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1. Chemical features and machine learning assisted predictions of protein-ligand short hydrogen bonds

   https://doi.org/10.1038/s41598-023-40614-7  

   Zhou, Shengmin ; Liu, Yuanhao ; Wang, Sijian ; Wang, Lu ( August 2023 , Scientific Reports)

   There are continuous efforts to elucidate the structure and biological functions of short hydrogen bonds (SHBs), whose donor and acceptor heteroatoms reside more than 0.3 Å closer than the sum of their van der Waals radii. In this work, we evaluate 1070 atomic-resolution protein structures and characterize the common chemical features of SHBs formed between the side chains of amino acids and small molecule ligands. We then develop a machine learning assisted prediction of protein-ligand SHBs (MAPSHB-Ligand) model and reveal that the types of amino acids and ligand functional groups as well as the sequence of neighboring residues are essential factors that determine the class of protein-ligand hydrogen bonds. The MAPSHB-Ligand model and its implementation on our web server enable the effective identification of protein-ligand SHBs in proteins, which will facilitate the design of biomolecules and ligands that exploit these close contacts for enhanced functions.

    

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2. Effective prediction of short hydrogen bonds in proteins via machine learning method

   https://doi.org/10.1038/s41598-021-04306-4  

   Zhou, Shengmin ; Liu, Yuanhao ; Wang, Sijian ; Wang, Lu ( January 2022 , Scientific Reports)

   Short hydrogen bonds (SHBs), whose donor and acceptor heteroatoms lie within 2.7 Å, exhibit prominent quantum mechanical characters and are connected to a wide range of essential biomolecular processes. However, exact determination of the geometry and functional roles of SHBs requires a protein to be at atomic resolution. In this work, we analyze 1260 high-resolution peptide and protein structures from the Protein Data Bank and develop a boosting based machine learning model to predict the formation of SHBs between amino acids. This model, which we name as machine learning assisted prediction of short hydrogen bonds (MAPSHB), takes into account 21 structural, chemical and sequence features and their interaction effects and effectively categorizes each hydrogen bond in a protein to a short or normal hydrogen bond. The MAPSHB model reveals that the type of the donor amino acid plays a major role in determining the class of a hydrogen bond and that the side chain Tyr-Asp pair demonstrates a significant probability of forming a SHB. Combining electronic structure calculations and energy decomposition analysis, we elucidate how the interplay of competing intermolecular interactions stabilizes the Tyr-Asp SHBs more than other commonly observed combinations of amino acid side chains. The MAPSHB model, which is freely available on our web server, allows one to accurately and efficiently predict the presence of SHBs given a protein structure with moderate or low resolution and will facilitate the experimental and computational refinement of protein structures.

    

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3. Structural aspects of the topological model of the hydrogen bond in water on auto-dissociation via proton transfer

   https://doi.org/10.1039/c8cp02592d  

   Lentz, Jesse ; Garofalini, Stephen H. ( January 2018 , Physical Chemistry Chemical Physics)

   Molecular dynamics (MD) simulations were used to investigate the structure and lifetimes of hydrogen bonds and auto dissociation via proton transfer in bulk water using a reactive and dissociative all-atom potential that has previously been shown to match a variety of water properties and proton transfer. Using the topological model, each molecule's donated and accepted hydrogen bonds were labeled relative to the other hydrogen bonds on neighboring waters, providing a description of the effect of these details on the structure, dynamics and autoionization of water molecules. In agreement with prior data, asymmetric bonding at the sub-100 femtosecond timescale is observed, as well as the existence of linear, bifurcated, and dangling hydrogen bonds. The lifetime of the H-bond, 2.1 ps, is consistent with experimental data, with short time librations on the order of femtoseconds. The angular correlation functions, the presence of a second shell water entering the first shell, and OH vibrational stretch frequencies were all consistent with experiment or ab initio calculations. The simulations show short-lived (femtoseconds) dissociation of a small fraction of water molecules followed by rapid recombination. The role of the other H-bonds to the acceptor and on the donor plays an important part in proton transfer between the molecules in auto dissociation and is consistent with the role of a strong electric field caused by local (first and second shell) waters on initiating dissociation. The number of H-bonds to the donor water is 4.3 per molecule in the simulations, consistent with previous data regarding the number of hydrogen bonds required to generate this strong local electric field that enhances dissociation. The continuous lifetime autocorrelation function of the H-bond for those molecules that experience dissociation is considerably longer than that for all molecules that show no proton transfer. 

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4. 31 P spin–lattice and singlet order relaxation mechanisms in pyrophosphate studied by isotopic substitution, field shuttling NMR, and molecular dynamics simulation

   https://doi.org/10.1039/D2CP03801C  

   Korenchan, David E. ; Lu, Jiaqi ; Sabba, Mohamed ; Dagys, Laurynas ; Brown, Lynda J. ; Levitt, Malcolm H. ; Jerschow, Alexej ( October 2022 , Physical Chemistry Chemical Physics)

   Nuclear spin relaxation mechanisms are often difficult to isolate and identify, especially in molecules with internal flexibility. Here we combine experimental work with computation in order to determine the major mechanisms responsible for 31 P spin–lattice and singlet order (SO) relaxation in pyrophosphate, a physiologically relevant molecule. Using field-shuttling relaxation measurements (from 2 μT to 9.4 T) and rates calculated from molecular dynamics (MD) trajectories, we identified chemical shift anisotropy (CSA) and spin–rotation as the major mechanisms, with minor contributions from intra- and intermolecular coupling. The significant spin–rotation interaction is a consequence of the relatively rapid rotation of the –PO 3 2− entities around the bridging P–O bonds, and is treated by a combination of MD simulations and quantum chemistry calculations. Spin–lattice relaxation was predicted well without adjustable parameters, and for SO relaxation one parameter was extracted from the comparison between experiment and computation (a correlation coefficient between the rotational motion of the groups). 

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5. Crossover from hydrogen to chemical bonding

   https://doi.org/10.1126/science.abe1951  

   Dereka, Bogdan ; Yu, Qi ; Lewis, Nicholas H. C. ; Carpenter, William B. ; Bowman, Joel M. ; Tokmakoff, Andrei ( January 2021 , Science)

   Hydrogen bonds (H-bonds) can be interpreted as a classical electrostatic interaction or as a covalent chemical bond if the interaction is strong enough. As a result, short strong H-bonds exist at an intersection between qualitatively different bonding descriptions, with few experimental methods to understand this dichotomy. The [F-H-F]⁻ion represents a bare short H-bond, whose distinctive vibrational potential in water is revealed with femtosecond two-dimensional infrared spectroscopy. It shows the superharmonic behavior of the proton motion, which is strongly coupled to the donor-acceptor stretching and disappears on H-bond bending. In combination with high-level quantum-chemical calculations, we demonstrate a distinct crossover in spectroscopic properties from conventional to short strong H-bonds, which identify where hydrogen bonding ends and chemical bonding begins.

    

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