skip to main content

Title: Unraveling the structural and chemical features of biological short hydrogen bonds
The three-dimensional architecture of biomolecules often creates specialized structural elements, notably short hydrogen bonds that have donor–acceptor separations below 2.7 Å. In this work, we statistically analyze 1663 high-resolution biomolecular structures from the Protein Data Bank and demonstrate that short hydrogen bonds are prevalent in proteins, protein–ligand complexes and nucleic acids. From these biological macromolecules, we characterize the preferred location, connectivity and amino acid composition in short hydrogen bonds and hydrogen bond networks, and assess their possible functional importance. Using electronic structure calculations, we further uncover how the interplay of the structural and chemical features determines the proton potential energy surfaces and proton sharing conditions in biological short hydrogen bonds.
Award ID(s):
Publication Date:
Journal Name:
Chemical Science
Page Range or eLocation-ID:
7734 to 7745
Sponsoring Org:
National Science Foundation
More Like this
  1. Short hydrogen bonds (SHBs), which have donor and acceptor separations below 2.7 Å, occur extensively in small molecules and proteins. Due to their compact structures, SHBs exhibit prominent covalent characters with elongated Donor–H bonds and highly downfield (>14 ppm) 1 H NMR chemical shifts. In this work, we carry out first principles simulations on a set of model molecules to assess how quantum effects determine the symmetry and chemical shift of their SHBs. From simulations that incorporate the quantum mechanical nature of both the electrons and nuclei, we reveal a universal relation between the chemical shift and the position of the proton in a SHB, and unravel the origin of the observed downfield spectral signatures. We further develop a metric that allows one to accurately and efficiently determine the proton position directly from its 1 H chemical shift, which will facilitate the experimental examination of SHBs in both small molecules and biological macromolecules.
  2. Abstract

    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,more »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.

    « less
  3. Abstract

    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.

  4. Predicting the asymmetric structure and dynamics of solvated hydroxide and hydronium in water from ab initio molecular dynamics (AIMD) has been a challenging task. The difficulty mainly comes from a lack of accurate and efficient exchange–correlation functional in elucidating the amphiphilic nature and the ubiquitous proton transfer behaviors of the two ions. By adopting the strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation functional in AIMD simulations, we systematically examine the amphiphilic properties, the solvation structures, the electronic structures, and the dynamic properties of the two water ions. In particular, we compare these results to those predicted by the PBE0-TS functional, which is an accurate yet computationally more expensive exchange–correlation functional. We demonstrate that the general-purpose SCAN functional provides a reliable choice for describing the two water ions. Specifically, in the SCAN picture of water ions, the appearance of the fourth and fifth hydrogen bonds near hydroxide stabilizes the pot-like shape solvation structure and suppresses the structural diffusion, while the hydronium stably donates three hydrogen bonds to its neighbors. We apply a detailed analysis of the proton transfer mechanism of the two ions and find the two ions exhibit substantially different proton transfer patterns. Our AIMD simulations indicate thatmore »hydroxide diffuses more slowly than hydronium in water, which is consistent with the experimental results.« less
  5. 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.