Allosteric Mechanism of Calmodulin Revealed by Targeted Molecular Dynamics Simulation

Calmodulin （CAM） is involved in the regulation of a variety of cellular signaling pathways. To accomplish its physiological functions, CaM binds with Ca2＋ at its EF-hand Ca2＋ binding sites which induce the conformational switching of CaM. However, the molecular mechanism by which Ca2＋ binds with CaM and induces conformational switching is still obscure. Here we combine molecular dynamics with targeted molecular dynamics simulation and achieve the state-transition pathway of CaM. Our data show that Ca2＋ binding speeds up the conformational transition of CaM by weakening the interactions which stabilize the closed state. It spends about 6.5 ns and 5.25 ns for transition from closed state to open state for apo and holo CaM, respectively. Regarding the contribution of two EF-hands, our data indicate that the first EF-hand triggers the conformational transition and is followed by the second one. We determine that there are two interaction networks which contribute to stabilize the closed and open states, respectively.

Car-Parinello molecular dynamics simulations of thionitroxide and S-nitrosothiol in the gas phase,methanol,and water——A theoretical study of S-nitrosylation

A dilemma about whether thionitroxide radical (RSNHO) or S-nitrosothiol (RSNO) is observed in protein S-nitrosylation has arisen recently. To illustrate the effect of chemical environment on these structures, this paper presents quantum mechanical molecular dynamics of thionitroxide, and cis-and trans-S-nitrosothiols in the gas phase, methanol, and water. By using Car-Parrinello molecular dynamics (CPMD), we have observed that there is free rotation about the S-N bond at 300 K in thionitroxide, but no such rotation is observed for S-nitrosothiol. The C-S-N-O torsion angle distribution in thionitroxide is s-ignificantly dependent upon the surrounding environment, leading to either gauche-, cis-, or trans-conformation. In the case of S-nitrosothiol the C-S-N-O plane is twisted slightly by 5°-15° in the cis-isomer, while the periplanar structure is well-retained in the trans-isomer. The calculated results are in agreement with the X-ray crystallographic data of small molecular RSNO species. Interestingly, for both compounds, the CPMD simulations show that solvation can cause a decrease in the S-N bond length. Moreover, the oxygen atom of thionitroxide is found to be a good hydrogen-bond acceptor, forming an oxyanion-hole-like hydrogen bonding network.

Recent progress on the mechanics of sharply bent DNA

Despite extensive studies on the mechanics of DNA under external constrains, such as tension, torsion, and bending, several important aspects have remained poorly understood. One biologically important example is the mechanics of DNA under sharp bending conditions, which has been debated for a decade without thorough comprehension. The debate is about the interesting phenomenon raised from a series of different experiments: sharply bent DNA has a surprisingly high apparent bending flexibility that deviates from the canonical bending elasticity of DNA. This finding has motivated various theoretical models, which mainly incorporate the excitation of mechanical defects inside severely bent DNA molecules. Here, we review the recent progress on the understanding of the mechanics of sharply bent DNA and provide our view on this important question by interrogating the theoretical foundation of these experimental measurements.

Two-dimensional ultraviolet spectroscopy of proteins

Two-dimensional ultraviolet(2 DUV) spectroscopy is a novel technology for probing molecular structure. We have developed a generalized quantum mechanics/molecular mechanics(QM/MM) approach to simulate the electronic transitions of protein backbones and aromatic amino acids in aqueous solution. These transitions, which occur in the ultraviolet(UV) region, provide a sensitive probe of molecular structure. The features of 2 DUV spectra are accurately characterized and enable us to trace small variations in the structure and dynamics as well as evolution propensity with high accuracy. Various structures and dynamic phenomena are investigated to construct a systematic framework for 2 DUV simulation mechanisms, so as to explore further applications of this technique. In this feature article, we summarize the theory and applications of 2 DUV spectroscopy we have engaged in recently, present the important roles of 2 DUV spectroscopy, and outline directions for future development. We hope this article can offer a platform for more scientists in different research fields to gain a clear overview of 2 DUVand further attract more people to explore this promising field.

Modeling nanoscale ice adhesion

Anti-icing is crucial for numerous instruments and devices in low temperature circum- stance. One of the approaches in anti-icing is to reduce ice adhesion strength, seeking spontaneous de-icing processes by natural forces of gravity or by winds. In order to enable tai- lored surface icephobicity design, research requires a good theoretical understanding of the atomistic interacting mechanisms between water/ice molecules and their adhering substrates. Herein, this work focuses on using atomistic modeling and molecular dynamics simulation to build a nanosized ice-cube adhering onto silicon surface, with different contact modes of solid-solid and solid-liquid-solid patterns. This study provides atomistic models for probing nanoscale ice adhesion mechanics and theoretical platforms for explaining experimental results.

An empirical description for the hinge-like mechanism in single-layer black phosphorus:The angle–angle cross interaction

The single-layer black phosphorus is characterized by its puckered configuration that pos- sesses the hinge-like behavior, which leads to the highly anisotropic in-plane Poisson＇s ratios and the negative out-of-plane Poisson＇s ratio. We demonstrate that the hinge-like mechanism can be described by the angle-angle cross interaction, which, combined with the bond stretching and angle bending interactions, is able to provide a good description for the mechanical properties of single-layer black phosphorus. We also propose a nonlinear angle-angle cross interaction, which follows the form of Stillinger-Weber potential and can be advantageous for molecular dynamics simulations of single-layer black phosphorus under large deformation.