Molecular Properties of Ca2+ Transport Through TRPV2 Channel: A Molecular Dynamic Simulations Study

TRPV channels are a category of nonselective cation channels that activated by heat and ligands, and permeate monovalent and divalent ions. The mechanism of Ca2+ transfer through TRPV2 channel is not well known. Here, we investigated the reaction coordination and energy fluctuation of Ca2+ transition in TRPV2 channel by steered molecular dynamics (SMD) simulations and potential of mean force (PMF) calculation. Results showed that electrostatic interactions between Ca2+ and residues of the first and second gates had main roles in ions transfer through the channel, and also, we recognized important amino acids in this path. Moreover, results indicated that enter and exit of calcium ions needed to overcome barrier energies in first and second gates.

Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current coronavirus disease 2019 (COVID-19) pandemic. It is known that the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 interacts with the human angiotensin-converting enzyme 2 (ACE2) receptor, initiating the entry of SARS-CoV-2. Since its emergence, a number of SARS-CoV-2 variants have been reported, and the variants that show high infectivity are classified as the variants of concern according to the US CDC. In this study, we performed both all-atom steered molecular dynamics (SMD) simulations and microscale thermophoresis (MST) experiments to characterize the binding interactions between ACE2 and RBD of all current variants of concern (Alpha, Beta, Gamma, and Delta) and two variants of interest (Epsilon and Kappa). We report that the RBD of the Alpha (N501Y) variant requires the highest amount of force initially to be detached from ACE2 due to the N501Y mutation in addition to the role of N90-glycan, followed by Beta/Gamma (K417N/T, E484K, and N501Y) or Delta (L452R and T478K) variant. Among all variants investigated in this work, the RBD of the Epsilon (L452R) variant is relatively easily detached from ACE2. Our results combined SMD simulations and MST experiments indicate what makes each variant more contagious in terms of RBD and ACE2 interactions. This study could help develop new drugs to inhibit SARS-CoV-2 entry effectively.

Mechanical Properties of Spider Silk for Use As a Biomaterial: Molecular Dynamics Investigations

Even though silkworm are the most dominant type of silk fibers used for commercial applications, spider silk has a definitive role in biomedical applications due to its biocompatibility and excellent mechanical properties as biomaterials. In recent years, recombinant production of the silk proteins at a larger scale has found new interest. Spider silk composites with a combination of a variety of other biomaterials have also been used to improve properties such as bio-compatibility, mechanical strength and controlled degradation. [1] A major constituent of spider silk fibers, are spidroin proteins. These are made up of repetitive segments flanked by conserved non-repetitive domains. The fiber proteins consist of a light chain and a heavy chain that are connected via a single disulfide bond. [2] Present paper employed steered molecular dynamics (SMD) as the principal method of investigating the mechanical properties of these nanoscale spider silk protein 3LR2, with a residual count of 134 amino acids. [3]. SMD simulations were performed by pulling on β-chain of the protein in the x-direction, while holding the other fixed. The focus of this paper is to investigate the mechanical properties of the nanoscale spider silk proteins with lengths of about 4.5nm in a folded state, leading to understanding of their feasibility in bio-printing of a composite spider silk biomaterial with a blend of various other biomaterials such as collagen. An in-depth insight into the fraying and tensile deformation and structural properties of the spider silk proteins are of innovative significance for a multitude of biomedical engineering applications. A calculated Gibbs free energy value of 18.59 kCal/mol via umbrella sampling corresponds with a complete separation of a single chain from a spider silk protein in case of fraying. Force needed for complete separation of the chain from the spider silk protein is analyzed, and discussed in this paper. It is found that the protein molecule undergoes a tensile stretch at strain rates of ≅ 11.65. An elastic modulus of 20.136 GPa, calculated via simple SMD simulations by subjecting the silk β-chain to a tensile stretch is also presented.

Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism

ToxIN is a triangular structure formed by three protein toxins (ToxNs) and three specific noncoding RNA antitoxins (ToxIs). To respond to stimuli, ToxI is preferentially degraded, releasing the ToxN. Thus, the dynamic character is essential in the normal function interactions between ToxN and ToxI. Here, equilibrated molecular dynamics (MD) simulations were performed to study the stability of ToxN and ToxI. The results indicate that ToxI adjusts the conformation of 3′ and 5′ termini to bind to ToxN. Steered molecular dynamics (SMD) simulations combined with the recently developed thermodynamic integration in 3nD (TI3nD) method were carried out to investigate ToxN unbinding from the ToxIN complex. The potentials of mean force (PMFs) and atomistic pictures suggest the unbinding mechanism as follows: (1) dissociation of the 5′ terminus from ToxN, (2) missing the interactions involved in the 3′ terminus of ToxI without three nucleotides (G31, A32, and A33), (3) starting to unfold for ToxI, (4) leaving the binding package of ToxN for three nucleotides of ToxI, (5) unfolding of ToxI. This work provides information on the structure-function relationship at the atomistic level, which is helpful for designing new potent antibacterial drugs in the future.

Exploring the Binding Mechanism between Human Profilin (PFN1) and Polyproline-10 through Binding Mode Screening

The large magnitude of protein-protein interaction (PPI) pairs within the human interactome necessitates the development of predictive models and screening tools to better understand this fundamental molecular communication. However, despite enormous efforts from various groups to develop predictive techniques in the last decade, PPI complex structures are in general still very challenging to predict due to the large number of degrees of freedom. In this study, we use the binding complex of human profilin (PFN1) and polyproline-10 (P10) as a model system to examine various approaches, with the aim of going beyond normal protein docking for PPI prediction and evaluation. The potential of mean force (PMF) was first obtained from the timeconsuming umbrella sampling, which confirmed that the most stable binding structure identified by the maximal PMF difference is indeed the crystallographic binding structure. Moreover, crucial residues previously identified in experimental studies, W3, H133 and S137 of PFN1, were found to form favorable hydrogen bonds with P10, suggesting a zipping process during the binding between PFN1 and P10. We then explored both regular molecular dynamics (MD) and steered molecular dynamics (SMD) simulations, seeking for better criteria of ranking the PPI prediction. Despite valuable information obtained from conventional MD simulations, neither the commonly used interaction energy between the two binding parties nor the long-term root mean square displacement (RMSD) correlates well with the PMF results. On the other hand, with a sizable collection of trajectories, we demonstrated that the average rupture work calculated from SMD simulations correlates fairly well with the PMFs (R2 = 0.67), making it a promising PPI screening method.

Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes

Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered molecular dynamics (SMD) to assess the strength of protein-peptide interactions. The idea behind using SMD simulations is that the mechanical stability can be used as a promising and an efficient alternative to computationally highly demanding estimation of binding affinity. However, mechanical stability defined as a peak in force-extension profile depends on the choice of the pulling direction. Here we propose an uncommon choice of the pulling direction along resultant dipole moment (RDM) vector, which has not been explored in SMD simulations so far. Using explicit solvent all-atom MD simulations, we apply SMD technique to probe mechanical resistance of ligand-receptor system pulled along two different vectors. A novel pulling direction—when ligand unbinds along the RDM vector—results in stronger forces compared to commonly used ligand unbinding along center of masses vector. Our observation that RDM is one of the factors influencing the mechanical stability of protein-peptide complex can be used to improve the ranking of binding affinities by using mechanical stability as an effective scoring function.

Theoretical study of mechanisms for the hydrolytic deamination of cytosine via steered molecular dynamic simulations

Gibbs free energy profiles of the cytosine deamination assisted by a water molecule in a discrete aqueous medium were obtained by the application of Steered Molecular Dynamic (SMD) simulations.