Zeros of partition functions in the NPT ensemble

Investigating the Interaction Mechanism of CAT-BT-Br and Key Residue Mutations for Castration-Resistant Prostate Cancer through Molecular Dynamics Simulation

Prostate cancer is the second most common cancer in men, second only to lung cancer. Castration-resistant prostate cancer (CRPC) was formerly known as hormone-resistant prostate cancer. The aim of this study is to reveal the effect of key residue mutations on the binding mechanism between catalase (CAT) and benzaldehyde thiourea derivatives (BT-Br), providing theoretical support for the development of novel CAT inhibitors. This article analyzes the structural stability, binding energy and decomposition, hydrogen bonding, etc. of wild-type (WT) and multiple mutations systems. The results showed that, in addition to the R203A mutant, all mutation systems significantly enhanced the binding ability of CAT to BT-Br, and their binding free energy contribution mainly came from van der Waals interactions. Hydrogen bond analysis shows that the hydrogen bond occupancy rate of the WT system is relatively low, while mutations such as V302A have a hydrogen bond occupancy rate as high as 93.05%, indicating a significant enhancement in their binding ability. In addition, mutations have limited impact on the overall stability of proteins, but some mutations such as Y215A and V302A significantly alter the binding site and direction of proteins. The results of principal component analysis (PCA) in other systems are consistent with those of root mean square fluctuation (RMSF) analysis, and the binding site shows little movement. This study not only elucidates the microscopic effects of key residue mutations on the binding mechanism between CAT and BT-Br but also provides new targets and drug design ideas for prostate cancer treatment based on iron death induction strategies.

Molecular mechanism of ZER1-mediated recognition of N-terminal glycine in protein degradation

The N-terminal glycine (Gly/N-degron) serves as a degradation signal recognized by specific E3 ligases, playing a crucial role in protein quality control and maintaining intracellular protein homeostasis. Zinc finger E3 ubiquitin protein ligase 1 (ZER1), a substrate receptor of the Cullin 2-RING E3 ubiquitin ligase, recognizes N-terminal glycine and other small N-terminal residues (such as serine, alanine, and cysteine), mediating protein degradation through the Gly/N-degron pathway. In this study, we employed all-atom molecular dynamics (MD) simulations and binding free energy calculations to study the binding mode of ZER1 with N-terminal glycine and the effects of key residue mutations on this recognition process. The results show that the binding of glycine-containing peptides and key residue mutations have minimal impact on ZER1 structural stability. During ZER1-peptide binding, van der Waals and electrostatic interactions are the primary driving forces. Residues W552, N553, D556, N597, I678, N579, R681, and K716 play significant roles in the recognition process, with mutations in these residues affecting the electrostatic distribution and hydrophobic properties of the ZER1 binding site, thereby influencing peptide binding. Additionally, ZER1 forms a complex hydrogen-bond network with the peptide, which stabilizes the peptide like an anchor. D556A and N597A disrupt the hydrogen bond between the N-terminal residue (G1) and ZER1. These findings provide a molecular-level understanding of the N-terminal degron pathway and lay a foundation for future related research.

A Study on the Binding Mechanism and the Impact of Key Residue Mutations between SND1 and MTDH Peptide through Molecular Dynamics Simulations

Metastasis of breast cancer is the main cause of death for patients with breast cancer. The interaction between metadherin (MTDH) and staphylococcal nuclease domain 1 (SND1) plays a pivotal role in promoting breast cancer development. However, the binding details between MTDH and SND1 remain unclear. In this study, we employed all-atom molecular dynamics simulations (MDs) and conducted binding energy calculations to investigate the binding details and the impact of key residue mutations on binding. The mutations in key residues have not significantly affected the overall stability of the structure and the fluctuation of residues near the binding site; they have exerted a substantial impact on the binding of SND1 and MTDH peptide. The electrostatic interactions and van der Waals interactions play an important role in the binding of SND1 and the MTDH peptide. The mutations in the key residues have a significant impact on electrostatic and van der Waals interactions, resulting in weakened binding. The energy contributions of key residues mainly come from the electrostatic energy and van der Waals interactions of the side chain. In addition, the key residues form an intricate and stable network of hydrogen bonds and salt-bridge interactions with the MTDH peptide. The mutations in key residues have directly disrupt the interactions formed between SND1 and MTDH peptide, consequently leading to changes in the binding mode of the MTDH peptide. These analyses unveil the detailed atomic-level interaction mechanism between SND1 and the MTDH peptide, providing a molecular foundation for the development of antibreast cancer drugs.

Exploring binding modes of the selected inhibitors to SND1 by all-atom molecular dynamics simulations

Breast cancer is the leading cause of cancer-related deaths in women. Previous studies have indicated that disrupting the interaction between Metadherin (MTDH) and Staphylococcal nuclease domain containing 1 (SND1) can inhibit breast cancer development. Understanding the binding mode of small molecule inhibitors with SND1 is of great significance for designing drugs targeting the MTDH-SND1 complex. In this study, we conducted all-atom molecular dynamics (MD) simulations in solution and performed binding energy calculations to gain insights into the binding mechanism of small molecules to SND1. The binding site of SND1 for small molecules is relatively rigid, and the binding of the small molecule and the mutation of key residues have little effect on the conformation of the binding site. SND1 binds more tightly to C26-A6 than to C26-A2, as C26-A2 undergoes a 180° directional change during the simulation process. The key residue mutations have a direct effect on the position and orientation of small molecule in the binding site. The key residues make primary contributions to the binding energy through van der Waals interaction and nonpolar solvation energy, although the contribution from nonpolar solvation is relatively minor. The key residue mutations also affect the formation of hydrogen bonds and ultimately the stability of the small molecule-SND1 complex.Communicated by Ramaswamy H. Sarma.

Revealing the binding mechanism of BACE1 inhibitors through molecular dynamics simulations

Alzheimer's disease is a debilitating neurodegenerative disorder, and the Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1) is a key therapeutic target in its treatment. This study employs molecular dynamics simulations and binding energy analysis to investigate the binding interactions between BACE1 and four selected small molecules: CNP520, D9W, NB641, and NB360. The binding model analysis indicates that the binding of BACE1 with four molecules are stable, except the loop regions show significant fluctuation. The binding free energy analyses reveal that NB360 exhibits the highest binding affinity with BACE1, surpassing other molecules (CNP520, D9W, and NB641). Detailed energy component assessments highlight the critical roles of electrostatic interactions and van der Waals forces in the binding process. Furthermore, residue contribution analysis identifies key amino acids influencing the binding process across all systems. Hydrogen bond analysis reveals a limited number of bonds between BACE1 and each small molecule, highlighting the importance of structural modifications to enable more stable hydrogen bonds. This research provides valuable insights into the molecular mechanisms of potential Alzheimer's disease therapeutics, guiding the way for improved drug design and the development of effective treatments targeting BACE1.

Exploration of the Product Specificity of chitosanase CsnMY002 and Mutants Using Molecular Dynamics Simulations

Chitosanase CsnMY002 is a new type of enzyme isolated from Bacillus subtilis that is used to prepare chitosan oligosaccharide. Although mutants G21R and G21K could increase Chitosan yield and thus increase the commercial value of the final product, the mechanism by which this happens is not known. Herein, we used molecular dynamics simulations to explore the conformational changes in CsnMY002 wild type and mutants when they bind substrates. The binding of substrate changed the conformation of protein, stretching and deforming the active and catalytic region. Additionally, the mutants caused different binding modes and catalysis, resulting in different degrees of polymerization of the final Chitooligosaccharide degradation product. Finally, Arg37, Ile145 ~ Gly148 and Trp204 are important catalytic residues of CsnMY002. Our study provides a basis for the engineering of chitosanases.

Towards A Novel Multi-Epitopes Chimeric Vaccine for Simulating Strong Immune Responses and Protection against Morganella morganii

Morganella morganii is one of the main etiological agents of hospital-acquired infections and no licensed vaccine is available against the pathogen. Herein, we designed a multi-epitope-based vaccine against M. morganii. Predicted proteins from fully sequenced genomes of the pathogen were subjected to a core sequences analysis, followed by the prioritization of non-redundant, host non-homologous and extracellular, outer membrane and periplasmic membrane virulent proteins as vaccine targets. Five proteins (TonB-dependent siderophore receptor, serralysin family metalloprotease, type 1 fimbrial protein, flagellar hook protein (FlgE), and pilus periplasmic chaperone) were shortlisted for the epitope prediction. The predicted epitopes were checked for antigenicity, toxicity, solubility, and binding affinity with the DRB*0101 allele. The selected epitopes were linked with each other through GPGPG linkers and were joined with the cholera toxin B subunit (CTBS) to boost immune responses. The tertiary structure of the vaccine was modeled and blindly docked with MHC-I, MHC-II, and Toll-like receptors 4 (TLR4). Molecular dynamic simulations of 250 nanoseconds affirmed that the designed vaccine showed stable conformation with the receptors. Further, intermolecular binding free energies demonstrated the domination of both the van der Waals and electrostatic energies. Overall, the results of the current study might help experimentalists to develop a novel vaccine against M. morganii.

Electrolyte structure near electrodes with molecular-size roughness

Understanding electrodes' surface morphology influence on ions' distribution is essential for designing supercapacitors with enhanced energy density characteristics. We develop a model for the structure of electrolytes near the rough surface of electrodes. The model describes an effective electrostatic field's increase and associated intensification of ions' spatial separation at the electrode-electrolyte interface. These adsorption-induced local electric and structure properties result in notably increased values and a sharpened form of the differential capacitance dependence on the applied potential. Such capacitance behavior is observed in many published simulations, and its description is beyond the capabilities of the established flat-electrodes theories. The proposed approach could extend the quantitatively verified models providing a new instrument of the electrode surface-parameter optimization for specific electrolytes.

Construction of subcritical isotherms for model and real gases on the basis of Mayer's cluster expansion

Existing rigorous statistical approaches still cannot quantitatively describe condensation phenomena in real fluids and even model systems with some simplified interaction potential. Here, we present a method to evaluate the unlimited subcritical set of Mayer's reducible cluster integrals (the power coefficients of virial expansions) by using the information on several virial coefficients and empirical value of saturation activity. As to the requirements on the initial number of known virial coefficients, the calculations for the Lennard-Jones model indicate that only the second virial coefficient is sufficient to reproduce gas isotherms (including the flat phase-transition region) with high accuracy at low temperatures. This remarkable feature allows the simplification of the method for real fluids with an unknown interaction potential: In particular, the calculated isotherms of several real substances (including water) are in good agreement with experiments. Additionally, the obtained results indicate the existence of some important universality which needs serious future exploration.