Double-domain Structure Research Articles

Structure of CdTe(111)B grown by MBE on misoriented Si(001)

Single domain CdTe(111)B has been grown on Si(001) substrates tilted 1o 2o, and 4o toward [110]. All the layers started with a double-domain structure, then a transition from a double- to a single-domain was observed by reflection high energy electron diffraction. A microscopic picture of this transition is presented. We also measured the tilt between CdTe(111)B and Si(001). The result does not follow the tilt predicted by the currently existing model. A new model of the microscopic mechanism of CdTe(111)B growth is presented. New evidence indicates that optimizing the tilt of the substrate surface is very crucial in improving the CdTe(111)B crystal quality.

Atomic configuration dependent secondary electron emission from reconstructed silicon surfaces

We show that domains of reconstructed silicon surfaces can be imaged by secondary electrons (SEs) using an ultrahigh vacuum scanning electron microscope with a SE detector having angular resolvability. The SE images clearly show the double domain structure, alternate 2×1 and 1×2 domains on Si(100), as well as the coexistence of the reconstructed 7×7 domains and the nonreconstructed 1×1 domains on Si(111). These results demonstrate that SE emission is sensitive to the atomic configuration of the topmost layers. We call this scanning electron microscopy based technique for top layer imaging as scanning electron surface microscopy, which will evolve into a useful tool for surface characterization.

Epitaxial growth of yttrium silicide YSi 2− x on (100) Si

This paper reports the growth of epitaxial YSi 2− x layers on p-type (100) Si substrate. To grow the YSi 2− x , specimens were annealed between 300 and 900°C. By annealing above 550 °C, the hexagonal YSi 2− x grows epitaxially. The orientation relationships between the YSi 2− x and (100) Si substrate are identified as (1 100) YSi 2−x‖(100) Si with [0002] YSi 2−x‖[02 2] Si;OR1 (1 100) YSi 2−x‖(100) Si with [0002] YSi 2−x‖[0 22] Si;OR2 OR1 and OR2 are crystallographically equivalent, one being obtained by rotating 90° relative to the other around the common [1 1 00] YSi 2− x axis. The formation of this double-domain structure throughout the film is considered to be as a result of the relief of the large elastic strain energies induced by the anisotropy in the lattice mismatch. A portion of these strain energies is also likely to be relieved by the introduction of misfit dislocations in each domain.

Initial Growth Mechanism of Si on GaAs Studied by Reflection High-Energy Electron Diffraction Oscillations

We have studied the initial growth mechanism of Si on GaAs(100) and GaAs(111)B substrates by observing the behavior of the reflection high-energy electron diffraction (RHEED) specular beam intensity and the changes in the RHEED patterns. During the growth on just exactly substrates, we infer two-dimensional growth with nucleation on the terraces from the presence of RHEED oscillations. For the growth of Si on GaAs(100), a flat surface with bilayer steps (single domain) was obtained at ∼0.8 monolayers (ML) of growth. This structure was conserved up to ∼3 ML by a bilayer growth mode. With further growth, monolayer steps were formed on the surface and a double domain structure was observed. It is suggested that this change could be related to an alteration of the Si surface migration due to the high strain energy caused by the 4% lattice mismatch. A model is presented which includes some of the possible reactions between Si, Ga and As at the interface.

Eptiaxial Growth of bcc-Eu/Yb Superlattices - Stabilation of High Temperature Yb Metal Phase-

A bcc-Eu metal layer having a double-domain structure was grown by the molecular beam epitaxy technique on a cleaved NaCl (100) surface with the epitaxial relationship that Eu (110) [100] or [110] is parallel to NaCl (100) [100]. An epitaxial Eu/Yb superlattice was successfully prepared on this Eu buffer layer at a growth temperature of 260 K. The Yb layers in the prepared superlattices were found to be in the bec phase which is stable only at high temperatures above 1071 K. It was also shown that a bcc-Yb can be epitaxially grown on the bcc-Eu layer with thickness 1500 Å.

Epitaxial growth of bcc-Eu/Yb superlattices

A bcc-Eu metal layer having a double-domain structure was grown by the molecular-beam epitaxy (MBE) technique on a cleaved NaCl (100) surface with the epitaxial relationship that Eu (110) [100] or [110] is parallel to NaCl (100) [100]. An Eu/Yb superlattice was successfully prepared by MBE on this Eu buffer layer at a growth temperature of 260 K. The Yb layers in the prepared superlattices were found to be in the bcc phase which is stable only at high temperatures above 1071 K. It was also shown that a bcc-Yb can be epitaxially grown on the bcc-Eu layer up to a thickness of 1500 Å.

Molecular beam epitaxy of single domain InP films directly grown on Si(001) substrates

MBE growth of single domain InP films directly on Si(001) substrates was successfully achieved for the first time. Domain structures of the substrates and films were observed by RHEED during growth. The surface of the substrate showed a Si(001) 2×1 two domain structure. Initial thin ( ∽ 300Å) InP film grown on the substrate showed a double domain structure. With increasing film thickness, the domain structure of the film became single domain.

Sequence homologies, hydrophobic profiles and secondary structures of cathepsins B, H and L: comparison with papain and actinidin

The comparison of the amino acid sequences of 5 cysteine proteinases: papain, actinidin, rat cathepsins B and H and chicken cathepsin L, demonstrates a striking homology among their sequences. The N-terminal region (residues 1–70 in papain) and C-terminal region (residues 118–212 in papain) display the highest sequence homologies, whereas the lowest sequence homologies are observed in the middle region (residues 71–117 in papain); a segment where most insertions/deletions are observed. The highest sequence homology is observed between rat cathepsin H and chicken cathepsin L. As shown by X-ray studies, papain and actinidin have a clearly defined double domain structure. Each domain contains a core of non-polar side chains, which are retained in cathepsins B, H and L, except for the non-polar residue 203 of the core which is replaced by glutamic acid in cathepsin B. The percentage and the location of α-helix and β-sheets of cathepsins B, H and L, assessed using the methods of Garnier et al. (1978, J. Mol. Biol. 120, 97–120) and Chou and Fasman (1974, Biochemistry 13, 222–245), show that the main ordered structures in papain and actinidin are probably retained in cathepsins B, H and L. The differences observed occur essentially in the middle region, a place where sequences display the lowest homologies and which is far removed from the active site.

Structure of L-3-hydroxyacyl-coenzyme A dehydrogenase: preliminary chain tracing at 2.8-A resolution.

The conformation of L-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) has been derived from electron-density maps calculated at 2.8-A resolution with phases obtained from two heavy-atom derivatives and the bound coenzyme, NAD. Like other dehydrogenases, 3-hydroxyacyl-CoA dehydrogenase is a double-domain structure, but the bilobal nature of this enzyme is more pronounced than has been previously observed. The amino-terminal domain, which comprises approximately the first 200 residues, is responsible for binding the NAD cofactor and displays considerable structural homology with the dinucleotide binding domains observed in other NAD-, NADP-, and FAD-dependent enzymes. The carboxyl-terminal domain, comprising the remaining 107 residues, appears to be all alpha-helical and bears little homology to other known dehydrogenases. The subunit-subunit interface in the 3-hydroxyacyl-CoA dehydrogenase dimer is formed almost exclusively by residues in the smaller helical domain. A difference map between the apo and holo forms of the crystalline enzyme has been interpreted in terms of the NAD molecule being bound in a typically extended conformation. The location of the coenzyme binding site, along with the structural homology to other dehydrogenases, makes it possible to speculate about the location of the binding site for the fatty acyl-CoA substrate.

Characterization of the Antigen‐Specific T Cell Receptor from a Pigeon Cytochrome c‐Specific T Cell Hybrid

The monoclonal antibody, A2B4-2, specifically bound to and inhibited antigen-induced IL-2 release from the cloned pigeon cytochrome c-specific T cell hybrid, 2B4. The initial immunoprecipitation with these reagents demonstrated a protein of 85-90kd on non-reducing conditions, and two bands of 45-50 and 40-44 on reducing conditions. These data enabled us to conclude that this monoclonal antibody bound to the antigen receptor on the 2B4 cell. In this paper we have presented results that further define the receptor structure. The migration pattern of the protein on SDS-PAGE in the presence and absence of reducing agents was consistent with the interpretation that the receptor has intrachain disulfide bonds that create globular domains. Sequence data from the recently described cDNA clones that encode receptor genes confirm that there are cysteine residues in positions that could be involved in such disulfide bonding. Since both alpha and beta chains behave identically on the SDS-PAGE we predict that both chains have the same double domain structure. The antigen receptor has a heterodimeric structure. A relatively simple acidic alpha chain is bound to one of two forms of the beta chain. Some of the receptors have a beta chain equal in molecular weight to the alpha chain, while some of the beta chains (beta') are heavier and more acidic. The difference in beta chain forms appears to be due to different levels of glycosylation of this chain. The cDNA sequence data demonstrate that there are several possible carbohydrate addition sites on the protein encoded by this gene so it may be that 2B4 beta chains are present that are either completely or partially glycosylated at these sites. Finally, we have presented a preliminary experiment that indicates that a smaller 20-25kd molecule is associated with the antigen receptor. The well characterized T3 molecule appears to be in a complex with the clonotypic structure on human T cells. The crosslinking data that we present suggests that a similar molecule may be present in the murine system.

Structure of actinidin, after refinement at 1.7 Å resolution

The structure of the sulphydryl protease, actinidin, after refinement at 1.7 Å resolution, is described. The positions of most of the 1666 atoms have been determined with an accuracy better than 0.1 Å; only two residues (219 and 220) and the side-chain of a third (87) cannot be seen. In addition, the model contains 272 solvent molecules, all taken as water, except one which may be an ammonium ion. Atomic B values give a good indication of the mobility of different parts of the structure. Actinidin has a double domain structure, with one domain mostly helical in its secondary structure, and the other domain built around a twisted β-sheet. The geometry of hydrogen bonds in helices, β-structure and turns has been analysed. All are significantly non-linear, with the angle N-Ĥ…O ~160 °. Carbonyl groups are tilted outwards from the axis of each helix, the tilting apparently unaffected by whether or not additional hydrogen bonds are made (e.g. to water or side-chain atoms). Each domain is folded round a substantial core of non-polar side-chains, but the interface between domains is mostly polar. Interactions across this interface involve a network of eight buried water molecules, the buried carboxyl and amino groups of Glu35, Glu50, Lys181 and Lys17, other polar side-chains and a few hydrophobic groups. One other internal charged side-chain, that of Glu52, is adjacent to a buried solvent molecule, probably an ammonium ion. Other side-chain environments are described. One proline residue has a cis configuration. The sulphydryl group is oxidized, probably to SO 2 −, with one oxygen atom clearly visible but the other somewhat less certain. The active site geometry is otherwise compatible with the mechanism proposed by Drenth et al. (1975,1976) for papain. The positions of the 272 solvent molecules are described. The best-ordered water molecules are those that are internal (total of 17), in surface pockets, or in the intermolecular contact regions. These generally form three or four hydrogen bonds, two to proton acceptors and one or two to proton donors. Other water molecules make water bridges on the surface, sometimes covering the exposed edges of non-polar groups. Intermolecular contacts involve few protein atoms, but many water molecules.

Biochemical and structural studies of the tetragonal crystalline modification of the Escherichia coli elongation factor Tu.

The tetragonal crystalline form of the trypsin-treated Escherichia coli protein elongation factor Tu has been analyzed by biochemical and x-ray crystallographic techniques. The crystals contain two tightly associated polypeptide fragments of molecular weight 36,000 and 6,500 which represent 97% of the native enzyme. The crystals do not contain a short internal polypeptide fragment of 14 amino acids which dissociates from the native enzyme following mild trypsin digestion. The short fragment has been implicated in the aminoacyl-tRNA binding function and its location has been determined. The structure of the modified enzyme in the P4(3)2(1)2 crystal form has been determined to 5 A resolution by x-ray diffraction methods. The protein consists of two domains: the larger domain exhibits considerable alpha helical characteristics and the smaller domain has no identifiable secondary structural features. The relationship between the double domain structure of the enzyme and its biochemical properties is discussed.

The double domain structure of rhodanese.

A 3 A electron density map of bovine liver rhodanese shows, in conjunction with gel electrophoresis experiments, that rhodanese consists of a single polypeptide chain with molecular weight of 32,000. The map reveals a very clear double domain structure of the molecule. The two domains are of equal size and have very similar conformations. They are related by a pseudo dyad. Nevertheless, at a few places, distinct structural differences exist between the two domains. A four-stranded parallel β -structure occurs in each domain, with one of the helices running antiparallel to the β -sheet. The relationship of this super secondary structure with similar structures in other proteins is discussed briefly.