Microfabrication as a scientific tool

Research in microfabrication not only serves the microelectronics industry but also can provide research tools for studying the behavior of matter at submicrometer dimensions. A variety of techniques including optical, x-ray, and electron beam lithography and reactive ion etching can be used to make structures, devices, and arrays only hundreds of atoms across. Microfabrication techniques have been applied to experiments on surface-enhanced Raman scattering, transport in one-dimensional conductors, and macroscopic quantum tunneling. Recent progress is extending these techniques to scales of less than 100 angstroms.     

A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G

The high-resolution three-dimensional structure of a single immunoglobulin binding domain (B1, which comprises 56 residues including the NH2-terminal Met) of protein G from group G Streptococcus has been determined in solution by nuclear magnetic resonance spectroscopy on the basis of 1058 experimental restraints. The average atomic root-mean-square distribution about the mean coordinate positions is 0.27 angstrom (A) for the backbone atoms, 0.65 A for all atoms, and 0.39 A for atoms excluding disordered surface side chains. The structure has no disulfide bridges and is composed of a four-stranded beta sheet, on top of which lies a long helix. The central two strands (beta 1 and beta 4), comprising the NH2- and COOH-termini, are parallel, and the outer two strands (beta 2 and beta 3) are connected by the helix in a +3x crossover. This novel topology (-1, +3x, -1), coupled with an extensive hydrogen-bonding network and a tightly packed and buried hydrophobic core, is probably responsible for the extreme thermal stability of this small domain (reversible melting at 87 degrees C).     

Structures from anomalous diffraction of native biological macromolecules

Crystal structure analyses for biological macromolecules without known structural relatives entail solving the crystallographic phase problem. Typical de novo phase evaluations depend on incorporating heavier atoms than those found natively; most commonly, multi- or single-wavelength anomalous diffraction (MAD or SAD) experiments exploit selenomethionyl proteins. Here, we realize routine structure determination using intrinsic anomalous scattering from native macromolecules. We devised robust procedures for enhancing the signal-to-noise ratio in the slight anomalous scattering from generic native structures by combining data measured from multiple crystals at lower-than-usual x-ray energy. Using this multicrystal SAD method (5 to 13 equivalent crystals), we determined structures at modest resolution (2.8 to 2.3 angstroms) for native proteins varying in size (127 to 1148 unique residues) and number of sulfur sites (3 to 28). With no requirement for heavy-atom incorporation, such experiments provide an attractive alternative to selenomethionyl SAD experiments.     

X-ray structure of the major adduct of the anticancer drug cisplatin with DNA: cis-[Pt(NH3)2(d(pGpG))

Crystals of the adduct of the anticancer drug cis-diamminedichloroplatinum(II), cis-DDP, with d(pGpG), its putative target on DNA in the cancer cell, have been obtained and used in an x-ray crystallographic study to elucidate the molecular structure to atomic resolution. Each of the four crystallographically independent cis-[Pt(NH3)2(d(pGpG))] molecules is comprised of a square-planar platinum atom bonded to two ammonia ligands and two N(7) atoms of guanosine nucleosides from the same chain. Base stacking of the two adjacent guanine rings is completely disrupted by coordination to the cis-(Pt(NH3)2)2+ unit. Comparison of the backbone and deoxyribose ring torsion angles with those found by previous (nuclear magnetic resonance spectroscopy) studies of this adduct in solution demonstrates that the solid state geometry is substantially the same as that in solution. The relevance of these results to the molecular mechanism of action of cis-DDP is discussed.     

X-ray Photographs of a Solar Active Region with a Multilayer Telescope at Normal Incidence

An astronomical photograph was obtained with a multilayer x-ray telescope. A 4-centimeter tungsten-carbon multilayer mirror was flown as part of an experimental solar rocket payload, and successful images were taken of the sun at normal incidence at a wavelength of 44 angstroms. Coronal Si-XII emission from an active region was recorded on film; as expected, the structure is very similar to that observed at O-VIII wavelengths by the Solar Maximum Mission flat crystal spectrometer at the same time. The small, simple optical system used in this experiment appears to have achieved a resolution of 5 to 10 arc seconds.     

Multiple-quantum nuclear magnetic resonance spectroscopy

A nuclear magnetic resonance (NMR) event is popularly viewed as the flip of a single spin in a magnetc field, stimulated by the absorption or emission of only one quantum of radio-frequency energy. Nevertheless, resonances between nuclear spin states that differ by more than one unit in the Zeeman quantum number also can be induced in systems of coupled spins by suitably designed sequences of radio-frequency pulses. Pairs of states excited in this way oscillate coherently at the frequencies of the corresponding multiple-quantum transitions and produce a response that may be monitored indirectly in a two-dimensional time-domain experiment. The pattern of multiple-quantum excitation and response, influenced largely by the concerted interactions of groups of coupled nuclei, simplifies the NMR spectrum in some instances and provides significant new information in others. Applications of multiple-quantum NMR extend to problems in many different areas, ranging from studies of the structure and function of proteins and nucleic acids in solution to investigations of the arrangements of atoms in amorphous semiconductors. The specific spectroscopic techniques are varied as well and include methods designed, for example, to simplify spectral analysis for liquids and liquid crystals, eliminate inhomogeneous broadening, study interatomic connectivity in liquid-state molecules, identify clusters of atoms in solids, enhance the spatial resolution in solid-state imaging experiments, and probe correlated molecular motions.     

Nitrogenase MoFe-protein at 1.16 A resolution: a central ligand in the FeMo-cofactor

A high-resolution crystallographic analysis of the nitrogenase MoFe-protein reveals a previously unrecognized ligand coordinated to six iron atoms in the center of the catalytically essential FeMo-cofactor. The electron density for this ligand is masked in structures with resolutions lower than 1.55 angstroms, owing to Fourier series termination ripples from the surrounding iron and sulfur atoms in the cofactor. The central atom completes an approximate tetrahedral coordination for the six iron atoms, instead of the trigonal coordination proposed on the basis of lower resolution structures. The crystallographic refinement at 1.16 angstrom resolution is consistent with this newly detected component being a light element, most plausibly nitrogen. The presence of a nitrogen atom in the cofactor would have important implications for the mechanism of dinitrogen reduction by nitrogenase.     

Soft X-ray Images of the Solar Corona with a Normal-Incidence Cassegrain Multilayer Telescope

High-resolution images of the sun in the soft x-ray to extreme ultraviolet(EUV) regime have been obtained with normal-incidence Cassegrain multilayer telescopes operated from a sounding rocket in space. The inherent energy-selective property of multilayer-coated optics allowed distinct groups of emission lines to be isolated in the solar corona and the transition region. The Cassegrain telescopes provided images in bands centered at 173 and 256 angstroms. The bandpass centered at 173 angstroms is dominated by emission from the ions Fe IX Fe X. This emission is from coronal plasma in the temperature range 0.8 x 10(6) to 1.4 x 10(6)K. The images have angular resolution of about 1.0 to 1.5 arc seconds, and show no degradation because of x-ray scattering. Many features of coronal structure, including magnetically confined loops of hot plasma, coronal plumes, polar coronal holes, faint structures on the size scale of supergranulation and smaller, and features due to overlying cool prominences are visible in the images. The density structure of polar plumes, which are thought to contribute to the solar wind, has been derived from the observations out to 1.7 solar radii.     

Crystalline transfer RNA: the three-dimensional Patterson function at 12-angstrom resolution

An orthorhombic form of crystalline formylmethionine transter RNA has been obtained which contains one molecule as the asymmetric unit of the unit cell. Three-dimensional x-ray diffraction data have been collected up to a resolution of 12 angstroms, and from this a Patterson function has been calculated. The function contains an elongated ridge of interatomic vectors parallel to the c-axis of the crystal. Analysis of the function suggests that the molecules are elogated and dimerized in an overlapping antiparrael fashion along the c-axis. The dimer has a length near 109 angstroms and a width of 35 angstroms in one direction. The individual molecular length is approximately 80 angstroms with an irregular cross section measuring 25 by 35 angstrms.     

Studying enzyme mechanism by 13C nuclear magnetic resonance

High-resolution carbon-13 nuclear magnetic resonance (NMR) spectra of enzyme-inhibitor and enzyme-substrate complexes provide detailed structural and stereochemical information on the mechanism of enzyme action. The proteases trypsin and papain are shown to form tetrahedrally coordinated complexes and acyl derivatives with a variety of compounds artificially enriched at the site or sites of interest. These results are compared with the structural information derived from x-ray diffraction. Detailed NMR studies have provided a clearer picture of the ionization state of the residues participating in enzyme-catalyzed processes than other more classical techniques. The dynamics of enzymic catalysis can be observed at sub-zero temperatures by a combination of cryoenzymology and carbon-13 NMR spectroscopy. With these powerful techniques, transient, covalently bound intermediates in enzyme-catalyzed reactions can be detected and their structures rigorously assigned.     

Three-dimensional solution structure of a single zinc finger DNA-binding domain

The three-dimensional solution structure of a zinc finger nucleic acid binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. Spectra of a synthetic peptide corresponding to a single zinc finger from the Xenopus protein Xfin yielded distance and dihedral angle constraints that were used to generate structures from distance geometry and restrained molecular dynamics calculations. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding.     

Three-dimensional readout of flash x-ray images of living sperm in water by atomic-force microscopy

The imaging of living specimens in water by x-ray microscopy can be greatly enhanced with the use of an intense flash x-ray source and sophisticated technologies for reading x-ray images. A subnanosecond [corrected] x-ray pulse from a laser-produced plasma was used to record the x-ray image of living sea urchin sperm in an x-ray resist. The resist relief was visualized at high resolution by atomic-force microscopy. Internal structure of the sperm head was evident, and the carbon density in a flagellum was estimated from the relief height.     

Study by synchrotron radiation of the structure of a working catalyst at high temperatures and pressures

A relation among activity, composition, and structure was determined for a working catalyst by means of a stainless-steel reactor cell of novel design that permitted operation at temperatures and pressures similar to those in industrial reactors. Molybdenum K-edge x-ray absorption spectra were used to probe the structural environment of molybdenum in CoMoS/[unknown]-alumina catalysts while hydro-desulfurization of benzothiophene was proceeding at high temperature and pressure. For catalyst samples with different contents of cobalt, radial structure functions obtained from extended x-ray absorption fine structure data presented the same features as those obtained from the spectra of MoS(2)/[unknown]-alumina reference samples. Moreover, Mo-S and Mo-Mo coordination numbers were maximum for the sample with an atomic ratio of Co to (Co + Mo) of 0.33; this sample was also the most active catalyst tested.     

Time-resolved holography with photoelectrons

Ionization is the dominant response of atoms and molecules to intense laser fields and is at the basis of several important techniques, such as the generation of attosecond pulses that allow the measurement of electron motion in real time. We present experiments in which metastable xenon atoms were ionized with intense 7-micrometer laser pulses from a free-electron laser. Holographic structures were observed that record underlying electron dynamics on a sublaser-cycle time scale, enabling photoelectron spectroscopy with a time resolution of almost two orders of magnitude higher than the duration of the ionizing pulse.     

An isomorphous heavy-atom derivative of crystaline formylmethionine transfer RNA

An isomorphous osmium derivative of crystalline yeast initiator transfer RNA has been prepared and interpreted to 6-angstrom resolution. The coordinates of the heavy atoms have been determined by Patterson and "direct" methods applied to the difference coefficients of the centric projections, followed by least-squares refinement. There is one dominant site per asymmetric unit, consistent with the finding by neutron-activation analysis that there is approximately one osmium atom per molecule of transfer RNA. The osmium derivative appears to be a normal substrate for enzymatic aminoacylation.     

X-ray diffraction and computation yield the structure of alkanethiols on gold(111)

The structure of self-assembled monolayers (SAMs) of long-chain alkyl sulfides on gold(111) has been resolved by density functional theory-based molecular dynamics simulations and grazing incidence x-ray diffraction for hexanethiol and methylthiol. The analysis of molecular dynamics trajectories and the relative energies of possible SAM structures suggest a competition between SAM ordering, driven by the lateral van der Waals interaction between alkyl chains, and disordering of interfacial Au atoms, driven by the sulfur-gold interaction. We found that the sulfur atoms of the molecules bind at two distinct surface sites, and that the first gold surface layer contains gold atom vacancies (which are partially redistributed over different sites) as well as gold adatoms that are laterally bound to two sulfur atoms.     

Crystallographic structure of the octameric histone core of the nucleosome at a resolution of 3.3 A

The structure of the (H2A-H2B-H3-H4)2 histone octamer has been determined by means of x-ray crystallographic techniques at a resolution of 3.3 angstroms. The octamer is a prolate ellipsoid 110 angstroms long and 65 to 70 angstroms in diameter, and its general shape is that of a rugby ball. The size and shape are radically different from those determined in earlier studies. The most striking feature of the histone octamer is its tripartite organization, that is, a central (H3-H4)2 tetramer flanked by two H2A-H2B dimers. The DNA helix, placed around the octamer in a path suggested by the features on the surface of the protein, appears like a spring holding the H2A-H2B dimers at either end of the (H3-H4)2 tetramer.     

Tetraplex formation of a guanine-containing nonameric DNA fragment

A combination of spectroscopic and calorimetric techniques has been used to characterize the structures formed by a family of short, guanine-containing DNA single strands of the form d[GGTTXTTGG], X = A, C, G, T. In 1 molar NaCl at low temperatures, these molecules do not behave like single strands, but rather exhibit properties consistent with tetraplex formation. The standard state enthalpies, entropies, and free energies for formation of each tetraplex have been measured, as have preliminary nuclear magnetic resonance (NMR) spectra. In 1 molar KCl, the melting behavior of the structure or structures is more complex than in 1 molar NaCl. This observation may be related to the recently proposed "sodium-potassium switch."     

Atomic structure of ferredoxin-NADP+ reductase: prototype for a structurally novel flavoenzyme family

The three-dimensional structure of spinach ferredoxin-NADP+ reductase (NADP+, nicotinamide adenine dinucleotide phosphate) has been determined by x-ray diffraction at 2.6 angstroms (A) resolution and initially refined to an R factor of 0.226 at 2.2 A resolution. The model includes the flavin-adenine dinucleotide (FAD) prosthetic group and the protein chain from residue 19 through the carboxyl terminus at residue 314 and is composed of two domains. The FAD binding domain (residues 19 to 161) has an antiparallel beta barrel core and a single alpha helix for binding the pyrophosphate of FAD. The NADP binding domain (residues 162 to 314) has a central five-strand parallel beta sheet and six surrounding helices. Binding of the competitive inhibitor 2'-phospho-AMP (AMP, adenosine monophosphate) places the NADP binding site at the carboxyl-terminal edge of the sheet in a manner similar to the nucleotide binding of the dehydrogenase family. The structures reveal the key residues that function in cofactor binding and the catalytic center. With these key residues as a guide, conclusive evidence is presented that the ferredoxin reductase structure is a prototype for the nicotinamide dinucleotide and FAD binding domains of the enzymes NADPH-cytochrome P450 reductase, NADPH-sulfite reductase, NADH-cytochrome b5 reductase, and NADH-nitrate reductase. Thus this structure provides a structural framework for the NADH- or NADPH-dependent flavoenzyme parts of five distinct enzymes involved in photosynthesis, in the assimilation of inorganic nitrogen and sulfur, in fatty-acid oxidation, in the reduction of methemoglobin, and in the metabolism of many pesticides, drugs, and carcinogens.