A hydrogen bond is a non-covalent interaction between a hydrogen convalently bond to a very electronegative atom (N, O, F) and another very electronegative atom. The interaction in a hydrogen bond is dominantly electrostatic, which leads to a pronounced flexibility in the bond length and angle. However, the distance between X and H, when X = N or O, is most optimal around 2 Å and the angle between the covalent bond and the hydrogen bond between 150º and 180º.

Hydrogen bond networks are webs or hydrogen bonds that connect the sidechain of multiple residues across the protein.

Hydrogen bond networks help to stabilize the entire protein structure and have also been observed to play a role in activation and allostery. For example, it has been observed that GPCRs present an extensive hydrogen bond network that spans all functional motifs of the protein in the active state, suggesting it might contribute to their activation mechanism [1].

Ligand binding has also shown to perturb the interresidue interactions and shift hydrogen bond networks, which drive a major redistribution of energy [2].

Given that hydrogen networks can mediate coupling between remote regions of the protein, they are paramount in modulating allostery, function, and stability. Thus, methods to easily compute hydrogen networks in proteins are key to understand protein function.

In ProteinTools, we protonate the user-given protein coordinates with PROPKA [3] and PDB2PQR [4]. Then, we compute all hydrogen networks in the protein sidechains using the Baker-Hubbard algorithm [5]. This algorithm presents cutoffs of ϑ > 120º and d < 2.5 Å.

We thus consider to be in the same network cluster any two residues that have a path of hydrogen bond networks between them.

• [1] Éva Bertalan, Samo Lešnik, Urban Bren, Ana-Nicoleta Bondar. "Protein-water hydrogen-bond networks of G protein-coupled receptors: Graph-based analyses of static structures and molecular dynamics". J Struct Biol. 2020 Sep 29;212(3):107634. doi: 10.1016/j.jsb.2020.107634
• [2] Amit Kumawata, Suman Chakrabarty. "Hidden electrostatic basis of dynamic allostery in a PDZ domain". PNAS July 18, 2017 114 (29) E5825-E5834;
• [3] Olsson, Mats HM, Chresten R. Sondergaard, Michal Rostkowski, and Jan H. Jensen. "PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions." Journal of Chemical Theory and Computation 7, no. 2 (2011): 525-537. doi:10.1021/ct100578z
• [4] Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. "PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations." Nucleic Acids Res. 2007 Jul;35(Web Server issue):W522-5.
• [5] Baker, E. N., and R. E. Hubbard. “Hydrogen bonding in globular proteins.” Progress in Biophysics and Molecular Biology 44.2 (1984): 97-179.