Force field parameters for S-nitrosocysteine and molecular dynamics simulations of S-nitrosated thioredoxin

Estimation of structural perturbation induced by S-nitrosation is important to understand the mode of cellular signal transduction mediated by nitric oxide. Crystal structures of S-nitrosated proteins have been solved only for a few cases, however, so that molecular dynamics simulation may provide an alternative tool for probing structural perturbation. In this study AMBER-99 force field parameters for S-nitrosocysteine were developed and applied to molecular dynamics simulations of S-nitrosated thioredoxin. Geometry optimization at the level of HF/6-31G∗ was followed by a restrained electrostatic potential charge-fitting to obtain the atomic charges of S-nitrosocysteine. Force constants for bonds and angles were obtained from generalized AMBER force field. Torsional force constants for CC-SN and CS-NO were determined by fitting the torsional profiles obtained from geometry optimization with those from molecular mechanical energy minimization. Finally molecular dynamics simulations were performed with theses parameters on oxidized and reduced thioredoxin with and without S-nitrosocysteine. In all cases the root-mean-square deviations of α-carbons yielded well-behaved trajectories. The CC-SH dihedral angle which fluctuated severely during the simulation became quiet upon S-nitrosation. In conclusion the force field parameters developed in this study for S-nitrosocysteine appear to be suitable for molecular dynamics simulations of S-nitrosated proteins.     

The role of thioredoxin in the regulation of cellular processes by S-nitrosylation

Background

S-nitrosylation (or S-nitrosation) by Nitric Oxide (NO), i.e., the covalent attachment of a NO group to a cysteine thiol and formation of S-nitrosothiols (R-S-N=O or RSNO), has emerged as an important feature of NO biology and pathobiology. Many NO-related biological functions have been directly associated with the S-nitrosothiols and a considerable number of S-nitrosylated proteins have been identified which can positively or negatively regulate various cellular processes including signaling and metabolic pathways.

Scope of the review

Taking account of the recent progress in the field of research, this review focuses on the regulation of cellular processes by S-nitrosylation and Trx-mediated cellular homeostasis of S-nitrosothiols.

Major conclusions

Thioredoxin (Trx) system in mammalian cells utilizes thiol and selenol groups to maintain a reducing intracellular environment to combat oxidative/nitrosative stress. Reduced glutathione (GSH) and Trx system perform the major role in denitrosylation of S-nitrosylated proteins. However, under certain conditions, oxidized form of mammalian Trx can be S-nitrosylated and then it can trans-S-nitrosylate target proteins, such as caspase 3.

General significance

Investigations on the role of thioredoxin system in relation to biologically relevant RSNOs, their functions, and the mechanisms of S-denitrosylation facilitate the development of drugs and therapies. This article is part of a Special Issue entitled Regulation of Cellular Processes.     

Molecular and enzymatic characterisation of Schistosoma mansoni thioredoxin

Defense against oxidative damage can be mediated through glutathione and/or thioredoxin utilising systems. Here, we report the identification and characterisation of a thioredoxin from Schistosoma mansoni. The predicted protein has similarity to previously characterised thioredoxins including conservation of the redox active site. Recombinant six-histidine tagged schistosome thioredoxin had insulin reduction activity and supported the enzymatic function of thioredoxin reductase and thioredoxin peroxidase. By Western blotting, all mammalian stages of the schistosome lifecycle expresses thioredoxin. Thioredoxin is present in egg secretory products and antibodies against the recombinant protein produce the circumoval precipitin reaction. This is the first identification of defined antigen producing this reaction. Furthermore, thioredoxin is a novel egg immunogen as it elicits an antibody response in schistosome-infected mice. The most significant IgG production against thioredoxin occurs after parasite oviposition commences. These observations suggest that thioredoxin participates in processes vital to the parasite and may facilitate the passage and survival of eggs across inflamed host tissues.     

Molecular dynamics simulations of membrane proteins

Membrane proteins control the traffic across cell membranes and thereby play an essential role in cell function from transport of various solutes to immune response via molecular recognition. Because it is very difficult to determine the structures of membrane proteins experimentally, computational methods have been increasingly used to study their structure and function. Here we focus on two classes of membrane proteins—ion channels and transporters—which are responsible for the generation of action potentials in nerves, muscles, and other excitable cells. We describe how computational methods have been used to construct models for these proteins and to study the transport mechanism. The main computational tool is the molecular dynamics (MD) simulation, which can be used for everything from refinement of protein structures to free energy calculations of transport processes. We illustrate with specific examples from gramicidin and potassium channels and aspartate transporters how the function of these membrane proteins can be investigated using MD simulations.     

Molecular expression and enzymatic characterization of thioredoxin from the carcinogenic human liver fluke Opisthorchis viverrini

The human liver fluke, Opisthorchis viverrini, induces inflammation of the hepatobiliary system. Despite being constantly exposed to inimical oxygen radicals released from inflammatory cells, the parasite survives for years. Defense against oxidative damage can be mediated through glutathione and/or thioredoxin utilizing systems. Here, we report the molecular expression and biochemical characterization of a thioredoxin (Trx) from O. viverrini. O. viverrini Trx cDNA encoded a polypeptide of 105 amino acid residues, of molecular mass 11.63 kDa. The predicted protein has similarity to previously characterized thioredoxins with 26-51% identity. Recombinant O. viverrini Trx (Ov-Trx-1) was expressed as soluble protein in E. coli. The recombinant protein showed insulin reduction activity and supported the enzymatic function of O. viverrini thioredoxin peroxidase. Expression of Ov-Trx-1 at mRNA and protein levels was observed in all obtainable developmental stages of the liver fluke. Ov-Trx-1 was also detected in excretory-secretory products released by adult O. viverrini. Immunohistochemistry, Ov-Trx-1 was expressed in nearly all parasite tissue excepted ovary and mature sperms. Interestingly, Ov-Trx-1 was observed in the infected biliary epithelium but not in normal bile ducts. These results suggest that Ov-Trx-1 is essential for the parasite throughout the life cycle. In the host-parasite interaction aspect, Ov-Trx-1 may support thioredoxin peroxidase in protecting the parasite against damage induced by reactive oxygen species from inflammation.     

Molecular dynamics simulations of polyampholytes inside a slit

Alternating and diblock polyampholytes confined in a slit with and without an electric field have been simulated by the molecular dynamics method with a Langevin thermostat. It is shown that the slit has a strong effect on the properties of the polyampholyte. The effect is stronger when the electric field is weak, or the temperature is not too high. When a polyampholyte chain moves close to the slit wall, its radius of gyration perpendicular to the wall becomes smaller but that parallel to the wall becomes larger. Owing to the confinement of the slit, the polyampholyte chain closer to the slit wall tends to lie on the wall and becomes more flat. The width of the slit has only a little influence on the properties of solutions near the slit wall, values of several physical statistics are very close with different widths. However, when the electric field strength is strong enough in a narrow slit, the obtained properties obviously differ.     

Molecular dynamics simulations of ion distribution in nanochannels

Molecular dynamics simulations of ion distribution in a nanochannel were performed using a three region simulation domain including two bulk regions on each side of the nanochannel. This scheme allows the study of ion concentration and distribution inside the nanochannel under a given bulk electrolyte concentration, i.e. when the molecular system reaches equilibrium, the concentrations of the counter- and co-ions inside the nanochannel corresponding to a bulk electrolyte will emerge naturally. Our approach is in sharp contrast to the common practice in modeling electric double layers where the number of ions in the nanochannel is assigned somewhat arbitrarily, corresponding to an unknown bulk concentration.     

Molecular dynamics simulations of human DNA methyltransferase 3B with selective inhibitor nanaomycin A

DNA methyltransferases (DNMTs) are involved in epigenetic regulation of the genome and are promising targets for therapeutic intervention in cancer and other diseases. Until now, very limited information is available concerning the molecular dynamics of DNMTs. The natural product nanaomycin A is the first selective inhibitor of DNMT3B that induce genomic demethylation. Herein we report long (>100 ns) molecular dynamics simulations for human DNMT3B bound to nanaomycin A with and without the presence of the cofactor S-adenosyl-l-methionine (SAM). We concluded that SAM favors the binding of nanaomycin A to DNMT3B. Key interactions of nanaomycin A with DNMT3B involve long lasting interactions with Arg731, Arg733, Arg832, and the catalytic Cys651. Results further support the previous hypothesis that nanaomycin A has key interactions with amino acid residues involved in the mechanism of methylation. This work represents one of the first molecular dynamics studies of DNMT3B. Results of this work shed light on the structure and binding recognition process of a key epigenetic enzyme with a small molecule inhibitor.     

Molecular dynamics simulations on HIV-1 Tat

Molecular dynamics simulations are used to investigate dynamics and intramolecular interactions of the HIV-1 transactivator (Tat) in aqueous solution. The calculations are based on the AMBER force field with particle mesh Ewald treatment for long-range electrostatics. The Tat structure exhibits a large flexibility, consistent with its absence of secondary structure elements. From an analysis of the correlation matrix and of electrostatic interactions we suggest that segments expressed by the two exons (amino acids 1-72 and 73-86, respectively) exhibit rather separated dynamic and energetic properties. We also identify intramolecular interactions of importance for structure stabilization. In particular, significant electrostatic interactions are recognized between the N-terminus and the basic domain of the protein, consistent with site-directed mutagenesis performed in this work.     

Evidence for a subgroup of thioredoxin h that requires GSH/Grx for its reduction

Poplar thioredoxin h4 (popTrxh4) and a related CXXS type (popCXXS3) are both members of a plant thioredoxin h subgroup. PopTrxh4 exhibits the usual catalytic site WCGPC, whereas popCXXS3 harbors the non-typical active site WCMPS. Recombinant popTrxh4 and popCXXS3 are not reduced either by Arabidopsis thaliana NADPH-dependent thioredoxin reductases (NTR) A and B or by Escherichia coli NTR. We report here evidence that a poplar glutaredoxin as well as three E. coli Grxs are able to reduce popTrxh4. PopTrxh4 is able to reduce several thioredoxin targets as peroxiredoxins or methionine sulfoxide reductases. On the other hand, popCXXS3 exhibits an activity in the presence of glutathione and hydroxyethyldisulfide. Except for examples of glutathiolation, these are the first two examples of a direct interconnection between the thioredoxin and glutathione/glutaredoxin systems.     

Structure of thioredoxin from Trypanosoma brucei brucei

The three-dimensional structure of thioredoxin from Trypanosoma brucei brucei has been determined at 1.4 A resolution. The overall structure is more similar to that of human thioredoxin than to any other thioredoxin structure. The most striking difference to other thioredoxins is the absence of a buried carboxylate behind the active site cysteines. Instead of the common Asp, there is a Trp that binds an ordered water molecule probably involved in the protonation/deprotonation of the more buried cysteine during catalysis. The conserved Trp in the WCGPC sequence motif has an exposed position that can interact with target proteins.     

Molecular dynamics simulations of noble gases encapsulated in C60 Fullerene

Molecular dynamics simulations of Helium (He), Neon (Ne), Argon (Ar), Krpton (Kr) and Xenon (Xe) encapsulated in C₆₀ are discussed, as well simulations of Fullerenes containing anywhere from two to four He atoms. Even for single atom encapsulates, no species resides at the geometric center of the Fullerene cage. Smaller atoms sit more off-center than larger ones, and He appears to be a special case in both centering and dynamics. Some encapsulated species stabilize the cage by stifling radial fluctuations and others disrupt it; adding Ne seems to have the most stabilizing effect, while Kr and Xe cause the largest radial atomic excursions. Multiple He encapsulates tend to stabilize the cage; such systems are very stressed and show structure over a wide temperature range. Based on dynamical information quadruple He seems to be close to the packing limit for C₆₀.     

Molecular dynamics simulations of local anesthetic articaine in a lipid bilayer

In order to investigate structural and dynamical properties of local anesthetic articaine in a model lipid bilayer, a series of molecular dynamics simulations have been performed. Simulations were carried out for neutral and charged (protonated) forms of articaine inserted in fully hydrated dimyristoylphosphatidylcholine (DMPC) lipid bilayer. For comparison purpose, a fully hydrated DMPC bilayer without articaine was also simulated. The length of each simulation was 200 ns. Various properties of the lipid bilayer systems in the presence of both charged and uncharged forms of articaine taken at two different concentrations have been examined: membrane area per lipid, mass density distributions, order parameters, radial distribution functions, head group tilt, diffusion coefficients, electrostatic potential, etc, and compared with results of previous simulations of DMPC bilayer in the presence of lidocaine. It was shown that addition of both charged and neutral forms of articaine causes increase of the dipole electrostatic potential in the membrane interior.     

Characterization of mitochondrial thioredoxin reductase from C. elegans

Thioredoxin reductase catalyzes the NADPH-dependent reduction of the catalytic disulfide bond of thioredoxin. In mammals and other higher eukaryotes, thioredoxin reductases contain the rare amino acid selenocysteine at the active site. The mitochondrial enzyme from Caenorhabditis elegans, however, contains a cysteine residue in place of selenocysteine. The mitochondrial C. elegans thioredoxin reductase was cloned from an expressed sequence tag and then produced in Escherichia coli as an intein-fusion protein. The purified recombinant enzyme has a kcat of 610 min(-1) and a Km of 610 microM using E. coli thioredoxin as substrate. The reported kcat is 25% of the kcat of the mammalian enzyme and is 43-fold higher than a cysteine mutant of mammalian thioredoxin reductase. The enzyme would reduce selenocysteine, but not hydrogen peroxide or insulin. The flanking glycine residues of the GCCG motif were mutated to serine. The mutants improved substrate binding, but decreased the catalytic rate.     

Molecular dynamics simulations of phenylimidazole inhibitor complexes of cytochrome P450 cam

Molecular dynamics simulations have been performed on three phenylimidazole inhibitor complexes ofP450 _cam, utilizing the X-ray structures and the AMBER suite of programs. Compared to their corresponding optimized X-ray structures, very similar features were observed for the 1-phenylimidazole (1-PI) and 2-phenylimidazole (2-PI) complexes during a 100 ps MD simulation. The 1-PI inhibitor binds as a Type II complex with the imidazole nitrogen as a ligand of the heme iron. Analysis of the inhibitor-enzyme interctions during the MD simulations reveals that electrostatic interactions of the imidazole with the heme and van der Waals interactions of the phenyl ring with nearby hydrophobic residues are dominant. By contrast, 2-PI binds as a Type I inhibitor in the substrate binding pocket, but not as a ligand of the iron. The interactions of this inhibitor are qualitatively different from that of the Type II 1-PI, being mainly electrostatic/H-bonding interactions with a bound water and polar residues. Although the third compound, 4-PI, in common with 1-PI, also binds as a Type II inhibitor, with one nitrogen of the imidazole as a ligand to the iron, the MD average binding orientation deviates significantly from the X-ray structure. The most important changes observed include: (1) the rotation of the imidazole ring of this inhibitor by about 90° to enhance electrostatic interactions of the imidazole NH group with the carbonyl group of LEU244, and (2) the rotation of the carbonyl group of ASP251 to form a H-bond with VAL254. An analysis of the H-bonding network surrounding this substrate in the optimized crystal structure revealed that there is no H-bonding partner either for the free polar NH group in the imidazole ring of 4-phenylimidazole or for the polar carbonyl group of the nearby ASP251 residue. The deviation of the dynamically averaged inhibitor-enzyme structure of the 4-PI complex from the optimized crystal structure can therefore be rationalized as a consequence of the optimization of the electrostatic interactions among the polar groups.     

Molecular dynamics simulations of a fibrillogenic peptide derived from apolipoprotein C-II

The pathway to amyloid fibril formation in proteins involves specific structural changes leading to the combination of misfolded intermediates into oligomeric assemblies. Recent NMR studies showed the presence of “turns” in amyloid peptides, indicating that turn formation may play an important role in the nucleation of the intramolecular folding and possible assembly of amyloid. Fully solvated all-atom molecular dynamics simulations were used to study the structure and dynamics of the apolipoprotein C-II peptide 56 to 76, associated with the formation of amyloid fibrils. The peptide populated an ensemble of turn structures, stabilized by hydrogen bonds and hydrophobic interactions enabling the formation of a strong hydrophobic core which may provide the conditions required to initiate aggregation. Two competing mechanisms discussed in the literature were observed. This has implications in understanding the mechanism of amyloid formation in not only apoC-II and its fragments, but also in other amyloidogenic peptides.     

Reactive nitrogen species derived activation of rat liver microsomal glutathione S-transferase

The effect of reactive nitrogen species on rat liver microsomal glutathione S-transferase (MGST1) was investigated using microsomes and purified MGST1. When microsomes or the purified enzyme were incubated with peroxynitrite (ONOO(-)), the GST activity was increased to 2.5-6.5 fold in concentration-dependent manner and a small amount of the MGST1 dimer was detected. MGST1 activity was increased by ONOO(-) in the presence of high amounts of reducing agents including glutathione (GSH) and the activities increased by ONOO(-) or ONOO(-) plus GSH treatment were decreased by 30-40% by further incubation with dithiothreitol (DTT, reducing disulfide) or by sodium arsenite (reducing sulfenic acid). Furthermore, GSH was detected by HPLC from the MGST1 which was incubated with ONOO(-) plus GSH or S-nitrosoglutathione followed by DTT treatment. In addition, the MGST1 activity increased by nitric oxide (NO) donors such as S-nitrosoglutathione, S-nitrosocysteine or the non-thiol NO donor 1-hydroxy-2-oxo-3 (3-aminopropyl)-3-isopropyl was restored by the DTT treatment. Since DTT can reduce S-nitrosothiol and disulfide bond to thiol, S-nitrosylation and a mixed disulfide bond formation of MGST1 were suggested. Thus, it was demonstrated that MGST1 is activated by reactive nitrogen species through a forming dimeric protein, mixed disulfide bond, nitrosylation and sulfenic acid.     

Molecular dynamics simulations of palmitate entry into the hydrophobic pocket of the fatty acid binding protein

The entry of substrate into the active site is the first event in any enzymatic reaction. However, due to the short time interval between the encounter and the formation of the stable complex, the detailed steps are experimentally unobserved. In the present study, we report a molecular dynamics simulation of the encounter between palmitate molecule and the Toad Liver fatty acid binding protein, ending with the formation of a stable complex resemblance in structure of other proteins of this family. The forces operating on the system leading to the formation of the tight complex are discussed.     

Molecular dynamics simulations on hydrogen adsorption in finite single walled carbon nanotube bundles

Molecular dynamics simulations of the adsorption of hydrogen molecules in finite single-walled carbon nanotube bundles are presented using a curvature dependent force field. The heat of formation and the effective adsorption capacity are expressed as a function of H₂ distance from adsorbent. The heat of adsorption decreases rapidly with the distance and increasing H₂ loading results in weakening adsorption strength. The effects of nanotube packing and bundle thickness on hydrogen adsorption strength were investigated and the results show that the heat of adsorption can be improved slightly if hydrogen molecules are placed in thicker and inhomogeneously packed nanotube bundles. Only very small diameter nanotube bundles were found to hold promise for significant hydrogen storage for onboard applications.