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Comparative Analysis of Hydrogen-Bonding Vibrations of Ice VI.

ABSTRACT: It is difficult to investigate the hydrogen-bonding dynamics of hydrogen-disordered ice VI. Here, we present a comparative method based on our previous study of its counterpart hydrogen-ordered phase, ice XV. The primitive cell of ice XV is a 10 molecule unit, and the vibrational normal modes were analyzed individually. We constructed an 80 molecule supercell of ice VI to mimic the periodic unit and performed first-principles density functional theory calculations. As the two vibrational spectra show almost identical features, we compared the molecular translation vibrations. Inspired by the phonon analysis of ice XV, we found that the vibrational modes in the translation band of ice VI are classifiable into three groups. The lowest-strength vibration modes represent vibrations between two sublattices that lack hydrogen bonding. The highest-strength vibration modes represent the vibration of four hydrogen bonds of one molecule. The middle-strength vibration modes mainly represent the molecular vibrations of only two hydrogen bonds. Although there are many overlapping stronger and middle modes, there are only two main peaks in the inelastic neutron scattering (INS) spectra. This work explains the origin of the two main peaks in the far-infrared region of ice VI and illustrates how to analyze a hydrogen-disordered ice structure.

SUBMITTER: Wang XC

PROVIDER: S-EPMC8190920 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Hydrogen exchange (HX) studies have provided critical insight into our understanding of protein folding, structure, and dynamics. More recently, hydrogen exchange mass spectrometry (HX-MS) has become a widely applicable tool for HX studies. The interpretation of the wealth of data generated by HX-MS experiments as well as other HX methods would greatly benefit from the availability of exchange predictions derived from structures or models for comparison with experiment. Most reported computational HX modeling studies have employed solvent-accessible-surface-area based metrics in attempts to interpret HX data on the basis of structures or models. In this study, a computational HX-MS prediction method based on classification of the amide hydrogen bonding modes mimicking the local unfolding model is demonstrated. Analysis of the NH bonding configurations from molecular dynamics (MD) simulation snapshots is used to determine partitioning over bonded and nonbonded NH states and is directly mapped into a protection factor (PF) using a logistics growth function. Predicted PFs are then used for calculating deuteration values of peptides and compared with experimental data. Hydrogen exchange MS data for fatty acid synthase thioesterase (FAS-TE) collected for a range of pHs and temperatures was used for detailed evaluation of the approach. High correlation between prediction and experiment for observable fragment peptides is observed in the FAS-TE and additional benchmarking systems that included various apo/holo proteins for which literature data were available. In addition, it is shown that HX modeling can improve experimental resolution through decomposition of in-exchange curves into rate classes, which correlate with prediction from MD. Successful rate class decompositions provide further evidence that the presented approach captures the underlying physical processes correctly at the single residue level. This assessment is further strengthened in a comparison of residue resolved protection factor predictions for staphylococcal nuclease with NMR data, which was also used to compare prediction performance with other algorithms described in the literature. The demonstrated transferable and scalable MD based HX prediction approach adds significantly to the available tools for HX-MS data interpretation based on available structures and models.

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Comparative Analysis of Hydrogen-Bonding Vibrations of Ice VI.

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