Protein Folding Simulations: Confinement, External Fields and Sequence Design

The present Thesis looks at the problem of protein folding using Monte Carlo and Langevin simulations, three topics in protein folding have been studied: 1) the effect of confining potential barriers, 2) the effect of a static external field and 3) the design of amino acid sequences which fold in a short time and which have a stable native state (global minimum). Regarding the first topic, we studied the confinement of a small protein of 16 amino acids known as 1NJ0 (PDB code) which has a beta-sheet structure as a native state. The confinement of proteins occurs frequently in the cell environment. Some molecules called Chaperones, present in the cytoplasm, capture the unfolded proteins in their interior and avoid the formation of aggregates and misfolded proteins. This mechanism of confinement mediated by Chaperones is not yet well understood. In the present work we considered two kinds of potential barriers which try to mimic the confinement induced by a Chaperon molecule. The first kind of potential was a purely repulsive barrier whose only effect is to create a cavity where the protein folds up correctly. The second kind of potential was a barrier which includes both attractive and repulsive effects. We performed Wang-Landau simulations to calculate the thermodynamical properties of 1NJ0. From the free energy landscape plot we found that 1NJ0 has two intermediate states in the bulk (without confinement) which are clearly separated from the native and the unfolded states. For the case of the purely repulsive barrier we found that the intermediate states get closer to each other in the free energy landscape plot and eventually they collapse into a single intermediate state. The unfolded state is more compact, compared to that in the bulk, as the size of the barrier decreases. For an attractive barrier modifications of the states (native, unfolded and intermediates) are observed depending on the degree of attraction between the protein and the walls of the barrier. The strength of the attraction is measured by the parameter $\epsilon$. A purely repulsive barrier is obtained for $\epsilon=0$ and a purely attractive barrier for $\epsilon=1$. The states are changed slightly for magnitudes of the attraction up to $\epsilon=0.4$. The disappearance of the intermediate states of 1NJ0 is already observed for $\epsilon =0.6$. A very high attractive barrier ($\epsilon \sim 1.0$) produces a completely denatured state. In the second topic of this Thesis we dealt with the interaction of a protein with an external electric field. We demonstrated by means of computer simulations, specifically by using the Wang-Landau algorithm, that the folded, unfolded, and intermediate states can be modified by means of a field. We have found that an external field can induce several modifications in the thermodynamics of these states: for relatively low magnitudes of the field ($<2.06 \times 10^8$ V/m) no major changes in the states are observed. However, for higher magnitudes than ($6.19 \times 10^8$ V/m) one observes the appearance of a new native state which exhibits a helix-like structure. In contrast, the original native state is a $\beta$-sheet structure. In the new native state all the dipoles in the backbone structure are aligned parallel to the field. The design of amino acid sequences constitutes the third topic of the present work. We have tested the Rate of Convergence criterion proposed by D. Gridnev and M. Garcia ({\it work unpublished}). We applied it to the study of off-lattice models. The Rate of Convergence criterion is used to decide if a certain sequence will fold up correctly within a relatively short time. Before the present work, the common way to decide if a certain sequence was a good/bad folder was by performing the whole dynamics until the sequence got its native state (if it existed), or by studying the curvature of the potential energy surface. There are some difficulties in the last two approaches. In the first approach, performing the complete dynamics for hundreds of sequences is a rather challenging task because of the CPU time needed. In the second approach, calculating the curvature of the potential energy surface is possible only for very smooth surfaces. The Rate of Convergence criterion seems to avoid the previous difficulties. With this criterion one does not need to perform the complete dynamics to find the good and bad sequences. Also, the criterion does not depend on the kind of force field used and therefore it can be used even for very rugged energy surfaces.

First-principles electronic theory of non-collinear magnetic order in transition-metal nanowires

The structural, electronic and magnetic properties of one-dimensional 3d transition-metal (TM) monoatomic chains having linear, zigzag and ladder geometries are investigated in the frame-work of first-principles density-functional theory. The stability of long-range magnetic order along the nanowires is determined by computing the corresponding frozen-magnon dispersion relations as a function of the 'spin-wave' vector q. First, we show that the ground-state magnetic orders of V, Mn and Fe linear chains at the equilibrium interatomic distances are non-collinear (NC) spin-density waves (SDWs) with characteristic equilibrium wave vectors q that depend on the composition and interatomic distance. The electronic and magnetic properties of these novel spin-spiral structures are discussed from a local perspective by analyzing the spin-polarized electronic densities of states, the local magnetic moments and the spin-density distributions for representative values q. Second, we investigate the stability of NC spin arrangements in Fe zigzag chains and ladders. We find that the non-collinear SDWs are remarkably stable in the biatomic chains (square ladder), whereas ferromagnetic order (q =0) dominates in zigzag chains (triangular ladders). The different magnetic structures are interpreted in terms of the corresponding effective exchange interactions J(ij) between the local magnetic moments μ(i) and μ(j) at atoms i and j. The effective couplings are derived by fitting a classical Heisenberg model to the ab initio magnon dispersion relations. In addition they are analyzed in the framework of general magnetic phase diagrams having arbitrary first, second, and third nearest-neighbor (NN) interactions J(ij). The effect of external electric fields (EFs) on the stability of NC magnetic order has been quantified for representative monoatomic free-standing and deposited chains. We find that an external EF, which is applied perpendicular to the chains, favors non-collinear order in V chains, whereas it stabilizes the ferromagnetic (FM) order in Fe chains. Moreover, our calculations reveal a change in the magnetic order of V chains deposited on the Cu(110) surface in the presence of external EFs. In this case the NC spiral order, which was unstable in the absence of EF, becomes the most favorable one when perpendicular fields of the order of 0.1 V/Å are applied. As a final application of the theory we study the magnetic interactions within monoatomic TM chains deposited on graphene sheets. One observes that even weak chain substrate hybridizations can modify the magnetic order. Mn and Fe chains show incommensurable NC spin configurations. Remarkably, V chains show a transition from a spiral magnetic order in the freestanding geometry to FM order when they are deposited on a graphene sheet. Some TM-terminated zigzag graphene-nanoribbons, for example V and Fe terminated nanoribbons, also show NC spin configurations. Finally, the magnetic anisotropy energies (MAEs) of TM chains on graphene are investigated. It is shown that Co and Fe chains exhibit significant MAEs and orbital magnetic moments with in-plane easy magnetization axis. The remarkable changes in the magnetic properties of chains on graphene are correlated to charge transfers from the TMs to NN carbon atoms. Goals and limitations of this study and the resulting perspectives of future investigations are discussed.

Poly-Si₁₋xGex Film Growth for Ni Germanosilicided Metal Gate

Scaling down of the CMOS technology requires thinner gate dielectric to maintain high performance. However, due to the depletion of poly-Si gate, it is difficult to reduce the gate thickness further especially for sub-65 nm CMOS generation. Fully silicidation metal gate (FUSI) is one of the most promising solutions. Furthermore, FUSI metal gate reduces gate-line sheet resistance, prevents boron penetration to channels, and has good process compatibility with high-k gate dielectric. Poly-SiGe gate technology is another solution because of its enhancement of boron activation and compatibility with the conventional CMOS process. Combination of these two technologies for the formation of fully germanosilicided metal gate makes the approach very attractive. In this paper, the deposition of undoped Poly-Si₁₋xGex (0 < x < 30% ) films onto SiO₂ in a low pressure chemical vapor deposition (LPCVD) system is described. Detailed growth conditions and the characterization of the grown films are presented.

A review of studies performed to assess metal uptake by earthworms

Earthworms perform a number of essential functions in soil; the impacts of metals on earthworms are often investigated. In this review we consider the range of earthworm species, types of soil and forms of metal for which metal uptake and accumulation have been studied, the design of these experiments and the quantitative relationships that have been derived to predict earthworm metal body burden. We conclude that there is a need for more studies on earthworm species other than Eisenia fetida in order to apply the large existing database on this earthworm to other, soil dwelling species. To aid comparisons between studies agreement is needed on standard protocols that define exposure and deputation periods and the parameters, such as soil solution composition, soil chemical and physical properties to be measured. It is recommended that more field or terrestrial model ecosystem studies using real contaminated soil rather than metal-amended artificial soils are performed. (c) 2006 Elsevier Ltd. All rights reserved.

Aldose reductase and the importance of experimental design

Kinetic studies on the AR (aldose reductase) protein have shown that it does not behave as a classical enzyme in relation to ring aldose sugars. As with non-enzymatic glycation reactions, there is probably a free radical element involved derived from monosaccharide autoxidation. in the case of AR, there is free radical oxidation of NADPH by autoxidizing monosaccharides, which is enhanced in the presence of the NADPH-binding protein. Thus any assay for AR based on the oxidation of NADPH in the presence of autoxidizing monosaccharides is invalid, and tissue AR measurements based on this method are also invalid, and should be reassessed. AR exhibits broad specificity for both hydrophilic and hydrophobic aldehydes that suggests that the protein may be involved in detoxification. The last thing we would want to do is to inhibit it. ARIs (AR inhibitors) have a number of actions in the cell which are not specific, and which do not involve them binding to AR. These include peroxy-radical scavenging and effects of metal ion chelation. The AR/ARI story emphasizes the importance of correct experimental design in all biocatalytic experiments. Developing the use of Bayesian utility functions, we have used a systematic method to identify the optimum experimental designs for a number of kinetic model data sets. This has led to the identification of trends between kinetic model types, sets of design rules and the key conclusion that such designs should be based on some prior knowledge of K-m and/or the kinetic model. We suggest an optimal and iterative method for selecting features of the design such as the substrate range, number of measurements and choice of intermediate points. The final design collects data suitable for accurate modelling and analysis and minimizes the error in the parameters estimated, and is suitable for simple or complex steady-state models.

4,4 '-Dipyridyl-N,N '-dioxide complexes of metal-thiocyanate/selenocyanate: pi-stacked molecular rods as three-dimensional support for two-dimensional polymeric sheets and intra/interchain S center dot center dot center dot S interaction dependent architecture of the R-2(2)(8) synthon driven assembly of one-dimensional polymeric chains

Three supramolecular complexes of Co(II) using SCN-/SeCN- in combination with 4,4'-dipyridyl-N,N'-dioxide (dpyo), i.e., {[Co(SCN)(2)(dpyo)(2)].(dpyo)}(n) ( 1), {[Co(SCN)(2)(dpyo)(H2O)(2)].(H2O)}(n) ( 2), {[Co(SeCN)(2)(dpyo)(H2O)(2)]center dot(H2O)}(n) ( 3), have been synthesized and characterized by single-crystal X-ray analysis. Complex 1 is a rare example of a dpyo bridged two-dimensional (2D) coordination polymer, and pi-stacked dpyo supramolecular rods are generated by the lattice dpyo, passing through the rhombic grid of stacked layers, resulting in a three-dimensional (3D) superstructure. Complexes 2 and 3 are isomorphous one-dimensional (1D) coordination polymers [-Co-dpyo-Co-] that undergo self-assembly leading to a bilayer architecture derived through an R-2(2)(8) H-bonding synthon between coordinated water and dpyo oxygen. A reinvestigation of coordination polymers [Mn(SCN)(2)(dpyo)( H2O)(MeOH)](n) ( 4) and {[Fe(SCN)(2)(dpyo)(H2O)(2)]center dot(H2O)}(n) ( 5) reported recently by our group [ Manna et al. Indian J. Chem. 2006, 45A, 1813] reveals brick wall topology rather than bilayer architecture is due to the decisive role of S center dot center dot center dot S/Se center dot center dot center dot Se interactions in determining the helical nature in 4 and 5 as compared to zigzag polymeric chains in 2 and 3, although the same R-2(2)(8) synthon is responsible for supramolecular assembly in these complexes.

Design and theoretical study of nickel catalysts for syndiotactic polyolefins

A nickel catalyst was modeled with ligand L-2, [ NH = CH-CH = CH-O](-), which should have potential use as a syndiotactic polyolefin catalyst, and the reaction mechanism was studied by theoretical calculations using the density functional method at the B3LYP/ LANL2MB level. The mechanism involves the formation of the intermediate [(NiLMe)-Me-2](+), in which the metal occuples a T-shaped geometry. - This intermediate has two possible structures with the methyl group trans either to the oxygen or to the nitrogen atom of L-2. The results show that both structures can lead to the desired product via similar reaction paths, A and B. Thus, the polymerization could be considered as taking place either with the alkyl group occupying the position trans to the Ni-O or trans to the Ni-N bond in the catalyst. The polymerization process thus favors the catalysis of syndiotactic polyolefins. The syndiotactic synthesis effects could also be enhanced by variations in the ligand substituents. From energy considerations, we can conclude that it is more favorable for the methyl group to occupy the trans-O position to form a complex than to occupy the trans-N position. From bond length considerations, it is also more favoured for ethene to occupy the trans-O position than to occupy the trans-N position.

Engineering Pt in ceria for a maximum metal-support interaction in catalysis

Conventional supported metal catalysts are metal nanoparticles deposited on high surface area oxide supports with a poorly defined metal−support interface. Typically, the traditionally prepared Pt/ceria catalyzes both methanation (H2/CO to CH4) and water−gas shift (CO/H2O to CO2/H2) reactions. By using simple nanochemistry techniques, we show for the first time that Pt or PtAu metal can be created inside each CeO2 particle with tailored dimensions. The encapsulated metal is shown to interact with the thin CeO2 overlayer in each single particle in an optimum geometry to create a unique interface, giving high activity and excellent selectivity for the water−gas shift reaction, but is totally inert for methanation. Thus, this work clearly demonstrates the significance of nanoengineering of a single catalyst particle by a bottom-up construction approach in modern catalyst design which could enable exploitation of catalyst site differentiation, leading to new catalytic properties.

Comparison of white metal and resin socket terminations for wire ropes

Previously the authors have presented both theoretical and experimental work discussing the operating mechanism of a wire rope held in a tapered socket by means of a cast resin cone. The work reported here extends the investigation to address the question of whether the same socket fabricated with white metal operates in the same manner. To date, previous investigations have compared the operational efficiency of resin and white metal in terms of both strength and/or fatigue endurance. Some other work has analysed the operation of resin sockets or specific cast metal terminations. This paper seeks to draw the results from this work together, and, in addition to a theoretical analysis, presents experimental data obtained from a direct comparison of the operation mechanism for the same sockets filled with resin or white metal. Results show that white metal terminations have a very different distribution of stresses along the length of the socket basket from resin terminations, and a smaller but still significant amount of socket draw. For both types of termination the socket draw develops high frictional gripping forces which can transfer the load from the rope to the socket. The different stress distributions mean that the consequences of termination fabrication defects may not be the same for resin and white metal terminations.

Construction of supramolecular helices and breaking the helicity by forming supramolecular β-sheet structures using suitable self-assembling pseudopeptide building blocks

Bis-valine derivatives or malonamide (Guha,S.; Drew, M.G.B. Small 2008, 4, 1993-2005) and a bis-valine derivative of 1,1-cyclopropone dicarboxamide were used as building blocks for the construction of supramolecular helical structures. The six-membered intramolecular hydrogen-bonded scaffold is formed, and this acts as a unique supramolecular synthon for the construction of a pseudopeptide-based supramolecular helical structure. However, in absence of this intramolecular hydrogen bond. intermolecular hydrogen bonds are formed among the peptide strands. This leads to a supramolecular beta-sheet structure. Proper selection of the supramolecular synthon (six-membered intramolecular hydrogenbonded scaffold) promotes supramolecular helix formation, and a deviation from this molecular structure dictates the disruption of supramolecular helicity. In this study, six crystal structures have been used to demonstrate that a change in the central angle and/or the central core structure of dicarboxamides can be used to design either a supramolecular helix or a beta-sheet.

Design of a biomimetic skin for an octopus-inspired robot - Part II: Development of the skin artefact

In order to develop skin artefact for an octopus-inspired robot arm, which is designed to be able to elongate 60% of its original length, silicone rubber and knitted nylon sheet were selected to manufacture an artificial skin, due to their higher elastic strain and high flexibility. Tensile and scissors cutting tests were conducted to characterise the matrix and reinforcing materials and the skin artefact. Material properties of the individual and the composite materials were compared with the measured properties of real octopus skin presented in Part I. The Young’s modulus of the skin should be below 20 MPa and the elastic strain range should be over 60%. The fracture toughness should be at least 0.9 kJ·m−2. Tubes made of the skin artefact filled with liquid were tested to study volume change under deformation. Finite element analysis model was developed to simulate the material and arm structure under tensile loading. Results show that the skin artefact developed has similar mechanical properties as the real octopus skin and satisfies all the design specifications of the OCTOPUS robot.

Synthesis and evaluation of lipophilic BTBP ligands for An/Ln separation in nuclear waste treatment: the effect of alkyl substitution on extraction properties and implications for ligand design

Four new 6,6′-bis(1,2,4-triazin-3-yl)-2,2′-bipyridine (BTBP) ligands, which contain either additional alkyl groups on the pyridine rings or seven-membered aliphatic rings attached to the triazine rings, have been synthesized, and the effects of the additional alkyl substitution in the 4- and 4′-positions of the pyridine rings on their extraction properties with LnIII and AnIII cations in simulated nuclear waste solutions have been studied. The speciation of ligand 13 with some trivalent lanthanide nitrates was elucidated by 1H NMR spectroscopic titrations and ESI-MS. Although 13 formed both 1:1 and 1:2 complexes with LaIII and YIII, only 1:2 complexes were observed with EuIII and CeIII. Quite unexpectedly, both alkyl-substituted ligands 12 and 13 showed lower solubilities in certain diluents than the unsubstituted ligand CyMe4-BTBP. Compared to CyMe4-BTBP, alkyl-substitution was found to decrease the rates of metal-ion extraction of the ligands in both 1-octanol and cyclohexanone. A highly efficient (DAm > 10) and selective (SFAm/Eu > 90) extraction was observed for 12 and 13 in cyclohexanone and for 13 in 1-octanol in the presence of a phase-transfer agent. The implications of these results for the design of improved extractants for radioactive waste treatment are discussed.

Effect of uncertainty in surface mass balance--elevation feedback on projections of the future sea level contribution of the Greenland ice sheet

We apply a new parameterisation of the Greenland ice sheet (GrIS) feedback between surface mass balance (SMB: the sum of surface accumulation and surface ablation) and surface elevation in the MAR regional climate model (Edwards et al., 2014) to projections of future climate change using five ice sheet models (ISMs). The MAR (Modèle Atmosphérique Régional: Fettweis, 2007) climate projections are for 2000–2199, forced by the ECHAM5 and HadCM3 global climate models (GCMs) under the SRES A1B emissions scenario. The additional sea level contribution due to the SMB– elevation feedback averaged over five ISM projections for ECHAM5 and three for HadCM3 is 4.3% (best estimate; 95% credibility interval 1.8–6.9 %) at 2100, and 9.6% (best estimate; 95% credibility interval 3.6–16.0 %) at 2200. In all results the elevation feedback is significantly positive, amplifying the GrIS sea level contribution relative to the MAR projections in which the ice sheet topography is fixed: the lower bounds of our 95% credibility intervals (CIs) for sea level contributions are larger than the “no feedback” case for all ISMs and GCMs. Our method is novel in sea level projections because we propagate three types of modelling uncertainty – GCM and ISM structural uncertainties, and elevation feedback parameterisation uncertainty – along the causal chain, from SRES scenario to sea level, within a coherent experimental design and statistical framework. The relative contributions to uncertainty depend on the timescale of interest. At 2100, the GCM uncertainty is largest, but by 2200 both the ISM and parameterisation uncertainties are larger. We also perform a perturbed parameter ensemble with one ISM to estimate the shape of the projected sea level probability distribution; our results indicate that the probability density is slightly skewed towards higher sea level contributions.

Systematic structural studies of iron superoxide dismutases from human parasites and a statistical coupling analysis of metal binding specificity

Superoxide dismutases (SODs) are a crucial class of enzymes in the combat against intracellular free radical damage. They eliminate superoxide radicals by converting them into hydrogen peroxide and oxygen. In spite of their very different life cycles and infection strategies, the human parasites Plasmodium falciparum, Trypanosoma cruzi and Trypanosoma brucei are known to be sensitive to oxidative stress. Thus the parasite Fe-SODs have become attractive targets for novel drug development. Here we report the crystal structures of FeSODs from the trypanosomes T. brucei at 2.0 angstrom and T. cruzi at 1.9 angstrom resolution, and that from P. falciparum at a higher resolution (2.0 angstrom) to that previously reported. The homodimeric enzymes are compared to the related human MnSOD with particular attention to structural aspects which are relevant for drug design. Although the structures possess a very similar overall fold, differences between the enzymes at the entrance to the channel which leads to the active site could be identified. These lead to a slightly broader and more positively charged cavity in the parasite enzymes. Furthermore, a statistical coupling analysis (SCA) for the whole Fe/MnSOD family reveals different patterns of residue coupling for Mn and Fe SODs, as well as for the dimeric and tetrameric states. In both cases, the statistically coupled residues lie adjacent to the conserved core surrounding the metal center and may be expected to be responsible for its fine tuning, leading to metal ion specificity.