First-principles quantum chemistry in the life sciences

Elucidating the fundamental forces in protein crystal formation: the case of crambin

This study demonstrates the feasibility of periodic all-electron hybrid density functional theory calculations in the description of protein crystals, using crambin as a test case.

Molecular simulations of proteins have been usually accomplished through empirical or semi-empirical potentials, due to the large size and inherent complexity of these biological systems. On the other hand, a theoretical description of proteins based on quantum-mechanical methods would however provide an unbiased characterization of their electronic properties, possibly offering a link between these and the ultimate biological activity. Yet, such approaches have been historically hindered by the large amount of requested computational power. Here we demonstrate the feasibility of periodic all-electron density functional theory calculations in the description of the crystal of the protein crambin (46 aminoacids), which is determined with exceptional structural accuracy. We have employed the hybrid B3LYP functional, coupled to an empirical description of London interactions (D*) to simulate the crambin crystal with an increasing amount of lattice water molecules in the cell (up to 172H₂O per cell). The agreement with the experiment is good for both protein geometry and protein–water interactions. The energetics was computed to predict crystal formation energies, protein–water and protein–protein interaction energies. We studied the role of dispersion interactions which are crucial for holding the crambin crystal in place. B3LYP-D* electrostatic potential and dipole moment of crambin as well as the electronic charge flow from crambin to the solvating water molecules (0.0015e per H₂O) have also been predicted. These results proved that quantum-mechanical simulations of small proteins, both free and in their crystalline state, are now feasible in a reasonable amount of time, by programs capable of exploiting high performance computing architectures, allowing the study of protein properties not easily amenable through classical force fields.

QM and QM/MM simulations of proteins

Molecular dynamics simulations of biomolecules have matured into powerful tools of structural biology. In addition to the commonly used empirical force field potentials, quantum mechanical descriptions are gaining popularity for structure optimization and dynamic simulations of peptides and proteins. In this chapter, we introduce methodological developments such as the QM/MM framework and linear-scaling QM that make efficient calculations on large biomolecules possible. We identify the most common scenarios in which quantum descriptions of peptides and proteins are employed, such as structural refinement, force field development, treatment of unusual residues, and predicting spectroscopic and exited state properties. The benefits and shortcomings of QM potentials, in comparison to classical force fields, are discussed, with special emphasis on the sampling problems of protein conformational space. Finally, recent examples of QM/MM calculations in light-sensitive membrane proteins illustrate typical applications of the reviewed methods.

Water-chloride and water-bromide hydrogen-bonded networks: influence of the nature of the halide ions on the stability of the supramolecular assemblies

Two compounds, namely, [TTPH(2)](Cl)(2) x 4 H(2)O (1) and [TTPH(2)](Br)(2) x 4 H(2)O (2), (TTP = 4'-p-tolyl-2,2':6',2''-terpyridine) were synthesized from purely aqueous media and characterized by physical techniques. In the solid-state structures of these compounds, interesting supramolecular assemblies are observed. In 1, an unusual staircase-like architecture of the tape of edge-shared planar water hexamer is of importance, where the chloride ions are at the two edges of the tape. In 2, the polymeric nature of the water-bromide assembly is of interest, where discrete open-cube water octamers are doubly bridged by bromide ions. Semiempirical and DFT calculations confirm that the nature of the anion indeed affects the topology of the water-halide assemblies. We conclude that the protonated [TTPH(2)](2+) species can act as appropriate receptors for halide ions, which in turn act as a matrix for the formation of polymeric 1D water-halide assemblies.