Rigid Structural Units Research Articles

Pronounced Negative Thermal Expansion from a Simple Structure: Cubic ScF3

Scandium trifluoride maintains a cubic ReO(3) type structure down to at least 10 K, although the pressure at which its cubic to rhombohedral phase transition occurs drops from >0.5 GPa at ∼300 K to 0.1-0.2 GPa at 50 K. At low temperatures it shows strong negative thermal expansion (NTE) (60-110 K, α(l) ≈ -14 ppm K(-1)). On heating, its coefficient of thermal expansion (CTE) smoothly increases, leading to a room temperature CTE that is similar to that of ZrW(2)O(8) and positive thermal expansion above ∼1100 K. While the cubic ReO(3) structure type is often used as a simple illustration of how negative thermal expansion can arise from the thermally induced rocking of rigid structural units, ScF(3) is the first material with this structure to provide a clear experimental illustration of this mechanism for NTE.

Independent and Cooperative Motions of the Kv1.2 Channel: Voltage Sensing and Gating

Voltage-gated potassium (Kv) channels, such as Kv1.2, are involved in the generation and propagation of action potentials. The Kv channel is a homotetramer, and each monomer is composed of a voltage-sensing domain (VSD) and a pore domain (PD). We analyzed the fluctuations of a model structure of Kv1.2 using elastic network models. The analysis suggested a network of coupled fluctuations of eight rigid structural units and seven hinges that may control the transition between the active and inactive states of the channel. For the most part, the network is composed of amino acids that are known to affect channel activity. The results suggested allosteric interactions and cooperativity between the subunits in the coupling between the motion of the VSD and the selectivity filter of the PD, in accordance with recent empirical data. There are no direct contacts between the VSDs of the four subunits, and the contacts between these and the PDs are loose, suggesting that the VSDs are capable of functioning independently. Indeed, they manifest many inherent fluctuations that are decoupled from the rest of the structure. In general, the analysis suggests that the two domains contribute to the channel function both individually and cooperatively.

Molecular analysis of receptor protein tyrosine phosphatase mu-mediated cell adhesion.

Type IIB receptor protein tyrosine phosphatases (RPTPs) are bi-functional cell surface molecules. Their ectodomains mediate stable, homophilic, cell-adhesive interactions, whereas the intracellular catalytic regions can modulate the phosphorylation state of cadherin/catenin complexes. We describe a systematic investigation of the cell-adhesive properties of the extracellular region of RPTPmu, a prototypical type IIB RPTP. The crystal structure of a construct comprising its N-terminal MAM (meprin/A5/mu) and Ig domains was determined at 2.7 A resolution; this assigns the MAM fold to the jelly-roll family and reveals extensive interactions between the two domains, which form a rigid structural unit. Structure-based site-directed mutagenesis, serial domain deletions and cell-adhesion assays allowed us to identify the four N-terminal domains (MAM, Ig, fibronectin type III (FNIII)-1 and FNIII-2) as a minimal functional unit. Biophysical characterization revealed at least two independent types of homophilic interaction which, taken together, suggest that there is the potential for formation of a complex and possibly ordered array of receptor molecules at cell contact sites.

A new borazine-type single source precursor for Si/B/N/C ceramics

The new borazine derivative [B{CH(CH3)(SiCl3)}NH]3 (TSEB) was prepared by reacting Cl3Si–CH(CH3)–BCl2 (TSDE) with hexamethyldisilazane (hmds) at ambient conditions. TSEB was characterized by infrared spectroscopy (IR), nuclear magnetic resonance (NMR), and by mass spectrometry (MS). The specially designed molecule serves as a single source precursor for the synthesis of a highly durable Si/B/N/C ceramic material via the well known ‘polymer route’. Pursuing this philosophy, polymerization of TSEB with methylamine as the cross-linking reagent has lead to a highly homogeneous pre-ceramic polymer, which was further characterized by spectroscopic methods. Subsequent thermal degradation of the as-obtained polyborocarbosilazane was monitored by means of DTA/TG/MS up to 1400 °C. The resulting amorphous silicon boron carbonitride of the approximate elemental composition Si3B3N5C4 exhibits an outstanding thermal durability at 2000 °C under inert conditions and is also stable in pure oxygen up to at least 1300 °C. The ceramic material still contains borazine rings from the TSEB precursor molecule embedded in the covalent Si/B/N/C network, acting as rigid structural units which reinforce the ceramic material on an atomic scale.

Comparison of tRNA Motions in the Free and Ribosomal Bound Structures

A general method is presented that allows the separation of the rigid body motions from the nonrigid body motions of structural subunits when bound in a complex. The application presented considers the motions of the tRNAs: free, bound to the ribosome and to a synthase. We observe that both the rigid body and nonrigid body motions of the structural subunits are highly controlled by the large ribosomal assembly and are important for the functional motions of the assembly. For the intact ribosome, its major parts, the 30S and the 50S subunits, are found to have counterrotational motions in the first few slowest modes, which are consistent with the experimentally observed ratchet motion. The tRNAs are found to have on average ∼72–75% rigid body motions and principally translational motions within the first 100 slow modes of the complex. Although the three tRNAs exhibit different apparent total motions, after the rigid body motions are removed, the remaining internal motions of all three tRNAs are essentially the same. The direction of the translational motions of the tRNAs are in the same direction as the requisite translocation step, especially in the first slowest mode. Surprisingly the small intrinsically flexible mRNA has all of its internal motions completely inhibited and shows mainly a rigid-body translation in the slow modes of the ribosome complex. On the other hand, the required nonrigid body motions of the tRNA during translocation reveal that the anticodon-stem-loop, as well as the acceptor arm, of the tRNA enjoy a large mobility but act as rigid structural units. In summary, the ribosome exerts its control by enforcing rigidity in the functional parts of the tRNAs as well as in the mRNA.

Synthesis and yeast mediated bioreduction of α-keto-β-lactams bearing a functionalized and rigid side chain

Bakers' yeast (Saccharomyces cerevisiae) mediated reductions were investigated for the potential of a fermentation approach towards novel paclitaxel C-13 side-chain analogs bearing a polar methoxy-functionality in combination with a rigid structural core unit. Synthesis of correspondingly substituted α-keto-β-lactam compounds as biotransformation precursors was carried out following a straightforward strategy involving Staudinger (2+2) cyclization. Bioreductions were carried out using growing whole-cells of S. cerevisiae and the dia- and enantioselectivity of the process was studied.

Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition?

Structural studies of protein-DNA complexes have shown that there are many distinct families of DNA-binding proteins, and have shown that there is no simple “code” describing side-chain/base interactions. However, systematic analysis and comparison of protein-DNA complexes has been complicated by the diversity of observed contacts, the sheer number of complexes currently available and the absence of any consistent method of comparison that retains detailed structural information about the protein-DNA interface. To address these problems, we have developed geometric methods for characterizing the local structural environment in which particular side-chain/base interactions are observed. In particular, we develop methods for analyzing and comparing spatial relationships at the protein-DNA interface. Our method involves attaching local coordinate systems to the DNA bases and to the Cα atoms of the peptide backbone (these are relatively rigid structural units). We use these tools to consider how the position and orientation of the polypeptide backbone (with respect to the DNA) helps to determine what contacts are possible at any given position in a protein-DNA complex. Here, we focus on base contacts that are made in the major groove, and we use spatial relationships in analyzing: (i) the observed patterns of side-chain/base interactions; (ii) observed helix docking orientations; (iii) family/subfamily relationships among DNA-binding proteins; and (iv) broader questions about evolution, altered specificity mutants and the limits for the design of new DNA-binding proteins. Our analysis, which highlights differences in spatial relationships in different complexes and at different positions in a complex, helps explain why there is no simple, general code for protein-DNA recognition.

Dynamic Mechanical Characterization of Molecular Motion in a Wide Temperature Range of Various Polymers Containing Propylene Units

The temperature transitions for a series of flexible polymers containing propylene units were studied by dynamic mechanical spectroscopy. It was found that the gradual activation of the local motion of different structural units involved in polymers occurs with increasing temperature. Initially, the rotation of the side groups, such as side methyl groups, is activated and on further heating the main chain structural units show their local motions. It is important that the temperature interval of the appearance of the local motion of each structural unit is almost independent of the presence of other structural units. Accordingly, the polymers investigated can be divided into two groups. The activation of the local motion of the most rigid structural unit determines the glass transition in the first group of polymers. The glass transition of the polymers of the second group takes place at a higher temperature which depends on the content of side methyl groups and the intermolecular interaction. The increased influence of both these factors on the cooperative amorphous motion of polymers of the second group leads to their increased Tg values.

Lengthening the Second Stalk of F1F0 ATP Synthase in Escherichia coli

In Escherichia coli F(1)F(0) ATP synthase, the two b subunits dimerize forming the peripheral second stalk linking the membrane F(0) sector to F(1). Previously, we have demonstrated that the enzyme could accommodate relatively large deletions in the b subunits while retaining function (Sorgen, P. L., Caviston, T. L., Perry, R. C., and Cain, B. D. (1998) J. Biol. Chem. 273, 27873-27878). The manipulations of b subunit length have been extended by construction of insertion mutations into the uncF(b) gene adding amino acids to the second stalk. Mutants with insertions of seven amino acids were essentially identical to wild type strains, and mutants with insertions of up to 14 amino acids retained biologically significant levels of activity. Membranes prepared from these strains had readily detectable levels of F(1)F(0)-ATPase activity and proton pumping activity. However, the larger insertions resulted in decreasing levels of activity, and immunoblot analysis indicated that these reductions in activity correlated with reduced levels of b subunit in the membranes. Addition of 18 amino acids was sufficient to result in the loss of F(1)F(0) ATP synthase function. Assuming the predicted alpha-helical structure for this area of the b subunit, the 14-amino acid insertion would result in the addition of enough material to lengthen the b subunit by as much as 20 A. The results of both insertion and deletion experiments support a model in which the second stalk is a flexible feature of the enzyme rather than a rigid rod-like structure.

Nanoscale Fibrils and Grids: Aggregated Structures from Rigid-Rod Conjugated Polymers

Langmuir−Blodgett (LB) molecular processing of conjugated polymers [poly(phenylene ethynylenes)] into highly aligned films has revealed conditions for the formation of liquid crystalline monolayer films that structurally evolve into fibril aggregates. The structural requirements for poly(phenylene ethynylene)s to display liquid crystalline phases capable or alignment by LB methods were determined. The reconstruction of monolayers into fibril structures was found to require a low glass-transition temperature (Tg), weak surface anchoring, and a monolayer with a high energy that can be stabilized by reorganization. This assembly of polymers into aggregated structures produces rigid structural units analogous to naturally occurring fibrous proteins such as collagen and elastin. These oriented, shape-persistent nanoscale structures create new possibilities for the construction of complex supramolecular structures, and this capability has been demonstrated by the formation of a nanoscale grid.

Tensile drawing of poly(aryl ether ether ketone): 2. Analysis of the stress-strain-orientation relationships through the Brown and Windle model

The deformation behaviour of amorphous poly(aryl ether ether ketone) films above the glass transition temperature is studied by analysing the amorphous orientation function and shrinkage stress variations versus draw ratio in the framework of the two component model of Brown and Windle which considers separate orientational and extensional contributions to the overall strain. This analysis is in line with our previous conclusion of the existence of two regimes dominated by orientation of rigid structural units and extension of the chains before and after the threshold of the strain-induced crystallization, respectively. Also supported is the disentanglement trend of the chains prior to the crystallization which brings about a physical crosslinking effect to the macromolecular network. The identification of the rigid structural unit with a single monomer unit is remarkably consistent with our previous determination of the size of the random link. The study of isothermally-crystallized samples supports the conclusion about the efficiency of the crystallites for preventing chain slippage. The estimation of the molecular weight between entanglements as a function of draw ratio for both amorphous and crystallized samples suggests that the physical crosslinking effect of the crystallites is much more efficient than the intertwining of the chains.

Bulk properties and monolayer behaviour of diol-based mesogens and their acetonides

Amphiphilic 1,2-diol derivatives and their acetonides, incorporating rigid aromatic structural units, have been prepared. They exhibit liquid-crystalline behaviour and form stable monolayers at the air/water interface. The force–area isotherms obtained depend largely on the chemical structure of the rigid core.

Investigation of bulk properties and monolayer behaviour of amphiphilic mesogens: structural variations of the head group

Non-ionic amphiphilic compounds—butane-1.2,3-triol derivatives, 2-hydroxycarboxylic acids and carboxylic acids—incorporating rigid aromatic structural units like 1,4-disubstituted benzene, 4,4′-disubstituted biphenyl or the 2-phenyl-1,3,4-thiadiazole have been prepared. In most cases these compounds exhibit smectic liquid crystalline phases which can be stabilized by the addition of water. Their mesomorphic properties are compared with those of the structurally related 1,2-diol derivatives. Surprisingly, also some ω-(4-alkylphenoxy)alkanoic acids which have no thermotropic mesophases were found to aggregate to lyotropic mesophases in the presence of water. Most of the new compounds form stable monolayers at the air–water interface. The force–area isotherms of the thiadiazole derivatives have been recorded and it was found that they strongly depend on the chemical structure of the head group.

Molecular design of amphotropic materials: double-headed diol-based mesogens incorporating rigid structural units

The syntheses of novel bolaamphiphilic triol and tetraol compounds incorporating rigid structural units are described. Their liquid-crystalline properties were investigated by polarizing microscopy, differential scanning calorimetry and in some cases also by means of X-ray diffraction. Most 4,4-disubstituted biphenyl derivatives exhibit one or more smectic phases (predominantly SA but also Sc, SB, SG and Sk) and extraordinarily high clearing temperatures. No thermotropic liquid-crystalline properties could be detected for bolaamphiphiles incorporating a single 1,4-disubstituted phenyl ring or a 2,6-disubstituted naphthalene ring system, but for naphthalene derivatives a lyotropic smectic A phase was induced by addition of water. If one of the diol groups of the biphenyl-derived bolaamphiphiles is replaced by a single hydroxy group or by a carboxylic acid group the mesophase stability is decreased. Mesomorphic properties are lost if the hydrogen-bonding density is further diminished by the replacement of one diol group by an ethyl carboxylate group. However, in these cases lyotropic liquid-crystalline phases can be induced by the addition of water.

Rigidity, Connectivity, and Glass‐Forming Ability

Following the ideas of Zachariasen and of Cooper, it is argued that the glass‐forming ability of a system can be rationalized in terms of the degrees of freedom available to form an infinitely large topologically disordered network composed of rigid structural units connected at vertices, edges, or faces. Expressions are derived for the degrees of freedom for regular and irregular networks composed of regular or distorted polytopes sharing vertices, edges, or faces. The condition that degrees of freedom must be nonnegative for such a disordered network to exist is in agreement with the empirical results on glass‐forming abilities of a variety of covalent, ionic, and metallic systems. The present approach can be used to screen the proposed models of structure of a glass and to predict the boundaries of glass‐forming regions in composition spaces.

A structure–property rationalization of some poly(carboxyl–epoxy) thermosets

AbstractThe glass transition temperatures, Tg, and strength properties have been determined for an acrylic‐based prepolymer containing 25 mole‐% carboxyl functionality crosslinked with five different diepoxides. The Tg values vary from 100° to 200°C, and ultimate elongations of 2% to 7% at 25°C are observed with the different crosslinking agents. These variations are rationalized in terms of the structural elements present in the diepoxides. Thermosets possessing rigid structural units at the crosslink points connected by flexible segments have the best all‐around combination of Tg and tensile properties. A decline in these properties was noted when the epoxide/carboxyl ratio exceeded unity owing to the formation of mixed networks and free chain ends.