Role of Specific Cations and Water Entropy on the Stability of Branched DNA Motif Structures

DNA three-way junctions (TWJs) are important intermediates in various cellular processes and are the simplest of a family of branched nucleic acids being considered as scaffolds for biomolecular nanotechnology. Branched nucleic acids are stabilized by divalent cations such as Mg2+, presumably due to condensation and neutralization of the negatively charged DNA backbone. However, electrostatic screening effects point to more complex solvation dynamics and a large role of interfacial waters in thermodynamic stability. Here, we report extensive computer simulations in explicit water and salt on a model TWJ and use free energy calculations to quantify the role of ionic character and strength on stability. We find that enthalpic stabilization of the first and second hydration shells by Mg2+ accounts for 1/3 and all of the free energy gain in 50% and pure MgCl2 solutions, respectively. The more distorted DNA molecule is actually destabilized in pure MgCl2 compared to pure NaCl. Notably, the first shell, interfacial waters have very low translational and rotational entropy (i.e., mobility) compared to the bulk, an entropic loss that is overcompensated by increased enthalpy from additional electrostatic interactions with Mg2+. In contrast, the second hydration shell has anomalously high entropy as it is trapped between an immobile and bulklike layer. The nonmonotonic entropic signature and long-range perturbations of the hydration shells to Mg2+ may have implications in the molecular recognition of these motifs. For example, we find that low salt stabilizes the parallel configuration of the three-way junction, whereas at normal salt we find antiparallel configurations deduced from the NMR. We use the 2PT analysis to follow the thermodynamics of this transition and find that the free energy barrier is dominated by entropic effects that result from the decreased surface area of the antiparallel form which has a smaller number of low entropy waters in the first monolayer.

Ca2+ Binding to the ExDxD Motif Regulates the DNA Cleavage Specificity of a Promiscuous Endonuclease

Most of the restriction endonucleases (REases) are dependent on Mg2+ for DNA cleavage, and in general, Ca2+ inhibits their activity. RKpnI, an HNH active site containing beta beta alpha-Me finger nuclease, is an exception. In presence of Ca2+, the enzyme exhibits high-fidelity DNA cleavage and complete suppression of Mg2+-induced promiscuous activity. To elucidate the mechanism of unusual Ca2+-mediated activity, we generated alanine variants in the putative Ca-2+ binding motif, E(132)xD(134)xD(136), of the enzyme. Mutants showed decreased levels of DNA cleavage in the presence of Ca2+. We demonstrate that ExDxD residues are involved in Ca2+ coordination; however, the invariant His of the catalytic HNH motif acts as a general base for nucleophile activation, and the other two active site residues, D148 and Q175, also participate in Ca2+-mediated cleavage. Insertion of a 10-amino acid linker to disrupt the spatial organization of the ExDxD and HNH motifs impairs Ca2+ binding and affects DNA cleavage by the enzyme. Although ExDxD mutant enzymes retained efficient cleavage at the canonical sites in the presence of Mg2+, the promiscuous activity was greatly reduced, indicating that the carboxyl residues of the acidic triad play an important role in sequence recognition by the enzyme. Thus, the distinct Ca2+ binding motif that confers site specific cleavage upon Ca2+ binding is also critical for the promiscuous activity of the Mg2+-bound enzyme, revealing its role in metal ion-mediated modulation of DNA cleavage.

Cloning, expression, purification, and biochemical characterisation of the FIC motif containing protein of Mycobacterium tuberculosis

The role of FIC (Filamentation induced by cAMP)(2) domain containing proteins in the regulation of many vital pathways, mostly through the transfer of NMPs from NTPs to specific target proteins (NMPylation), in microorganisms, higher eukaryotes, and plants is emerging. The identity and function of FIC domain containing protein of the human pathogen, Mycobacterium tuberculosis, remains unknown. In this regard, M. tuberculosis fic gene (Mtfic) was cloned, overexpressed, and purified to homogeneity for its biochemical characterisation. It has the characteristic FIC motif, HPFREGNGRSTR (HPFxxGNGRxxR), spanning 144th to 155th residue. Neither the His-tagged nor the GST-tagged MtFic protein, overexpressed in Escherichia coil, nor expression of Mtfic in Mycobacterium smegmatis, yielded the protein in the soluble fraction. However, the maltose binding protein (MBP) tagged MtFic (MBP-MtFic) could be obtained partly in the soluble fraction. The cloned, overexpressed, and purified recombinant MBP-MtFic showed conversion of ATP, GTP, CTP, and UTP into AMP. GMP, CMP, and UMP, respectively. Sequence alignment with several FIC motif containing proteins, complemented with homology modeling on the FIC motif containing protein, VbhT of Bartonella schoenbuchensis as the template, showed conservation and interaction of residues constituting the FIC domain. Site-specific mutagenesis of the His144, or Glu148, or Asn150 of the FIC motif, or of Arg87 residue that constitutes the FIC domain, or complete deletion of the FIC motif, abolished the NTP to NMP conversion activity. The design of NMP formation assay using the recombinant, soluble MtFic would enable identification of its target substrate for NMPylation. (C) 2012 Elsevier Inc. All rights reserved.

A cyclic peptide mimic of an RNA recognition motif of human La protein is a potent inhibitor of hepatitis C virus

Due to limited available therapeutic options, developing new lead compounds against hepatitis C virus is an urgent need. Human La protein stimulates hepatitis C virus translation through interaction with the hepatitis C viral RNA. A cyclic peptide mimicking the beta-turn of the human La protein that interacts with the viral RNA was synthesized. It inhibits hepatitis C viral RNA translation significantly better than the corresponding linear peptide at longer post-treatment times. The cyclic peptide also inhibited replication as measured by replicon RNA levels using real time RT-PCR. The cyclic peptide emerges as a promising lead compound against hepatitis C.

Structural Integrity of the Greek Key Motif in beta gamma-Crystallins Is Vital for Central Eye Lens Transparency

Background: We highlight an unrecognized physiological role for the Greek key motif, an evolutionarily conserved super-secondary structural topology of the beta gamma-crystallins. These proteins constitute the bulk of the human eye lens, packed at very high concentrations in a compact, globular, short-range order, generating transparency. Congenital cataract (affecting 400,000 newborns yearly worldwide), associated with 54 mutations in beta gamma-crystallins, occurs in two major phenotypes nuclear cataract, which blocks the central visual axis, hampering the development of the growing eye and demanding earliest intervention, and the milder peripheral progressive cataract where surgery can wait. In order to understand this phenotypic dichotomy at the molecular level, we have studied the structural and aggregation features of representative mutations. Methods: Wild type and several representative mutant proteins were cloned, expressed and purified and their secondary and tertiary structural details, as well as structural stability, were compared in solution, using spectroscopy. Their tendencies to aggregate in vitro and in cellulo were also compared. In addition, we analyzed their structural differences by molecular modeling in silico. Results: Based on their properties, mutants are seen to fall into two classes. Mutants A36P, L45PL54P, R140X, and G165fs display lowered solubility and structural stability, expose several buried residues to the surface, aggregate in vitro and in cellulo, and disturb/distort the Greek key motif. And they are associated with nuclear cataract. In contrast, mutants P24T and R77S, associated with peripheral cataract, behave quite similar to the wild type molecule, and do not affect the Greek key topology. Conclusion: When a mutation distorts even one of the four Greek key motifs, the protein readily self-aggregates and precipitates, consistent with the phenotype of nuclear cataract, while mutations not affecting the motif display `native state aggregation', leading to peripheral cataract, thus offering a protein structural rationale for the cataract phenotypic dichotomy ``distort motif, lose central vision''.

Generalized model predictive static programming and its application to 3D impact angle constrained guidance of air-to-surface missiles

A new `generalized model predictive static programming (G-MPSP)' technique is presented in this paper in the continuous time framework for rapidly solving a class of finite-horizon nonlinear optimal control problems with hard terminal constraints. A key feature of the technique is backward propagation of a small-dimensional weight matrix dynamics, using which the control history gets updated. This feature, as well as the fact that it leads to a static optimization problem, are the reasons for its high computational efficiency. It has been shown that under Euler integration, it is equivalent to the existing model predictive static programming technique, which operates on a discrete-time approximation of the problem. Performance of the proposed technique is demonstrated by solving a challenging three-dimensional impact angle constrained missile guidance problem. The problem demands that the missile must meet constraints on both azimuth and elevation angles in addition to achieving near zero miss distance, while minimizing the lateral acceleration demand throughout its flight path. Both stationary and maneuvering ground targets are considered in the simulation studies. Effectiveness of the proposed guidance has been verified by considering first order autopilot lag as well as various target maneuvers.

Catalytic Reduction of Graphene Oxide Nanosheets by Glutathione Peroxidase Mimetics Reveals a New Structural Motif in Graphene Oxide

A catalytic reduction of graphene oxide (GO) by glutathione peroxidase (GPx) mimics is reported. This study reveals that GO contains peroxide functionalities, in addition to the epoxy, hydroxyl and carboxylic acid groups that have been identified earlier. It also is shown that GO acts as a peroxide substrate in the GPx-like catalytic activity of organoselenium/tellurium compounds. The reaction of tellurol, generated from the corresponding ditelluride, reduces GO through the glutathione (GSH)-mediated cleavage of the peroxide linkage. The mechanism of GO reduction by the tellurol in the presence of GSH involves the formation of a tellurenic acid and tellurenyl sulfide intermediates. Interestingly, the GPx mimics also catalyze the decarboxylation of the carboxylic acid functionality in GO at ambient conditions. Whereas the selenium/tellurium-mediated catalytic reduction/decarboxylation of GO may find applications in bioremediation processes, this study suggests that the modification of GO by biologically relevant compounds such as redox proteins must be taken into account when using GO for biomedical applications because such modifications can alter the fundamental properties of GO.

Robust Reentry Guidance of a Reusable Launch Vehicle Using Model Predictive Static Programming

A robust suboptimal reentry guidance scheme is presented for a reusable launch vehicle using the recently developed, computationally efficient model predictive static programming. The formulation uses the nonlinear vehicle dynamics with a spherical and rotating Earth, hard constraints for desired terminal conditions, and an innovative cost function having several components with associated weighting factors that can account for path and control constraints in a soft constraint manner, thereby leading to smooth solutions of the guidance parameters. The proposed guidance essentially shapes the trajectory of the vehicle by computing the necessary angle of attack and bank angle that the vehicle should execute. The path constraints are the structural load constraint, thermal load constraint, bounds on the angle of attack, and bounds on the bank angle. In addition, the terminal constraints include the three-dimensional position and velocity vector components at the end of the reentry. Whereas the angle-of-attack command is generated directly, the bank angle command is generated by first generating the required heading angle history and then using it in a dynamic inversion loop considering the heading angle dynamics. Such a two-loop synthesis of bank angle leads to better management of the vehicle trajectory and avoids mathematical complexity as well. Moreover, all bank angle maneuvers have been confined to the middle of the trajectory and the vehicle ends the reentry segment with near-zero bank angle, which is quite desirable. It has also been demonstrated that the proposed guidance has sufficient robustness for state perturbations as well as parametric uncertainties in the model.

Generalized State Estimation and Model Predictive Guidance for Spiraling and Ballistic Targets

An extended Kalman filter based generalized state estimation approach is presented in this paper for accurately estimating the states of incoming high-speed targets such as ballistic missiles. A key advantage of this nine-state problem formulation is that it is very much generic and can capture spiraling as well as pure ballistic motion of targets without any change of the target model and the tuning parameters. A new nonlinear model predictive zero-effort-miss based guidance algorithm is also presented in this paper, in which both the zero-effort-miss as well as the time-to-go are predicted more accurately by first propagating the nonlinear target model (with estimated states) and zero-effort interceptor model simultaneously. This information is then used for computing the necessary lateral acceleration. Extensive six-degrees-of-freedom simulation experiments, which include noisy seeker measurements, a nonlinear dynamic inversion based autopilot for the interceptor along with appropriate actuator and sensor models and magnitude and rate saturation limits for the fin deflections, show that near-zero miss distance (i.e., hit-to-kill level performance) can be obtained when these two new techniques are applied together. Comparison studies with an augmented proportional navigation based guidance shows that the proposed model predictive guidance leads to a substantial amount of conservation in the control energy as well.

Estimation of the 2.0(5) helix type i -> i hydrogen bond energy at Aib*-Oxa motif: an isodesmic approach

Bending at the valence angle N-C-alpha-C' (tau) is a known control feature for attenuating the stability of the rare intramolecular hydrogen bonded pseudo five-membered ring C-5 structures, the so called 2.0(5) helices, at Aib. The competitive 3(10)-helical structures still predominate over the C5 structures at Aib for most values of tau. However at Aib*, a mimic of Aib where the carbonyl 0 of Aib is replaced with an imidate N (in 5,6-dihydro-4H-1,3-oxazine = Oxa), in the peptidomimic Piv-Pro-Aib*-Oxa (1), the C(5)i structure is persistent in both crystals and in solution. Here we show that the i -> i hydrogen bond energy is a more determinant control for the relative stability of the C5 structure and estimate its value to be 18.5 +/- 0.7 kJ/mol at Aib* in 1, through the computational isodesmic reaction approach, using two independent sets of theoretical isodesmic reactions. (C) 2014 Elsevier Ltd. All rights reserved.

Generalized Model Predictive Static Programming and Angle-Constrained Guidance of Air-to-Ground Missiles

A new generalized model predictive static programming technique is presented for rapidly solving a class of finite-horizon nonlinear optimal control problems with hard terminal constraints. Two key features for its high computational efficiency include one-time backward integration of a small-dimensional weighting matrix dynamics, followed bya static optimization formulation that requires only a static Lagrange multiplier to update the control history. It turns out that under Euler integration and rectangular approximation of finite integrals it is equivalent to the existing model predictive static programming technique. In addition to the benchmark double integrator problem, usefulness of the proposed technique is demonstrated by solving a three-dimensional angle-constrained guidance problem for an air-to-ground missile, which demands that the missile must meet constraints on both azimuth and elevation angles at the impact point in addition to achieving near-zero miss distance, while minimizing the lateral acceleration demand throughout its flight path. Simulation studies include maneuvering ground targets along with a first-order autopilot lag. Comparison studies with classical augmented proportional navigation guidance and modern general explicit guidance lead to the conclusion that the proposed guidance is superior to both and has a larger capture region as well.

Optimal control of grinding mill circuit using model predictive static programming: A new nonlinear MPC paradigm

The recently developed reference-command tracking version of model predictive static programming (MPSP) is successfully applied to a single-stage closed grinding mill circuit. MPSP is an innovative optimal control technique that combines the philosophies of model predictive control (MPC) and approximate dynamic programming. The performance of the proposed MPSP control technique, which can be viewed as a `new paradigm' under the nonlinear MPC philosophy, is compared to the performance of a standard nonlinear MPC technique applied to the same plant for the same conditions. Results show that the MPSP control technique is more than capable of tracking the desired set-point in the presence of model-plant mismatch, disturbances and measurement noise. The performance of MPSP and nonlinear MPC compare very well, with definite advantages offered by MPSP. The computational speed of MPSP is increased through a sequence of innovations such as the conversion of the dynamic optimization problem to a low-dimensional static optimization problem, the recursive computation of sensitivity matrices and using a closed form expression to update the control. To alleviate the burden on the optimization procedure in standard MPC, the control horizon is normally restricted. However, in the MPSP technique the control horizon is extended to the prediction horizon with a minor increase in the computational time. Furthermore, the MPSP technique generally takes only a couple of iterations to converge, even when input constraints are applied. Therefore, MPSP can be regarded as a potential candidate for online applications of the nonlinear MPC philosophy to real-world industrial process plants. (C) 2014 Elsevier Ltd. All rights reserved.

A predictive approach to CVD of crystalline layers of TMDs: the case of MoS2

Layered transition metal dichalcogenides (TMDs), such as MoS2, are candidate materials for next generation 2-D electronic and optoelectronic devices. The ability to grow uniform, crystalline, atomic layers over large areas is the key to developing such technology. We report a chemical vapor deposition (CVD) technique which yields n-layered MoS2 on a variety of substrates. A generic approach suitable to all TMDs, involving thermodynamic modeling to identify the appropriate CVD process window, and quantitative control of the vapor phase supersaturation, is demonstrated. All reactant sources in our method are outside the growth chamber, a significant improvement over vapor-based methods for atomic layers reported to date. The as-deposited layers are p-type, due to Mo deficiency, with field effect and Hall hole mobilities of up to 2.4 cm(2) V-1 s(-1) and 44 cm(2) V-1 s(-1) respectively. These are among the best reported yet for CVD MoS2.

The nuclease activities of both the Smr domain and an additional LDLK motif are required for an efficient anti-recombination function of Helicobacter pyloriMutS2

Helicobacter pylori, a human pathogen, is a naturally and constitutively competent bacteria, displaying a high rate of intergenomic recombination. While recombination events are essential for evolution and adaptation of H.pylori to dynamic gastric niches and new hosts, such events should be regulated tightly to maintain genomic integrity. Here, we analyze the role of the nuclease activity of MutS2, a protein that limits recombination during transformation in H.pylori. In previously studied MutS2 proteins, the C-terminal Smr domain was mapped as the region responsible for its nuclease activity. We report here that deletion of Smr domain does not completely abolish the nuclease activity of HpMutS2. Using bioinformatics analysis and mutagenesis, we identified an additional and novel nuclease motif (LDLK) at the N-terminus of HpMutS2 unique to Helicobacter and related epsilon-proteobacterial species. A single point mutation (D30A) in the LDLK motif and the deletion of Smr domain resulted in approximate to 5-10-fold loss of DNA cleavage ability of HpMutS2. Interestingly, the mutant forms of HpMutS2 wherein the LDLK motif was mutated or the Smr domain was deleted were unable to complement the hyper-recombination phenotype of a mutS2(-) strain, suggesting that both nuclease sites are indispensable for an efficient anti-recombinase activity of HpMutS2.

PLAStiCC: Predictive Look-Ahead Scheduling for Continuous dataflows on Clouds

Scalable stream processing and continuous dataflow systems are gaining traction with the rise of big data due to the need for processing high velocity data in near real time. Unlike batch processing systems such as MapReduce and workflows, static scheduling strategies fall short for continuous dataflows due to the variations in the input data rates and the need for sustained throughput. The elastic resource provisioning of cloud infrastructure is valuable to meet the changing resource needs of such continuous applications. However, multi-tenant cloud resources introduce yet another dimension of performance variability that impacts the application's throughput. In this paper we propose PLAStiCC, an adaptive scheduling algorithm that balances resource cost and application throughput using a prediction-based lookahead approach. It not only addresses variations in the input data rates but also the underlying cloud infrastructure. In addition, we also propose several simpler static scheduling heuristics that operate in the absence of accurate performance prediction model. These static and adaptive heuristics are evaluated through extensive simulations using performance traces obtained from Amazon AWS IaaS public cloud. Our results show an improvement of up to 20% in the overall profit as compared to the reactive adaptation algorithm.