AMOEBA Force Field Predicts Accurate Hydrogen Bond Counts of Nitriles in SNase by Revealing Water-Protein Interaction in Vibrational Absorption Frequencies

TinkerModeller: An Efficient Tool for Building Biological Systems in Tinker Simulations

Polarizable force fields advance our understanding of electrostatic interactions in molecular systems; however, their widespread application is limited by the complexity of required molecular modeling. We here present TinkerModeller (TKM), a versatile software package designed to streamline the construction of biological systems in the Tinker molecular simulation software. The core functionality of TKM lies in its capacity to generate input files for complex molecular systems and facilitate the conversion from classical to polarizable force fields. With a user-friendly, standalone script, TKM provides an intuitive interface that supports users from molecular modeling through to postanalysis, creating a comprehensive platform for molecular dynamics simulations within Tinker. Furthermore, TKM includes an electric field (EF) postanalysis module, introducing a novel approach that employs charge methods and point charge approximations for efficient internal EF estimation. This module offers a computationally low-demand solution for high-throughput EF estimation. Our work paves the way for broader, more accessible use of polarizable force fields within Tinker and introduces a new method for EF estimation, advancing our capacity to explore electrostatic effects in biological and materials science applications.

Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications

The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or complexes thereof, are strongly influenced by protonation changes of their typically many titratable groups, which explains their sensitivity to pH changes. Conversely, conformational and environmental changes of the biomolecule affect the protonation state of these groups. With few exceptions, conventional force field-based molecular dynamics (MD) simulations neither account for these effects nor do they allow for coupling to a pH buffer. Here, we present design decisions and applications of a rigorous Hamiltonian interpolation λ-dynamics constant pH method in GROMACS, which rests on GPU-accelerated Fast Multipole Method (FMM) electrostatics. Our implementation supports both CHARMM36m and Amber99sb*-ILDN force fields and is largely automated to enable seamless switching from regular MD to constant pH MD, involving minimal changes to the input files. Here, the first of two companion papers describes the underlying constant pH protocol and sample applications to several prototypical benchmark systems such as cardiotoxin V, lysozyme, and staphylococcal nuclease. Enhanced convergence is achieved through a new dynamic barrier height optimization method, and high pKa accuracy is demonstrated. We use Functional Mode Analysis (FMA) and Mutual Information (MI) to explore the complex intra- and intermolecular couplings between the protonation states of titratable groups as well as those between protonation states and conformational dynamics. We identify striking conformation-dependent pKa variations and unexpected inter-residue couplings. Conformation-protonation coupling is identified as a primary cause of the slow protonation convergence notorious to constant pH simulations involving multiple titratable groups, suggesting enhanced sampling methods to accelerate convergence.

Unusual Hydrophobic Property of Blue Fluorescent Amino Acid 4-Cyanotryptophan

It is a common belief that the negative heat capacity change (ΔCp) associated with protein folding, which is a manifestation of the hydrophobic effect, results from a decrease in the solvent accessible hydrophobic surface area. Herein, we investigate the conformational energy landscape and dynamics of a tetrapeptide composed of two glycine and two 4-cyanotryptophan residues using time-resolved fluorescence spectroscopy, molecular dynamics simulations, and density functional theory calculations and find that, contrary to this expectation, the hydrophobic association of two 4-cyanotryptophan side chains leads to a positive ΔCp (approximately 543 J K-1 mol-1). Furthermore, we find that promoting one of the 4-cyanotryptophans to its excited electronic state strengthens this self-association. Taken together, our results provide not only insight into how modification of an aromatic amino acid can affect its hydrophobicity but also a potential strategy for designing protein sequences that can fold (unfold) at high (low) temperatures.

Exploring the inflammation-related mechanisms of Lingguizhugan decoction on right ventricular remodeling secondary to pulmonary arterial hypertension based on integrated strategy using UPLC-HRMS, systems biology approach, and experimental validation

BACKGROUND

Pulmonary arterial hypertension (PAH) and the consequent right heart dysfunction persist with high morbidity and mortality, and the mechanisms and pharmacologic interventions for chronic right-sided heart failure (RHF) have not been adequately investigated. Research has shown that prolonged inflammation is critical in precipitating the progression of PAH-associated right heart pathology. Some research demonstrated that Lingguizhugan decoction (LGZGD), as a classical Chinese medicine formula, had beneficial effects in alleviating PAH and RHF, while its underlying mechanisms involved are not fully elucidated.

PURPOSE

Based on that, this study aims to investigate the effects and underlying mechanisms of LGZGD on PAH-induced RHF.

STUDY DESIGN

In this study, we identified the serum constituents and deciphered the potential anti-inflammatory mechanism and crucial components of LGZGD using combined approaches of UPLC-HRMS, transcriptomic analysis, and molecular docking techniques. Finally, we used in vivo experiments to verify the expression of key targets in the monocrotaline (MCT)-induced RHF model and the intervene effect of LGZGD.

RESULTS

Integrated strategies based on UPLC-HRMS and systems biology approach combined with in vivo experimental validation showed that LGZGD could improve right heart fibrosis and dysfunction via regulating diverse inflammatory signaling pathways and the activity of immune cells, including chemokine family CCL2, CXCR4, leukocyte integrins family ITGAL, ITGB2, and M2 macrophage infiltration, as well as lipid peroxidation-associated HMOX1, NOX4, and 4-HNE.

CONCLUSION

The present research demonstrated for the first time that LGZGD might improve PAH-induced RHF through multiple anti-inflammatory signaling and inhibition of ferroptosis, which could provide certain directions for future research in related fields.

Critical Evaluation of Polarizable and Nonpolarizable Force Fields for Proteins Using Experimentally Derived Nitrile Electric Fields

Molecular dynamics (MD) simulations are frequently carried out for proteins to investigate the role of electrostatics in their biological function. The choice of force field (FF) can significantly alter the MD results, as the simulated local electrostatic interactions lack benchmarking in the absence of appropriate experimental methods. We recently reported that the transition dipole moment (TDM) of the popular nitrile vibrational probe varies linearly with the environmental electric field, overcoming well-known hydrogen bonding (H-bonding) issues for the nitrile frequency and, thus, enabling the unambiguous measurement of electric fields in proteins (J. Am. Chem. Soc. 2022, 144 (17), 7562-7567). Herein, we utilize this new strategy to enable comparisons of experimental and simulated electric fields in protein environments. Specifically, previously determined TDM electric fields exerted onto nitrile-containing o-cyanophenylalanine residues in photoactive yellow protein are compared with MD electric fields from the fixed-charge AMBER FF and the polarizable AMOEBA FF. We observe that the electric field distributions for H-bonding nitriles are substantially affected by the choice of FF. As such, AMBER underestimates electric fields for nitriles experiencing moderate field strengths; in contrast, AMOEBA robustly recapitulates the TDM electric fields. The FF dependence of the electric fields can be partly explained by the presence of additional negative charge density along the nitrile bond axis in AMOEBA, which is due to the inclusion of higher-order multipole parameters; this, in turn, begets more head-on nitrile H-bonds. We conclude by discussing the implications of the FF dependence for the simulation of nitriles and proteins in general.