On the Uses of PCA to Characterise Molecular Dynamics Simulations of Biological Macromolecules: Basics and Tips for an Effective Use

Principal Component Analysis (PCA) is a procedure widely used to examine data collected from molecular dynamics simulations of biological macromolecules. It allows for greatly reducing the dimensionality of their configurational space, facilitating further qualitative and quantitative analysis. Its simplicity and relatively low computational cost explain its extended use. However, a judicious implementation of PCA requires the knowledge of its theoretical grounds as well as its weaknesses and capabilities. In this article, we review these issues and discuss several strategies developed over the last years to mitigate the main PCA flaws and enhance the reproducibility of its results.

Application and Comprehensive Analysis of Neighbor Approximated Information Theoretic Configurational Entropy Methods to Protein-Ligand Binding Cases

The binding entropy is an important thermodynamic quantity which has numerous applications in studies of the biophysical process, and configurational entropy is often one of the major contributors in it. Therefore, its accurate estimation is important, though it is challenging mostly due to sampling limitations, anharmonicity, and multimodality of atomic fluctuations. The present work reports a Neighbor Approximated Maximum Information Spanning Tree (A-MIST) method for conformational entropy and presents its performance and computational advantage over conventional Mutual Information Expansion (MIE) and Maximum Information Spanning Tree (MIST) for two protein-ligand binding cases: indirubin-5-sulfonate to Plasmodium falciparum Protein Kinase 5 (PfPK5) and P. falciparum RON2-peptide to P. falciparum Apical Membrane Antigen 1 (PfAMA1). Important structural regions considering binding configurational entropy are identified, and physical origins for such are discussed. A thorough performance evaluation is done of a set of four entropy estimators (Maximum Likelihood (ML), Miller-Madow (MM), Chao-Shen (CS), and James and Stein shrinkage (JS)) with known varying degrees of sensitivity of the entropy estimate on the extent of sampling, each with two schemes for discretization of fluctuation data of Degrees of Freedom (DFs) to estimate Probability Density Functions (PDFs). Our comprehensive evaluation of influences of variations of parameters shows Neighbor Approximated MIE (A-MIE) outperforms MIE in terms of convergence and computational efficiency. In the case of A-MIE/MIE, results are sensitive to the choice of root atoms, graph search algorithm used for the Bond-Angle-Torsion (BAT) conversion, and entropy estimator, while A-MIST/MIST are not. A-MIST yields binding entropy within 0.5 kcal/mol of MIST with only 20-30% computation. Moreover, all these methods have been implemented in an OpenMP/MPI hybrid parallel C++11 code, and also a python package for data preprocessing and entropy contribution analysis is developed and made available. A comparative analysis of features of current implementation and existing tools is also presented.

Rational design and chemical modification of TEAD coactivator peptides to target hippo signaling pathway against gastrointestinal cancers

Human Hippo signaling pathway has been recognized as a new and promising therapeutic target of gastrointestinal cancers, which is regulated by the intermolecular recognition between the TEA domain (TEAD) transcription factor and its prime coactivators. The coactivator proteins adopt two hotspot sites, namely α-helix and Ω-loop, to interact with TEAD. Here, we demonstrate that both the α-helix and Ω-loop peptides cannot maintain in structured state when splitting from the full-length coactivator proteins; they exhibit a large intrinsic disorder in free state that prevents the coactivator peptide recognition by TEAD. Rational design is used to optimize the interfacial residues of coactivator α-helix peptides, which can effectively improve the favorable direct readout effect upon the peptide binding to TEAD. Chemical modification is employed to constrain the free α-helix peptide into native ordered conformation. The method introduces an all-hydrocarbon bridge across i and i + 4 residues to stabilize the helical structure of a free coactivator peptide, which can considerably reduce the unfavorable indirect readout effect upon the peptide binding to TEAD. The all-hydrocarbon bridge is designed to point out of the TEAD-peptide complex interface, which would not disrupt the direct intermolecular interaction between the TEAD and peptide. Therefore, the stapling only improves peptide affinity, but does not alter peptide specificity, to TEAD. Affinity assay confirms that the binding potency of coactivator α-helix peptides is improved substantially by >5-fold upon the rational design and chemical modification. Structural analysis reveals that the optimized/stapled peptides can form diverse nonbonded interactions such as hydrogen bonds and hydrophobic contacts with TEAD, thus conferring stability and specificity to the TEAD-peptide complex systems.

3D-QSAR, Molecular Docking and Molecular Dynamics Simulation of Pseudomonas aeruginosa LpxC Inhibitors

As an important target for the development of novel antibiotics, UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) has been widely studied. Pyridone methylsulfone hydroxamate (PMH) compounds can effectively inhibit the catalytic activity of LpxC. In this work, the three-dimensional quantitative structure-activity relationships of PMH inhibitors were explored and models with good predictive ability were established using comparative molecular field analysis and comparative molecular similarity index analysis methods. The effect of PMH inhibitors' electrostatic potential on the inhibitory ability of Pseudomonas aeruginosa LpxC (PaLpxC) is revealed at the molecular level via molecular electrostatic potential analyses. Then, two molecular dynamics simulations for the PaLpxC and PaLpxC-inhibitor systems were also performed respectively to investigate the key residues of PaLpxC hydrolase binding to water molecules. The results indicate that orderly alternative water molecules can form stable hydrogen bonds with M62, E77, T190, and H264 in the catalytic center, and tetracoordinate to zinc ion along with H78, H237, and D241. It was found that the conformational transition space of PaLpxC changes after association with PMH inhibitors through free energy landscape and cluster analyses. Finally, a possible inhibitory mechanism of PMH inhibitors was proposed, based on our molecular simulation. This paper will provide a theoretical basis for the molecular design of LpxC-targeting antibiotics.

Entropy in bimolecular simulations: A comprehensive review of atomic fluctuations-based methods

Entropy of binding constitutes a major, and in many cases a detrimental, component of the binding affinity in biomolecular interactions. While the enthalpic part of the binding free energy is easier to calculate, estimating the entropy of binding is further more complicated. A precise evaluation of entropy requires a comprehensive exploration of the complete phase space of the interacting entities. As this task is extremely hard to accomplish in the context of conventional molecular simulations, calculating entropy has involved many approximations. Most of these golden standard methods focused on developing a reliable estimation of the conformational part of the entropy. Here, we review these methods with a particular emphasis on the different techniques that extract entropy from atomic fluctuations. The theoretical formalisms behind each method is explained highlighting its strengths as well as its limitations, followed by a description of a number of case studies for each method. We hope that this brief, yet comprehensive, review provides a useful tool to understand these methods and realize the practical issues that may arise in such calculations.

Replica-exchange molecular dynamics simulations of cellulose solvated in water and in the ionic liquid 1-butyl-3-methylimidazolium chloride

Ionic liquids have become a popular solvent for cellulose pretreatment in biorefineries due to their efficiency in dissolution and their reusability. Understanding the interactions between cations, anions, and cellulose is key to the development of better solvents and the improvement of pretreatment conditions. While previous studies described the interactions between ionic liquids and cellulose fibers, shedding light on the initial stages of the cellulose dissolution process, we study the end state of that process by exploring the structure and dynamics of a single cellulose decamer solvated in 1-butyl-3-methyl-imidazolium chloride (BmimCl) and in water using replica-exchange molecular dynamics. In both solvents, global structural features of the cellulose chain are similar. However, analyses of local structural properties show that cellulose explores greater conformational variability in the ionic liquid than in water. For instance, in BmimCl the cellulose intramolecular hydrogen bond O3H'···O5 is disrupted more often resulting in greater flexibility of the solute. Our results indicate that the cellulose chain is more dynamic in BmimCl than in water, which may play a role in the favorable dissolution of cellulose in the ionic liquid. Calculation of the configurational entropy of the cellulose decamer confirms its higher conformational flexibility in BmimCl than in water at elevated temperatures.

Exploring binding properties of agonists interacting with a δ-opioid receptor

Ligand-receptor interactions are at the basis of the mediation of our physiological responses to a large variety of ligands, such as hormones, neurotransmitters and environmental stimulants, and their tuning represents the goal of a large variety of therapies. Several molecular details of these interactions are still largely unknown. In an effort to shed some light on this important issue, we performed a computational study on the interaction of two related compounds differing by a single methyl group (clozapine and desmethylclozapine) with a -opioid receptor. According to experiments, desmethylclozapine is more active than clozapine, providing a system well suited for a comparative study. We investigated stable configurations of the two drugs inside the receptor by simulating their escape routes by molecular dynamics simulations. Our results point out that the action of the compounds might be related to the spatial and temporal distribution of the affinity sites they visit during their permanency. Moreover, no particularly pronounced structural perturbations of the receptor were detected during the simulations, reinforcing the idea of a strong dynamical character of the interaction process, with an important role played by the solvent in addition.

A molecular simulation based assessment of binding of metal ions on micelles

An assessment of the ability of a micellar surface to bind different metal ions using molecular simulation is presented in this study. Sodium dodecyl sulfate (SDS) is considered as the anionic surfactant. Various relevant characteristics of SDS-metal ion systems are estimated to quantify preferential binding of metal ions. These are electrostatic energy, total potential energy of the system, radial distribution function, and entropy and free energy change of the system. By examining these parameters, the relative extents of binding of different metal ions to the micellar surface are assessed.