Combination of Enveloping Distribution Sampling (EDS) of a Soft-Core Reference-State Hamiltonian with One-Step Perturbation to Predict the Effect of Side Chain Substitution on the Relative Stability of Right- and Left-Helical Folds of β-Peptides

Effect of Oxidative Damage on the Stability and Dimerization of Superoxide Dismutase 1

During their life cycle, proteins are subject to different modifications involving reactive oxygen species. Such oxidative damage to proteins may lead to the formation of insoluble aggregates and cytotoxicity and is associated with age-related disorders including neurodegenerative diseases, cancer, and diabetes. Superoxide dismutase 1 (SOD1), a key antioxidant enzyme in human cells, is particularly susceptible to such modifications. Moreover, this homodimeric metalloenzyme has been directly linked to both familial and sporadic amyotrophic lateral sclerosis (ALS), a devastating, late-onset motor neuronal disease, with more than 150 ALS-related mutations in the SOD1 gene. Importantly, oxidatively damaged SOD1 aggregates have been observed in both familial and sporadic forms of the disease. However, the molecular mechanisms as well as potential implications of oxidative stress in SOD1-induced cytotoxicity remain elusive. In this study, we examine the effects of oxidative modification on SOD1 monomer and homodimer stability, the key molecular properties related to SOD1 aggregation. We use molecular dynamics simulations in combination with thermodynamic integration to study microscopic-level site-specific effects of oxidative "mutations" at the dimer interface, including lysine, arginine, proline and threonine carbonylation, and cysteine oxidation. Our results show that oxidative damage of even single residues at the interface may drastically destabilize the SOD1 homodimer, with several modifications exhibiting a comparable effect to that of the most drastic ALS-causing mutations known. Additionally, we show that the SOD1 monomer stability decreases upon oxidative stress, which may lead to partial local unfolding and consequently to increased aggregation propensity. Importantly, these results suggest that oxidative stress may play a key role in development of ALS, with the mutations in the SOD1 gene being an additional factor.

The key to predicting the stability of protein mutants lies in an accurate description and proper configurational sampling of the folded and denatured states

BACKGROUND

The contribution of particular hydrogen bonds to the stability of a protein fold can be investigated experimentally as well as computationally by the construction of protein mutants which lack particular hydrogen-bond donors or acceptors with a subsequent determination of their structural stability. However, the comparison of experimental data with computational results is not straightforward. One of the difficulties is related to the representation of the unfolded state conformation.

METHODS

A series of molecular dynamics simulations of the 34-residue WW domain of protein Pin1 and 20 amide-to-ester mutants started from the X-ray crystal structure and the NMR solution structure are analysed in terms of backbone-backbone hydrogen bonding and differences in free enthalpies of folding in order to provide a structural interpretation of the experimental data available.

RESULTS

The contribution of the different β-sheet hydrogen bonds to the relative stability of the mutants with respect to wild type cannot be directly inferred from experimental thermal denaturation temperatures or free enthalpies of chaotrope denaturation for the different mutants, because some β-sheet hydrogen bonds show sizeable variation in occurrence between the different mutants.

CONCLUSIONS

A proper representation of unfolded state conformations appears to be essential for an adequate description of relative stabilities of protein mutants.

GENERAL SIGNIFICANCE

The simulations may be used to link the structural Boltzmann ensembles to relative free enthalpies of folding between mutants and wild-type protein and show that unfolded conformations have to be treated with a sufficient level of detail in free energy calculations of protein stability. This article is part of a Special Issue entitled Recent developments of molecular dynamics.

Integrated Hamiltonian sampling: a simple and versatile method for free energy simulations and conformational sampling

Motivated by specific applications and the recent work of Gao and co-workers on integrated tempering sampling (ITS), we have developed a novel sampling approach referred to as integrated Hamiltonian sampling (IHS). IHS is straightforward to implement and complementary to existing methods for free energy simulation and enhanced configurational sampling. The method carries out sampling using an effective Hamiltonian constructed by integrating the Boltzmann distributions of a series of Hamiltonians. By judiciously selecting the weights of the different Hamiltonians, one achieves rapid transitions among the energy landscapes that underlie different Hamiltonians and therefore an efficient sampling of important regions of the conformational space. Along this line, IHS shares similar motivations as the enveloping distribution sampling (EDS) approach of van Gunsteren and co-workers, although the ways that distributions of different Hamiltonians are integrated are rather different in IHS and EDS. Specifically, we report efficient ways for determining the weights using a combination of histogram flattening and weighted histogram analysis approaches, which make it straightforward to include many end-state and intermediate Hamiltonians in IHS so as to enhance its flexibility. Using several relatively simple condensed phase examples, we illustrate the implementation and application of IHS as well as potential developments for the near future. The relation of IHS to several related sampling methods such as Hamiltonian replica exchange molecular dynamics and λ-dynamics is also briefly discussed.

Influence of variation of a side chain on the folding equilibrium of a β-peptide: limitations of one-step perturbation

In a recent study (Lin et al., Helv. Chim. Acta 2011, 94, 597), the one-step perturbation method was applied to tackle a challenging computational problem, that is, the calculation of the folding free enthalpies ΔGF,U of six hepta-β-peptides with different, Ala, Val, Leu, Ile, Ser, or Thr, side chains in the fifth residue. The ΔGF,U values obtained using one-step perturbation based on a single molecular dynamics simulation of a judiciously chosen reference state with soft-core atoms in the side chain of the fifth residue showed an overall accuracy of about kB T for the four peptides with nonpolar side chains, but twice as large deviations were observed for the peptides with polar side chains. Here, alternative reference-state Hamiltonians that better cover the conformational space relevant to these peptides are investigated, and post simulation rotational sampling of the χ1 and χ2 torsional angles of the fifth residue is carried out to sample different orientations of the side chain. A reference state with rather soft atoms yields accurate ΔGF,U values for the peptides with the Ser and Thr side chains, but it failed to correctly predict the folding free enthalpy for one peptide with a nonpolar side chain, that is, Leu. Based on the results and those of earlier studies, possible ways to improve the accuracy of the efficient one-step perturbation technique to compute free enthalpies of folding are discussed.