Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 33
Filter
1.
Head Neck ; 2024 Apr 29.
Article in English | MEDLINE | ID: mdl-38680087

ABSTRACT

BACKGROUND: Post-treatment surveillance recommendations for oropharyngeal cancer do not vary with p16 status despite the differences in outcomes. The optimal algorithm personalizing follow-up for these patients remains undefined. Here, we evaluate the feasibility and utility of incorporating electronic patient-reported outcomes (ePROs) and circulating tumor DNA (ctDNA) into routine surveillance for patients treated for p16+ oropharynx cancer. METHODS: A prospective registry was developed in which ePROs and ctDNA were incorporated into routine surveillance among patients with oropharynx cancer. ePROs were emailed monthly for 1 year and blood HPV ctDNA testing was performed every 3-6 months. The primary objective was to assess patient compliance with ePRO-based surveillance with adequate compliance defined as ≥85% of patients completing monthly ePROs. Sensitivity, specificity, and positive/negative predictive values to detect recurrence were calculated for ePROs, HPV ctDNA, or the combination. RESULTS: Of 122 patients who initially expressed interest, 76 completed the electronic consent process and 44/76 (58%) were compliant with monthly surveys over 1 year; thus adequate compliance was not achieved. Technical difficulties associated with ePRO receipt through email largely limited participation. Provider feedback was significantly associated with heightened ePRO compliance. One hundred and six patients had ctDNA testing with a mean number of three tests per patient. Sensitivity to detect recurrence was 75% for the combination of ePROs and ctDNA. CONCLUSION: Despite lower than anticipated compliance with ePROs, our findings show promise for incorporation of HPV ctDNA into surveillance paradigms for HPV-related oropharynx cancer with suggestions of methods to optimize ePRO formats for personalized surveillance.

2.
EMBO J ; 43(8): 1634-1652, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38467832

ABSTRACT

During bacterial cell growth, hydrolases cleave peptide cross-links between strands of the peptidoglycan sacculus to allow new strand insertion. The Pseudomonas aeruginosa carboxyl-terminal processing protease (CTP) CtpA regulates some of these hydrolases by degrading them. CtpA assembles as an inactive hexamer composed of a trimer-of-dimers, but its lipoprotein binding partner LbcA activates CtpA by an unknown mechanism. Here, we report the cryo-EM structures of the CtpA-LbcA complex. LbcA has an N-terminal adaptor domain that binds to CtpA, and a C-terminal superhelical tetratricopeptide repeat domain. One LbcA molecule attaches to each of the three vertices of a CtpA hexamer. LbcA triggers relocation of the CtpA PDZ domain, remodeling of the substrate binding pocket, and realignment of the catalytic residues. Surprisingly, only one CtpA molecule in a CtpA dimer is activated upon LbcA binding. Also, a long loop from one CtpA dimer inserts into a neighboring dimer to facilitate the proteolytic activity. This work has revealed an activation mechanism for a bacterial CTP that is strikingly different from other CTPs that have been characterized structurally.


Subject(s)
Endopeptidases , Pseudomonas aeruginosa , Pseudomonas aeruginosa/metabolism , Endopeptidases/metabolism , Proteolysis
3.
Nat Commun ; 15(1): 660, 2024 Jan 22.
Article in English | MEDLINE | ID: mdl-38253530

ABSTRACT

The molecular chaperone DnaK is essential for viability of Mycobacterium tuberculosis (Mtb). DnaK hydrolyzes ATP to fold substrates, and the resulting ADP is exchanged for ATP by the nucleotide exchange factor GrpE. It has been unclear how GrpE couples DnaK's nucleotide exchange with substrate release. Here we report a cryo-EM analysis of GrpE bound to an intact Mtb DnaK, revealing an asymmetric 1:2 DnaK-GrpE complex. The GrpE dimer ratchets to modulate both DnaK nucleotide-binding domain and the substrate-binding domain. We further show that the disordered GrpE N-terminus is critical for substrate release, and that the DnaK-GrpE interface is essential for protein folding activity both in vitro and in vivo. Therefore, the Mtb GrpE dimer allosterically regulates DnaK to concomitantly release ADP in the nucleotide-binding domain and substrate peptide in the substrate-binding domain.


Subject(s)
Mycobacterium tuberculosis , Tuberculosis , Humans , Nucleotides , Polymers , Adenosine Triphosphate
4.
mSphere ; 7(5): e0027422, 2022 Oct 26.
Article in English | MEDLINE | ID: mdl-35993699

ABSTRACT

Mycobacterium tuberculosis possesses a Pup-proteasome system analogous to the eukaryotic ubiquitin-proteasome pathway. We have previously shown that the hexameric mycobacterial proteasome ATPase (Mpa) recruits pupylated protein substrates via interactions between amino-terminal coiled-coils in Mpa monomers and the degradation tag Pup. However, it is unclear how Mpa rings interact with a proteasome due to the presence of a carboxyl-terminal ß-grasp domain unique to Mpa homologues that makes the interaction highly unstable. Here, we describe newly identified critical interactions between Mpa and 20S core proteasomes. Interestingly, the Mpa C-terminal GQYL motif binds the 20S core particle activation pocket differently than the same motif of the ATP-independent proteasome accessory factor PafE. We further found that the ß-hairpin of the Mpa ß-grasp domain interacts variably with the H0 helix on top of the 20S core particle via a series of ionic and hydrogen-bond interactions. Individually mutating several involved residues reduced Mpa-mediated protein degradation both in vitro and in vivo. IMPORTANCE The Pup-proteasome system in Mycobacterium tuberculosis is critical for this species to cause lethal infections in mice. Investigating the molecular mechanism of how the Mpa ATPase recruits and unfolds pupylated substrates to the 20S proteasomal core particle for degradation will be essential to fully understand how degradation is regulated, and the structural information we report may be useful for the development of new tuberculosis chemotherapies.


Subject(s)
Mycobacterium tuberculosis , Animals , Mice , Adenosine Triphosphatases/genetics , Adenosine Triphosphate/metabolism , Bacterial Proteins/metabolism , Hydrogen/metabolism , Mycobacterium tuberculosis/genetics , Mycobacterium tuberculosis/metabolism , Proteasome Endopeptidase Complex/chemistry , Proteasome Endopeptidase Complex/metabolism , Ubiquitins/genetics , Ubiquitins/chemistry , Ubiquitins/metabolism
5.
mBio ; 13(1): e0368021, 2022 02 22.
Article in English | MEDLINE | ID: mdl-35038915

ABSTRACT

Pseudomonas aeruginosa CtpA is a carboxyl-terminal processing protease that partners with the outer membrane lipoprotein LbcA to degrade at least five cell wall-associated proteins, four of which are cell wall hydrolases. This activity plays an important role in supporting P. aeruginosa virulence in a mouse model of acute pneumonia. However, almost nothing is known about the molecular mechanisms underlying CtpA and LbcA function. Here, we used structural analysis to show that CtpA alone assembles into an inactive hexamer comprising a trimer of dimers, which limits its substrate access and prevents nonspecific degradation. The adaptor protein LbcA is a right-handed open spiral with 11 tetratricopeptide repeats, which might wrap around a substrate to deliver it to CtpA for degradation. By structure-guided mutagenesis and functional assays, we also showed that the interfaces of the CtpA trimer of dimers and an N-terminal helix of LbcA are important for LbcA-mediated substrate degradation by CtpA both in vitro and in vivo. This work improves our understanding of the molecular mechanism of the LbcA-CtpA proteolytic system and reveals some striking differences from the arrangements found in some other bacterial CTPs. IMPORTANCE Carboxyl-terminal processing proteases (CTPs) are found in all three domains of life. In bacteria, some CTPs have been associated with virulence, raising the possibility that they could be therapeutic targets. However, relatively little is known about their molecular mechanisms of action. In Pseudomonas aeruginosa, CtpA supports virulence by working in complex with the outer membrane lipoprotein LbcA to degrade cell wall hydrolases. Here, we report structure-function analyses of CtpA and LbcA, which reveals that CtpA assembles into an inactive hexamer comprising a trimer of dimers. LbcA is monomeric, with the first N-terminal helix important for binding to and activating CtpA, followed by a spiral structure composed of 11 tetratricopeptide repeats, which could wrap around a substrate for delivery to CtpA. This work reveals a unique mutimeric arrangement for a CTP and insight into how the important LbcA-CtpA proteolytic system functions.


Subject(s)
Bacterial Proteins , Pseudomonas aeruginosa , Animals , Mice , Pseudomonas aeruginosa/metabolism , Bacterial Proteins/metabolism , Proteolysis , Membrane Proteins/metabolism , Lipoproteins/metabolism
6.
Nat Commun ; 12(1): 5207, 2021 09 01.
Article in English | MEDLINE | ID: mdl-34471127

ABSTRACT

Uropathogenic Escherichia coli assemble surface structures termed pili or fimbriae to initiate infection of the urinary tract. P pili facilitate bacterial colonization of the kidney and pyelonephritis. P pili are assembled through the conserved chaperone-usher pathway. Much of the structural and functional understanding of the chaperone-usher pathway has been gained through investigations of type 1 pili, which promote binding to the bladder and cystitis. In contrast, the structural basis for P pilus biogenesis at the usher has remained elusive. This is in part due to the flexible and variable-length P pilus tip fiber, creating structural heterogeneity, and difficulties isolating stable P pilus assembly intermediates. Here, we circumvent these hindrances and determine cryo-electron microscopy structures of the activated PapC usher in the process of secreting two- and three-subunit P pilus assembly intermediates, revealing processive steps in P pilus biogenesis and capturing new conformational dynamics of the usher assembly machine.


Subject(s)
Escherichia coli Proteins/chemistry , Escherichia coli Proteins/metabolism , Fimbriae, Bacterial/chemistry , Fimbriae, Bacterial/metabolism , Uropathogenic Escherichia coli/metabolism , Cryoelectron Microscopy , Escherichia coli Proteins/genetics , Fimbriae Proteins/metabolism , Fimbriae, Bacterial/genetics , Models, Molecular , Molecular Chaperones/metabolism , Protein Binding , Protein Conformation , Uropathogenic Escherichia coli/genetics
7.
Cell Rep ; 35(8): 109166, 2021 05 25.
Article in English | MEDLINE | ID: mdl-34038719

ABSTRACT

The M. tuberculosis (Mtb) ClpB is a protein disaggregase that helps to rejuvenate the bacterial cell. DnaK is a protein foldase that can function alone, but it can also bind to the ClpB hexamer to physically couple protein disaggregation with protein refolding, although the molecular mechanism is not well understood. Here, we report the cryo-EM analysis of the Mtb ClpB-DnaK bi-chaperone in the presence of ATPγS and a protein substrate. We observe three ClpB conformations in the presence of DnaK, identify a conserved TGIP loop linking the oligonucleotide/oligosaccharide-binding domain and the nucleotide-binding domain that is important for ClpB function, derive the interface between the regulatory middle domain of the ClpB and the DnaK nucleotide-binding domain, and find that DnaK binding stabilizes, but does not bend or tilt, the ClpB middle domain. We propose a model for the synergistic actions of aggregate dissolution and refolding by the Mtb ClpB-DnaK bi-chaperone system.


Subject(s)
Bacterial Proteins/metabolism , Endopeptidase Clp/metabolism , Escherichia coli Proteins/metabolism , Mycobacterium tuberculosis/genetics , Models, Molecular , Protein Refolding
8.
J Biol Chem ; 296: 100713, 2021.
Article in English | MEDLINE | ID: mdl-33930464

ABSTRACT

Although many bacterial species do not possess proteasome systems, the actinobacteria, including the human pathogen Mycobacterium tuberculosis, use proteasome systems for targeted protein removal. Previous structural analyses of the mycobacterial proteasome ATPase Mpa revealed a general structural conservation with the archaeal proteasome-activating nucleotidase and eukaryotic proteasomal Rpt1-6 ATPases, such as the N-terminal coiled-coil domain, oligosaccharide-/oligonucleotide-binding domain, and ATPase domain. However, Mpa has a unique ß-grasp domain that in the ADP-bound crystal structure appears to interfere with the docking to the 20S proteasome core particle (CP). Thus, it is unclear how Mpa binds to proteasome CPs. In this report, we show by cryo-EM that the Mpa hexamer in the presence of a degradation substrate and ATP forms a gapped ring, with two of its six ATPase domains being highly flexible. We found that the linkers between the oligonucleotide-binding and ATPase domains undergo conformational changes that are important for function, revealing a previously unappreciated role of the linker region in ATP hydrolysis-driven protein unfolding. We propose that this gapped ring configuration is an intermediate state that helps rearrange its ß-grasp domains and activating C termini to facilitate engagement with proteasome CPs. This work provides new insights into the crucial process of how an ATPase interacts with a bacterial proteasome protease.


Subject(s)
Adenosine Triphosphatases/metabolism , Mycobacterium tuberculosis/enzymology , Proteasome Endopeptidase Complex/metabolism , Adenosine Triphosphatases/chemistry , Models, Molecular , Protein Domains , Protein Multimerization , Protein Structure, Quaternary
9.
Elife ; 92020 12 15.
Article in English | MEDLINE | ID: mdl-33320091

ABSTRACT

The P4 ATPases use ATP hydrolysis to transport large lipid substrates across lipid bilayers. The structures of the endosome- and Golgi-localized phosphatidylserine flippases-such as the yeast Drs2 and human ATP8A1-have recently been reported. However, a substrate-binding site on the cytosolic side has not been found, and the transport mechanisms of P4 ATPases with other substrates are unknown. Here, we report structures of the S. cerevisiae Dnf1-Lem3 and Dnf2-Lem3 complexes. We captured substrate phosphatidylcholine molecules on both the exoplasmic and cytosolic sides and found that they have similar structures. Unexpectedly, Lem3 contributes to substrate binding. The conformational transitions of these phosphatidylcholine transporters match those of the phosphatidylserine transporters, suggesting a conserved mechanism among P4 ATPases. Dnf1/Dnf2 have a unique P domain helix-turn-helix insertion that is important for function. Therefore, P4 ATPases may have retained an overall transport mechanism while evolving distinct features for different lipid substrates.


Subject(s)
ATP-Binding Cassette Transporters/metabolism , Adenosine Triphosphatases/metabolism , Membrane Transport Proteins/metabolism , P-type ATPases/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Adenosine Triphosphate/metabolism , Biological Transport, Active/physiology , Cell Membrane/metabolism , Hydrolysis , Lipid Bilayers/metabolism , Phosphatidylcholines/metabolism , Protein Conformation , Saccharomyces cerevisiae/enzymology , Saccharomyces cerevisiae/metabolism
10.
Nature ; 584(7821): 475-478, 2020 08.
Article in English | MEDLINE | ID: mdl-32494008

ABSTRACT

The endoplasmic reticulum (ER) membrane complex (EMC) cooperates with the Sec61 translocon to co-translationally insert a transmembrane helix (TMH) of many multi-pass integral membrane proteins into the ER membrane, and it is also responsible for inserting the TMH of some tail-anchored proteins1-3. How EMC accomplishes this feat has been unclear. Here we report the first, to our knowledge, cryo-electron microscopy structure of the eukaryotic EMC. We found that the Saccharomyces cerevisiae EMC contains eight subunits (Emc1-6, Emc7 and Emc10), has a large lumenal region and a smaller cytosolic region, and has a transmembrane region formed by Emc4, Emc5 and Emc6 plus the transmembrane domains of Emc1 and Emc3. We identified a five-TMH fold centred around Emc3 that resembles the prokaryotic YidC insertase and that delineates a largely hydrophilic client protein pocket. The transmembrane domain of Emc4 tilts away from the main transmembrane region of EMC and is partially mobile. Mutational studies demonstrated that the flexibility of Emc4 and the hydrophilicity of the client pocket are required for EMC function. The EMC structure reveals notable evolutionary conservation with the prokaryotic insertases4,5, suggests that eukaryotic TMH insertion involves a similar mechanism, and provides a framework for detailed understanding of membrane insertion for numerous eukaryotic integral membrane proteins and tail-anchored proteins.


Subject(s)
Cryoelectron Microscopy , Endoplasmic Reticulum/enzymology , Intracellular Membranes/enzymology , Multiprotein Complexes/chemistry , Multiprotein Complexes/ultrastructure , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/ultrastructure , Saccharomyces cerevisiae , Binding Sites , Endoplasmic Reticulum/chemistry , Endoplasmic Reticulum/ultrastructure , Evolution, Molecular , Hydrophobic and Hydrophilic Interactions , Intracellular Membranes/chemistry , Intracellular Membranes/ultrastructure , Models, Molecular , Multiprotein Complexes/genetics , Multiprotein Complexes/metabolism , Mutation , Protein Domains , Protein Subunits/chemistry , Protein Subunits/genetics , Protein Subunits/metabolism , Saccharomyces cerevisiae/chemistry , Saccharomyces cerevisiae/enzymology , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/ultrastructure , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Substrate Specificity
11.
Mil Med ; 185(3-4): 512-518, 2020 03 02.
Article in English | MEDLINE | ID: mdl-31865375

ABSTRACT

INTRODUCTION: Breast cancer is the most common cancer diagnosed among women and the second most common cause of cancer death among women. There are ways to reduce a woman's risk of breast cancer; however, most eligible women in the United States are neither offered personalized screening nor chemoprevention. Surveys have found that primary care providers are largely unaware of breast cancer risk assessment models or chemoprevention. This survey aims to investigate Veterans Health Administration primary care providers' comfort level, practice patterns, and knowledge of breast cancer risk assessment and chemoprevention. MATERIALS AND METHODS: An online, Research Electronic Data Capture-generated survey was distributed to VHA providers in internal medicine, family medicine, and obstetrics/gynecology. Survey domains were provider demographics, women's health experience, comfort level, practice patterns, barriers to using risk models and chemoprevention, and knowledge of chemoprevention. RESULTS: Of the 167 respondents, 33.1% used the Gail model monthly or more often and only 2.4% prescribed chemoprevention in the past 2 years. Most VHA primary care providers did not answer chemoprevention knowledge questions correctly. Designated women's health providers were more comfortable with risk assessment (P < 0.018) and chemoprevention (P < 0.011) and used both breast cancer risk models (P < 0.0045) and chemoprevention more often (P < 0.153). Reported barriers to chemoprevention were lack of education and provider time. CONCLUSIONS: VHA providers and women Veterans would benefit from a system to ensure that women at increased risk of breast cancer are identified with risk modeling and that risk reduction options, such as chemoprevention, are offered when appropriate. VHA providers requested risk reduction education, which could improve primary care provider comfort level with chemoprevention.


Subject(s)
Breast Neoplasms , Chemoprevention , Veterans , Breast Neoplasms/epidemiology , Breast Neoplasms/prevention & control , Female , Humans , Primary Health Care , Risk Assessment , United States , United States Department of Veterans Affairs
12.
Nat Commun ; 10(1): 4142, 2019 09 12.
Article in English | MEDLINE | ID: mdl-31515475

ABSTRACT

The heterodimeric eukaryotic Drs2p-Cdc50p complex is a lipid flippase that maintains cell membrane asymmetry. The enzyme complex exists in an autoinhibited form in the absence of an activator and is specifically activated by phosphatidylinositol-4-phosphate (PI4P), although the underlying mechanisms have been unclear. Here we report the cryo-EM structures of intact Drs2p-Cdc50p isolated from S. cerevisiae in apo form and in the PI4P-activated form at 2.8 Å and 3.3 Å resolution, respectively. The structures reveal that the Drs2p C-terminus lines a long groove in the cytosolic regulatory region to inhibit the flippase activity. PIP4 binding in a cytosol-proximal membrane region triggers a 90° rotation of a cytosolic helix switch that is located just upstream of the inhibitory C-terminal peptide. The rotation of the helix switch dislodges the C-terminus from the regulatory region, activating the flippase.


Subject(s)
Calcium-Transporting ATPases/antagonists & inhibitors , Lipids/chemistry , Saccharomyces cerevisiae Proteins/antagonists & inhibitors , Saccharomyces cerevisiae/enzymology , Adenosine Triphosphate/metabolism , Binding Sites , Calcium-Transporting ATPases/chemistry , Calcium-Transporting ATPases/metabolism , Calcium-Transporting ATPases/ultrastructure , Models, Molecular , Phosphatidylinositol Phosphates/metabolism , Protein Conformation , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/ultrastructure , Substrate Specificity
13.
Nat Struct Mol Biol ; 26(8): 704-711, 2019 08.
Article in English | MEDLINE | ID: mdl-31285605

ABSTRACT

In eukaryotes, a nascent peptide entering the endoplasmic reticulum (ER) is scanned by two Sec61 translocon-associated large membrane machines for protein N-glycosylation and protein O-mannosylation, respectively. While the structure of the eight-protein oligosaccharyltransferase complex has been determined recently, the structures of mannosyltransferases of the PMT family, which are an integral part of ER protein homeostasis, are still unknown. Here we report cryo-EM structures of the Saccharomyces cerevisiae Pmt1-Pmt2 complex bound to a donor and an acceptor peptide at 3.2-Å resolution, showing that each subunit contains 11 transmembrane helices and a lumenal ß-trefoil fold termed the MIR domain. The structures reveal the substrate recognition model and confirm an inverting mannosyl-transferring reaction mechanism by the enzyme complex. Furthermore, we found that the transmembrane domains of Pmt1 and Pmt2 share a structural fold with the catalytic subunits of oligosaccharyltransferases, confirming a previously proposed evolutionary relationship between protein O-mannosylation and protein N-glycosylation.


Subject(s)
Mannosyltransferases/ultrastructure , Multienzyme Complexes/ultrastructure , Saccharomyces cerevisiae Proteins/ultrastructure , Saccharomyces cerevisiae/enzymology , Cryoelectron Microscopy , Glycosylation , Humans , Image Processing, Computer-Assisted , Mannose/metabolism , Mannosyltransferases/chemistry , Mannosyltransferases/genetics , Mannosyltransferases/metabolism , Models, Molecular , Multienzyme Complexes/chemistry , Multienzyme Complexes/metabolism , Protein Conformation , Protein Domains , Protein Folding , Protein Processing, Post-Translational , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/metabolism , Species Specificity , Substrate Specificity , Walker-Warburg Syndrome/genetics
14.
J Bacteriol ; 201(14)2019 07 15.
Article in English | MEDLINE | ID: mdl-31036728

ABSTRACT

We characterized an operon in Mycobacterium tuberculosis, Rv3679-Rv3680, in which each open reading frame is annotated to encode "anion transporter ATPase" homologues. Using structure prediction modeling, we found that Rv3679 and Rv3680 more closely resemble the guided entry of tail-anchored proteins 3 (Get3) chaperone in eukaryotes. Get3 delivers proteins into the membranes of the endoplasmic reticulum and is essential for the normal growth and physiology of some eukaryotes. We sought to characterize the structures of Rv3679 and Rv3680 and test if they have a role in M. tuberculosis pathogenesis. We solved crystal structures of the nucleotide-bound Rv3679-Rv3680 complex at 2.5 to 3.2 Å and show that while it has some similarities to Get3 and ArsA, there are notable differences, including that these proteins are unlikely to be involved in anion transport. Deletion of both genes did not reveal any conspicuous growth defects in vitro or in mice. Collectively, we identified a new class of proteins in bacteria with similarity to Get3 complexes, the functions of which remain to be determined.IMPORTANCE Numerous bacterial species encode proteins predicted to have similarity with Get3- and ArsA-type anion transporters. Our studies provide evidence that these proteins, which we named BagA and BagB, are unlikely to be involved in anion transport. In addition, BagA and BagB are conserved in all mycobacterial species, including the causative agent of leprosy, which has a highly decayed genome. This conservation suggests that BagAB constitutes a part of the core mycobacterial genome and is needed for some yet-to-be-determined part of the life cycle of these organisms.


Subject(s)
Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Mycobacterium tuberculosis/chemistry , Mycobacterium tuberculosis/genetics , Adenosine Triphosphatases/chemistry , Adenosine Triphosphatases/genetics , Animals , Anion Transport Proteins/genetics , Female , Genome, Bacterial , Guanine Nucleotide Exchange Factors/chemistry , Guanine Nucleotide Exchange Factors/genetics , Mice , Mice, Inbred C57BL , Models, Molecular , Operon , Protein Binding , Protein Conformation , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/genetics
15.
Proc Natl Acad Sci U S A ; 115(41): E9560-E9569, 2018 10 09.
Article in English | MEDLINE | ID: mdl-30257943

ABSTRACT

The protein disaggregase ClpB hexamer is conserved across evolution and has two AAA+-type nucleotide-binding domains, NBD1 and NBD2, in each protomer. In M. tuberculosis (Mtb), ClpB facilitates asymmetric distribution of protein aggregates during cell division to help the pathogen survive and persist within the host, but a mechanistic understanding has been lacking. Here we report cryo-EM structures at 3.8- to 3.9-Šresolution of Mtb ClpB bound to a model substrate, casein, in the presence of the weakly hydrolyzable ATP mimic adenosine 5'-[γ-thio]triphosphate. Mtb ClpB existed in solution in two closed-ring conformations, conformers 1 and 2. In both conformers, the 12 pore-loops on the 12 NTDs of the six protomers (P1-P6) were arranged similarly to a staircase around the bound peptide. Conformer 1 is a low-affinity state in which three of the 12 pore-loops (the protomer P1 NBD1 and NBD2 loops and the protomer P2 NBD1 loop) are not engaged with peptide. Conformer 2 is a high-affinity state because only one pore-loop (the protomer P2 NBD1 loop) is not engaged with the peptide. The resolution of the two conformations, along with their bound substrate peptides and nucleotides, enabled us to propose a nucleotide-driven peptide translocation mechanism of a bacterial ClpB that is largely consistent with several recent unfoldase structures, in particular with the eukaryotic Hsp104. However, whereas Hsp104's two NBDs move in opposing directions during one step of peptide translocation, in Mtb ClpB the two NBDs move only in the direction of translocation.


Subject(s)
Adenosine Triphosphate/chemistry , Bacterial Proteins/chemistry , Endopeptidase Clp/chemistry , Mycobacterium tuberculosis/enzymology , Adenosine Triphosphate/metabolism , Bacterial Proteins/metabolism , Endopeptidase Clp/metabolism , Hydrolysis , Protein Domains , Protein Transport
16.
Nature ; 555(7696): 328-333, 2018 03 15.
Article in English | MEDLINE | ID: mdl-29466327

ABSTRACT

N-glycosylation is a ubiquitous modification of eukaryotic secretory and membrane-bound proteins; about 90% of glycoproteins are N-glycosylated. The reaction is catalysed by an eight-protein oligosaccharyltransferase (OST) complex that is embedded in the endoplasmic reticulum membrane. Our understanding of eukaryotic protein N-glycosylation has been limited owing to the lack of high-resolution structures. Here we report a 3.5 Å resolution cryo-electron microscopy structure of the Saccharomyces cerevisiae OST complex, revealing the structures of subunits Ost1-Ost5, Stt3, Wbp1 and Swp1. We found that seven phospholipids mediate many of the inter-subunit interactions, and an Stt3 N-glycan mediates interactions with Wbp1 and Swp1 in the lumen. Ost3 was found to mediate the OST-Sec61 translocon interface, funnelling the acceptor peptide towards the OST catalytic site as the nascent peptide emerges from the translocon. The structure provides insights into co-translational protein N-glycosylation, and may facilitate the development of small-molecule inhibitors that target this process.


Subject(s)
Cryoelectron Microscopy , Hexosyltransferases/chemistry , Hexosyltransferases/ultrastructure , Membrane Proteins/chemistry , Membrane Proteins/ultrastructure , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/ultrastructure , Saccharomyces cerevisiae/enzymology , Allosteric Regulation , Biocatalysis , Catalytic Domain , Glycosylation , Hexosyltransferases/metabolism , Membrane Proteins/metabolism , Models, Molecular , Phospholipids/metabolism , Protein Subunits/chemistry
17.
J Biol Chem ; 293(13): 4713-4723, 2018 03 30.
Article in English | MEDLINE | ID: mdl-29414791

ABSTRACT

In all domains of life, proteasomes are gated, chambered proteases that require opening by activators to facilitate protein degradation. Twelve proteasome accessory factor E (PafE) monomers assemble into a single dodecameric ring that promotes proteolysis required for the full virulence of the human bacterial pathogen Mycobacterium tuberculosis Whereas the best characterized proteasome activators use ATP to deliver proteins into a proteasome, PafE does not require ATP. Here, to unravel the mechanism of PafE-mediated protein targeting and proteasome activation, we studied the interactions of PafE with native substrates, including a newly identified proteasome substrate, the ParA-like protein, Rv3213c, and with proteasome core particles. We characterized the function of a highly conserved feature in bacterial proteasome activator proteins: a glycine-glutamine-tyrosine-leucine (GQYL) motif at their C termini that is essential for stimulating proteolysis. Using cryo-electron microscopy (cryo-EM), we found that the GQYL motif of PafE interacts with specific residues in the α subunits of the proteasome core particle to trigger gate opening and degradation. Finally, we also found that PafE rings have 40-Å openings lined with hydrophobic residues that form a chamber for capturing substrates before they are degraded, suggesting PafE has a previously unrecognized chaperone activity. In summary, we have identified the interactions between PafE and the proteasome core particle that cause conformational changes leading to the opening of the proteasome gate and have uncovered a mechanism of PafE-mediated substrate degradation. Collectively, our results provide detailed insights into the mechanism of ATP-independent proteasome degradation in bacteria.


Subject(s)
Adenosine Triphosphate/chemistry , Bacterial Proteins/chemistry , Molecular Chaperones/chemistry , Mycobacterium tuberculosis/chemistry , Proteasome Endopeptidase Complex/chemistry , Proteolysis , Adenosine Triphosphate/metabolism , Amino Acid Motifs , Bacterial Proteins/metabolism , Molecular Chaperones/metabolism , Mycobacterium tuberculosis/metabolism , Proteasome Endopeptidase Complex/metabolism , Protein Domains
18.
J Biol Chem ; 292(30): 12653-12666, 2017 07 28.
Article in English | MEDLINE | ID: mdl-28615457

ABSTRACT

AMP-activated protein kinase (AMPK) is a central cellular energy sensor that adapts metabolism and growth to the energy state of the cell. AMPK senses the ratio of adenine nucleotides (adenylate energy charge) by competitive binding of AMP, ADP, and ATP to three sites (CBS1, CBS3, and CBS4) in its γ-subunit. Because these three binding sites are functionally interconnected, it remains unclear how nucleotides bind to individual sites, which nucleotides occupy each site under physiological conditions, and how binding to one site affects binding to the other sites. Here, we comprehensively analyze nucleotide binding to wild-type and mutant AMPK protein complexes by quantitative competition assays and by hydrogen-deuterium exchange MS. We also demonstrate that NADPH, in addition to the known AMPK ligand NADH, directly and competitively binds AMPK at the AMP-sensing CBS3 site. Our findings reveal how AMP binding to one site affects the conformation and adenine nucleotide binding at the other two sites and establish CBS3, and not CBS1, as the high affinity exchangeable AMP/ADP/ATP-binding site. We further show that AMP binding at CBS4 increases AMP binding at CBS3 by 2 orders of magnitude and reverses the AMP/ATP preference of CBS3. Together, these results illustrate how the three CBS sites collaborate to enable highly sensitive detection of cellular energy states to maintain the tight ATP homeostastis required for cellular metabolism.


Subject(s)
AMP-Activated Protein Kinases/metabolism , Adenine/metabolism , Nucleotides/metabolism , AMP-Activated Protein Kinases/chemistry , AMP-Activated Protein Kinases/genetics , Adenine/chemistry , Binding Sites , Humans , Models, Molecular , Nucleotides/chemistry
19.
Environ Sci Technol ; 49(13): 7762-9, 2015 Jul 07.
Article in English | MEDLINE | ID: mdl-26018982

ABSTRACT

Opposing hypotheses posit that increasing primary productivity should result in either greater or lesser contaminant accumulation in stream food webs. We conducted an experiment to evaluate primary productivity effects on MeHg accumulation in stream consumers. We varied light for 16 artificial streams creating a productivity gradient (oxygen production =0.048-0.71 mg O2 L(-1) d(-1)) among streams. Two-level food webs were established consisting of phytoplankton/filter feeding clam, periphyton/grazing snail, and leaves/shredding amphipod (Hyalella azteca). Phytoplankton and periphyton biomass, along with MeHg removal from the water column, increased significantly with productivity, but MeHg concentrations in these primary producers declined. Methylmercury concentrations in clams and snails also declined with productivity, and consumer concentrations were strongly correlated with MeHg concentrations in primary producers. Heterotroph biomass on leaves, MeHg in leaves, and MeHg in Hyalella were unrelated to stream productivity. Our results support the hypothesis that contaminant bioaccumulation declines with stream primary production via the mechanism of bloom dilution (MeHg burden per cell decreases in algal blooms), extending patterns of contaminant accumulation documented in lakes to lotic systems.


Subject(s)
Food Chain , Methylmercury Compounds/analysis , Rivers , Water Pollutants, Chemical/analysis , Amphipoda/drug effects , Animals , Biomass , Bivalvia/drug effects , Bivalvia/metabolism , Eutrophication , Heterotrophic Processes , Methylmercury Compounds/pharmacokinetics , Oxygen/metabolism , Phytoplankton/metabolism , Plant Leaves/drug effects , Plant Leaves/metabolism , Snails/drug effects , Snails/metabolism , Water Pollutants, Chemical/pharmacokinetics
20.
Psychol Serv ; 12(3): 303-12, 2015 Aug.
Article in English | MEDLINE | ID: mdl-25938855

ABSTRACT

This report describes the results of a randomized controlled feasibility study of the Mindfulness Intervention for Rehabilitation and Recovery in Schizophrenia (MIRRORS). MIRRORS is an adaptation of Mindfulness-Based Stress Reduction designed to help persons with schizophrenia to persist and perform better at work. Thirty-four participants with schizophrenia or schizoaffective disorder who were engaged in outpatient services were enrolled in a vocational rehabilitation program that included a job placement and then were randomized to receive MIRRORS (n = 18) or Intensive Support (n = 16) over a period of 16 weeks. The number of hours worked was recorded weekly and job performance was assessed monthly using the Work Behavior Inventory. Results of t-tests revealed that participants in the MIRRORS group worked a significantly greater number of hours and performed significantly better at the end of the 4-month intervention than those in the Intensive Support condition. Repeated-measures analysis of variance revealed that the MIRRORS group worked more hours each week on average and that this difference increased over time as well as having generally better work performance compared with the Intensive Support group. Results suggest a link between MIRRORS and higher levels of work performance and persistence in people with schizophrenia. Further research is indicated to evaluate MIRRORS in a fully powered randomized controlled trial.


Subject(s)
Mindfulness/methods , Psychotic Disorders/rehabilitation , Rehabilitation, Vocational/methods , Schizophrenia/rehabilitation , Work Performance , Adult , Feasibility Studies , Female , Humans , Male , Middle Aged , Treatment Outcome
SELECTION OF CITATIONS
SEARCH DETAIL
...