Host Template Research Articles

Sequence-structure specificity of a knowledge based energy function at the secondary structure level.

This paper investigates the sequence-structure specificity of a representative knowledge based energy function by applying it to threading at the level of secondary structures of proteins. Assessing the strengths and weaknesses of an energy function at this fundamental level provides more detailed and insightful information than at the tertiary structure level and the results obtained can be useful in tertiary level threading. We threaded each of the 293 non-redundant proteins onto the secondary structures contained in its respective native protein (host template). We also used 68 pairs of proteins with similar folds and low sequence identity. For each pair, we threaded the sequence of one protein onto the secondary structures of the other protein. The discerning power of the total energy function and its one-body, pairwise, and mutation components is studied. We then applied our energy function to a recent study which demonstrated how a designed 11-amino acid sequence can replace distinct segments (one segment is an alpha-helix, the other is a beta-sheet) of a protein without changing its fold. We conducted random mutations of the designed sequence to determine the patterns for favorable mutations. We also studied the sequence-structure specificity at the boundaries of a secondary structure. Finally, we demonstrated how to speed up tertiary level threading by filtering out alignments found to be energetically unfavorable during the secondary structure threading. The program is available on request from the authors. xud@ornl.gov

Processing, Characterization, and Measurement of the Seebeck Coefficient of Bismuth Microwire Array Composites

ABSTRACTWe have fabricated Bi microwire array composites ranging in diameter from 10 to 50 micrometer using the method of high-pressure-injection (HPI) of the Bi melt into microchannel arrays (MCA) templates. The composites are dense, with Bi volume fraction in excess of 70 %. The parallel Bi nanowires, whose length appears to be limited only by the thickness of the host template (up to 2 mm), terminate at both sides of the composite in the Bi bulk. The individual Bi microwire crystal structure is rhombohedral, with the same lattice parameters as that of bulk Bi; the wires crystalline orientation is predominantly perpendicular to the (113) lattice plane. The transversal magnetoresistance and Seebeck effect of the wires has been measured in magnetic fields up to 0.8 Tesla and for temperatures ranging between 77 K and room temperature.

Modelling of structure, sorption, synthesis and reactivity in catalytic systems

We illustrate the current status of the application of computer modelling methods to catalytic systems by taking recent examples from modelling of both long range and local structural properties of microporous materials, surface structures of oxides, sorption in zeolites, host–template interactions in aluminophosphates and reaction mechanisms on oxide surfaces and at acid sites in zeolites. We emphasise the role of modelling techniques in the interpretation of experimental studies in catalysis.

Porphyrin Blocking Groups in Amide‐Based Rotaxanes

AbstractThe synthesis of amide‐based symmetrical rotaxanes2a,bbearing porphyrin blocking groups is firstly described. These compounds can be obtained by a one‐step one‐pot reaction only if the macromonocyclic host template complementary to the threading guest is found. The symmetry of the axle is removed by introducing an unsymmetrical central part, leading to the formation of rotaxane2c. Different blocking groups were used to obtain the non‐symmetrical rotaxane3a. The bis‐Zn2+complex10aof the rotaxane2awas isolated. A nonionic supramolecular complex7was assumed as threaded intermediate, which was blocked by reaction with the stopper components. The amide‐type rotaxane system thus proved to be variable with respect to all its parts including stopper components of different reactivity, bulkiness and supramolecular functionality.

Reinitiation at the λ DNA origin accompanies the host SOS response

Abnormal reinitiation of replication from λ origins has previously been found during infection in the presence of caffeine or cis-diamminedichloroplatinum II ( cis-Pt) or when λ infects a P2 lysogen. It was further shown that the reinitiations arising from cis-Pt treatment took place during the SOS response induced by the template damage caused by the drug. It is now shown that SOS induction by uv irradiation of the host also results in reinitiation events and that it is the SOS response itself rather than some other direct effect of the damaged host template that is responsible for the phenomenon. Parental sections of λ replicative intermediates can supercoil, whereas daughter segments cannot. To explain the control that prevents reinitiation, it is proposed that normally the origin sequence has to be under superhelical tension to be a suitable substrate for the initiating machinery; once a round is in progress, the daughter origin sequences would not be under such tension and would therefore be inactive. It is shown that in an SOS environment the proposed requirement for a superhelical origin sequence is relaxed and consequently the control against reinitiation lost. Under such conditions, primary growing points that have encountered template lesions terminate and a new wave of replication initiates.

Localization of host poly(A)+ mRNA in the ribosome profile of mengovirus-infected Ehrlich ascites tumor cells

The distribution of poly(A)+ mRNA among polysomes, monosomes, and ribosome-free supernatant fractions after mengovirus infection of Ehrlich ascites tumor (EAT) cells was investigated employing sucrose gradient centrifugation of their corresponding postnuclear supernatants. Poly(A)+ mRNA was isolated from sucrose gradient fractions and quantitated in a cell-free protein synthesizing system from uninfected EAT cells. It was also localized by annealing [3H]-poly(U) to the poly(A)-tracts of mRNA present in the sucrose gradient fractions. Both experiments revealed a gradual shift of host poly(A)+ mRNA from large to small polysomes and monosomes, respectively, with the time postinfection. The greatest part of host template RNA appears to remain ribosome-bound and only a fraction seems to be detached from the ribosomes in the course of mengovirus infection. At the end of the infectious cycle, 8 h postinfection, approximately 70% of the poly(A)+ mRNA detected in uninfected cells is still biologically active, but not translated in vivo, in agreement with data from the [3H]poly(U)hybridization experiment.

Coding capacity of poly(A)+ mRNA isolated from mengovirus-infected Ehrlich ascites tumor cells

Total poly (A)+mRNA was isolated from mengovirus-infected Ehrlich ascites tumor cells at various times postinfection and quantitated in a cell-free system derived from uninfected ascites cells. Basic proteins were separated from acidic proteins by carboxymethyl cellulose chromatography. At the end of the infectious cycle, 8h postinfection, the cellular contents of most mRNAs coding for basic ribosomal proteins are still between 70 and 90 percent of those measured at the beginning of infection or in uninfected cells. On the basis of this result, the rapid shutoff of host protein synthesis after mengovirus infection of Ehrlich ascites tumor cells cannot be the consequence of the inactivation of host template RNA.

Selective translation of T4 template RNA by ribosomes from T4-infected Escherichia coli.

The present studies indicate that T4 infection induces an alteration in host ribosomes which restricts the translation of host and other T4-unrelated template RNAs but permits normal translation of T4 RNA. A heat-labile factor has been isolated from T4-infected cell ribosomes which, when combined with normal cell ribosomes, confers upon the latter the property of selective T4 template RNA translation.