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.

Download Full Text

The manuscripts available on our site are provided for your personal use only and may not be retransmitted or redistributed without written permissions from the paper's publisher and author. You may not upload any of this site's material to any public server, on-line service, network, or bulletin board without prior written permission from the publisher and author. You may not make copies for any commercial purpose. Reproduction or storage of materials retrieved from this web site is subject to the U.S. Copyright Act of 1976, Title 17 U.S.C.

Download full text: Journal, Request a Copy