Structural flexibility in transcription complex formation revealed by protein–DNA photocrosslinking

The Oct-1 POU domain binds diverse DNA-sequence elements and forms a higher-order regulatory complex with the herpes simplex virus coregulator VP16. The POU domain contains two separate DNA-binding domains joined by a flexible linker. By protein–DNA photocrosslinking we show that the relative positioning of the two POU DNA-binding domains on DNA varies depending on the nature of the DNA target. On a single VP16-responsive element, the POU domain adopts multiple conformations. To determine the structure of the Oct-1 POU domain in a multiprotein complex with VP16, we allowed VP16 to interact with previously crosslinked POU-domain–DNA complexes and found that VP16 can associate with multiple POU-domain conformations. These results reveal the dynamic potential of a DNA-binding domain in directing transcriptional regulatory complex formation.

Effects of structural flexibility on entry vehicle control systems. [Prepared for NASA under the cognizance of the Jet Propulsion Laboratory, California Institute of Technology.

Cover title.

Structural flexibility and oxygen diffusion pathways in monomeric fluorescent proteins

Fluorescent proteins are valuable tools as biochemical markers for studying cellular processes. Red fluorescent proteins (RFPs) are highly desirable for in vivo applications because they absorb and emit light in the red region of the spectrum where cellular autofluorescence is low. The naturally occurring fluorescent proteins with emission peaks in this region of the spectrum occur in dimeric or tetrameric forms. The development of mutant monomeric variants of RFPs has resulted in several novel FPs known as mFruits. Though oxygen is required for maturation of the chromophore, it is known that photobleaching of FPs is oxygen sensitive, and oxygen-free conditions result in improved photostabilities. Therefore, understanding oxygen diffusion pathways in FPs is important for both photostabilites and maturation of the chromophores. We used molecular dynamics calculations to investigate the protein barrel fluctuations in mCherry, which is one of the most useful monomeric mFruit variants, and its GFP homolog citrine. We employed implicit ligand sampling and locally enhanced sampling to determine oxygen pathways from the bulk solvent into the mCherry chromophore in the interior of the protein. The pathway contains several oxygen hosting pockets, which were identified by the amino acid residues that form the pocket. We calculated the free-energy of an oxygen molecule at points along the path. We also investigated an RFP variant known to be significantly less photostable than mCherry and find much easier oxygen access in this variant. We showed that oxygen pathways can be blocked or altered, and barrel fluctuations can be reduced by strategic amino acid substitutions. The results provide a better understanding of the mechanism of molecular oxygen access into the fully folded mCherry protein barrel and provide insight into the photobleaching process in these proteins.

Flexibility of short-strand RNA in aqueous solution as revealed by molecular dynamics simulation:are A′-RNA and A-RNA distinct conformational structures?

We use molecular dynamics simulations to compare the conformational structure and dynamics of a 21-base pair RNA sequence initially constructed according to the canonical A-RNA and A'-RNA forms in the presence of counterions and explicit water. Our study aims to add a dynamical perspective to the solid-state structural information that has been derived from X-ray data for these two characteristic forms of RNA. Analysis of the three main structural descriptors commonly used to differentiate between the two forms of RNA namely major groove width, inclination and the number of base pairs in a helical twist over a 30 ns simulation period reveals a flexible structure in aqueous solution with fluctuations in the values of these structural parameters encompassing the range between the two crystal forms and more. This provides evidence to suggest that the identification of distinct A-RNA and A'-RNA structures, while relevant in the crystalline form, may not be generally relevant in the context of RNA in the aqueous phase. The apparent structural flexibility observed in our simulations is likely to bear ramifications for the interactions of RNA with biological molecules (e.g. proteins) and non-biological molecules (e.g. non-viral gene delivery vectors). © CSIRO 2009.

The role of disulfide bridges in the 3-D structures of the antimicrobial peptides gomesin and protegrin-1: a molecular dynamics study

Some antimicrobial peptides have a broad spectrum of action against many different kinds of microorganisms. Gomesin and protegrin-1 are examples of such antimicrobial peptides, and they were studied by molecular dynamics in this research. Both have a beta-hairpin conformation stabilized by two disulfide bridges and are active against Gram-positive and Gram-negative bacteria, as well as fungi. In this study, the role of the disulfide bridge in the maintenance of the tertiary peptide structure of protegrin-1 and gomesin is analyzed by the structural characteristics of these peptides and two of their respective variants, gomy4 and proty4, in which the four cysteines are replaced by four tyrosine residues. The absence of disulfide bridges in gomy4 and proty4 is compensated by overall reinforcement of the original hydrogen bonds and extra attractive interactions between the aromatic rings of the tyrosine residues. The net effects on the variants with respect to the corresponding natural peptides are: i) maintenance of the original beta-hairpin conformation, with great structural similarities between the mutant and the corresponding natural peptide; ii) combination of positive F and. Ramachandran angles within the hairpin head region with a qualitative change to a combination of positive (F) and negative (.) angles, and iii) significant increase in structural flexibility. Experimental facts about the antimicrobial activity of the gomesin and protegrin-1 variants have also been established here, in the hope that the detailed data provided in the present study may be useful for understanding the mechanism of action of these peptides.

Assessing protein stability of the dimeric DNA-binding domain of E2 human papillomavirus 18 with molecular dynamics

The objective of this study is to understand the structural flexibility and curvature of the E2 protein of human papillomavirus type 18 using molecular dynamics (6 ns). E2 is required for viral DNA replication and its disruption could be an anti-viral strategy. E2 is a dimer, with each monomer folding into a stable open-faced β-sandwich. We calculated the mobility of the E2 dimer and found that it was asymmetric. These different mobilities of E2 monomers suggest that drugs or vaccines could be targeted to the interface between the two monomers.

Role of the HCF-1 basic region in sustaining cell proliferation.

BACKGROUND: The human herpes simplex virus-associated host cell factor 1 (HCF-1) is a conserved human transcriptional co-regulator that links positive and negative histone modifying activities with sequence-specific DNA-binding transcription factors. It is synthesized as a 2035 amino acid precursor that is cleaved to generate an amino- (HCF-1(N)) terminal subunit, which promotes G1-to-S phase progression, and a carboxy- (HCF-1(C)) terminal subunit, which controls multiple aspects of cell division during M phase. The HCF-1(N) subunit contains a Kelch domain that tethers HCF-1 to sequence-specific DNA-binding transcription factors, and a poorly characterized so called "Basic" region (owing to a high ratio of basic vs. acidic amino acids) that is required for cell proliferation and has been shown to associate with the Sin3 histone deacetylase (HDAC) component. Here we studied the role of the Basic region in cell proliferation and G1-to-S phase transition assays. METHODOLOGY/PRINCIPAL FINDINGS: Surprisingly, much like the transcriptional activation domains of sequence-specific DNA-binding transcription factors, there is no unique sequence within the Basic region required for promoting cell proliferation or G1-to-S phase transition. Indeed, the ability to promote these activities is size dependent such that the shorter the Basic region segment the less activity observed. We find, however, that the Basic region requirements for promoting cell proliferation in a temperature-sensitive tsBN67 cell assay are more stringent than for G1-to-S phase progression in an HCF-1 siRNA-depletion HeLa-cell assay. Thus, either half of the Basic region alone can support G1-to-S phase progression but not cell proliferation effectively in these assays. Nevertheless, the Basic region displays considerable structural plasticity because each half is able to promote cell proliferation when duplicated in tandem. Consistent with a potential role in promoting cell-cycle progression, the Sin3a HDAC component can associate independently with either half of the Basic region fused to the HCF-1 Kelch domain. CONCLUSIONS/SIGNIFICANCE: While conserved, the HCF-1 Basic region displays striking structural flexibility for controlling cell proliferation.

Rakenteellisen jouston kuvaus reaaliaikasimuloinnissa

Työn tavoitteena oli tuottaa rakenteellisen jouston huomioiva monikappaledynmiikan simulointiohjelma Matlab-ympäristöön. Rakenteellinen jousto huomioitiin kelluvan koordinaatiston menetelmällä ja joustavuutta kuvaavat muodot ratkaistiin elementtimenetelmällä. Tehdyn ohjelman avulla voidaan koostaa joustavista kappaleista koostuvia avaruusmekanismeja ja tutkia niiden dynaamista käyttäytymistä. Simulointitulosta verrattiin kaupallisen ohjelmiston tuottamaan tulokseen. Työssä havaittiin, että kelluvan koordinaatiston menetelmä on käyttökelpoinen reaaliaikaiseen simulointiin. Työssä toteutetun ohjelman tulokset vastasivat kaupallisen simulointiohjelman tuloksia.

Use of neural networks in robot positioning of large flexible redundant manipulators

Deflection compensation of flexible boom structures in robot positioning is usually done using tables containing the magnitude of the deflection with inverse kinematics solutions of a rigid structure. The number of table values increases greatly if the working area of the boom is large and the required positioning accuracy is high. The inverse kinematics problems are very nonlinear, and if the structure is redundant, in some cases it cannot be solved in a closed form. If the structural flexibility of the manipulator arms is taken into account, the problem is almost impossible to solve using analytical methods. Neural networks offer a possibility to approximate any linear or nonlinear function. This study presents four different methods of using neural networks in the static deflection compensation and inverse kinematics solution of a flexible hydraulically driven manipulator. The training information required for training neural networks is obtained by employing a simulation model that includes elasticity characteristics. The functionality of the presented methods is tested based on the simulated and measured results of positioning accuracy. The simulated positioning accuracy is tested in 25 separate coordinate points. For each point, the positioning is tested with five different mass loads. The mean positioning error of a manipulator decreased from 31.9 mm to 4.1 mm in the test points. This accuracy enables the use of flexible manipulators in the positioning of larger objects. The measured positioning accuracy is tested in 9 separate points using three different mass loads. The mean positioning error decreased from 10.6 mm to 4.7 mm and the maximum error from 27.5 mm to 11.0 mm.

New studies on the versatile roles of Polyaniline and its composites in polymer based optoelectronic and energy storage devices

From the early stages of the twentieth century, polyaniline (PANI), a well-known and extensively studied conducting polymer has captured the attention of scientific community owing to its interesting electrical and optical properties. Starting from its structural properties, to the currently pursued optical, electrical and electrochemical properties, extensive investigations on pure PANI and its composites are still much relevant to explore its potentialities to the maximum extent. The synthesis of highly crystalline PANI films with ordered structure and high electrical conductivity has not been pursued in depth yet. Recently, nanostructured PANI and the nanocomposites of PANI have attracted a great deal of research attention owing to the possibilities of applications in optical switching devices, optoelectronics and energy storage devices. The work presented in the thesis is centered around the realization of highly conducting and structurally ordered PANI and its composites for applications mainly in the areas of nonlinear optics and electrochemical energy storage. Out of the vast variety of application fields of PANI, these two areas are specifically selected for the present studies, because of the following observations. The non-linear optical properties and the energy storing properties of PANI depend quite sensitively on the extent of conjugation of the polymer structure, the type and concentration of the dopants added and the type and size of the nano particles selected for making the nanocomposites. The first phase of the work is devoted to the synthesis of highly ordered and conducting films of PANI doped with various dopants and the structural, morphological and electrical characterization followed by the synthesis of metal nanoparticles incorporated PANI samples and the detailed optical characterization in the linear and nonlinear regimes. The second phase of the work comprises the investigations on the prospects of PANI in realizing polymer based rechargeable lithium ion cells with the inherent structural flexibility of polymer systems and environmental safety and stability. Secondary battery systems have become an inevitable part of daily life. They can be found in most of the portable electronic gadgets and recently they have started powering automobiles, although the power generated is low. The efficient storage of electrical energy generated from solar cells is achieved by using suitable secondary battery systems. The development of rechargeable battery systems having excellent charge storage capacity, cyclability, environmental friendliness and flexibility has yet to be realized in practice. Rechargeable Li-ion cells employing cathode active materials like LiCoO2, LiMn2O4, LiFePO4 have got remarkable charge storage capacity with least charge leakage when not in use. However, material toxicity, chance of cell explosion and lack of effective cell recycling mechanism pose significant risk factors which are to be addressed seriously. These cells also lack flexibility in their design due to the structural characteristics of the electrode materials. Global research is directed towards identifying new class of electrode materials with less risk factors and better structural stability and flexibility. Polymer based electrode materials with inherent flexibility, stability and eco-friendliness can be a suitable choice. One of the prime drawbacks of polymer based cathode materials is the low electronic conductivity. Hence the real task with this class of materials is to get better electronic conductivity with good electrical storage capability. Electronic conductivity can be enhanced by using proper dopants. In the designing of rechargeable Li-ion cells with polymer based cathode active materials, the key issue is to identify the optimum lithiation of the polymer cathode which can ensure the highest electronic conductivity and specific charge capacity possible The development of conducting polymer based rechargeable Li-ion cells with high specific capacity and excellent cycling characteristics is a highly competitive area among research and development groups, worldwide. Polymer based rechargeable batteries are specifically attractive due to the environmentally benign nature and the possible constructional flexibility they offer. Among polymers having electrical transport properties suitable for rechargeable battery applications, polyaniline is the most favoured one due to its tunable electrical conducting properties and the availability of cost effective precursor materials for its synthesis. The performance of a battery depends significantly on the characteristics of its integral parts, the cathode, anode and the electrolyte, which in turn depend on the materials used. Many research groups are involved in developing new electrode and electrolyte materials to enhance the overall performance efficiency of the battery. Currently explored electrolytes for Li ion battery applications are in liquid or gel form, which makes well-defined sealing essential. The use of solid electrolytes eliminates the need for containment of liquid electrolytes, which will certainly simplify the cell design and improve the safety and durability. The other advantages of polymer electrolytes include dimensional stability, safety and the ability to prevent lithium dendrite formation. One of the ultimate aims of the present work is to realize all solid state, flexible and environment friendly Li-ion cells with high specific capacity and excellent cycling stability. Part of the present work is hence focused on identifying good polymer based solid electrolytes essential for realizing all solid state polymer based Li ion cells.The present work is an attempt to study the versatile roles of polyaniline in two different fields of technological applications like nonlinear optics and energy storage. Conducting form of doped PANI films with good extent of crystallinity have been realized using a level surface assisted casting method in addition to the generally employed technique of spin coating. Metal nanoparticles embedded PANI offers a rich source for nonlinear optical studies and hence gold and silver nanoparticles have been used for making the nanocomposites in bulk and thin film forms. These PANI nanocomposites are found to exhibit quite dominant third order optical non-linearity. The highlight of these studies is the observation of the interesting phenomenon of the switching between saturable absorption (SA) and reverse saturable absorption (RSA) in the films of Ag/PANI and Au/PANI nanocomposites, which offers prospects of applications in optical switching. The investigations on the energy storage prospects of PANI were carried out on Li enriched PANI which was used as the cathode active material for assembling rechargeable Li-ion cells. For Li enrichment or Li doping of PANI, n-Butyllithium (n-BuLi) in hexanes was used. The Li doping as well as the Li-ion cell assembling were carried out in an argon filled glove box. Coin cells were assembled with Li doped PANI with different doping concentrations, as the cathode, LiPF6 as the electrolyte and Li metal as the anode. These coin cells are found to show reasonably good specific capacity around 22mAh/g and excellent cycling stability and coulombic efficiency around 99%. To improve the specific capacity, composites of Li doped PANI with inorganic cathode active materials like LiFePO4 and LiMn2O4 were synthesized and coin cells were assembled as mentioned earlier to assess the electrochemical capability. The cells assembled using the composite cathodes are found to show significant enhancement in specific capacity to around 40mAh/g. One of the other interesting observations is the complete blocking of the adverse effects of Jahn-Teller distortion, when the composite cathode, PANI-LiMn2O4 is used for assembling the Li-ion cells. This distortion is generally observed, near room temperature, when LiMn2O4 is used as the cathode, which significantly reduces the cycling stability of the cells.

Modeling Robot Dynamic Performance for Endpoint Force Control

This research aims to understand the fundamental dynamic behavior of servo-controlled machinery in response to various types of sensory feedback. As an example of such a system, we study robot force control, a scheme which promises to greatly expand the capabilities of industrial robots by allowing manipulators to interact with uncertain and dynamic tasks. Dynamic models are developed which allow the effects of actuator dynamics, structural flexibility, and workpiece interaction to be explored in the frequency and time domains. The models are used first to explain the causes of robot force control instability, and then to find methods of improving this performance.

Hydrolyzable tannin structures influence relative globular and random coil protein binding strengths

Binding parameters for the interactions of pentagalloyl glucose (PGG) and four hydrolyzable tannins (representing gallotannins and ellagitannins) with gelatin and bovine serum albumin (BSA) have been determined from isothermal titration calorimetry data. Equilibrium binding constants determined for the interaction of PGG and isolated mixtures of tara gallotannins and of sumac gallotannins with gelatin and BSA were of the same order of magnitude for each tannin (in the range of 10(4)-10(5) M-1 for stronger binding sites when using a binding model consisting of two sets of multiple binding sites). In contrast, isolated mixtures of chestnut ellagitannins and of myrabolan ellagitannins exhibited 3-4 orders of magnitude greater equilibrium binding constants for the interaction with gelatin (similar to 2 x 10(6) M-1) than for that with BSA (similar to 8 x 10(2) M-1). Binding stoichiometries revealed that the stronger binding sites on gelatin outnumbered those on BSA by a ratio of at least similar to 2:1 for all of the hydrolyzable tannins studied. Overall, the data revealed that relative binding constants for the interactions with gelatin and BSA are dependent on the structural flexibility of the tannin molecule.

On the discourse of construction competitiveness

It is contended that competitiveness is better understood as a discourse rather than as a characteristic that is supposedly possessed. The discourse of competitiveness derives its legitimacy from the enterprise culture that came to dominance during the 1980s. Current popularized theories of competitiveness are constituent parts of this broader discourse, which has had significant material implications for the UK construction sector. The dominant discourse of competitiveness amongst contracting firms is shaped by the need to achieve structural flexibility to cope with fluctuations in demand. Fashionable espoused improvement recipes such as total quality management, business process re-engineering, and lean construction legitimize and reinforce the material manifestations of the enterprise culture. In consequence, the UK industry is characterized by a plethora of hollowed-out firms that have failed to invest in their human capital. While the adopted model may be rational for individual firms, the systemic effect across the sector as a whole equates to a form of anorexia. However, the discourse of competitiveness is by no means monolithic and continues to be contested locally. There have also been numerous counter-discourses that have been mobilized in response to the undesirable externalities of unbridled enterprise. Currently, important counter-discourses promote the ideas of sustainability and corporate social responsibility.

Lean construction: Arenas of enactment, models of diffusion and the meaning of 'leanness'

The existing literature on lean construction is overwhelmingly prescriptive with little recognition of the social and politicised nature of the diffusion process. The prevailing production-engineering perspective too often assumes that organizations are unitary entities where all parties strive for the common goal of 'improved performance'. An alternative perspective is developed that considers the diffusion of lean construction across contested pluralistic arenas. Different actors mobilize different storylines to suit their own localized political agendas. Multiple storylines of lean construction continuously compete for attention with other management fashions. The conceptualization and enactment of lean construction therefore differs across contexts, often taking on different manifestations from those envisaged. However, such localized enactments of lean construction are patterned and conditioned by pre-existing social and economic structures over which individual managers have limited influence. Taking a broader view, 'leanness' can be conceptualized in terms of a quest for structural flexibility involving restructuring, downsizing and outsourcing. From this perspective, the UK construction industry can be seen to have embarked upon leaner ways of working in the mid-1970s, long before the terminology of lean thinking came into vogue. Semi-structured interviews with construction sector policy-makers provide empirical support for the view that lean construction is a multifaceted concept that defies universal definition.

Novel Zn(2+)-binding Sites in Human Transthyretin IMPLICATIONS FOR AMYLOIDOGENESIS AND RETINOL-BINDING PROTEIN RECOGNITION

Human transthyretin (TTR) is a homotetrameric protein involved in several amyloidoses. Zn(2+) enhances TTR aggregation in vitro, and is a component of ex vivo TTR amyloid fibrils. We report the first crystal structure of human TTR in complex with Zn(2+) at pH 4.6-7.5. All four structures reveal three tetra-coordinated Zn(2+)-binding sites (ZBS 1-3) per monomer, plus a fourth site (ZBS 4) involving amino acid residues from a symmetry-related tetramer that is not visible in solution by NMR.Zn(2+) binding perturbs loop E-alpha-helix-loop F, the region involved in holo-retinol-binding protein (holo-RBP) recognition, mainly at acidic pH; TTR affinity for holo-RBP decreases similar to 5-fold in the presence of Zn(2+). Interestingly, this same region is disrupted in the crystal structure of the amyloidogenic intermediate of TTR formed at acidic pH in the absence of Zn(2+). HNCO and HNCA experiments performed in solution at pH 7.5 revealed that upon Zn(2+) binding, although the alpha-helix persists, there are perturbations in the resonances of the residues that flank this region, suggesting an increase in structural flexibility. While stability of the monomer of TTR decreases in the presence of Zn(2+), which is consistent with the tertiary structural perturbation provoked by Zn(2+) binding, tetramer stability is only marginally affected by Zn(2+). These data highlight structural and functional roles of Zn(2+) in TTR-related amyloidoses, as well as in holo-RBP recognition and vitamin A homeostasis.