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Scanning probe microscopy is used to image nucleation sites leading to dewetting of polystyrene films (

The CD4 molecule interacts with the alpha2 and beta2 domains of the MHC class II molecules. However, the class II contact sites on CD4 are less clear. Involvement of different regions throughout D1, D2, and D3 domains have been suggested. To further delineate the class II MHC contact sites on CD4, a crystal structure-informed mutagenesis was performed. Alanine scan mutants were generated for exposed residues located throughout D1 and the FG loop of D2, and in the "hinge-like" region, a short and flexible region between D2 and D3. Mutants were tested in a co-ligand (Dd stimulation) and a co-receptor (staphylococcal enterotoxin B stimulation) assay. In the co-ligand assay, TCR and CD4 interact with two distinct ligands (Dd or HLA-DR), while in the co-receptor assay both molecules interact with the same ligand, namely HLA-DR. Results show that residues from both lateral faces of D1 and the FG loop of D2 are implicated in interaction with class II, although a bigger surface of CD4 was involved in co-receptor compared with co-ligand function. The potential involvement of residues on both the top and two side faces of CD4 is consistent with a bivalent model, which involves the interaction between a single CD4 and two class II molecules. Alternatively, our results can be interpreted with a model of a specifically organized CD4 and/or class II oligomerization event. Finally, results from the hinge region mutants revealed a very important role in maintaining the overall structural integrity of CD4, its topology, and function.

A general method has been developed for determining the number of molecules per asymmetric unit, Za, of a protein crystal. The method, volume-specific amino acid analysis, relies on the direct measurement of the number of protein molecules in a crystal as normalized by the crystal volume. The method is accurate, straightforward to implement and sensitive enough for application to small (0.002 m3) crystals. Although the procedures described here are specific to proteins, extension to nucleic acid crystals should be possible.

Scanning tunneling and atomic force images of polystyrene spin-coated onto silicon surfaces as a function of polymer molecular weight and concentration are presented.

Scanning tunneling microscopy images of strands, microislands, and thin films formed by the conducting polymers polypyrrole tosylate, polypyrrole tetrafluoroborate, and polythiophene tetrafluoroborate are presented. The polymer strands and microislands contain two types of helical structures with diameters of 1.5-1.8 nm, a simple helix, and 5-6 nm, a superhelix. The polymer films gradually transform from an ordered crystalline array located at the anode surface to an amorphous material at the air-polymer interface.

Single-wavelength Cu K alpha anomalous scattering has been used to determine the structure of a crystalline complex of gramicidin A and caesium chloride. The asymmetric unit in these crystals, with space group P2(1)2(1)2(1) and a = 32.118 (6), b = 52.103 (12), c = 31.174 (7) A, contains four independent monomers (two dimers) of the pentadecapeptide. This structure falls in an intermediate size range for which direct methods and multiple isomorphous replacement are generally not successful for obtaining phase information. However, using the Bijvoet differences and the partial structure of the caesium atoms which have been incorporated in the crystals, it has been possible to obtain information on this crystal form. Because the caesium atoms dominate the scattering of these crystals, inclusion of the Friedel mate information in the restrained least-squares refinement has been essential. These studies extend the utility of single-wavelength anomalous-scattering phase determination to a macromolecular structure in which the partial structure of the anomalous scatterer is large.

A procedure has been developed to incorporate stereo-chemical restraints information for new groups into the dictionary of ideal groups used by the program PROTIN which prepares the input file needed by the reciprocal-space least-squares refinement program PROLSQ. It requires the availability of Cartesian coordinates for the group to be added to the dictionary, usually obtained from crystallographic analysis of crystals of the compound. If no such information is available these coordinates can be generated by an ancillary program, MOLBLD, which makes use of specified bond lengths, bond angles and dihedral angles to produce the required coordinates. The program is written in standard Fortran 77 and has been used in the refinement of several structures.

The scanning tunneling microscope (STM) has grown and evolved at an incredible rate. Now STM not only is used as a powerful imaging tool to provide atomic resolution surface topography but also quickly becomes a nanoscale manipulator after slight modification. In this paper, we describe a nanoscale lithography technique, which was developed by combining STM with an electrochemical cell. We have demonstrated the feasibility of this technique, which allows us to write, read, and erase letters at a nanoscale level. At present, there still exist some difficulties but we believe that the ability to write, edit, and archive symbols and patterns on a nanoscale level constitutes a significant advance and an enabling concept in nanolithography

PhoQ is a transmembrane histidine kinase belonging to the family of two-component signal transducing systems common in prokaryotes and lower eukaryotes. In response to changes in environmental Mg(2+) concentration, PhoQ regulates the level of phosphorylated PhoP, its cognate transcriptional response-regulator. The PhoQ cytoplasmic region comprises two independently folding domains: the histidine-containing phosphotransfer domain and the ATP-binding kinase domain. We have determined the structure of the kinase domain of Escherichia coli PhoQ complexed with the non-hydrolyzable ATP analog adenosine 5'-(beta,gamma-imino)triphosphate and Mg(2+). Nucleotide binding appears to be accompanied by conformational changes in the loop that surrounds the ATP analog (ATP-lid) and has implications for interactions with the substrate phosphotransfer domain. The high resolution (1.6 A) structure reveals a detailed view of the nucleotide-binding site, allowing us to identify potential catalytic residues. Mutagenic analyses of these residues provide new insights into the catalytic mechanism of histidine phosphorylation in the histidine kinase family. Comparison with the active site of the related GHL ATPase family reveals differences that are proposed to account for the distinct functions of these proteins.

Scanning tunneling spectroscopy (STS) has been used to determine the band structure of polypyrrole. The polypyrrole films were electropolymerized onto a highly oriented pyrolytic graphite surface using a rotating disk electrode. Differential conductance spectra measurements allowed us to follow the evolution of the band gap as a function of doping level. Before and after the STS measurements, the film structure was imaged by scanning tunneling microscopy. The STS results agree with data obtained by inverse photoemission spectroscopy

The biological activity of the transcription factor NF-kappaB is differentially controlled by three IkappaB proteins, Ikappa Balpha, Ikappa Bbeta, and Ikappa Bepsilon. We have examined the molecular basis for the differential inhibitory strengths of IkappaB proteins by constructing hybrid IkappaBs and found that the first ankyrin repeat of Ikappa Balpha is responsible for its strong inhibitory effect. Swapping a putative beta-turn within the first ankyrin repeat between the strong Ikappa Balpha and the weak IkappaBbeta inhibitors switches their in vivo inhibitory activity on NF-kappaB. The qualitatively distinct contacts made by this beta-turn in Ikappa Balpha and Ikappa Bbeta with NF-kappaB determine the efficiency by which IkappaBs sequester NF-kappaB to the cytoplasm, thus explaining their distinct effects on gene activity.

Scanning tunneling microscopy images of single, double, and multistranded helical structures of bulk poly(ethylene oxide) polymers (PEO) are presented. The single-stranded helix appears to contain seven PEO monomer units with two turns per repeat unit consistent with the model proposed by Tadokoro; individual monomer units are visible. The multistranded STM images are similar to those obtained by transmission electron microscopy, but smaller in scale. A hierarchy of superhelical structures is proposed to account for the observed images

Streptavidin binds 2'-iminobiotin in a pH-dependent fashion--affinity decreases as the pH is lowered. This property makes the purification of compounds conjugated to streptavidin or immobiotin possible under mild conditions by affinity chromatography. In order to understand the molecular details of this pH-dependent binding, we analyzed the crystal structures of the complex of core streptavidin with 2'-iminobiotin at pH values 4.0 and 7.5. The two structures are very similar to each other even at their binding sites. Although the relative abundance of the protonated species of the ligand is increased more than 3,000-fold on going from pH 7.5 to pH 4.0, both structures contain only the nonprotonated from of the ligand. Streptavidin selects the nonprotonated form, which, at pH 4.0, is one part in 7.9 x 10(7).

The CD4 molecule interacts with the alpha2 and beta2 domains of the MHC class II molecules. However, the class II contact sites on CD4 are less clear. Involvement of different regions throughout D1, D2, and D3 domains have been suggested. To further delineate the class II MHC contact sites on CD4, a crystal structure-informed mutagenesis was performed. Alanine scan mutants were generated for exposed residues located throughout D1 and the FG loop of D2, and in the "hinge-like" region, a short and flexible region between D2 and D3. Mutants were tested in a co-ligand (Dd stimulation) and a co-receptor (staphylococcal enterotoxin B stimulation) assay. In the co-ligand assay, TCR and CD4 interact with two distinct ligands (Dd or HLA-DR), while in the co-receptor assay both molecules interact with the same ligand, namely HLA-DR. Results show that residues from both lateral faces of D1 and the FG loop of D2 are implicated in interaction with class II, although a bigger surface of CD4 was involved in co-receptor compared with co-ligand function. The potential involvement of residues on both the top and two side faces of CD4 is consistent with a bivalent model, which involves the interaction between a single CD4 and two class II molecules. Alternatively, our results can be interpreted with a model of a specifically organized CD4 and/or class II oligomerization event. Finally, results from the hinge region mutants revealed a very important role in maintaining the overall structural integrity of CD4, its topology, and function.

Crystals of both native and mutant Escherichia coli UmuD' protein were obtained using the hanging drop method. Soaking the native crystals in solutions of heavy metal ions failed to produce good isomorphous derivatives, and selenomethionine substituted wild-type protein did not crystallize under conditions that gave native crystals. Site-directed mutagenesis was used to change the penultimate residue, a methionine amino acid, to either a valine or a threonine amino acid. Crystals were subsequently obtained from these mutant proteins with and without selenomethionine incorporation. Crystals of the native, the mutant, and the selenomethionine incorporated protein were all similar, crystallizing in the P4(1)2(1)2 space group.

Many membrane proteins feature autonomously folded extramembranous domains which, when isolated from the intact protein, perform biochemical functions relevant to biological activity. Whereas intact membrane proteins usually require detergent solubilization for purification, most extramembranous fragments are soluble in aqueous solution. If appropriately constructed, such fragments are often crystallizable and the resulting atomic structures can lead to important biological insight. In most instances, these fragments are produced in recombinant expression systems. To be crystallizable, molecular fragments should be uniform in composition and conformation and be available in abundance. Considerations for the production of crystallizable fragments of membrane proteins include the definition of fragment boundaries, the control of nonuniformities introduced by glycosylation of phosphorylation, and optimization of expression systems. These aspects are addressed here in general terms and in the case studies of applications to CD4, CD8, the insulin receptor kinase, and N-cadherin.

A portion of rat mannose-binding protein A (MBP-A), a Ca(2+)-dependent animal lectin, has been overproduced in a bacterial expression system, biochemically characterized, and crystallized. A fragment corresponding to the COOH-terminal 115 residues of native MBP-A, produced by subtilisin digestion of the bacterially expressed protein, contains the carbohydrate-recognition domain (CRD). Gel filtration, chemical cross-linking, and crystallographic self-rotation function analyses indicate that the subtilisin fragment is a dimer, although the complete bacterially expressed fragment, containing the neck and CRD of MBP-A, is a trimer. Crystals of the minimal CRD, obtained only as a complex with a Man6GlcNAc2Asn glycopeptide, diffract to Bragg spacings of at least 1.7 A. Several trivalent lanthanide ions (Ln3+) can substitute for Ca2+, as assessed by their ability to support carbohydrate binding and to protect the CRD from proteolysis in a manner similar to that observed for Ca2+. These assays indicate that Ln2+ binds about 30 times more tightly than Ca2+ to the CRD, and that two Ca2+ or Ln3+ bind to each monomer, a result confirmed by determination of the Ho3+ positions in a Ho(3+)-containing crystal of the CRD. Crystals grown in the presence of Ln3+ belong to different space groups from those obtained with Ca2+ and are therefore not useable for traditional crystallographic phase determination methods, but are well-suited for high resolution structure determination by multiwavelength anomalous dispersion phasing.

Atomic force microscopy (AFM) and scanning tunneling microscopy (STM) have been successfully used to observe four systems of organic macromolecules; spin‐coated polystyrene; polyethylene oxide; polythiophene and polypyrrole; and phosphorylase kinase and phosphorylase b. Images shown demonstrate the ability of AFM and STM to resolve the structure of these systems with subnanometer resolution. Further discussion supports these two techniques as valuable research tools in this area.

The analysis of X-ray diffraction intensities is complicated by the anisotropy of anomalous scattering (AAS) that can occur due to resonance associated with transitions between core electrons and valence molecular orbitals. Substantial AAS has been observed directly in diffraction data near the K edge of selenium in selenolanthionine [Templeton & Templeton (1988). Acta Cryst. A44, 1045-1051] and in pleiochroism of X-ray absorption in selenobiotinyl streptavidin [Hendrickson, Pahler, Smith, Satow, Merritt & Phizackerley (1989). Proc. Natl Acad. Sci. USA, 86, 2190-2194]. The impact of AAS on the multiple-wavelength anomalous diffraction (MAD) method for phase determination is of particular interest in the context of this chemical state of selenium in the light of a general method that has been developed to incorporate selenomethionine into proteins for use in MAD phasing [Hendrickson, Horton & LeMaster (1990). EMBO J. 9, 1665-1672]. The first step of the MAD phasing method necessarily assumes that the anomalous-scattering factors are isotropic and our first aim here is to evaluate the effect of this approximation on initially determined phases. To obtain ultimate phases free from the effects of anisotropy, a least-squares procedure has been written in which global parameters (i.e. pertaining to the whole data set) are refined simultaneously with local parameters (i.e. pertaining to a given node h). The AAS is taken explicitly into account by considering f′ and f” as tensors instead of scalars [Templeton & Templeton (1982). Acta Cryst. A38, 62-67], and the components of the f′ and f′′ tensors are among the refinable global parameters. The effectiveness of this procedure is tested with data simulated from the refined atomic model of selenobiotinyl streptavidin. The application of this procedure to actual Photon Factory measurements is also described. The results show that AAS does not cripple the MAD method, and that phases uncorrupted by these effects can be recovered.

Ribonuclease H (RNase H) from Escherichia coli is an endonuclease that specifically degrades the RNAs of RNA:DNA hybrids. The enzyme is a single polypeptide chain of 155 amino acid residues, of which 4 are methionines. To solve the crystallographic three-dimensional structure of E. coli RNase H by the multi-wavelength anomalous diffraction technique, we have constructed methionine auxotrophic strains of E. coli that overexpress selenomethionyl RNase H. MIC88 yields about 10 mg of selenomethionyl RNase H per liter of culture, which is comparable to the overexpression of the natural recombinant protein. We have purified both proteins to homogeneity and crystallized them isomorphously in the presence of sulfate. These are Type I crystals of space group P2(1)2(1)2(1) with the cell parameters a = 41.8 A, b = 86.4 A, c = 36.4 A, one monomer per asymmetric unit, and approximately 36% (v/v) solvent. Crystals of both proteins diffract to beyond 2-A Bragg spacings and are relatively durable in an x-ray beam. On replacement of sulfate with NaCl, crystals of natural RNase H grow as Type I' (very similar to Type I) at pH between 7.0 and 8.0; at pH 8.8, crystals of Type II are obtained in space group P2(1)2(1)2(1) with a = 44.3 A, b = 87.3 A, and c = 35.7 A. Type II crystals can be converted to Type I by soaking in phosphate buffer. RNase H crystals of Type II have also been reported by Kanaya et al. (Kanaya, S., Kohara, A., Miyakawa, M., Matsuzaki, T., Morikawa, K., and Ikehara, M. (1989) J. Biol. Chem. 264, 11546-11549).

The origin of replication of the Escherichia coli chromosomal DNA binds with high affinity to outer membrane preparations. This specific binding requires a 463-base-pair region of origin DNA between positions -45 and +417 of the oriC map. We show that binding does not require the presence of adjacent regions. From further analysis, we conclude that more than one binding site resides within the 325-base-pair fragment between positions +38 (BamHI) and +417 (XhoI). When this fragment is cut, two pieces bind with high affinity and one binds with lesser affinity. The binding ability of one of the high affinity sites is abolished by cutting it at position +92 with BamHI.

The molecular model of myohemerythrin, an oxygen-carrying protein from sipunculan worms, has been refined by stereochemically restrained least-squares minimization at 1.7/1.3 A resolution to a conventional R-value of 0.158. The estimated positional standard deviation is better than 0.15 A for most of the 979 protein atoms. The average isotropic displacement parameter, B, for the protein atoms is 23.1 A2. This high average B parameter appears to be due to the overall motion of the molecule, which correlates with the observed anisotropic diffraction. The side-chains of seven residues were modeled in two conformations, i.e. the side-chains were discretely disordered, and B parameters for several lysine and glutamate side-chains indicate that they are poorly localized. Of the residues in myohemerythrin, 66% are helical, with 62% occurring in four long alpha-helices with mean values for the backbone torsion angles of phi = -65 degrees, psi = -42 degrees, and for the hydrogen bonds distances of N ... O, 3.0 A and H ... O, 2.1 A, and angles of N ... O = C, 153 degrees, N-H ... O, 157 degrees, and H ... O = C, 147 degrees. For two-thirds of the alpha-helical residues, the torsional rotation of the C alpha-C beta bond, chi 1, is approximately -60 degrees, and for one-third chi 1 is approximately 180 degrees. Although most turns in myohemerythrin are well-categorized by previous classification, two do not fit in established patterns. Also included in the refined model are three sulfate ions, all partially occupied, and 157 water molecules, 40% of which are modeled fully occupied. Only one water molecule is internal to the protein, the remainder occur on the surface and are observed principally between symmetry-related molecules contributing, along with van der Waals' contacts, most of the interactions between molecules. There are eight intermolecular protein-protein hydrogen bonds, of which only four are between well-located atoms.

Phospholipases in some snake venoms are potent neurotoxins that target their enzymatic action to the synaptic membrane. One of these is the heterodimeric neurotoxin, beta-bungarotoxin, which binds with a protease inhibitor-like subunit to a presynaptic potassium channel and then blocks neurotransmission with a second subunit that has phospholipase A2 activity. We have prepared and characterized well ordered crystals of the most toxic beta-bungarotoxin isoform, beta 1-bungarotoxin. The crystals are monoclinic, space group C2, with unit cell parameters: a = 176.5 A, b = 39.3 A, c = 92.7 A, and beta = 114.8 degrees. Rotation-function analysis of the Patterson function, as calculated from a 2.3-A data set, reveals an asymmetric unit composed of four heterodimers. These heterodimers appear to be associated as two crystallographically distinct (AB)4 tetramers, each having dihedral D2 symmetry. The two are positioned with equivalent molecular 2-fold axes coincident with crystallographic dyads, but rotated by 55 degrees relative to one another. X-ray analysis of these crystals will permit direct visualization of the specific structural motifs and chemical features that underlie phospholipase neurotoxicity.

We have characterized a streptavidin product that had been reduced to a minimal size that still retained full biotin-binding activity. This core streptavidin is proteolyzed at both ends at points that correspond closely with the termini of hen egg white avidin. Core streptavidin is more soluble than is the parent molecule. We have grown three different types of crystals of core streptavidin. The symmetry properties of these crystals prove that the molecule is a tetramer organized in tetrahedral (D2) point symmetry. The crystallographic response to the interaction of biotin with core streptavidin indicates that some conformational change accompanies ligand binding. We are attempting to determine the three-dimensional structure of streptavidin and its complex with selenobiotin from these crystals of core streptavidin.

The three-dimensional structure of the protein myohemerythrin from retractor muscles of the sipunculan worn Themiste zostericola has been explored for the existance of approximately symmetry operators that locally interrelate portions of the molecule. First, the electron denisty distribution at 5.5 A resolution was examined. A local 2-fold axis that transposes the C-D helix pair into the A-B helix pair was found and refined by the method of least squares. The match in electron densities for a pure 2-fold rotation had a correlation coefficient of 0.56. Next, a comprehensive search was made for rotational symmetry in the Patterson function of an isolated molecule. The rotation function based on data to 6 A spacings showed a major peak, 72% of the self-peak height, that confirmed the result from electron density correlations. In addition, a pattern of lower level peaks revealed approximate point group symmetry as high as D4. Finally, the amino acid sequence has been inspected for evidence of a repeated structure. The level of amino acid identities between positions in the A-B and C-D helix pairs is 28%. Several factors are discussed to suggest that this homology, although low, is nonetheless significant.

The crystal structure of Clostridium acidi-urici ferredoxin has been determined using multiple wavelength anomalous diffraction (MAD) techniques at 5.0-A resolution. The electron density map shows striking similarity to a map of Peptococcus aerogenes ferredoxin computed at the same resolution from the atomic coordinates reported by Adman et al. (Adman, E. T., Sieker, L. C., and Jensen, L. H. (1973) J. Biol. Chem. 248, 3987-3996). Such similarity is expected from the high degree of identity between amino acid sequences of the two proteins. The use of MAD methods has in the relatively recent past become a practical possibility due to instrumental advances enabling the collection of accurate data at several wavelengths at synchrotrons and due to theoretical and computational advances that facilitate the analysis of these data for the determination of phases. These methods hold great promise as an alternative to the multiple isomorphous replacement method in macromolecular structure determination. The present report represents one of the first applications of the MAD techniques to the determination of the structure of a protein which was previously unknown in detail.

Treatment of gently prepared lysates of Escherichia coli with single-strand-specific endonuclease (SI or from mung beans) results in the release of about 90% of the DNA from membranes, as determined by the M band technique. The released DNA has an average molecular weight of about 1.2 X 10(8). Data obtained with endonuclease S1 fit a mathematical model in which substrate sites are at or near membrane attachment sites. Data obtained with pancreatic deoxyribonuclease or x-rays fit a model for double-strand breaks at random sites along the DNA. Fitting data to these models, we estimate that there are 18+/-5 membrane attachment sites. The DNA remaining after S1 nuclease treatment is enriched for the region near the origin of chromosome replication. Therefore, attachment at this region near the origin of chromosome replication. Therefore, attachment at this region appears to be chemically different from that at the other sites along the DNA.

A complex consisting of replicative origin DNA and several proteins was isolated from Escherichia coli. Cells of temperature-sensitive mutants were labeled at the origin and fractionated by sucrose gradient centrifugation. A complex highly purified in origin DNA sedimented as a unique band. This complex dissociated at high concentration, above 0.2 M KCl. Upon dialysis, the complex reformed, allowing further purification of its constituents. Three major protein bands were found, corresponding to proteins of the outer membrane. The complex did not sediment with membrane fractions, but adhered to the outer membrane in the presence of magnesium.

X-ray diffraction data to a minimum Bragg spacing of 5.5 A have been collected from crystals of Lumbricus terrestris erthrocruorin, a 3.9 x 10(6)-dalton respiratory protein. Self-rotation function calculations from these data reveal D6 symmetry to a resolution of at least 6 A. These calculations show that erythrocruorin molecules pack in their crystals with molecular diads coincident with crystallographic diads along the a axis. Packing constraints limit the position of the molecular center to within 40 A of x = 1/4a.