Molecular Dynamics Simulation for Probing the Flexibility of the 35 Nucleotide SL1 Sequence Kissing Complex from HIV-1Lai Genomic RNA

Abstract

The SL1 stem-loop located in the encapsidation domain is responsible for initiating the dimerisation of HIV-1 genomic RNA by means of a loop-loop interaction known as Kissing Complex (KC). The SL1 secondary structure has been predicted as a 35 nucleotides [K. G. Murti, M. Bondurant, and A. Tereba. J Virol 37, 411–419 (1981)] stem-loop composed of a 4 base pairs (bp) terminal duplex, a 4 nt asymmetrical internal loop, a 7 bp internal duplex, and a 9 nt apical loop. Several high resolution structures of the monomer and of KC of a 23 nt sequence containing only the internal duplex and the apical loop of SL1 are available in the literature. No experimental high resolution structure of the complete native SL1 sequence has been reported so far, either for the monomer or for KC. The asymmetrical internal loop has been described from NMR studies of different monomeric hairpin sequences, leading to divergent results, which suggests its high flexibility. In this work, we built a SL1₃₅ KC model which was submitted to a 31 ns molecular dynamics simulation (MD).

Our results allows to describe the internal dynamics of SL1₃₅ KC and the differences of behavior of the different parts of the dimer. Thus, we could show the stability of the interactions between the two apical loops and of the terminal duplexes, the destabilization of the internal duplexes and the high flexibility of the asymmetrical internal loops.     

Molecular Dynamics and Free Energy Calculations of the B and Z Forms of C8-Arylguanine Modified Oligonucleotides

Abstract

Arylhydrazines found in the mushroom Agaricus bisporus have been shown to be carcinogenic. Upon metabolic activation, arylhydrazines are transformed into aryl radicals, forming 8-arylpurines, which may play a role in arylhydrazine carcinogenesis. These adducts are poorly read and inhibit chain extension but do alter the conformational preferences of oligonucleotides. We have shown that C8-phenylguanine modification of d(CGCGCG*CGCG) (G*= 8-phenylguanine) stabilizes it in the Z-DNA conformation (B/Z-DNA=1:1, 200 mM NaCl, pH 7.4). Here we have conducted molecular dynamics and free energy calculations to determine the sources(s) of these conformational affects and to predict the affect of the related C8- tolyl and C8-hydroxymethylphenyl guanine adducts on B/Z-DNA equilibrium. Force field parameters for the modified guanines were first developed using Guassian98 employing the B3LYP method and the standard 6–31G* basis set and fit to the Cornell 94 force field with RESP. Molecular dynamics simulations and free energy calculations, using the suite of programs contained in Amber 6 and 7 with the Cornell 94 force field, were used to determine the structural and thermodynamic properties of the DNA. The principal factors that drive conformation are stacking of the aryl group over the 5′-cytosine in the phenyl and tolyl modified oligonucleotides while hydrogen bonding opposes stacking in the hydroxymethylphenyl derivative. The phenyl and tolyl-modified DNA's favored the Z-DNA form as did the hydroxymethylphenyl derivative when hydrogen bonding was not present. The B-DNA conformation was preferred by the unmodified oligonucleotide and by the hydroxymethylphenyl-modified oligonucleotide when hydrogen bonding was considered. Z-DNA stability was not found to directly correlated with carcinogenicity and additional biological factors, such as recognition and repair, may also need to be considered in addition to Z-DNA formation.     

Molecular modeling of the three-dimensional structure of GLP-1R and its interactions with several agonists

Glucagon-like peptide-1 receptor (GLP-1R) is a promising molecular target for developing drugs treating type 2 diabetes. We have predicted the complete three-dimensional structure of GLP-1R and the binding modes of several GLP-1R agonists, including GLP-1, Boc5, and Cpd1, through a combination of homology modeling, molecular docking, and long-time molecular dynamics simulation on a lipid bilayer. Our model can reasonably interpret the results of a number of mutation experiments regarding GLP-1R as well as the successful modification to GLP-1 by Liraglutide. Our model is also validated by a recently revealed crystal structure of the extracellular domain of GLP-1R. An activation mechanism of GLP-1R agonists is proposed based on the principal component analysis and normal mode analysis on our predicted GLP-1R structure. Before the complete structure of GLP-1R is determined through experimental means, our model may serve as a valuable reference for characterizing the interactions between GLP-1R and its agonists. Figure Comparison of our predicted model of rGLP-1R (left) with the recently revealed crystal structure of hGLP-1R (right)     

A Molecular Dynamics Study of the Repressor/Operator(OR1,OR3) Complexes from Bacteriophage 434

We have performed three molecular dynamics simulations using the CHARMM molecular modeling program to study the repressor protein from bacteriophage 434 complexed with DNA operators of two different sequences. Two approaches to the modeling of the solvent were used. In the first method, applied to the R1-69/OR1 truncated complex, water molecules were included explicitly in conjunction with a stochastic boundary force to solvate the complex. In the second approach, used for simulations of the R1-69/OR1 and the R1-69/OR3 complexes, the solvent was omitted and implicitly represented by using a distance-dependent dielectric constant and a scaling of the charges on the exposed residues. The simulation with the model which explicitly includes the solvent serves as a validation of the simulations using a simpler solvent representation. In our discussion of the results we focus upon the important interactions between the DNA binding motif of the 434 repressor (motif helix turn helix) and the operators and how the structures of the complexes change with time.Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1007/s0089460020427     

Molecular Dynamics Simulation Studies of the Limiting Conductances of MgCl2 and CaCl2 in Supercritical Water Using SPC/E Model for Water

We report results of molecular dynamics (MD) simulations of the limiting conductances of MgCl² and CaCl² in supercritical water as a function of water density using the SPC/E model for water. The limiting conductances of Mg²⁺, Ca²⁺ and Cl^- over the whole range of water density considered exhibits a linear dependence of the limiting conductance on the water density. In the cases of Mg²⁺ and Ca²⁺, a solventberg picture for the behavior of small divalent cation emerges from our studies. From the view of the solventberg picture, the ion and its shell moving together as an entity interacts with the second hydration shell water molecules, and its mobility is restricted mostly by the number of the second hydration shell water which is proportional to the water density of the whole system. In the case of Cl^-, the range of water density considered in this study belongs to the higher-density region (above 0.45?g/cm³) in which the effect of the number of hydration water molecules around ions dominated. As the water density increases, the water molecules of the first hydration shell restrict the mobility of Cl^- and the limiting conductance of Cl^- decreases nearly linearly. Significant different dependence on the water density is observed between the calculated limiting conductances of MgCl² and CaCl² at 673?K and the experimental results over the water density of 0.60–0.90?g/cm³. Possible limitation of the extended simple point charge (SPC/E) model with regard to this difference should be pointed out and the use of a more precise model like the revised polarizable (RPOL) model is indispensable for a further MD study to gain a complete picture of the chemical circumstance around the ions.     

On the Approximation of Solvent Effects on the Conformation and Dynamics of Cyclosporin A by Stochastic Dynamics Simulation Techniques

Abstract

The molecular simulation technique of stochastic dynamics (SD) is tested by application to the immunosuppressive drug cyclosporin A (CPA). Two stochastic dynamics simulations are performed, one (SD_CCl4 ) with atomic friction coefficients proportional to the viscosity of the nonpolar solvent CCl₄, and one (SD_H2O) with atomic friction coefficients corresponding to an aqueous solution. The atomic friction coefficients are also taken proportional to an approximate expression for the atomic accessible surface area. The properties of both stochastic dynamics simulations are compared to those of two full molecular dynamics (MD) simulations of cyclosporin A, one in a box with 591 CCl₄ molecules, and one in a box with 632 H₂O molecules.

The properties of cyclosporin A as found in the molecular dynamics simulation in CCl₄ are well reproduced by the SD_CCl4 simulation. This indicates that the neglect of a mean force reresenting the average solvent effects on the solute is justified in the case of nonpolar solvents. For polar solvents, like water, this mean force may not be neglected. The SD_H2O simulation of cyclosporin A clearly fails to reproduce the amount of hydrogen bonding found in the molecular dynamics stimulation of cyclosporin A in water.

A comparison with a molecular dynamics simulation of cyclosporin A in vacuo shows that both the SD_CCl4 and the SD_H2O simulation come closer to the properties of the molecular dynamics simulations in CCl₄ and in H₂O than a molecular dynamics simulation in vacuo.     

Molecular Dynamics Simulation Studies of the Limiting Conductances of CaCl2 using Extended Simple Point Charge and Revised Polarizable Models

We have carried out molecular dynamics (MD) simulations of the limiting conductances of CaCl₂ in ambient and supercritical states as a function of water density using extended simple point charge (SPC/E) and revised polarizable (RPOL) models for ions and water molecules. Both models predict the limiting conductances of CaCl₂ in supercritical water that are a linear dependence on water density. The effect of the electronic polarization on the limiting conductances is too small to cause a deduction in the lower water density of 0.6?～?0.7?g/cc in this study. The most significant effect of the electronic polarization is appeared in a decrease in the ion–water potential energy and, as a result, an increase in the limiting conductances for both ions. Different charge distributions of water molecules in the first hydration shell around the ions lead the opposite behavior of the induced dipole moment with water density for a positive and a negative ion in supercritical water; the induced dipole moment of Ca²⁺ decreases with increasing water density but for Cl^-, the opposite is observed. The same kind of opposite behavior due to the structure of water molecules around the ions is also found in hydrogen-bond correlations of water around the ions and of bulk water; hydrogen bonding around Ca²⁺ persists longer than in bulk water whereas the opposite is observed for Cl^-.     

Identification of Four New Chemical Series of Small Drug-Like Natural Products as Potential Neuropilin-1 Inhibitors by Structure-Based Virtual Screening: Pharmacophore-Based Molecular Docking and Dynamics Simulation

Neuropilin-1 (NRP-1), a surface transmembrane glycoprotein, is one of the most important co-receptors of VEGF-A165 (vascular endothelial growth factor) responsible for pathological angiogenesis. In general, NRP-1 overexpression in cancer correlates with poor prognosis and more tumor aggressiveness. NRP-1 role in cancer has been mainly explained by mediating VEGF-A165-induced effects on tumor angiogenesis. NRP-1 was recently identified as a co-receptor and an independent gateway for SARS-CoV-2 through binding subunit S2 of Spike protein in the same way as VEGF-A165. Thus, NRP-1 is of particular value as a target for cancer therapy and other angiogenesis-dependent diseases as well as for SARS-CoV-2 antiviral intervention. Herein, The Super Natural II, the largest available database of natural products (∼0.33 M), pre-filtered with drug-likeness criteria (absorption, distribution, metabolism and excretion/toxicity), was screened against NRP-1. NRP-1/VEGF-A165 interaction is one of protein-protein interfaces (PPIs) known to be challenging when approached in-silico. Thus, a PPI-suited multi-step virtual screening protocol, incorporating a derived pharmacophore with molecular docking and followed by MD (molecular dynamics) simulation, was designed. Two stages of pharmacophorically constrained molecular docking (standard and extra precisions), a mixed Torsional/Low-mode conformational search and MM-GBSA ΔG binding affinities calculation, resulted in the selection of 100 hits. These 100 hits were subjected to 20 ns MD simulation, that was extended to 100 ns for top hits (20) and followed by post-dynamics analysis (atomic ligand-protein contacts, RMSD, RMSF, MM-GBSA ΔG, Rg, SASA and H-bonds). Post-MD analysis showed that 19 small drug-like nonpeptide natural molecules, grouped in four chemical scaffolds (purine, thiazole, tetrahydropyrimidine and dihydroxyphenyl), well verified the derived pharmacophore and formed stable and compact complexes with NRP-1. The discovered molecules are promising and can serve as a base for further development of new NRP-1 inhibitors.     

From Molecular to Process Simulation: Novel Approaches to the Prediction of Phase Equilibria and PVT Behavior Based on Molecular/Quantum Mechanics and Molecular Dynamics Simulations

Abstract

Actually, in modern process simulators, more than 75% of the code implemented is dedicated to physical properties estimation, calculation and predictions. Data banks storing pure component parameters and binary interaction parameters for phase equilibrium calculations are extensively used and continuously implemented in actual process simulators. This gives an idea of the important role physical properties availability plays in process simulation.

In this paper we propose a new way for coupling molecular and process simulation. The basic machinery is to resort to molecular/quantum mechanics and molecular dynamics simulation techniques for generating the parameters of some equations of state that will subsequently be used for the prediction of phase equilibria and PVT behavior of small and polymeric molecules as well. This information, in turn, will be used as input in the process simulator, thus creating a final and well-defined bridge between molecular and process simulations in chemical engineering.     

Molecular Dynamics Simulation in Solvent of the Estrogen Receptor Protein DNA Binding Domain in Complex with a Non-Consensus Estrogen Response Element DNA Sequence

Abstract

We investigated protein/DNA interactions, using molecular dynamics simulations computed between a 10 Angstom water layer model of the estrogen receptor (ER) protein DNA binding domain (DBD) amino acids and DNA of a non-consensus estrogen response element (ERE) consisting of 29 nucleotide base pairs. This ERE nucleotide sequence occurs naturally upstream of the Xenopus laevis Vitelligenin AI gene. The ER DBD is encoded by three exons. Namely, exons 2 and 3 which encode the two zinc binding motifs and a sequence of exon 4 which encodes a predicted alpha helix. We generated a computer model of the ER DBD using atomic coordinates derived from the average of 30 nuclear magnetic resonance (NMR) spectroscopy coordinate sets. Amino acids on the carboxyl end of the ER DBD were disordered in both X-ray crystallography and NMR determinations and no coordinates were reported. This disordered region includes 10 amino acids of a predicted alpha helix encoded in exon 4 at the exon 3/4 splice junction. These amino acids are known to be important in DNA binding and are also believed to function as a nuclear translocation signal sequence for the ER protein. We generated a computer model of the predicted alpha helix consisting of the 10 amino acids encoded in exon 4 and attached this helix to the carboxyl end of the ER DBD at the exon 3/4 splice junction site. We docked the ER DBD model within the DNA major groove halfsites of the 29 base pair non-consensus ERE and flanking nucleotides. We constructed a solvated model with the ER DBD/ERE complex surrounded by a ten Angstrom water layer and conducted molecular dynamics simulations. Hydrogen bonding interactions were monitored. In addition, van der Waals and electrostatic interaction energies were calculated. Amino acids of the ER DBD DNA recognition helix formed both direct and water mediated hydrogen bonds at cognate codon-anticodon nucleotide base and backbone sites within the ERE DNA right major groove halfsite. Amino acids of the ER DBD exon 4 encoded predicted alpha helix formed direct and water mediated H-bonds with base and backbone sites of their cognate codon-anticodon nucleotides within the minor grooves flanking the ERE DNA major groove halfsites. These interactions together induced bending of the DNA into the protein.     

Disruption Mechanism in the Helix of SPF Peptide by Interchanging E5 and K10 Residues: Inference from Molecular Dynamics Study

Abstract

Seminalplasmin (SPLN) is a 47-residue peptide (SDEKASPDKHHRFSLSRYAKLANR LANPKLLETFLSKWIGDRGNRSV) from bovine seminal plasma. It has broad spectrum antimicrobial activity, without any hemolytic activity. The 28–40 segment of SPLN with the sequence PKLLETFLSKWIG, designated as SPF, is the most hydrophobic stretch of SPLN and primarily responsible for the membrane-perturbing activity of SPLN. It was reported that SPF has a helical structure and the interchange of E5 and K10 residues disrupted the helical structure. The present paper reports a possible mechanism of disruption of the helical structure of SPF peptide during the interchange of E5 and K10 residues. The result is based on simulated annealing and molecular dynamics simulation studies on SPF and its four analogues with K10E, K10D, E5K, and E5K & K10E substitutions. It showed that K10 residue has a critical role in maintaining the highest helical content and the positions of charged residues are also very important for maintaining the helical structure of the SPF peptide. Formation of some new long-range hydrogen bonds and the rupture of some shortrange hydrogen bonds involving the tenth residue led to the disruption of helical structure of SPF peptide when E5 and K10 residues are interchanged.     

The Implementation of the Iterative Diagonalization Scheme and ab initio Molecular Dynamics Simulation with the LAPW Method

Abstract

A new ab initio molecular dynamics method based on the full-potential linearized-augmented-plane-wave (LAPW) basis set has been implemented. The LAPW basis set has been successfully employed for systems containing localized electrons such as first row atoms and transition metals. In our implementation of the LAPW-MD scheme, iterative residual minimization algorithm is used to solve the electronic states problem. The atoms are moved according to forces derived from the Hellman–Feynman theorem and incomplete basis set correction terms. The performance of the program is further enhanced by parallelization. We will discuss technical details of the program implementation and present results obtained from this code to the equilibrium structures and vibrational properties of simple diatomic molecules.     

On the Permeation by Dioxygen of the Cofactor‐Independent Unusual Oxygenase RhCC,in Complex with Substrate 4‐Hydroxyphenylenolpyruvate. A Molecular Dynamics Investigation

This work deals with a trimeric bacterial protein, RhCC, which, although belonging to the tautomerase superfamily, shows oxygenase activity. A model of the complex from RhCC and substrate 4‐hydroxyphenylenolpyruvate (4HPP), fitting the observation of extra electron densities from X‐ray diffraction of the crystal, could be built by autodocking. When subjected to molecular dynamics (MD) aided by an external random force applied to a O₂ molecule placed above 4HPP, this model evolved with O₂ egressing toward the bulk solvent from two nearly opposite gates. These were located between the nearly parallel helices 75 – 91 and 15 – 33 of either chain C (gate SE) or chain B (gate FL). Alternatively, with four O₂ molecules in the bulk solvent, unbiased MD led to O₂ entering the protein from gate SE and getting to 4HPP, while forming a stabilizing salt bridge between the 4HPP carboxylate and P1.C ⁺NH₂, thus providing scientific ground for a refined model of the complex.     

Molecular Dynamics Simulations on Pars Intercerebralis Major Peptide-C (PMP-C) Reveal the Role of Glycosylation and Disulfide Bonds in its Enhanced Structural Stability and Function

Abstract

Fucosylation of Thr 9 in pars intercerebralis major peptide-C (PMP-C) enhances its structural stability and functional ability as a serine protease inhibitor. In order to understand the role of disulfide bonds and glycosylation on the structure and function of PMP-C, we have carried out multiple explicit solvent molecular dynamics (MD) simulations on fucosylated and non-fucosylated forms of PMP-C, both in the presence and absence of the disulfide bonds. Our simulations revealed that there were no significant structural changes in the native disulfide bonded forms of PMP-C due to fucosylation. On the other hand, the non-fucosylated form of PMP-C without disulfide bonds showed larger deviations from the starting structure than the fucosylated form. However, the structural deviations were restricted to the terminal regions while core β-sheet retained its hydrogen bonded structure even in absence of disulfide bonds as well as fucosylation. Interestingly, fucosylation of disulfide bonded native PMP-C led to a decreased thermal flexibility in the residue stretch 29–32 which is known to interact with the active site of the target proteases. Our analysis revealed that disulfide bonds covalently connect the residue stretch 29–32 to the central β-sheet of PMP-C and using a novel network of side chain interactions and disulfide bonds fucosylation at Thr 9 is altering the flexibility of the stretch 29–32 located at a distal site. Thus, our simulations explain for the first time, how presence of disulfide bonds between conserved cysteines and fucosylation enhance the function of PMP-C as a protease inhibitor.     

On the Permeation by Dioxygen of Urate Oxidase from Aspergillus flavus in Complex with Xanthine Anion: Dioxygen Pathways and a Portrait of the Enzyme Cavities from Molecular Dynamics Simulations in Water Solution

This work describes molecular dynamics (MD) simulations in aqueous media for the complex of the homotetrameric urate oxidase (UOX) from Aspergillus flavus with xanthine anion ( 5 ) in the presence of dioxygen (O₂). After 196.6 ns of trajectory from unrestrained MD, a O₂ molecule was observed leaving the bulk solvent to penetrate the enzyme between two subunits, A/C. From here, the same O₂ molecule was observed migrating, across subunit C, to the hydrophobic cavity that shares residue V227 with the active site. The latter was finally attained, after 378.3 ns of trajectory, with O₂ at a bonding distance from 5 . The reverse same O₂ pathway, from 5 to the bulk solvent, was observed as preferred pathway under random acceleration MD (RAMD), where an external, randomly oriented force was acting on O₂. Both MD and RAMD simulations revealed several cavities populated by O₂ during its migration from the bulk solvent to the active site or backwards. Paying attention to the last hydrophobic cavity that apparently serves as O₂ reservoir for the active site, it was noticed that its volume undergoes ample fluctuations during the MD simulation, as expected from the thermal motion of a flexible protein, independently from the particular subunit and no matter whether the cavity is filled or not by O₂.     

Molecular dynamics studies on HIV-1 protease: a comparison of the flap motions between wild type protease and the M46I/G51D double mutant

The emergence of drug-resistant mutants of HIV-1 is a tragic effect associated with conventional long-treatment therapies against acquired immunodeficiency syndrome. These mutations frequently involve the aspartic protease encoded by the virus; knowledge of the molecular mechanisms underlying the conformational changes of HIV-1 protease mutants may be useful in developing more effective and longer lasting treatment regimes. The flap regions of the protease are the target of a particular type of mutations occurring far from the active site. These mutations modify the affinity for both substrate and ligands, thus conferring resistance. In this work, molecular dynamics simulations were performed on a native wild type HIV-1 protease and on the drug-resistant M46I/G51D double mutant. The simulation was carried out for a time of 3.5 ns using the GROMOS96 force field, with implementation of the SPC216 explicit solvation model. The results show that the flaps may exist in an ensemble of conformations between a “closed” and an “open” conformation. The behaviour of the flap tips during simulations is different between the native enzyme and the mutant. The mutation pattern leads to stabilization of the flaps in a semi-open configuration.     

A QM/MM study of the complexes formed by aluminum and iron with serum transferrin at neutral and acidic pH

Serum transferrin (sTf) transports iron in serum and internalizes in cells via receptor mediated endocytosis. Additionally, sTf has been identified as the predominant aluminum carrier in serum. Some questions remain unclear about the exact mechanism for the metal release or whether the aluminum and iron show the same binding mode during the entire process. In the present work, simulation techniques at quantum and atomic levels have been employed in order to gain access into a molecular level understanding of the metal-bound sTf complex, and to describe the binding of Al(III) and Fe(III) ions to sTf. First, hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations were carried out in order to analyze the dynamics of the aluminum-loaded complex, taking into account the different pH conditions in blood and into the cell. Moreover, the complexes formed by transferrin with Al(III) and Fe(III) were optimized with high level density functional theory (DFT)/MM methods. All these results indicate that the interaction mode of Al(III) and Fe(III) with sTf change upon different pH conditions, and that the coordination of Al(III) and Fe(III) is not equivalent during the metal intake, transport and release processes. Our results emphasize the importance of the pH on the metal binding and release mechanism and suggest that Al(III) can follow the iron pathway to get access into cells, although once there, it may show a different binding mode, leading to a different mechanism for its release.     

Identification of Distinct Conformations of the Angiotensin-II Type 1 Receptor Associated with the Gq/11 Protein Pathway and the β-Arrestin Pathway Using Molecular Dynamics Simulations

Biased signaling represents the ability of G protein-coupled receptors to engage distinct pathways with various efficacies depending on the ligand used or on mutations in the receptor. The angiotensin-II type 1 (AT₁) receptor, a prototypical class A G protein-coupled receptor, can activate various effectors upon stimulation with the endogenous ligand angiotensin-II (AngII), including the G_q/11 protein and β-arrestins. It is believed that the activation of those two pathways can be associated with distinct conformations of the AT₁ receptor. To verify this hypothesis, microseconds of molecular dynamics simulations were computed to explore the conformational landscape sampled by the WT-AT₁ receptor, the N111G-AT₁ receptor (constitutively active and biased for the G_q/11 pathway), and the D74N-AT₁ receptor (biased for the β-arrestin1 and -2 pathways) in their apo-forms and in complex with AngII. The molecular dynamics simulations of the AngII-WT-AT₁, N111G-AT₁, and AngII-N111G-AT₁ receptors revealed specific structural rearrangements compared with the initial and ground state of the receptor. Simulations of the D74N-AT₁ receptor revealed that the mutation stabilizes the receptor in the initial ground state. The presence of AngII further stabilized the ground state of the D74N-AT₁ receptor. The biased agonist [Sar¹,Ile⁸]AngII also showed a preference for the ground state of the WT-AT₁ receptor compared with AngII. These results suggest that activation of the G_q/11 pathway is associated with a specific conformational transition stabilized by the agonist, whereas the activation of the β-arrestin pathway is linked to the stabilization of the ground state of the receptor.     

Insights Into the Enzymatic Mechanism of 6-Phosphogluconolactonase from Trypanosoma brucei Using Structural Data and Molecular Dynamics Simulation

Trypanosoma brucei is the causative agent of African sleeping sickness. Current work for the development of new drugs against this pathology includes evaluation of enzymes of the pentose phosphate pathway (PPP), which first requires a clear understanding of their function and mechanism of action. In this context, we focused on T. brucei 6-phosphogluconolactonase (Tb6PGL), which converts δ-6-phosphogluconolactone into 6-phosphogluconic acid in the second step of the PPP. We have determined the crystal structure of Tb6PGL in complex with two ligands, 6-phosphogluconic acid and citrate, at 2.2 Å and 2.0 Å resolution, respectively. We have performed molecular dynamics (MD) simulations on Tb6PGL in its empty form and in complex with δ-6-phosphogluconolactone, its natural ligand. Analysis of the structural data and MD simulations allowed us to propose a detailed enzymatic mechanism for 6PGL enzymes.     

PASylation Enhances the Stability,Potency, and Plasma Half‐Life of Interferon α‐2a: A Molecular Dynamics Simulation

In this study, the effectiveness of PASylation in enhancing the potency and plasma half‐life of pharmaceutical proteins has been accredited as an alternative technique to the conventional methods such as PEGylation. Proline, alanine, and serine (PAS) chain has shown some advantages including biodegradability improvement and plasma half‐life enhancement while lacking immunogenicity or toxicity. Although some experimental studies have been performed to find the mechanism behind PASylation, the detailed mechanism of PAS effects on the pharmaceutical proteins has remained obscure, especially at the molecular level. In this study, the interaction of interferon α‐2a (IFN) and PAS chain is investigated using molecular dynamics simulation method. Several important parameters including secondary structure, root‐mean‐square distance, and solvent accessible surface area to investigate the stability, bioavailability, and bioactivity of the PASylated protein are studied. The results demonstrate that IFN conformation is not affected critically through PASylation while it results in improvement of the protein stability and bioactivity. Therefore, PASylation can be considered as a proper biological alternative technique to increase the plasma half‐life of the biopharmaceutical proteins through enlarging apparent volume. The proposed simulation represents a computational approach that would provide a basis for the study of PASylated pharmaceutical proteins for different future applications.