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Francisco J Asturias

Publications and source records attributed to Francisco J Asturias.

15 recordsLinked to original sources
PubMed2006

The parallelization of SPIDER on distributed-memory computers using MPI.

We describe the strategies and implementation details we employed to parallelize the SPIDER software package on distributed-memory parallel computers using the message passing interface (MPI). The MPI-enabled SPIDER preserves the interactive command line and batch interface used in the sequential version of SPIDER, thus does not require users to modify their existing batch programs. We show the excellent performance of the MPI-enabled SPIDER when it is used to perform multi-reference alignment and 3-D reconstruction operations on a number of different computing platforms. We point out some performance issues when the MPI-enabled SPIDER is used for a complete 3-D projection matching refinement run, and propose several ways to further improve the parallel performance of SPIDER on distributed-memory machines.

Algorithms↗
PubMed2006

Mammalian fatty acid synthase: X-ray structure of a molecular assembly line.

Mammalian fatty acid synthase (FAS) is a homodimeric, multifunctional polypeptide which comprises two full sets of catalytic subunits that carry out fatty acid synthesis. A recently published X-ray structure of FAS reveals, for the first time, the organization of all active sites involved in acyl chain elongation and provides a structural framework for interpretation of extensive functional studies. Further analysis with techniques capable of providing information about single molecule conformations will eventually provide a more complete understanding of FAS.

Amino Acid Substitution↗
PubMed2005

Structure of Saccharomyces cerevisiae DNA polymerase epsilon by cryo-electron microscopy.

The structure of the multisubunit yeast DNA polymerase epsilon (Pol epsilon) was determined to 20-A resolution using cryo-EM and single-particle image analysis. A globular domain comprising the catalytic Pol2 subunit is flexibly connected to an extended structure formed by subunits Dpb2, Dpb3 and Dpb4. Consistent with the reported involvement of the latter in interaction with nucleic acids, the Dpb portion of the structure directly faces a single cleft in the Pol2 subunit that seems wide enough to accommodate double-stranded DNA. Primer-extension experiments reveal that Pol epsilon processivity requires a minimum length of primer-template duplex that corresponds to the dimensions of the extended Dpb structure. Together, these observations suggest a mechanism for interaction of Pol epsilon with DNA that might explain how the structure of the enzyme contributes to its intrinsic processivity.

Catalysis↗
PubMed2005

Preponderance of free mediator in the yeast Saccharomyces cerevisiae.

Biochemical evidence suggesting that the predominant form of Mediator in the yeast Saccharomyces cerevisiae might be one in which the complex is associated with RNA polymerase II to form a holoenzyme has led to the proposition of a holoenzyme-based model for transcription initiation. We report that polymerase-free Mediator, isolated early on during a whole-cell extract fractionation protocol, is in fact the most abundant form of the Mediator complex. The existence of free Mediator would make possible independent recruitment of Mediator and RNA polymerase II to the pre-initiation complex. This is in agreement with reports from in vivo studies of time and spatial independence of Mediator and RNA polymerase II promoter interaction, with current models of pre-initiation complex structure in which promoter DNA upstream of the transcription start site is positioned between Mediator and polymerase, and with the proposed role of Mediator as the major component of the Scaffold complex involved in transcription reinitiation.

Cell Fractionation↗
PubMed2005

Structure and molecular organization of mammalian fatty acid synthase.

De novo synthesis of fatty acids in the cytosol of animal cells is carried out by the multifunctional, homodimeric fatty acid synthase (FAS). Cryo-EM analysis of single FAS particles imaged under conditions that limit conformational variability, combined with gold labeling of the N termini and structural analysis of the FAS monomers, reveals two coiled monomers in an overlapping arrangement. Comparison of dimeric FAS structures related to different steps in the fatty acid synthesis process indicates that only limited local rearrangements are required for catalytic interaction among different functional domains. Monomer coiling probably contributes to FAS efficiency and provides a structural explanation for the reported activity of a FAS monomer dimerized to a catalytically inactive partner. The new FAS structure provides a new paradigm for understanding the architecture of FAS and the related modular polyketide synthases.

Animals↗
PubMed2005

Structure of eukaryotic Mediator complexes.

Mediator, a macromolecular complex comprising approximately 20 different protein components, is largely responsible for the tight control of transcription that underpins cell development, differentiation, and maintenance in eukaryotes from yeast to human. In the past five years, macromolecular electron microscopy has been used to characterize the structure of Mediator, and of the complexes it forms with other components of the transcription machinery. The results reveal how Mediator interacts with RNA polymerase II, and suggest that regulatory information could be conveyed through changes in Mediator conformation that would influence the transcription initiation process.

Animals↗
PubMed2004

Head-to-head coiled arrangement of the subunits of the animal fatty acid synthase.

The role of the beta-ketoacyl synthase domains in dimerization of the 2505 residue subunits of the multifunctional animal FAS has been evaluated by a combination of crosslinking and characterization of several truncated forms of the protein. Polypeptides containing only the N-terminal 971 residues can form dimers, but polypeptides lacking only the N-terminal 422 residue beta-ketoacyl synthase domain cannot. FAS subunits can be crosslinked with spacer lengths as short as 6 A, via cysteine residues engineered near the N terminus of the full-length polypeptides. The proximity of the N-terminal beta-ketoacyl synthase domains and their essential role in dimerization is consistent with a revised model for the FAS in which a head-to-head arrangement of two coiled subunits facilitates functional interactions between the dimeric beta-ketoacyl synthase and the acyl carrier protein domains of either subunit.

Animals↗
PubMed2004

RNA polymerase II structure, and organization of the preinitiation complex.

Recent X-ray and cryo-electron microscopy studies have provided information about the basal eukaryotic transcription machinery and about Mediator, the complex involved in transcription regulation during initiation. On the basis of this structural information, a model describing the minimal transcription complex and its interaction with Mediator has been proposed. The model provides insight into the possible mechanisms of transcription initiation and regulation.

Animals↗
PubMed2003

RNA polymerase II/TFIIF structure and conserved organization of the initiation complex.

The structure of an RNA polymerase II/general transcription factor TFIIF complex was determined by cryo-electron microscopy and single particle analysis. Density due to TFIIF was not concentrated in one area but rather was widely distributed across the surface of the polymerase. The largest subunit of TFIIF interacted with the dissociable Rpb4/Rpb7 polymerase subunit complex and with the mobile "clamp." The distribution of the second largest subunit of TFIIF was very similar to that previously reported for the sigma subunit in the bacterial RNA polymerase holoenzyme, consisting of a series of globular domains extending along the polymerase active site cleft. This result indicates that the second TFIIF subunit is a true structural homolog of the bacterial sigma factor and reveals an important similarity of the transcription initiation mechanism between bacteria and eukaryotes. The structure of the RNAPII/TFIIF complex suggests a model for the organization of a minimal transcription initiation complex.

Animals↗
PubMed2002

Structural analysis of the RSC chromatin-remodeling complex.

Electron microscopy of the RSC chromatin-remodeling complex reveals a ring of protein densities around a central cavity. The size and shape of the cavity correspond closely to those of a nucleosome. Results of nuclease protection analysis are consistent with nucleosome binding in the cavity. Such binding could explain the ability of RSC to expose nucleosomal DNA in the presence of ATP without loss of associated histones.

Adenosine Triphosphate↗
PubMed2002

Structure of yeast RNA polymerase II in solution: implications for enzyme regulation and interaction with promoter DNA.

An 18 A resolution structure of the 12-subunit yeast RNA polymerase II (RNAPII) calculated from electron microscope images of single particles preserved in amorphous ice reveals the conformation of the enzyme in solution. The Rpb4/Rpb7 polymerase subunit complex was localized and found to be ideally positioned to determine the path of the nascent RNA transcript. The RNAPII structure suggests a revised mode of interaction with promoter DNA and demonstrates that regulation of RNAPII must involve structural changes that render the enzyme competent for initiation.

Binding Sites↗