On-chip deposition of carbon nanotubes using CMOS microhotplates.

The direct deposition of carbon nanotubes on CMOS microhotplates is demonstrated in this paper. Tungsten microhotplates, fabricated on thin SOI membranes aside CMOS control circuitry, are used to locally grow carbon nanotubes by chemical vapour deposition. Unlike bulk heating of the entire chip, which could cause degradation to CMOS devices and interconnects due to high growth temperatures in excess of 500 °C, this novel technique allows carbon nanotubes to be grown on-chip in localized regions. The microfabricated heaters are thermally isolated from the rest of the CMOS chip as they are on the membranes. This allows carbon nanotubes to be grown alongside CMOS circuitry on the same wafer without any external heating, thus enabling new applications (e.g. smart gas sensing) where the integration of CMOS and carbon nanotubes is required.

Modeling and solution structure probing of the HIV-1 TAR stem-loop.

We present a model for the three-dimensional structure of the HIV TAR stem-loop, based on a modeling algorithm which makes use of the known X-ray coordinates of tRNAs to generate a model structure, which has then been tested experimentally in solution by enzymatic and chemical structure probing of ribo-oligonucleotides encompassing the TAR sequence. The modeling suggested that the structure of TAR was similar to that of the anti-codon loop of tRNA(Asp), having a loop of just three single-stranded residues with a mismatched adenine excluded from the helical stem on the 3' side of the loop. The structural probing is consistent with such a structure for the loop, and reveals an unusual structure around the 5' uridine-rich bulge, which is the binding target for the transactivator protein Tat. These data may be useful in understanding the interaction of TAR with the Tat protein and may aid in the design of anti-AIDS drugs. The coordinates of the model are available on request.

A robust and efficient automated docking algorithm for molecular recognition.

A completely automated method is described for determining the most likely mode of binding of two (macro)molecules from the knowledge of their three-dimensional structures alone. The method is based on well-known graph theoretical techniques and has been used successfully to determine and rationalize the binding of a number of known macromolecular complexes. In this article we present results for a special case of the general molecular recognition problem--given the information concerning the particular atoms involved in the binding for one of the molecules, the algorithm can correctly identify the corresponding (contacting) atoms of the other molecule. The approach used can be easily extended to the general molecular recognition problem and requires the extraction of maximal common subgraphs. In these studies the docking of the macromolecules was achieved without the aid of computer graphics or other visual aids. The algorithm has been used to determine the correct mode of binding of a protein antigen to an antibody in approximately 100 min on a DEC micro VAX 3600.

Defining topological equivalences in macromolecules.

We describe a completely automated and objective method for defining topological equivalents in macromolecules. The method is based on well established techniques for identifying topologically and topographically equivalent atoms in small molecules and has been used in structural alignment of proteins and RNA molecules, and to extract fragments of molecules (protein secondary structures and RNA and DNA double helices) from structural databases consistent with some specified template structure.

Hyperreactivity of adenines and conformational flexibility of a translational repression site.

We have used a diethylpyrocarbonate (DEPC) modification [(1976) Prog. Nucl. Acids Res. 16, 189-262] to probe the accessibility of adenines essential for coat protein binding in the MS2 translational operator [(1983) Biochemistry 22, 2601-2610, 2610-2615, 4723-4730; (1987) Biochemistry 26, 1563-1568]. The essential adenines are apparently hyperreactive with this reagent relative to other sites within the same molecule. Variation of ionic strength, pH and divalent cation concentrations reveal the existence of two distinct conformers of the RNA operator as judged by DEPC reactivity. We propose that the hyperreactivity observed is due to the participation of neighbouring bases in the DEPC modification reaction and can be used as a novel structural probe.

Calculation of binding energies using a robust molecular mechanics technique: application to an antibody-antigen complex.

A novel molecular mechanics technique, which is both computationally efficient and robust, for calculation of relative stability of macromolecules and binding energies is presented. The technique delivers exact results for a number of hypothetical systems; the technique can be used to energy minimize a number of similar macromolecules simultaneously; simultaneous minimization of many structures requires computer time only fractionally over that needed to energy minimize one such structure. The method has been used to successfully calculate the relative stability and binding of two avian lysozymes to the monoclonal antibody D1.3.

Modeling loop structures in proteins and nucleic acids: an RNA stem-loop.

We have used a novel modeling technique, based on combining information from several preexisting structures, to generate a three-dimensional (3D) model for the RNA stem-loop responsible for translational repression of the MS2 RNA bacteriophage replicase. Specific features of the model have been tested experimentally by chemical and enzymatic structural probes; results from these experiments have been used to "improve" the model by fixing initial assumptions. The new model and chemical modification data are in part consistent, and further predictions are being tested. The modeling algorithm has a wide range of potential applications, particularly to loop regions in proteins and nucleic acids.

Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures.

An approach is described for modelling the three-dimensional structure of a protein from the tertiary structures of several homologous proteins that have been determined by X-ray analysis. A method is developed for the simultaneous superposition of several protein molecules and for the calculation of an 'average structure' or 'framework'. Investigation of the convergence properties of this method, in the case of both weighted and unweighted least squares, demonstrates that both give a unique answer and the latter is robust for an homologous family of proteins. Multi-dimensional scaling is used to subgroup of the proteins with respect to structural homology. The framework calculated on the basis of the family of homologous proteins, or of an appropriate subgroup, is used to align fragments of the known protein structures of high sequence homology with the unknown. This alignment provides a basis for model building the tertiary structure. Different techniques for using the framework to model the mainchain of various globins and an immunoglobulin domain in the structurally conserved regions are investigated.

Anisotropic thermal motion and polypeptide secondary structure studied by X-ray analysis at 0.98A resolution.

aPP is a 36-amino acid polypeptide which forms a stable globular structure stabilised by hydrophobic interactions between a polyproline-like helix and an alpha-helix. Crystals contain dimers and are crosslinked by coordination through zinc ions leading to a well-ordered lattice which diffracts X-rays to a resolution of 0.98A. This gives a 5:1 ratio of observations-to-parameters even when anisotropic thermal ellipsoids defined by six parameters for each non-hydrogen atom were refined using least-squares techniques. Rigid body refinement of groups within the polypeptide was also undertaken. The relationship of the principal axes of individual thermal ellipsoids and the librations of rigid side groups to features of secondary, tertiary, and quaternary structures of aPP and its interactions with water molecules are described.

Specificity of pancreatic ribonuclease-A. An X-ray study of a protein-nucleotide complex.

The modified purine nucleotide 8-oxo-guanosine-2'-phosphate binds at the pyrimidine binding site of ribonuclease-A. The O8-2'GMP inhibitor is in a syn conformation, with an intramolecular hydrogen bond between the N-3 atom of the base and the O-5' atom of the ribose. The essential groups of the protein involved in base recognition are O gamma 45 and N-45, which form hydrogen bonds to the five-membered ring of the heterocyclic base. Mobility of enzyme side-chains (viz. Lys41, Lys66, His119) close to the catalytic cleft of the protein allows conformational flexibility in the substrate binding region of ribonuclease-A. Inhibitor binding alters the solvent structure of the protein but the overall shape of the enzyme is not effected.