Predicting and interpreting EPR spectra of POPC lipid bilayers with transmembrane α-helical peptides from all-atom molecular dynamics simulations

This study reports a large-scale all-atom MD simulation of POPC lipid bilayers in the presence of different concentrations of the transmembrane peptide acetyl-K2(LA)12K2-amide ((LA)12) and doped with 5-PC paramagnetic spin probes used in EPR studies. We apply a combined MD-EPR simulation methodology for the prediction of EPR spectra directly and completely from MD trajectories. This approach serves three major purposes. Firstly, comparing predicted EPR spectra with experimental ones, which are highly sensitive to motions, provides an ultimate test bed for the force fields currently employed for modeling lipid bilayer systems with embedded proteins or peptides. Secondly, simulations of EPR spectra directly from the atomistic MD models simplify the interpretation of the EPR line shapes and their changes induced by the presence of peptides in the lipid bilayer. These changes are directly linked to the dynamics and order of spin probes and POPC host molecules. Lastly and importantly, we demonstrate how the MD-EPR methodology can be employed to test the validity and limitations of the widely used approach for the estimation of the order parameter of lipids directly from the EPR experimental line shapes.

Unravelling Guest Dynamics in Crystalline Molecular Organics Using 2H Solid-State NMR and Molecular Dynamics Simulation

2H solid-state NMR and atomistic molecular dynamics (MD) simulations are used to understand the disorder of guest solvent molecules in two cocrystal solvates of the pharmaceutical furosemide. Traditional approaches to interpreting the NMR data fail to provide a coherent model of molecular behavior and indeed give misleading kinetic data. In contrast, the direct prediction of the NMR properties from MD simulation trajectories allows the NMR data to be correctly interpreted in terms of combined jump-type and libration-type motions. Time-independent component analysis of the MD trajectories provides additional insights, particularly for motions that are invisible to NMR. This allows a coherent picture of the dynamics of molecules restricted in molecular-sized cavities to be determined.

The 'hidden side' of spin labelled oligonucleotides: Molecular dynamics study focusing on the EPR-silent components of base pairing

Nitroxide labels are combined with nucleic acid structures and are studied using electron paramagnetic resonance experiments (EPR). As X-ray/NMR structures are unavailable with the nitroxide labels, detailed residue level information, down to atomic resolution, about the effect of these nitroxide labels on local RNA structures is currently lacking. This information is critical to evaluate the choice of spin label. In this study, we compare and contrast the effect of TEMPO-based (N^T) and rigid spin (Ç) labels (in both 2'-O methylated and not-methylated forms) on RNA duplexes. We also investigate sequence- dependent effects of N^T label on RNA duplex along with the more complex G-quadruplex RNA. Distances measured from molecular dynamics simulations between the two spin labels are in agreement with the EPR experimental data. To understand the effect of labelled oligonucleotides on the structure, we studied the local base pair geometries and global structure in comparison with the unlabelled structures. Based on the structural analysis, we can conclude that TEMPO-based and Ç labels do not significantly perturb the base pair arrangements of the native oligonucleotide. When experimental structures for the spin labelled DNA/RNA molecules are not available, general framework offered by the current study can be used to provide information critical to the choice of spin labels to facilitate future EPR studies.

Assessment of AMBER Force Fields for Simulations of ssDNA

Single-stranded DNA (ssDNA) plays an important role in biological processes and is used in DNA nanotechnology and other novel applications. Many important research questions can be addressed with molecular simulations of ssDNA molecules; however, no dedicated force field for ssDNA has been developed, and there is limited experimental information about ssDNA structures. This study assesses the accuracy and applicability of existing Amber force fields for all-atom simulations of ssDNA, such as ff99, bsc0, bsc1, and OL15, in implicit and explicit solvents via comparison to available experimental data, such as Forster resonance energy transfer and small angle X-ray scattering. We observed that some force fields agree better with experiments than others mainly due to the difference in parameterization of the propensity for hydrogen bonding and base stacking. Overall, the Amber ff99 force field in the IGB5 or IGB8 implicit solvent and the bsc1 force field in the explicit TIP3P solvent had the best agreement with experiment.

Orientation and dynamics of Cu2+ based DNA labels from force field parameterized MD elucidates the relationship between EPR distance constraints and DNA backbone distances

Pulsed electron paramagnetic resonance (EPR) based distance measurements using the recently developed Cu2+-DPA label present a promising strategy for measuring DNA backbone distance constraints. Herein we develop force field parameters for Cu2+-DPA in order to understand the features of this label at an atomic level. We perform molecular dynamics (MD) simulations using the force field parameters of Cu2+-DPA on four different DNA duplexes. The distance between the Cu2+ centers, extracted from the 2 μs MD trajectories, agrees well with the experimental distance for all the duplexes. Further analyses of the trajectory provide insight into the orientation of the Cu2+-DPA inside the duplex that leads to such agreement with experiments. The MD results also illustrate the ability of the Cu2+-DPA to report on the DNA backbone distance constraints. Furthermore, measurement of fluctuations of individual residues showed that the flexibility of Cu2+-DPA in a DNA depends on the position of the label in the duplex, and a 2 μs MD simulation is not sufficient to fully capture the experimental distribution in some cases. Finally, the MD trajectories were utilized to understand the key aspects of the double electron electron resonance (DEER) results. The lack of orientational selectivity effects of the Cu2+-DPA at Q-band frequency is rationalized in terms of fluctuations in the Cu2+ coordination environment and rotameric fluctuations of the label linker. Overall, a combination of EPR and MD simulations based on the Cu2+-DPA labelling strategy can contribute towards understanding changes in DNA backbone conformations during protein-DNA interactions.

Investigation of thermal properties of DNA structure with precise atomic arrangement via equilibrium and non-equilibrium molecular dynamics approaches

BACKGROUND AND OBJECTIVE

Thermal conductivity of Deoxyribonucleic acid molecules is important for nanotechnology applications. Theoretical simulations based on simple models predict thermal conductivity for these molecular structures.

METHODS

In this work, we calculate the thermal properties of Deoxyribonucleic acid with precise atomic arrangement via equilibrium and non-equilibrium molecular dynamics approaches. In these methods, each Deoxyribonucleic acid molecule is represented by C, N, O, and P atoms and implemented dreidng potential to describe their atomic interactions.

RESULTS

Our calculated rate for thermal conductivity via equilibrium and non-equilibrium molecular dynamics methods is 0.381 W/m K and 0.373 W/m K, respectively. By comparing results from these two methods, it was found that the results from equilibrium and non-equilibrium molecular dynamics methods are identical, approximately. On the other hand, the number of DNA molecules and the equilibrium temperature of the simulated structures were important factors in their thermal conductivity rates, and their thermal conductivity was calculated at 0.323 W/m K-0.381 W/m K intervals for equilibrium and 0.303 W/m K-0.373 W/m K interval for non-equilibrium calculations.

CONCLUSIONS

These results are in good agreement with thermal conductivity calculation with other research groups.

Trajectory-Based Simulation of EPR Spectra: Models of Rotational Motion for Spin Labels on Proteins

Direct time-domain simulation of continuous-wave (CW) electron paramagnetic resonance (EPR) spectra from molecular dynamics (MD) trajectories has become increasingly popular, especially for proteins labeled with nitroxide spin labels. Due to the time-consuming nature of simulating adequately long MD trajectories, two approximate methods have been developed to reduce the MD-trajectory length required for modeling EPR spectra: hindered Brownian diffusion (HBD) and hidden Markov models (HMMs). Here, we assess the accuracy of these two approximate methods relative to direct simulations from MD trajectories for three spin-labeled protein systems (a simple helical peptide, a soluble protein, and a membrane protein) and two nitroxide spin labels with differing mobilities (R1 and 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC)). We find that the HMMs generally outperform HBD. Although R1 dynamics partially resembles hindered Brownian diffusion, HMMs accommodate the multiple dynamic time scales for the transitions between rotameric states of R1 that cannot be captured accurately by a HBD model. The MD trajectories of the TOAC-labeled proteins show that its dynamics closely resembles slow multisite exchange between twist-boat and chair ring puckering states. This motion is modeled well by HMM but not by HBD. All MD-trajectory data processing, stochastic trajectory simulations, and CW EPR spectral simulations are implemented in EasySpin, a free software package for MATLAB.

Spin Probe Determination of Molecular Orientation Distribution and Rotational Mobility in Liquid Crystals: Model-Free Approach

A model-free approach for simulation of EPR spectra of nitroxide spin probes in liquid-crystalline materials was suggested and used to obtain parameters of molecular orientation and rotational mobility. The developed method is based on experimental recording and numerical simulation of the angular dependence of EPR spectra, which is shown to be much more informative in comparison with a single EPR spectrum. Quantitative spectral simulations considering both local orientational ordering and distribution of local directors in the sample were used for discrimination of models of rotational mobility and orientational alignment. The method was applied for detailed quantitative characterization of axial, orthorhombic, and low-symmetry non-orthorhombic molecular orientation distributions. It is shown that the ordinarily used model of rotational diffusion in a mean-field potential is suitable for the description of molecular mobility and orientational ordering only for relatively low sample temperatures and low-mobility probe molecules with large sizes. In cases of high molecular mobility, the more realistic jump mechanism of molecular moves can be approximately described as quasi-librations. For ordered liquid crystals it was found that mostly the order parameters up to rank 12-14 are essential and easily determined. When well-aligned materials are described, the order parameters up to 18th rank or even higher become meaningful. Both molecular and sample biaxiality is analyzed and quantitatively characterized. The local molecular ordering and sample orientational alignment are quantitatively characterized separately.