Joel Ireta

Energetics of infinite homopolypeptide chains: a new look at commonly used force fields.

We present a novel method for comparing the long-range part of force fields in the presence of a maximally cooperative network of nonbonded interactions. The method is based on mapping the potential energy surface of an infinite polypeptide chain in the gas phase by using cylindrical coordinates (the twist and pitch) as geometry descriptors. We apply our method to an infinite polyalanine chain and consider the AMBER99, AMBER99SB, CHARMM27, and OPLS-AA/L fixed partial-charge force fields and the protein-specific version of the AMOEBA polarizable force field. Results from our analysis are compared to those obtained from high-level density-functional theory (DFT) calculations. We find that all force fields produce stronger stabilization of the helical conformations as compared to DFT, with only AMBER99/AMBER99SB satisfactorily reproducing all three helical conformations (pi, alpha, and 3(10)).

First-principles free-energy analysis of helix stability: The origin of the low entropy in π-helices

The temperature dependence of the stability of infinite poly-L-alanine alpha, pi, and 310 helices with respect to the fully extended structure (FES) is calculated using density functional theory and the harmonic approximation. We find that the vibrational entropy strongly reduces the stability of the helical conformations with respect to the FES. By mapping the ab initio data on an approximate mechanical model, we show that this effect is exclusively due to the formation of hydrogen bonds, whereas changes in the backbone stiffness are practically negligible. We furthermore observe that the temperature dependence is largest for the pi helix and smallest for the 310 helix and demonstrate that these trends are a generic behavior related to the geometric peculiarities of the respective helical conformations and independent of the specific amino acid sequence.

Density functional theory study of the conformational space of an infinitely long polypeptide chain.

The backbone conformational space of infinitely long polyalanine is investigated with density-functional theory and mapping the potential energy surface in terms of (L, theta) cylindrical coordinates. A comparison of the obtained (L, theta) Ramachandran-like plot with results from an extended set of protein structures shows excellent conformity, with the exception of the polyproline II region. It is demonstrated the usefulness of infinitely long polypeptide models for investigating the influence of hydrogen bonding and its cooperative effect on the backbone conformations. The results imply that hydrogen bonding together with long-range electrostatics is the main actuator for most of the structures assumed by protein residues.

On cooperative effects and aggregation of GNNQQNY and NNQQNY peptides

Some health disturbances like neurodegenerative diseases are associated to the presence of amyloids. GNNQQNY and NNQQNY peptides are considered as prototypical examples for studying the formation of amyloids. These exhibit quite different aggregation behaviors despite they solely differ in size by one residue. To get insight into the reasons for such difference, we have examined association energies of aggregates (parallel β-sheets, fibril-spines, and crystal structures) from GNNQQNY and NNQQY using density functional theory. As we found that GNNQQNY tends to form a zwitterion in the crystal structure, we have investigated the energetics of parallel β-sheets and fibril-spines in the canonical and zwitterionic states. We found that the formation of GNNQQNY aggregates is energetically more favored than the formation of the NNQQNY ones. We show that the latter is connected to the network of hydrogen bonds formed by each aggregate. Moreover, we found that the formation of some NNQQNY aggregates is anticooperative, whereas cooperative with GNNQQNY. These results have interesting implications for deciphering the factors determining peptide aggregation propensities.

Plane waves basis sets in the description of diatomic anions and valence charge density

The performance of plane wave basis sets to describe bond lengths, and vibrational frequencies for diatomic anions is described within the context of ab initio total energy density functional pseudopotential method. Also, the behavior of the charge density as a function of the plane wave expansion size is studied for a molecule containing C, H, O, N, and S atoms. For the three properties studied, a critical size of the basis set that assures a reasonable description of them was found. These critical values are around a cutoff energy of at least 20 Ry below the cutoff energy used to design the pseudopotentials.

Sensing polarization effects through the analysis of the effective C6 dispersion coefficients in NaCl solutions

Density functional theory based ab initio molecular dynamics is used to obtain microscopic details of the interactions in sodium chloride solutions. By following the changes in the atomic C6 coefficients under the Tkatchenko-Schefflers scheme, we were able to identify two different coordination situations for the Cl(-) ion with significant different capabilities to perform dispersion interactions. This capability is enhanced when the ion-ion distance corresponds to the contact ion-pair situation. Also, the oxygen and hydrogen atoms of the water molecules change their aptitudes to interact through van der Waals like terms when they are close to the cation region of the ion-pair. These results have interesting implications on the design of force fields to model electrolyte solutions.

A density functional theory based estimation of the anharmonic contributions to the free energy of a polypeptide helix

We have employed density functional theory to determine the temperature dependence of the intrinsic stability of an infinite poly-L-alanine helix. The most relevant helix types, i.e., the α- and the 3(10)-helix, and several unfolded conformations, which serve as reference for the stability analysis, have been included. For the calculation of the free energies for the various chain conformations we have explicitly included both, harmonic and anharmonic contributions. The latter have been calculated by means of a thermodynamic integration approach employing stochastic Langevin molecular dynamics, which is shown to provide a dramatic increase in the computational efficiency as compared to commonly employed deterministic molecular dynamics schemes. Employing this approach we demonstrate that the anharmonic part of the free energy amounts to the order of 0.1-0.4 kcal/mol per peptide unit for all analysed conformations. Although small, the anharmonic contribution stabilizes the helical conformations with respect to the fully extended structure.

Theoretical investigations on the layer-anion interaction in Mg–Al layered double hydroxides: Influence of the anion nature and layer composition

The influence of the anion nature and layer composition on the anion-layer interaction in Mg-Al layered double hydroxides (LDHs) is investigated using density functional theory. Changes in the strength of the anion-layer interaction are assessed calculating the potential energy surface (PES) associated to the interlayer anion (OH(-)/Cl(-)) in Mg-Al-OH and Mg-Al-Cl LDHs. The layer composition is varied changing the divalent to trivalent cation proportion (R). Mg-Al-OH is thus investigated with R = 2, 3, 3.5 and Mg-Al-Cl with R = 3. It is found that the PES for OH(-) in Mg-Al-OH/R = 3 presents wider energy basins and lower energy barriers than any other of the investigated compositions. It is shown that the latter is connected to the number of hydrogen bonds formed by the anions. These results have interesting implications for understanding the enhancement of the physicochemical properties of LDHs upon changing composition.