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Adaptive quantum-mechanics/molecular-mechanics (QM/MM) dynamics simulations feature on-the-fly reclassification of atoms as QM or MM continuously and smoothly as trajectories are propagated. This allows one to use small, mobile QM subsystems, the contents of which are dynamically updated as needed. In this work, we report the first adaptive QM/MM simulations of H+transfer through a biological channel, in particular, the protein EcCLC, a chloride channel (CLC) Cl–/H+antiporter derived from E. coli. To this end, the H+indicator previously formulated for approximating the location of an excess H+in bulk water was extended to include Cl–ions and carboxyl groups as H+donors/acceptors. Furthermore, when setting up buffer groups, a new “sushi-roll” scheme was employed to group multiple water molecules, ions, and titratable residues along the one-dimensional channel for adaptive partitions. Our simulations reveal that the H+relay path, which consists of water molecules in the pore, a bound Cl–ion at the central binding site (Cl–cen) of the protein, and the external gating residue E148, exhibits certain mobility within the channel. A two-stage journey of H+migration was observed: the H+moves toward Cl–cenand is then shared between Cl–cenand nearby water molecules in the first stage and departs from Cl–cenvia nearly concerted transfer to protonate E148 in the second stage. Most of the simulated trajectories show the bound Cl–ion in the channel to be transiently protonated, a possibility that was previously suggested by experiments and computations. Comparisons with conventional QM/MM simulations revealed that both adaptive and conventional treatments yield similar qualitative pictures. This work demonstrates the feasibility of adaptive QM/MM in the simulations of H+migration through biological channels.

OBJECTIVE: The malignancy of thyroid oncocytic tumours, or oncocytomas, is higher than that of follicular tumours. The aim of this study was to investigate the role of thyroid-specific genes in oncocytic tumours and papillary carcinomas. DESIGN AND METHODS: We compared 29 oncocytic tumours with 12 papillary carcinomas. Real-time quantitative PCR was used to measure the expression of thyroid-specific differentiation markers (thyrotrophin-stimulation hormone receptor (TSHR), thyroglobulin (TG) and Na(+)/I(-) symporter (NIS)), transcription factors (thyroid transcription factor-1 (TTF-1) and paired box gene-8 (PAX8)) and nuclear receptors (peroxisome proliferator-activated receptor (PPARgamma1) and thyroid hormone receptor (TRbeta1)) involved in thyroid carcinogenesis. RESULTS: TSHR, TTF-1 and TRbeta1 levels were significantly lower in oncocytic tumours than in papillary carcinomas, as a result of specific biological changes in oncocytic tumours. However, PAX8 and PPARgamma1 did not seem to be involved in the process. Applying the criterion of the underexpression of the thyroid-specific differentiation markers, TSHR, TG and NIS, we classified the oncocytic tumours and papillary carcinomas into three groups. In the first, all three markers were underexpressed; in the second, TSHR was normal while TG and NIS were underexpressed; and in the third, only NIS was underexpressed. The expression patterns revealed that 13 of the 24 oncocytic adenomas underexpressing TSHR in our study, as did four of the five oncocytic carcinomas. CONCLUSION: Cases of oncocytic adenoma associated with low levels of TSHR could be putative oncocytic carcinomas and should therefore receive adequate follow-up [corrected].