanine was substantially decreased. Comparative analysis of the fluorescence lifetimes, the extinction coefficients, and the quantum yields of the individual tryptophan residues demonstrates that tryptophan residue 262 gives the highest contribution to the total fluorescence. The other tryptophan residues have a very low quantum yield. In the wild-type protein, the fluorescence of all tryptophan residues is partially quenched as compared to the mutants that contain single tryptophan residues, due to conformational effects. The fluorescence of tryptophan residue 262 is very likely also partially quenched by energy transfer to tryptophan residue 175.

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“…Hudson proposed a model that involves reversible ionization of the excited tryptophan residue due to collisional transfer of an electron to a neighboring residue (Hudson, 1999). Other groups have also suggested the involvement of an electron transfer process as the principal quenching mechanism in proteins and peptides (Antonini et al, 1997;Chen and Barkley, 1998;Ababou and Bombarda, 2001). In the absence of quenching side chains, the carbonyl group of the peptide itself is thought to be the responsible quencher (Ricci and Nesta, 1976;Chen et al, 1996;Adams et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

The Dead-End Elimination Method, Tryptophan Rotamers, and Fluorescence Lifetimes

Hellings

Maeyer

Verheyden

et al. 2003

Biophysical Journal

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The Dead-End Elimination method was used to identify 40 low energy microconformations of 16 tryptophan residues in eight proteins. Single Trp-mutants of these proteins all show a double- or triple-exponential fluorescence decay. For ten of these lifetimes the corresponding rotameric state could be identified by comparing the bimolecular acrylamide quenching constant (k(q)) and the relative solvent exposure of the side chain in that microstate. In the absence of any identifiable quencher, the origin of the lifetime heterogeneity is interpreted in terms of the electron transfer process from the indole C epsilon 3 atom to the carbonyl carbon of the peptide bond. Therefore it is expected that a shorter [C epsilon 3-C[double bond]O] distance leads to a shorter lifetime as observed for these ten rotamers. Applying the same rule to the other 30 lifetimes, a link with their corresponding rotameric state could also be made. In agreement with the theory of Marcus and Sutin, the nonradiative rate constant shows an exponential relationship with the [C epsilon 3-C[double bond]O] distance for the 40 datapoints.

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Molecular mechanics analysis of Tet repressor TRP-43 fluorescence

Cited by 23 publications

References 59 publications

Opposite allosteric mechanisms in TetR and CAP

Opposite allosteric mechanisms in TetR and CAP

Tryptophan Properties in Fluorescence and Functional Stability of Plasminogen Activator Inhibitor 1

The Dead-End Elimination Method, Tryptophan Rotamers, and Fluorescence Lifetimes

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