PubMed Health⌕ Search

Biomedical subjects

T A Baker

Publications and source records attributed to T A Baker.

At least 19 recordsLinked to original sources
PubMed1998

An ATP-ADP switch in MuB controls progression of the Mu transposition pathway.

MuB protein, an ATP-dependent DNA-binding protein, collaborates with Mu transposase to promote efficient transposition. MuB binds target DNA, delivers this target DNA segment to transposase and activates transposase's catalytic functions. Using ATP-bound, ADP-bound and ATPase-defective MuB proteins we investigated how nucleotide binding and hydrolysis control the activities of MuB protein, important for transposition. We found that both MuB-ADP and MuB-ATP stimulate transposase, whereas only MuB-ATP binds with high affinity to DNA. Four different ATPase-defective MuB mutants fail to activate the normal transposition pathway, further indicating that ATP plays critical regulatory roles during transposition. These mutant proteins fall into two classes: class I mutants are defective in target DNA binding, whereas class II mutants bind target DNA, deliver it to transposase, but fail to promote recombination with this DNA. Based on these studies, we propose that the switch from the ATP- to ADP-bound form allows MuB to release the target DNA while maintaining its stimulatory interaction with transposase. Thus, ATP-hydrolysis by MuB appears to function as a molecular switch controlling how target DNA is delivered to the core transposition machinery.

Adenosine Diphosphate↗
PubMed1997

PDZ-like domains mediate binding specificity in the Clp/Hsp100 family of chaperones and protease regulatory subunits.

ClpX, a molecular chaperone and the regulatory subunit of the ClpXP protease, is shown to contain tandem modular domains that bind to the C-terminal sequences of target proteins in a manner that parallels functional specificity. Nuclear magnetic resonance studies show that these C-terminal sequences are displayed as disordered peptides on the surface of otherwise folded proteins. The ClpX substrate-binding domains are homologous to sequences in other Clp/Hsp100 proteins and are related more distantly to PDZ domains, which also mediate C-terminal specific protein-protein interactions. Conservation of these binding domains indicates that the mode of substrate recognition characterized here for ClpX will be a conserved feature among Clp/Hsp100 family members and a distinguishing characteristic between this chaperone family and the Hsp70 chaperones.

ATPases Associated with Diverse Cellular Activitie↗
PubMed1997

Conduction in segmentally demyelinated mammalian central axons.

The prominent symptoms associated with central demyelinating diseases such as multiple sclerosis (MS) are primarily caused by conduction deficits in affected axons. The symptoms may go into remission, but the mechanisms underlying remissions are uncertain. One factor that could be important is the restoration of conduction to affected axons, but it is not known whether demyelinated central axons resemble their peripheral counterparts in being able to conduct in the absence of repair by remyelination. In the present study we have made intra-axonal recordings from central axons affected by a demyelinating lesion, and then the axons have been labeled ionophoretically to permit their subsequent identification. Ultrastructural examination of 23 labeled preparations has established that some segmentally demyelinated central axons can conduct, and that they can do so over continuous lengths of demyelination exceeding several internodes (2500 micron). Such segmentally demyelinated central axons were found to conduct with the anticipated reduction in velocity and a refractory period of transmission (RPT) as much as 34 times the value obtained from the nondemyelinated portion of the same axon; the RPT was typically prolonged to 2-5 times the normal value. We conclude that some segmentally demyelinated central axons can conduct, and we propose that the restoration of conduction to such axons is likely to contribute to the remissions commonly observed in diseases such as MS.

Action Potentials↗
PubMed1997

ClpX and MuB interact with overlapping regions of Mu transposase: implications for control of the transposition pathway.

Transposition of phage Mu is catalyzed by an extremely stable transposase-DNA complex. Once recombination is complete, the Escherichia coli ClpX protein, a member of the Clp/Hsp100 chaperone family, initiates disassembly of the complex for phage DNA replication to commence. To understand how the transition between recombination and replication is controlled, we investigated how transposase-DNA complexes are recognized by ClpX. We find that a 10-amino-acid peptide from the carboxy-terminal domain of transposase is required for its recognition by ClpX. This short, positively charged peptide is also sufficient to convert a heterologous protein into a ClpX substrate. The region of transposase that interacts with the transposition activator, MuB protein, is also defined further and found to overlap with that recognized by ClpX. As a consequence, MuB inhibits disassembly of several transposase-DNA complexes that are intermediates in recombination. This ability of MuB to block access to transposase suggests a mechanism for restricting ClpX-mediated remodeling to the proper stage during replicative transposition. We propose that overlap of sequences involved in subunit interactions and those that target a protein for remodeling or destruction may be a useful design for proteins that function in pathways where remodeling or degradation must be regulated.

ATPases Associated with Diverse Cellular Activitie↗
PubMed1996

The interwoven architecture of the Mu transposase couples DNA synapsis to catalysis.

Mu transposition occurs exclusively using a pair of recombination sites found at the ends of the phage genome. To address the mechanistic basis of this specificity, we have determined both where the individual subunits of the tetrameric transposase bind on the DNA and where they catalyze DNA joining. We demonstrate that subunits do not catalyze recombination at the site adjacent to where they are bound, but rather on the opposite end of the phage genome. Furthermore, subunits bound to two different sites contribute to catalysis of one reaction step. This interwoven subunit arrangement suggests a molecular explanation for the precision with which recombination occurs using a pair of DNA signals and provides an example of the way in which the architecture of a protein-DNA complex can define the reaction products.

Amino Acid Sequence↗
PubMed1995

Assembly of phage Mu transpososomes: cooperative transitions assisted by protein and DNA scaffolds.

Transposition of phage Mu takes place within higher order protein-DNA complexes called transpososomes. These complexes contain the two Mu genome ends synapsed by a tetramer of Mu transposase (MuA). Transpososome assembly is tightly controlled by multiple protein and DNA sequence cofactors. We find that assembly can occur through two distinct pathways. One previously described pathway depends on an enhancer-like sequence element, the internal activation sequence (IAS). The second pathway depends on a MuB protein-target DNA complex. For both pathways, all four MuA monomers in the tetramer need to interact with an assembly-assisting element, either the IAS or MuB. However, once assembled, not all MuA monomers within the transpososome need to interact with MuB to capture MuB-bound target DNA. The multiple layers of control likely are used in vivo to ensure efficient rounds of DNA replication when needed, while minimizing unwanted transposition products.

Bacteriophage mu↗
PubMed1995

Disassembly of the Mu transposase tetramer by the ClpX chaperone.

Mu transposition is promoted by an extremely stable complex containing a tetramer of the transposase (MuA) bound to the recombining DNA. Here we purify the Escherichia coli ClpX protein, a member of a family of multimeric ATPases present in prokaryotes and eukaryotes (the Clp family), on the basis of its ability to remove the transposase from the DNA after recombination. Previously, ClpX has been shown to function with the ClpP peptidase in protein turnover. However, neither ClpP nor any other protease is required for disassembly of the transposase. The released MuA is not modified extensively, degraded, or irreversibly denatured, and is able to perform another round of recombination in vitro. We conclude that ClpX catalyzes the ATP-dependent release of MuA by promoting a transient conformational change in the protein and, therefore, can be considered a molecular chaperone. ClpX is important at the transition between the recombination and DNA replication steps of transposition in vitro; this function probably corresponds to the essential contribution of ClpX for Mu growth. Deletion analysis reveals that the sequence at the carboxyl terminus of MuA is important for disassembly by ClpX and can target MuA for degradation by ClpXP in vitro. These data contribute to the emerging picture that members of the Clp family are chaperones specifically suited for disaggregating proteins and are able to function with or without a collaborating protease.

ATPases Associated with Diverse Cellular Activitie↗
PubMed1995

Replication arrest.

Explore the source record for details and available documents.

Bacterial Proteins↗
PubMed1994

Complete transposition requires four active monomers in the mu transposase tetramer.

A tetramer of Mu transposase (MuA) cleaves and joins multiple DNA strands to promote transposition. Derivatives of MuA altered at two acidic residues that are conserved among transposases and retroviral integrases form tetramers but are defective in both cleavage and joining. These mutant proteins were used to analyze the contribution of individual monomers to the activity of the tetramer. The performance of different protein combinations demonstrates that not all monomers need to be catalytically competent for the complex to promote an individual cleavage or joining reaction. Furthermore, the results indicate that each pair of essential residues is probably donated to the active complex by a single monomer. Although stable, tetramers composed of a mixture of mutant and wild-type MuA generate products cleaved at only one end and with only one end joined to the target DNA. The abundance of these abortive products and the ratios of the two proteins in complexes stalled at different steps indicate that the complete reaction requires the activity of all four monomers. Thus, each subunit of MuA appears to use the conserved acidic amino acids to promote one DNA cleavage or one DNA joining reaction.

Bacteriophage mu↗
PubMed1994

Identification of residues in the Mu transposase essential for catalysis.

A tetramer of Mu transposase (MuA) cleaves the phage Mu DNA and joins these ends to a target DNA to catalyze transposition. Substitution mutations at Asp-269 or Glu-392 within MuA destroy both the DNA cleavage and joining activities without blocking tetramer assembly, indicating that the mutations specifically affect catalysis. Although inactive under standard reaction conditions (10 mM Mg2+), the mutant proteins are partially resuscitated by 10-20 mM Mn2+, concentrations 5- to 10-fold higher than optimal for wild-type MuA. Amino acid sequence alignment and the similar effects of mutations suggests that Asp-269 and Glu-392 of MuA may be analogs of the first Asp and final Glu of a conserved triad of acidic amino acids present in many transposases and the retroviral integrases (the D-D-35-E motif). The higher Mn2+ optima observed with MuA derivatives altered at these positions supports a role for the conserved acidic amino acids in coordinating divalent metal ions in the active sites of transposases.

Amino Acid Sequence↗
PubMed1994

HIV/AIDS.

Explore the source record for details and available documents.

Acquired Immunodeficiency Syndrome↗
PubMed1993

Division of labor among monomers within the Mu transposase tetramer.

A single tetramer of Mu transposase (MuA) pairs the recombination sites, cleaves the donor DNA, and joins these ends to a target DNA by strand transfer. Analysis of C-terminal deletion derivatives of MuA reveals that a 30 amino acid region between residues 575 and 605 is critical for these three steps. Although inactive on its own, a deletion protein lacking this region assembles with the wild-type protein. These mixed tetramers carry out donor cleavage but do not promote strand transfer, even when the donor cleavage stage is bypassed. These data suggest that the active center of the transposase is composed of the C-terminus of four MuA monomers; one dimer carries out donor cleavage while all four monomers contribute to strand transfer.

Bacteriophage phi X 174↗
PubMed1993

Protein-DNA assemblies controlling lytic development of bacteriophage Mu.

Recent analysis of the mechanism and regulation of transposition by bacteriophage Mu has emphasized the importance of controlled assembly of specific protein-DNA complexes. Both the Mu transposase and the Mu repressor engage in multiple protein-protein and protein-DNA interactions that modulate the outcome of a phage infection.

Bacteriolysis↗
PubMed1993

Family practice and internal medicine office fees: an analysis of charge differences.

BACKGROUND: This study applies the concept of economic efficiency to primary health care physicians. Comparisons of charges made by family physicians and general internists would provide evidence of "optimal" health care delivery of primary care services. METHODS: A list of all active licensed primary care physicians was obtained from the office of the Oregon State Board of Medical Examiners. Two thousand eight hundred forty-three questionnaires were sent to Oregon primary care physicians. Of the 1365 responses, 484 were family physicians and 341 were general internists. RESULTS: The study found that family physicians had significantly lower mean office visit fees than general internists, while both groups had essentially similar patient mixes. This difference in fees could not be explained by patient case mix. CONCLUSIONS: The findings of this study and the body of literature available support the concept that family practice physicians provide economically efficient primary health care. If two similarly trained physicians provide a comparable level of medical care, with the same or similar outcome (or output), the physician who provides the care for the lowest cost should be used.

Diagnosis-Related Groups↗
PubMed1992

Assembly of the active form of the transposase-Mu DNA complex: a critical control point in Mu transposition.

Discovery and characterization of a new intermediate in Mu DNA transposition allowed assembly of the transposition machinery to be separated from the chemical steps of recombination. This stable intermediate, which accumulates in the presence of Ca2+, consists of the two ends of the Mu DNA synapsed by a tetramer of the Mu transposase. Within this stable synaptic complex (SSC), the recombination sites are engaged but not yet cleaved. Thus, the SSC is structurally related to both the cleaved donor and strand transfer complexes, but precedes them on the transposition pathway. Once the active protein-DNA complex is constructed, it is conserved throughout transposition. The participation of internal sequence elements and accessory factors exclusively during SSC assembly allows recombination to be controlled prior to the irreversible chemical steps.

Bacteriophage mu↗