TCB Publications - Abstract

TCB Publications - Abstract

Edgar Larios, Wei Y. Yang, Klaus Schulten, and Martin Gruebele. A similarity measure for partially folded proteins: application to unfolded and native-like conformational fluctuations. Chemical Physics, 307:217-225, 2004.

LARI2004A Computing the root-mean-square deviation (RMSD) of a partially folded protein structure from the folded state requires the two structures to be translationally and rotationally aligned. We examine the constraint matrix $\mathcal {L}$ that preserves orthogonality of the rotation matrix during minimization of the RMSD. $\mathcal {L}$ is proportional to the sensitivity of the RMSD to the rotational alignment matrix. Its trace yields an isotropic reaction coordinate, while its off-diagonal matrix elements are related to the moment of inertia derivative tensor that encodes anisotropic information about the structure. We use $\mathcal {L}$ to compare $\lambda$-repressor fragment 6-85 ( $\lambda_{6-85}$ ) to several partially folded structures obtained from molecular dynamics simulation (MD), and find that $\mathcal {L}$ as a reaction coordinate indeed encodes some information about protein topology. We also apply $C_\alpha$ RMSD, $\mathcal {L}$ and tryptophan sidechain mobility as criteria for native state structural fluctuations of several $\lambda_{6-85}$ mutants. The mutants denaturation curves and fluorescence quenching are measured experimentally for comparison. The results are in accord with a recent proposal that structural fluctuations near the chromophore can induce increased native state fluorescence or hyperfluorescence during unfolding of proteins.

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