Qiao Xue

Exploring the molecular basis of dsRNA recognition by Mss116p using molecular dynamics simulations and free-energy calculations.

DEAD-box proteins are the largest family of helicase that are important in nearly all aspects of RNA metabolism. However, it is unclear how these proteins recognize and bind RNA. Here, we present a detailed analysis of the related DEAD-box protein Mss116p-RNA interaction, using molecular dynamics simulations with MM-GBSA calculations. The energetic analysis indicates that the two strands of double strands RNA (dsRNA) are recognized asymmetrically by Mss116p. The strand 1 of dsRNA provides the main binding affinity. Meanwhile, the nonpolar interaction provides the main driving force for the binding process. Although the contribution of polar interaction is small, it is vital in stabilizing the protein-RNA interaction. Compared with the wild type Mss116p, two studied mutants Q412A and D441A have obviously reduced binding free energies with dsRNA because of the decreasing of polar interaction. Three important residues Lys409, Arg415 and Arg438 lose their binding affinity significantly in mutants. In conclusion, these results complement previous experiments to advance comprehensive understanding of Mss116p-dsRNA interaction. The results also would provide support for the application of similar approaches to the understanding of other DEAD-box protein-RNA complexes.

Influence of Hyperthermophilic Protein Cren7 on the Stability and Conformation of DNA: Insights from Molecular Dynamics Simulation and Free Energy Analysis

Cren7, a novel chromatin protein highly conserved among crenarchaea, plays an important role in genome packaging and gene regulation. However, the detail dynamical structural characteristic of the Cren7-DNA complex and the detail study of the DNA in the complex have not been done. Focused on two specific Cren7-DNA complexes (PDB codes 3LWH and 3LWI ), we applied molecular dynamics (MD) simulations at four different temperatures (300, 350, 400, and 450 K) and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation at 300 and 350 K to examine the role of Cren7 protein in enhancing the stability of DNA duplexes via protein-DNA interactions, and to study the structural transition in DNA. The simulation results indicate that Cren7 stabilizes DNA duplex in a certain temperature range in the binary complex compared with the unbound DNA molecules. At the same time, DNA molecules were found to undergo B-like to A-like form transitions with increased temperature. The results of statistical analyses of the H-bond and hydrophobic contacts show that some residues have significant influence on the structure of DNA molecules. Our work can give important information to understand the interactions of proteins with nucleic acids and other ligands.

Exploring the mechanism how Marburg virus VP35 recognizes and binds dsRNA by molecular dynamics simulations and free energy calculations.

Filoviruses often cause terrible infectious disease which has not been successfully dealt with pharmacologically. All filoviruses encode a unique protein termed VP35 which can mask doubled‐stranded RNA to deactivate interferon. The interface of VP35–dsRNA would be a feasible target for structure‐based antiviral agent design. To explore the essence of VP35–dsRNA interaction, molecular dynamics simulation combined with MM‐GBSA calculations were performed on Marburg virus VP35–dsRNA complex and several mutational complexes. The energetic analysis indicates that nonpolar interactions provide the main driving force for the binding process. Although the intermolecular electrostatic interactions play important roles in VP35–dsRNA interaction, the whole polar interactions are unfavorable for binding which result in a low binding affinity. Compared with wild type VP35, the studied mutants F228A, R271A, and K298A have obviously reduced binding free energies with dsRNA reflecting in the reduction of polar or nonpolar interactions. The results also indicate that the loss of binding affinity for one dsRNA strand would abolish the total binding affinity. Three important residues Arg271, Arg294, and Lys298 which makes the largest contribution for binding in VP35 lose their binding affinity significantly in mutants. The uncovering of VP35–dsRNA recognition mechanism will provide some insights for development of antiviral drug.

Constant pH molecular dynamics (CpHMD) and molecular docking studies of CquiOBP1 pH-induced ligand releasing mechanism

The odorant binding protein of Culex quinquefasciatus (CquiOBP1), expressed on the insect antenna, is crucial for the investigation of trapping baited with oviposition semi-chemicals and controlling mosquito populations. The acidic titratable residues pKa prediction and the ligand binding poses investigation in two systems (pH 7 and pH 5) are studied by constant pH molecular dynamics (CpHMD) and molecular docking methods. Research results reveal that the change of the protonation states would disrupt some important H-bonds, such as Asp 66-Asp 70, Glu 105-Asn 102, etc. The cleavage of these H-bonds leads to the movement of the relative position of hydrophobic tunnel, N- and C- termini loops and pH-sensing triad (His23-Tyr54-Val125) in acid solution. Ligand MOP has lower affinity and shows different binding poses to protein CquiOBP1 at pH 5. This ligand may be released from another tunnel between helices α3 and α4 in acidic environment. However, it would bind to the protein with high affinity in neutral environment. This work could provide more penetrating understanding of the pH-induced ligand-releasing mechanism.

Highlighting a π–π interaction: a protein modeling and molecular dynamics simulation study on Anopheles gambiae glutathione S-transferase 1-2

Cytosolic insect theta class glutathione S-transferases (GSTs) have not been studied completely and their physiological roles are unknown. A detailed understanding of Anopheles gambiae GST (Aggst1-2) requires an accurate structure, which has not yet been determined. A high quality model structure of Aggst1-2 was constructed using homology modeling and the ligand–protein complex was obtained by the docking method. Molecular dynamics (MD) simulations were carried out to study conformational changes and to calculate binding free energy. The results of MD simulation indicate that Aggst1-2 undergoes small conformational changes after ligands dock to the protein, which facilitate the catalytic reaction. An essential hydrogen bond was found between the sulfur atom of glutathione (GSH) and the hydrogen atom of hydroxyl group in Ser9, which was in good agreement with experimental data. A π–π interaction between Phe204 and CDNB ligand was also found. This interaction seems to be important in stabilization of the ligand. Further study of binding free energy decomposition revealed a van der Waals interaction between two ligands that may play a key role in nucleophilic addition reaction. This work will be a good starting point for further determination of the biological role of cytosolic insect theta class GSTs and will aid the design of structure-based inhibitors.

Insights into the thermal stabilization and conformational transitions of DNA by hyperthermophile protein Sso7d: molecular dynamics simulations and MM-PBSA analysis

In the assembly of DNA-protein complex, the DNA kinking plays an important role in nucleoprotein structures and gene regulation. Molecular dynamics (MD) simulations were performed on specific protein-DNA complexes in this study to investigate the stability and structural transitions of DNA depending on temperature. Furthermore, we introduced the molecular mechanics/Poisson–Boltzmann surface area (MM-PBSA) approach to analyze the interactions between DNA and protein in hyperthermophile. Focused on two specific Sso7d-DNA complexes (PDB codes: 1BNZ and 1BF4), we performed MD simulations at four temperatures (300, 360, 420, and 480 K) and MM-PBSA at 300 and 360 K to illustrate detailed information on the changes of DNA. Our results show that Sso7d stabilizes DNA duplex over a certain temperature range and DNA molecules undergo B-like to A-like form transitions in the binary complex with the temperature increasing, which are consistent with the experimental data. Our work will contribute to a better understanding of protein-DNA interaction.

Mutation and low pH effect on the stability as well as unfolding kinetics of transthyretin dimer.

Transthyretin (TTR) dissociation and aggregation appear to cause several amyloid diseases. TTR dimer is an important intermediate that is hard to be observed from the biological experiments. To date, the molecular origin and the structural motifs for TTR dimer dissociation, as well as the unfolding process have not been rationalized at atomic resolution. To this end, we have investigated the effect of low pH and mutation L55P on stability as well as the unfolding pathway of TTR dimer using constant pH molecular dynamics simulations. The result shows that acidic environment results in loose TTR dimer structure. Mutation L55P causes the disruption of strand D and makes the CE-loop very flexible. In acidic conditions, dimeric L55P mutant exhibits notable conformation changes and an evident trend to separate. Our work shows that the movements of strand C and the loops nearby are the beginning of the unfolding process. In addition, hydrogen bond network at the interface of the two monomers plays a part in stabilizing TTR dimer. The dynamic investigation on TTR dimer provides important insights into the structure-function relationships of TTR, and rationalizes the structural origin for the tendency of unfolding and changes of structure that occur upon introduction of mutation and pH along the TTR dimer dissociation and unfolding process.

Insights into the drug resistance induced by the BaDHPS mutations: molecular dynamic simulations and MM/GBSA studies.

Dihydropteroate synthase (DHPS) is essential for the folic acid biosynthetic pathway in prokaryotes; the mutation forms for DHPS are found to be relative to the urgent drug resistance problems. In our study, the Bacillus anthracis DHPS (BaDHPS) was selected for molecular dynamics and binding free energy studies to investigate the biochemistry behaviors of the wild-type and mutation form BaDHPS proteins (D184N and K220Q). It is found that the conformational change of the ligand dihydropteroate sulfathiazole binding site in mutation D184N and K220Q systems is mainly attributed from the Loop 1, Loop 2, and Loop 7 regions, and the binding free energy of these mutation systems is lower than that of the wild-type system. Additionally, some important hydrogen bonds of the mutation systems are disrupted during the simulations. But the shortening of the distance between residue Thr67 and the ligand would cause significant change of the binding pose in the K220Q system. These studies of DHPS family will be helpful for further drug resistance investigations. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:24

Molecular dynamics (MD) simulations and binding free energy calculation studies between inhibitors and type II dehydroquinase (DHQ2)

Type II dehydroquinase (DHQ2) is the third enzyme of the shikimic acid pathway, and it has been the effective target for tuberculosis (TB). So far, developing multiple potent inhibitors of the DHQ2 of Mycobacterium tuberculosis (DHQ2-Mt) has been considered to be the new therapy to TB. Molecular dynamics simulations followed by molecular mechanics-generalised Born surface area were carried out to calculate the free binding energy and to determine the affinity ability of the four chosen inhibitor molecules, L1, L2, L3 and L4. Energy decomposition analyses show the electrostatic interaction and van der Waals interaction of the ligands to every residue of the DHQ2-Mt. The results suggest that some important residues have different interactions with the four ligands, such as Arg19 and Tyr24. These interactions may have an effect on the ligand binding affinity. The binding affinity of monosubstituted inhibitor is higher than that of disubstituted inhibitor, due to some important interactions with the DHQ2-Mt residues. These computational works will be significant to the theoretical research in the future.