1
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Castillo HB, Shuster SO, Tarekegn LH, Davis CM. Oleic acid differentially affects lipid droplet storage of de novo synthesized lipids in hepatocytes and adipocytes. Chem Commun (Camb) 2024; 60:3138-3141. [PMID: 38329230 PMCID: PMC10939124 DOI: 10.1039/d3cc04829b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/29/2024] [Indexed: 02/09/2024]
Abstract
Lipogenesis is a vital but often dysregulated metabolic pathway. Here we use optical photothermal infrared imaging to quantify lipogenesis rates of isotopically labelled oleic acid and glucose concomitantly in live cells. In hepatocytes, but not adipocytes, we find that oleic acid feeding at 60 μM increases the number and size of lipid droplets (LDs) while simultaneously inhibiting storage of de novo synthesized lipids in LDs. Our results demonstrate alternate regulation of lipogenesis between cell types.
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Affiliation(s)
- Hannah B Castillo
- Department of Chemistry, Yale University, New Haven, Connecticut, 06511, USA.
| | - Sydney O Shuster
- Department of Chemistry, Yale University, New Haven, Connecticut, 06511, USA.
| | - Lydia H Tarekegn
- Department of Chemistry, Yale University, New Haven, Connecticut, 06511, USA.
| | - Caitlin M Davis
- Department of Chemistry, Yale University, New Haven, Connecticut, 06511, USA.
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2
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Sivadas A, McDonald EF, Shuster SO, Davis CM, Plate L. Site-specific crosslinking reveals Phosphofructokinase-L inhibition drives self-assembly and attenuation of protein interactions. Adv Biol Regul 2023; 90:100987. [PMID: 37806136 DOI: 10.1016/j.jbior.2023.100987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 09/25/2023] [Indexed: 10/10/2023]
Abstract
Phosphofructokinase is the central enzyme in glycolysis and constitutes a highly regulated step. The liver isoform (PFKL) compartmentalizes during activation and inhibition in vitro and in vivo, respectively. Compartmentalized PFKL is hypothesized to modulate metabolic flux consistent with its central role as the rate limiting step in glycolysis. PFKL tetramers self-assemble at two interfaces in the monomer (interface 1 and 2), yet how these interfaces contribute to PFKL compartmentalization and drive protein interactions remains unclear. Here, we used site-specific incorporation of noncanonical photocrosslinking amino acids to identify PFKL interactors at interface 1, 2, and the active site. Tandem mass tag-based quantitative interactomics reveals interface 2 as a hotspot for PFKL interactions, particularly with cytoskeletal, glycolytic, and carbohydrate derivative metabolic proteins. Furthermore, PFKL compartmentalization into puncta was observed in human cells using citrate inhibition. Puncta formation attenuated crosslinked protein-protein interactions with the cytoskeleton at interface 2. This result suggests that PFKL compartmentalization sequesters interface 2, but not interface 1, and may modulate associated protein assemblies with the cytoskeleton.
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Affiliation(s)
- Athira Sivadas
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Eli Fritz McDonald
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | | | - Caitlin M Davis
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Lars Plate
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
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3
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Castillo HB, Shuster SO, Tarekegn LH, Davis CM. Oleic acid differentially affects de novo lipogenesis in adipocytes and hepatocytes. bioRxiv 2023:2023.10.04.560581. [PMID: 37873279 PMCID: PMC10592964 DOI: 10.1101/2023.10.04.560581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Lipogenesis is a vital but often dysregulated metabolic pathway. We report super-resolution multiplexed vibrational imaging of lipogenesis rates and pathways using isotopically labelled oleic acid and glucose as probes in live adipocytes and hepatocytes. These findings suggest oleic acid inhibits de novo lipogenesis (DNL), but not total lipogenesis, in hepatocytes. No significant effect is seen in adipocytes. These differential effects may be due to alternate regulation of DNL between cell types and could help explain the complicated role oleic acid plays in metabolism.
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Affiliation(s)
- Hannah B. Castillo
- Department of Chemistry, Yale University, New Haven, Connecticut, 06511, United States
| | - Sydney O. Shuster
- Department of Chemistry, Yale University, New Haven, Connecticut, 06511, United States
| | - Lydia H. Tarekegn
- Department of Chemistry, Yale University, New Haven, Connecticut, 06511, United States
| | - Caitlin M. Davis
- Department of Chemistry, Yale University, New Haven, Connecticut, 06511, United States
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4
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Sivadas A, McDonald EF, Shuster SO, Davis CM, Plate L. Site-Specific Crosslinking Reveals Phosphofructokinase-L Inhibition Drives Self-Assembly and Attenuation of Protein Interactions. bioRxiv 2023:2023.09.19.558525. [PMID: 37781627 PMCID: PMC10541129 DOI: 10.1101/2023.09.19.558525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Phosphofructokinase is the central enzyme in glycolysis and constitutes a highly regulated step. The liver isoform (PFKL) compartmentalizes during activation and inhibition in vitro and in vivo respectively. Compartmentalized PFKL is hypothesized to modulate metabolic flux consistent with its central role as the rate limiting step in glycolysis. PFKL tetramers self-assemble at two interfaces in the monomer (interface 1 and 2), yet how these interfaces contribute to PFKL compartmentalization and drive protein interactions remains unclear. Here, we used site-specific incorporation of noncanonical photocrosslinking amino acids to identify PFKL interactors at interface 1, 2, and the active site. Tandem mass tag-based quantitative interactomics reveals interface 2 as a hotspot for PFKL interactions, particularly with cytoskeletal, glycolytic, and carbohydrate derivative metabolic proteins. Furthermore, PFKL compartmentalization into puncta was observed in human cells using citrate inhibition. Puncta formation attenuated crosslinked protein-protein interactions with the cytoskeleton at interface 2. This result suggests that PFKL compartmentalization sequesters interface 2, but not interface 1, and may modulate associated protein assemblies with the cytoskeleton.
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Affiliation(s)
- Athira Sivadas
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Eli Fritz McDonald
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | | | | | - Lars Plate
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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5
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Knab E, Davis CM. Chemical Interactions Modulate λ 6-85 Stability in Cells. Protein Sci 2023:e4698. [PMID: 37313657 DOI: 10.1002/pro.4698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/26/2023] [Accepted: 06/06/2023] [Indexed: 06/15/2023]
Abstract
Because steric crowding is most effective when the crowding agent is similar in size to the molecule that it acts upon and the average macromolecule inside cells is much larger than a small protein or peptide, steric crowding is not predicted to affect their folding inside cells. On the other hand, chemical interactions should perturb in-cell structure and stability because they arise from interactions between the surface of the small protein or peptide and its environment. Indeed, previous in vitro measurements of the λ-repressor fragment, λ6-85 , in crowding matrices comprised of Ficoll or protein crowders support these predictions. Here we directly quantify the in-cell stability of λ6-85 and distinguish the contribution of steric crowding and chemical interactions to its stability. Using a FRET-labeled λ6-85 construct, we find that the fragment is stabilized by 5 °C in-cells compared to in vitro. We demonstrate that this stabilization cannot be explained by steric crowding because, as anticipated, Ficoll has no effect on λ6-85 stability. We find that the in-cell stabilization arises from chemical interactions, mimicked in vitro by mammalian protein extraction reagent (M-PERTM ). Comparison between FRET values in-cell and in Ficoll confirms that U-2 OS cytosolic crowding is reproduced at macromolecule concentrations of 15 %w/v. Our measurements validate the cytomimetic of 15% Ficoll and 20% M-PERTM that we previously developed for protein and RNA folding studies. However, because the in-cell stability of λ6-85 is reproduced by 20 %v/v M-PERTM alone, we predict that this simplified mixture could be a useful tool to predict the in-cell behaviors of other small proteins and peptides. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Edward Knab
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Caitlin M Davis
- Department of Chemistry, Yale University, New Haven, CT, USA
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6
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Abstract
De novo lipogenesis (DNL) is a critical metabolic process that provides the majority of lipids for adipocyte and liver tissue. In cancer, obesity, type II diabetes, and nonalcoholic fatty liver disease DNL becomes dysregulated. A deeper understanding of the rates and of subcellular organization of DNL is necessary for identifying how this dysregulation occurs and varies across individuals and diseases. However, DNL is difficult to study inside the cell because labeling lipids and their precursors is not trivial. Existing techniques either can only measure parts of DNL, like glucose uptake, or do not provide spatiotemporal resolution. Here, we track DNL in space and time as isotopically labeled glucose is converted to lipids in adipocytes using optical photothermal infrared microscopy (OPTIR). OPTIR provides submicron resolution infrared imaging of the glucose metabolism in both living and fixed cells while also reporting on the identity of lipids and other biomolecules. We show significant incorporation of the labeled carbons into triglycerides in lipid droplets over the course of 72 h. Live cells had better preservation of lipid droplet morphology, but both showed similar DNL rates. Rates of DNL, as measured by the ratio of 13C-labeled lipid to 12C-labeled lipid, were heterogeneous, with differences within and between lipid droplets and from cell to cell. The high rates of DNL measured in adipocyte cells match upregulated rates of DNL previously reported in PANC1 pancreatic cancer cells. Taken together, our findings support a model where DNL is locally regulated to meet energy needs within cells.
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Affiliation(s)
- Sydney O Shuster
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06511, United States
| | - Michael J Burke
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06511, United States
| | - Caitlin M Davis
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06511, United States
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7
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Yoo H, Davis CM. An in vitro cytomimetic of in-cell RNA folding. Chembiochem 2022; 23:e202200406. [PMID: 35999178 DOI: 10.1002/cbic.202200406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/21/2022] [Indexed: 11/07/2022]
Abstract
To discover the cytomimetic that accounts for cytoplasmic crowding and sticking on RNA stability, we conducted a two-dimensional scan of mixtures of artificial crowding and sticking agents, PEG10k and M-PERTM. As our model RNA, we investigate the fourU RNA thermometer motif of Salmonella, a hairpin-structured RNA that regulates translation by unfolding and exposing its RBS in response to temperature perturbations. We found that the addition of artificial crowding and sticking agents leads to a stabilization and destabilization of RNA folding, respectively, through the excluded volume effect and surface interactions. FRET-labels were added to the fourU RNA and Fast Relaxation Imaging (FReI), fluorescence microscopy coupled to temperature-jump spectroscopy, probed differences between folding stability of RNA inside single living cells and in vitro. Our results suggest that the cytoplasmic environment affecting RNA folding is comparable to a combination of 20% v/v M-PERTM and 150 g/L PEG10k.
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Affiliation(s)
- Hyejin Yoo
- Yale University, Chemistry, 225 Prospect St, 06511, New Haven, UNITED STATES
| | - Caitlin M Davis
- Yale University, Chemistry, 225 Prospect St., 06511, New Haven, UNITED STATES
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8
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Gopan G, Ghaemi Z, Davis CM, Gruebele M. Spliceosomal SL1 RNA binding to U1-70K: the role of the extended RRM. Nucleic Acids Res 2022; 50:8193-8206. [PMID: 35876068 PMCID: PMC9371917 DOI: 10.1093/nar/gkac599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 06/19/2022] [Accepted: 06/29/2022] [Indexed: 11/24/2022] Open
Abstract
The RNA recognition motif (RRM) occurs widely in RNA-binding proteins, but does not always by itself support full binding. For example, it is known that binding of SL1 RNA to the protein U1-70K in the U1 spliceosomal particle is reduced when a region flanking the RRM is truncated. How the RRM flanking regions that together with the RRM make up an ‘extended RRM’ (eRRM) contribute to complex stability and structural organization is unknown. We study the U1-70K eRRM bound to SL1 RNA by thermal dissociation and laser temperature jump kinetics; long-time molecular dynamics simulations interpret the experiments with atomistic resolution. Truncation of the helix flanking the RRM on its N-terminal side, ‘N-helix,’ strongly reduces overall binding, which is further weakened under higher salt and temperature conditions. Truncating the disordered region flanking the RRM on the C-terminal side, ‘C-IDR’, affects the local binding site. Surprisingly, all-atom simulations show that protein truncation enhances base stacking interactions in the binding site and leaves the overall number of hydrogen bonds intact. Instead, the flanking regions of the eRRM act in a distributed fashion via collective interactions with the RNA when external stresses such as temperature or high salt mimicking osmotic imbalance are applied.
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Affiliation(s)
- Gopika Gopan
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Zhaleh Ghaemi
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Caitlin M Davis
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA.,Department of Physics, University of Illinois, Urbana, IL 61801, USA
| | - Martin Gruebele
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA.,Department of Physics, University of Illinois, Urbana, IL 61801, USA.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, IL 61801, USA
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9
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Abstract
While extensive studies have been carried out to determine protein-RNA binding affinities, mechanisms, and dynamics in vitro, such studies do not take into consideration the effect of the many weak nonspecific interactions in a cell filled with potential binding partners. Here we experimentally tested the role of the cellular environment on affinity and binding dynamics between a protein and RNA in living U-2 OS cells. Our model system is the spliceosomal protein U1A and its binding partner SL2 of the U1 snRNA. The binding equilibrium was perturbed by a laser-induced temperature jump and monitored by Förster resonance energy transfer. The apparent binding affinity in live cells was reduced by up to 2 orders of magnitude compared to in vitro. The measured in-cell dissociation rate coefficients were up to 2 orders of magnitude larger, whereas no change in the measured association rate coefficient was observed. The latter is not what would be anticipated due to macromolecular crowding or nonspecific sticking of the uncomplexed U1A and SL2 in the cell. A quantitative model fits our experimental results, with the major cellular effect being that U1A and SL2 sticking to cellular components are capable of binding, just not as strongly as the free complex. This observation suggests that high binding affinities measured or designed in vitro are necessary for proper binding in vivo, where competition with many nonspecific interactions exists, especially for strongly interacting species with high charge or large hydrophobic surface areas.
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10
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Acks ES, Davis CM. Mapping Internally and Environmentally Stimulated RNA Foci Formation. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.2001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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11
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Choi DD, Smith D, Davis CM, McCain JP. Arthroscopic diagnosis and medical management of calcium pyrophosphate deposition disease in the temporomandibular joint. Int J Oral Maxillofac Surg 2020; 49:1618-1621. [PMID: 32859458 DOI: 10.1016/j.ijom.2020.07.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 05/26/2020] [Accepted: 07/23/2020] [Indexed: 10/23/2022]
Abstract
Calcium pyrophosphate deposition disease (CPPD) is a crystal arthropathy that can involve the temporomandibular joint. It is known to accelerate the osteoarthritic process, often initially presenting with advanced level of disease. The management of CPPD in the rheumatology and orthopedic literature is one of early diagnosis and medical management of acute attacks. The cases of three patients who presented with initial complaints of joint pain and limited mouth opening are presented. Preoperative imaging identified calcifications in two of these patients. Definitive diagnosis was achieved through arthroscopic-assisted biopsy. Rheumatology referrals revealed chondrocalcinosis of the knee in one patient. All patients had improved mouth opening and pain.
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Affiliation(s)
- D D Choi
- Thomas Jefferson University Hospital, Philadelphia, PA, USA.
| | - D Smith
- Herbert Wertheim College of Medicine - Florida International University, Miami, FL, USA
| | - C M Davis
- University of Alberta Faculty of Medicine and Dentistry, Edmonton, Alberta, Canada
| | - J P McCain
- Massachusetts General Hospital, Harvard School of Dental Medicine, Boston, MA, USA
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12
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Kelm RC, Surmanowicz P, Lung KE, Davis CM. New technique for removing bone covering miniplates and screws. Br J Oral Maxillofac Surg 2020; 58:e119-e121. [PMID: 32654799 DOI: 10.1016/j.bjoms.2020.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/09/2020] [Indexed: 10/23/2022]
Abstract
Miniplate osteosynthesis has revolutionised the treatment of open reduction and internal fixation in craniomaxillofacial procedures. However, when complications arise necessitating the removal of previously placed miniplates, bony overgrowth may be present and must be eliminated before removal of the hardware is possible. Osteogenesis over the screws prevents proper engagement of the screwdriver with the screw drives. If bone remains embedded in the screw drive during attempted removal of the screw, the contact interference increases the risk of the screwdriver slipping and the screw drive being stripped. There remains a lack of adequate techniques to clear bony overgrowth from miniplates and screws to allow for easy removal, as conventional methods are ineffective, time-consuming, and may damage the screw drives. Herein, we describe a new laser-assisted miniplate removal technique to eliminate bone that has grown over miniplates and screws before the miniplate is removed. This technique is efficient, safe, and simple and, compared with conventional methods, may decrease the complications associated with the removal of miniplates and screws.
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Affiliation(s)
- R C Kelm
- Faculty of Medicine and Dentistry, Department of Oral and Maxillofacial Surgery, University of Alberta, #107E 14310 111 Ave NW, Edmonton, Alberta, Canada T5M 3Z7.
| | - P Surmanowicz
- Faculty of Medicine and Dentistry, Department of Oral and Maxillofacial Surgery, University of Alberta, #107E 14310 111 Ave NW, Edmonton, Alberta, Canada T5M 3Z7.
| | - K E Lung
- Clinical Professor, Director of Implant Surgery Clinic, Chief of Pediatric Oral and Maxillofacial Surgery, Faculty of Medicine and Dentistry, Department of Oral and Maxillofacial Surgery, University of Alberta, #107E 14310 111 Ave NW, Edmonton, Alberta, Canada T5M 3Z7.
| | - C M Davis
- Associate Clinical Professor, Faculty of Medicine and Dentistry, Department of Oral and Maxillofacial Surgery, University of Alberta, #107E 14310 111 Ave NW, Edmonton, Alberta, Canada T5M 3Z7.
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13
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Abstract
The dynamic cytoskeletal network of microtubules and actin filaments can be disassembled by drugs. Cytoskeletal drugs work by perturbing the monomer-polymer equilibrium, thus changing the size and number of macromolecular crowders inside cells. Changes in both crowding and nonspecific surface interactions ("sticking") following cytoskeleton disassembly can affect the protein stability, structure, and function directly or indirectly by changing the fluidity of the cytoplasm and altering the crowding and sticking of other macromolecules in the cytoplasm. The effect of cytoskeleton disassembly on protein energy landscapes inside cells has yet to be observed. Here we have measured the effect of several cytoskeletal drugs on the folding energy landscape of two FRET-labeled proteins with different in vitro sensitivities to macromolecular crowding. Phosphoglycerate kinase (PGK) was previously shown to be more sensitive to crowding, whereas variable major protein-like sequence expressed (VlsE) was previously shown to be more sensitive to sticking. The in-cell effects of drugs that depolymerize either actin filaments (cytochalasin D and latrunculin B) or microtubules (nocodazole and vinblastine) were compared. The crowding sensor protein CrH2-FRET verified that cytoskeletal drugs decrease the extent of crowding inside cells despite also reducing the overall cell volume. The decreased compactness and folding stability of PGK could be explained by the decreased extent of crowding induced by these drugs. VlsE's opposite response to the drugs shows that depolymerization of the cytoskeleton also changes sticking in the cellular milieu. Our results demonstrate that perturbation of the monomer-polymer cytoskeletal equilibrium, for example, during natural cell migration or stresses from drug treatment, has off-target effects on the energy landscapes of proteins in the cell.
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14
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Davis CM, Deutsch J, Gruebele M. An in vitro mimic of in-cell solvation for protein folding studies. Protein Sci 2020; 29:1060-1068. [PMID: 31994240 DOI: 10.1002/pro.3833] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 01/15/2023]
Abstract
Ficoll, an inert macromolecule, is a common in vitro crowder, but by itself it does not reproduce in-cell stability or kinetic trends for protein folding. Lysis buffer, which contains ions, glycerol as a simple kosmotrope, and mimics small crowders with hydrophilic/hydrophobic patches, can reproduce sticking trends observed in cells but not the crowding. We previously suggested that the proper combination of Ficoll and lysis buffer could reproduce the opposite in-cell folding stability trend of two proteins: variable major protein-like sequence expressed (VlsE) is destabilized in eukaryotic cells and phosphoglycerate kinase (PGK) is stabilized. Here, to discover a well-characterized solvation environment that mimics in-cell stabilities for these two very differently behaved proteins, we conduct a two-dimensional scan of Ficoll (0-250 mg/ml) and lysis buffer (0-75%) mixtures. Contrary to our previous expectation, we show that mixtures of Ficoll and lysis buffer have a significant nonadditive effect on the folding stability. Lysis buffer enhances the stabilizing effect of Ficoll on PGK and inhibits the stabilizing effect of Ficoll on VlsE. We demonstrate that a combination of 150 mg/ml Ficoll and 60% lysis buffer can be used as an in vitro mimic to account for both crowding and non-steric effects on PGK and VlsE stability and folding kinetics in the cell. Our results also suggest that this mixture is close to the point where phase separation will occur. The simple mixture proposed here, based on commercially available reagents, could be a useful tool to study a variety of cytoplasmic protein interactions, such as folding, binding and assembly, and enzymatic reactions. SIGNIFICANCE STATEMENT: The complexity of the in-cell environment is difficult to reproduce in the test tube. Here we validate a mimic of cellular crowding and sticking interactions in a test tube using two proteins that are differently impacted by the cell: one is stabilized and the other is destabilized. This mimic is a starting point to reproduce cellular effects on a variety of protein and biomolecular interactions, such as folding and binding.
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Affiliation(s)
- Caitlin M Davis
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Jonathan Deutsch
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Martin Gruebele
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
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15
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Abstract
Macromolecular crowding is widely accepted as one of the factors that can alter protein stability, structure, and function inside cells. Less often considered is that crowding can be dynamic: as cell volume changes, either as a result of external duress or in the course of the cell cycle, water moves in or out through membrane channels, and crowding changes in tune. Both theory and in vitro experiments predict that protein stability will be altered as a result of crowding changes. However, it is unclear how much the structural ensemble is altered as crowding changes in the cell. To test this, we look at the response of a FRET-labeled kinase to osmotically induced volume changes in live cells. We examine both the folded and unfolded states of the kinase by changing the temperature of the media surrounding the cell. Our data reveals that crowding compacts the structure of its unfolded ensemble but stabilizes the folded protein. We propose that the structure of proteins lacking a rigid, well-defined tertiary structure could be highly sensitive to both increases and decreases in cell volume. Our findings present a possible mechanism for disordered proteins to act as sensors and actuators of cell cycle or external stress events that coincide with a change in macromolecular crowding.
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Affiliation(s)
- Yuhan Wang
- Center for Biophysics and Computational Biology , University of Illinois , Urbana , Illinois 61801 , United States
| | - Shahar Sukenik
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States
| | - Caitlin M Davis
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States.,Department of Physics , University of Illinois , Urbana , Illinois 61801 , United States
| | - Martin Gruebele
- Center for Biophysics and Computational Biology , University of Illinois , Urbana , Illinois 61801 , United States.,Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States.,Department of Physics , University of Illinois , Urbana , Illinois 61801 , United States
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16
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Davis CM, Zanetti-Polzi L, Gruebele M, Amadei A, Dyer RB, Daidone I. A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy. Chem Sci 2018; 9:9002-9011. [PMID: 30647892 PMCID: PMC6301204 DOI: 10.1039/c8sc03786h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/02/2018] [Indexed: 11/23/2022] Open
Abstract
We break the barrier between simulation and experiment by comparing identical computed and experimental infrared observables.
For small molecule reaction kinetics, computed reaction coordinates often mimic experimentally measured observables quite accurately. Although nowadays simulated and measured biomolecule kinetics can be compared on the same time scale, a gap between computed and experimental observables remains. Here we directly compared temperature-jump experiments and molecular dynamics simulations of protein folding dynamics using the same observable: the time-dependent infrared spectrum. We first measured the stability and folding kinetics of the fastest-folding β-protein, the GTT35 WW domain, using its structurally specific infrared spectrum. The relaxation dynamics of the peptide backbone, β-sheets, turn, and random coil were measured independently by probing the amide I′ region at different frequencies. Next, the amide I′ spectra along folding/unfolding molecular dynamics trajectories were simulated by accurate mixed quantum/classical calculations. The simulated time dependence and spectral amplitudes at the exact experimental probe frequencies provided relaxation and folding rates in agreement with experimental observations. The calculations validated by experiment yield direct structural evidence for a rate-limiting reaction step where an intermediate state with either the first or second hairpin is formed. We show how folding switches from a more homogeneous (apparent two-state) process at high temperature to a more heterogeneous process at low temperature, where different parts of the WW domain fold at different rates.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry and Department of Physics , University of Illinois at Urbana-Champaign , IL 61801 , USA.,Department of Chemistry , Emory University , Atlanta , GA 30322 , USA .
| | - Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences , University of L'Aquila , 67010 L'Aquila , Italy .
| | - Martin Gruebele
- Department of Chemistry and Department of Physics , University of Illinois at Urbana-Champaign , IL 61801 , USA.,Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , IL 61801 , USA
| | - Andrea Amadei
- Department of Chemical and Technological Sciences , University of Rome "Tor Vergata" , 00133 Rome , Italy
| | - R Brian Dyer
- Department of Chemistry , Emory University , Atlanta , GA 30322 , USA .
| | - Isabella Daidone
- Department of Physical and Chemical Sciences , University of L'Aquila , 67010 L'Aquila , Italy .
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17
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Kisley L, Miller KA, Davis CM, Guin D, Murphy EA, Gruebele M, Leckband DE. Soluble Zwitterionic Poly(sulfobetaine) Destabilizes Proteins. Biomacromolecules 2018; 19:3894-3901. [PMID: 30064224 DOI: 10.1021/acs.biomac.8b01120] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The widespread interest in neutral, water-soluble polymers such as poly(ethylene glycol) (PEG) and poly(zwitterions) such as poly(sulfobetaine) (pSB) for biomedical applications is due to their widely assumed low protein binding. Here we demonstrate that pSB chains in solution can interact with proteins directly. Moreover, pSB can reduce the thermal stability and increase the protein folding cooperativity relative to proteins in buffer or in PEG solutions. Polymer-dependent changes in the tryptophan fluorescence spectra of three structurally-distinct proteins reveal that soluble, 100 kDa pSB interacts directly with all three proteins and changes both the local polarity near tryptophan residues and the protein conformation. Thermal denaturation studies show that the protein melting temperatures decrease by as much as ∼1.9 °C per weight percent of polymer and that protein folding cooperativity increases by as much as ∼130 J mol-1 K-1 per weight percent of polymer. The exact extent of the changes is protein-dependent, as some proteins exhibit increased stability, whereas others experience decreased stability at high soluble pSB concentrations. These results suggest that pSB is not universally protein-repellent and that its efficacy in biotechnological applications will depend on the specific proteins used.
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18
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Davis CM, Gruebele M. Non-Steric Interactions Predict the Trend and Steric Interactions the Offset of Protein Stability in Cells. Chemphyschem 2018; 19:2290-2294. [PMID: 29877016 DOI: 10.1002/cphc.201800534] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Indexed: 01/15/2023]
Abstract
Although biomolecules evolved to function in the cell, most biochemical assays are carried out in vitro. In-cell studies highlight how steric and non-steric interactions modulate protein folding and interactions. VlsE and PGK present two extremes of chemical behavior in the cell: the extracellular protein VlsE is destabilized in eukaryotic cells, whereas the cytoplasmic protein PGK is stabilized. VlsE and PGK are benchmarks in a systematic series of solvation environments to distinguish contributions from non-steric and steric interactions to protein stability, compactness, and folding rate by comparing cell lysate, a crowding agent, ionic buffer and lysate buffer with in-cell results. As anticipated, crowding stabilizes proteins, causes compaction, and can speed folding. Protein flexibility determines its sensitivity to steric interactions or crowding. Non-steric interactions alone predict in-cell stability trends, while crowding provides an offset towards greater stabilization. We suggest that a simple combination of lysis buffer and Ficoll is an effective new in vitro mimic of the intracellular environment on protein folding and stability.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry and Department of Physics, University of Illinois at Urbana-Champaign Urbana, Illinois, 61801, United States
| | - Martin Gruebele
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana, Illinois, 61801, United States.,Department of Chemistry and Department of Physics, University of Illinois at Urbana-Champaign Urbana, Illinois, 61801, United States
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19
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Abstract
Qualitative imaging of biomolecular localization and distribution inside cells has revolutionized cell biology. Most of these powerful techniques require modifications to the target biomolecule. Over the past 10 years, these techniques have been extended to quantitative measurements, from in-cell protein folding rates to complex dissociation constants to RNA lifetimes. Such measurements can be affected even when a target molecule is just mildly perturbed by its labels. Here, the impact of labeling on protein (and RNA) structure, stability, and function in cells is discussed via practical examples from the recent literature. General guidelines for selecting and validating modification sites are provided to bring the best from cell biology and imaging to quantitative biophysical experiments inside cells.
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20
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Davis CM, Gruebele M, Sukenik S. How does solvation in the cell affect protein folding and binding? Curr Opin Struct Biol 2018; 48:23-29. [PMID: 29035742 DOI: 10.1016/j.sbi.2017.09.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/19/2017] [Accepted: 09/22/2017] [Indexed: 12/21/2022]
Abstract
The cellular environment is highly diverse and capable of rapid changes in solute composition and concentrations. Decades of protein studies have highlighted their sensitivity to solute environment, yet these studies were rarely performed in situ. Recently, new techniques capable of monitoring proteins in their natural context within a live cell have emerged. A recurring theme of these investigations is the importance of the often-neglected cellular solvation environment to protein function. An emerging consensus is that protein processes in the cell are affected by a combination of steric and non-steric interactions with this solution. Here we explain how protein surface area and volume changes control these two interaction types, and give recent examples that highlight how even mild environmental changes can alter cellular processes.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Martin Gruebele
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Shahar Sukenik
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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21
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Reid KA, Davis CM, Dyer RB, Kindt JT. Binding, folding and insertion of a β-hairpin peptide at a lipid bilayer surface: Influence of electrostatics and lipid tail packing. Biochim Biophys Acta Biomembr 2017; 1860:792-800. [PMID: 29291379 DOI: 10.1016/j.bbamem.2017.12.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 12/12/2017] [Accepted: 12/25/2017] [Indexed: 12/11/2022]
Abstract
Antimicrobial peptides (AMPs) act as host defenses against microbial pathogens. Here we investigate the interactions of SVS-1 (KVKVKVKVdPlPTKVKVKVK), an engineered AMP and anti-cancer β-hairpin peptide, with lipid bilayers using spectroscopic studies and atomistic molecular dynamics simulations. In agreement with literature reports, simulation and experiment show preferential binding of SVS-1 peptides to anionic over neutral bilayers. Fluorescence and circular dichroism studies of a Trp-substituted SVS-1 analogue indicate, however, that it will bind to a zwitterionic DPPC bilayer under high-curvature conditions and folds into a hairpin. In bilayers formed from a 1:1 mixture of DPPC and anionic DPPG lipids, curvature and lipid fluidity are also observed to promote deeper insertion of the fluorescent peptide. Simulations using the CHARMM C36m force field offer complementary insight into timescales and mechanisms of folding and insertion. SVS-1 simulated at an anionic mixed POPC/POPG bilayer folded into a hairpin over a microsecond, the final stage in folding coinciding with the establishment of contact between the peptide's valine sidechains and the lipid tails through a "flip and dip" mechanism. Partial, transient folding and superficial bilayer contact are seen in simulation of the peptide at a zwitterionic POPC bilayer. Only when external surface tension is applied does the peptide establish lasting contact with the POPC bilayer. Our findings reveal the influence of disruption to lipid headgroup packing (via curvature or surface tension) on the pathway of binding and insertion, highlighting the collaborative effort of electrostatic and hydrophobic interactions on interaction of SVS-1 with lipid bilayers.
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Affiliation(s)
- Keon A Reid
- Department of Chemistry, Emory University, 201 Dowman Drive, Atlanta, GA 30322, United States
| | - Caitlin M Davis
- Department of Chemistry, Emory University, 201 Dowman Drive, Atlanta, GA 30322, United States; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - R Brian Dyer
- Department of Chemistry, Emory University, 201 Dowman Drive, Atlanta, GA 30322, United States
| | - James T Kindt
- Department of Chemistry, Emory University, 201 Dowman Drive, Atlanta, GA 30322, United States.
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22
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Zanetti-Polzi L, Davis CM, Gruebele M, Dyer RB, Amadei A, Daidone I. Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation. FEBS Lett 2017; 591:3265-3275. [PMID: 28881468 DOI: 10.1002/1873-3468.12836] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/21/2017] [Accepted: 08/31/2017] [Indexed: 11/06/2022]
Abstract
We present a calculation of the amide I' infrared (IR) spectra of the folded, unfolded, and intermediate states of the WW domain Fip35, a model system for β-sheet folding. Using an all-atom molecular dynamics simulation in which multiple folding and unfolding events take place we identify six conformational states and then apply perturbed matrix method quantum-mechanical calculations to determine their amide I' IR spectra. Our analysis focuses on two states previously identified as Fip35 folding intermediates and suggests that a three-stranded core similar to the folded state core is the main source of the spectroscopic differences between the two intermediates. In particular, we propose a hypothesis for why folding via one of these intermediates was not experimentally observed by IR T-jump.
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Affiliation(s)
| | - Caitlin M Davis
- Departments of Chemistry and Physics, University of Illinois at Urbana-Champaign, IL, USA
| | - Martin Gruebele
- Departments of Chemistry and Physics, University of Illinois at Urbana-Champaign, IL, USA.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, IL, USA
| | - R Brian Dyer
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Andrea Amadei
- Department of Chemical and Technological Sciences, University of Rome "Tor Vergata", Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, Italy
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23
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Davis CM, Reddish MJ, Dyer RB. Dual time-resolved temperature-jump fluorescence and infrared spectroscopy for the study of fast protein dynamics. Spectrochim Acta A Mol Biomol Spectrosc 2017; 178:185-191. [PMID: 28189834 PMCID: PMC5346054 DOI: 10.1016/j.saa.2017.01.069] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 01/27/2017] [Accepted: 01/31/2017] [Indexed: 05/30/2023]
Abstract
Time-resolved temperature-jump (T-jump) coupled with fluorescence and infrared (IR) spectroscopy is a powerful technique for monitoring protein dynamics. Although IR spectroscopy of the polypeptide amide I mode is more technically challenging, it offers complementary information because it directly probes changes in the protein backbone, whereas, fluorescence spectroscopy is sensitive to the environment of specific side chains. With the advent of widely tunable quantum cascade lasers (QCL) it is possible to efficiently probe multiple IR frequencies with high sensitivity and reproducibility. Here we describe a dual time-resolved T-jump fluorescence and IR spectrometer and its application to study protein folding dynamics. A Q-switched Ho:YAG laser provides the T-jump source for both time-resolved IR and fluorescence spectroscopy, which are probed by a QCL and Ti:Sapphire laser, respectively. The Ho:YAG laser simultaneously pumps the time-resolved IR and fluorescence spectrometers. The instrument has high sensitivity, with an IR absorbance detection limit of <0.2mOD and a fluorescence sensitivity of 2% of the overall fluorescence intensity. Using a computer controlled QCL to rapidly tune the IR frequency it is possible to create a T-jump induced difference spectrum from 50ns to 0.5ms. This study demonstrates the power of the dual time-resolved T-jump fluorescence and IR spectroscopy to resolve complex folding mechanisms by complementary IR absorbance and fluorescence measurements of protein dynamics.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry, Emory University, Atlanta, GA 30322, United States
| | - Michael J Reddish
- Department of Chemistry, Emory University, Atlanta, GA 30322, United States
| | - R Brian Dyer
- Department of Chemistry, Emory University, Atlanta, GA 30322, United States.
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24
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Abstract
Atomic-level molecular dynamic simulations are capable of fully folding structurally diverse proteins; however, they are limited in their ability to accurately represent electrostatic interactions. Here we have experimentally tested the role of charged residues on stability and folding kinetics of one of the most widely simulated β-proteins, the WW domain. The folding of wild type Pin1 WW domain, which has two positively charged residues in the first turn, was compared to the fast folding mutant FiP35 Pin1, which introduces a negative charge into the first turn. A combination of FTIR spectroscopy and laser-induced temperature-jump coupled with infrared spectroscopy was used to probe changes in the amide I region. The relaxation dynamics of the peptide backbone, β-sheets and β-turns, and negatively charged aspartic acid side chain of FiP35 were measured independently by probing the corresponding bands assigned in the amide I region. Folding is initiated in the turns and the β-sheets form last. While the global folding mechanism is in good agreement with simulation predictions, we observe changes in the protonation state of aspartic acid during folding that have not been captured by simulation methods. The protonation state of aspartic acid is coupled to protein folding; the apparent pKa of aspartic acid in the folded protein is 6.4. The dynamics of the aspartic acid follow the dynamics of the intermediate phase, supporting assignment of this phase to formation of the first hairpin. These results demonstrate the importance of electrostatic interactions in turn stability and formation of extended β-sheet structures.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
| | - R Brian Dyer
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
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25
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Abstract
The development of food allergy is an increasingly recognized form of morbidity after solid organ transplant. It occurs more commonly in liver transplant recipients, although it has also been reported in heart, lung, kidney, and intestinal transplants. Pediatric transplant recipients are more likely to develop symptoms compared to adults, and reports of frequency vary widely from 5% to 38% in pediatric liver transplant recipients. Multiple mechanisms have been proposed in the literature, although no single mechanism can yet account for all reported observations. As food allergy can have at worst potentially fatal consequences, and at best require lifestyle adjustment through food avoidance, it is important for recipients to be aware of the donor's food allergies and particularly in pediatrics, the possibility of completely de novo allergies. This review explores the recent reports surrounding food allergy after solid organ transplant, including epidemiology, proposed mechanisms, and implications for practice.
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Affiliation(s)
- J M Needham
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - S K Nicholas
- Section of Immunology, Allergy and Rheumatology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - C M Davis
- Section of Immunology, Allergy and Rheumatology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
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26
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Abstract
Comparison of experimental and computational protein folding studies can be difficult because of differences in structural resolution. Isotope-edited infrared spectroscopy offers a direct measure of structural changes involved in protein folding at the single-residue level. Here we demonstrate the increased resolution of site-specific infrared probes to the peptide backbone in the B domain of staphylococcal protein A (BdpA). (13)C═(18)O-labeled methionine was incorporated into each of the helices using recombinant protein expression. Laser-induced temperature jumps coupled with infrared spectroscopy were used to probe changes in the peptide backbone on the submillisecond time scale. The relaxation kinetics of the buried helices, solvated helices, and labeled positions were measured independently by probing the corresponding bands assigned in the amide I region. Using these wavelength-dependent measurements, we observe a fast nanosecond phase and slower microsecond phase at each position. We find at least partial formation of helices 1-3 in the fast intermediate state that precedes the transition state. These measurements provide direct, time-resolved experimental evidence of the early formation of partial helical structure in helices 1 and 3, supporting folding models proposed by computer simulations.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
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27
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Abstract
Although the intrinsic tryptophan fluorescence of proteins offers a convenient probe of protein folding, interpretation of the fluorescence spectrum is often difficult because it is sensitive to both global and local changes. Infrared (IR) spectroscopy offers a complementary measure of structural changes involved in protein folding, because it probes changes in the secondary structure of the protein backbone. Here we demonstrate the advantages of using multiple probes, infrared and fluorescence spectroscopy, to study the folding of the FBP28 WW domain. Laser-induced temperature jumps coupled with fluorescence or infrared spectroscopy have been used to probe changes in the peptide backbone on the submillisecond time scale. The relaxation dynamics of the β-sheets and β-turn were measured independently by probing the corresponding IR bands assigned in the amide I region. Using these wavelength-dependent measurements, we observe three kinetics phases, with the fastest process corresponding to the relaxation kinetics of the turns. In contrast, fluorescence measurements of the wild-type WW domain and tryptophan mutants exhibit single-exponential kinetics with a lifetime that corresponds to the slowest phase observed by infrared spectroscopy. Mutant sequences provide evidence of an intermediate dry molten globule state. The slowest step in the folding of this WW domain is the tight packing of the side chains in the transition from the dry molten globule intermediate to the native structure. This study demonstrates that using multiple complementary probes enhances the interpretation of protein folding dynamics.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
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28
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Abstract
Small fast folding subdomains with low contact order have been postulated to facilitate the folding of larger proteins. We have tested this idea by determining how the fastest folding linear β-hairpin, CLN025, which folds on the nanosecond time scale, folds within the context of a two-hairpin WW domain system, which folds on the microsecond time scale. The folding of the wild type FBP28 WW domain was compared to constructs in which each of the loops was replaced by CLN025. A combination of FTIR spectroscopy and laser-induced temperature-jump coupled with infrared spectroscopy was used to probe changes in the peptide backbone. The relaxation dynamics of the β-sheets and β-turn were measured independently by probing the corresponding bands assigned in the amide I region. The folding rate of the CLN025 β-hairpin is unchanged within the larger protein. Insertion of the β-hairpin into the second loop results in an overall stabilization of the WW domain and a relaxation lifetime five times faster than the parent WW domain. In both mutants, folding is initiated in the turns and the β-sheets form last. These results demonstrate that fast folding subdomains can be used to speed the folding of more complex proteins, and that the folding dynamics of the subdomain is unchanged within the context of the larger protein.
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Affiliation(s)
- Caitlin M. Davis
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - R. Brian Dyer
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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29
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Abstract
Understanding the folding of the β-hairpin is a crucial step in studying how β-rich proteins fold. We have studied CLN025, an optimized ten residue synthetic peptide, which adopts a compact, well-structured β-hairpin conformation. Formation of the component β-sheet and β-turn structures of CLN025 was probed independently using a combination of equilibrium Fourier transform infrared spectroscopy and laser-induced temperature jump coupled with time-resolved infrared and fluorescence spectroscopies. We find that CLN025 is an ultrafast folder due to its small free energy barrier to folding and that it exceeds the predicted speed limit for β-hairpin formation by an order of magnitude. We also find that the folding mechanism cannot be described by a simple two-state model, but rather is a heterogeneous process involving two independent parallel processes. Formation of stabilizing cross-strand hydrophobic interactions and turn alignment occur competitively, with relaxation lifetimes of 82 ± 10 and 124 ± 10 ns, respectively, at the highest probed temperature. The ultrafast and heterogeneous folding kinetics observed for CLN025 provide evidence for folding on a nearly barrierless free energy landscape, and recalibrate the speed limit for the formation of a β-hairpin.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
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30
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Abstract
Atopic disease occurs in solid organ transplant recipients with an increasingly recognized frequency. The time course for the development of these atopic diseases in liver transplantation has not been described. The objective was to characterize the atopic manifestations of children receiving chronic immunosuppression after orthotopic liver transplantation (OLT). Chart review and follow-up questionnaire were utilized for 176 OLT pediatric recipients at a single institution for manifestations of allergic disease. Atopic disease was present in 25 (14.2%) patients. Median age at transplant was 16 months with a median follow-up of 63 months. Food allergy and non-food related atopic symptoms presented at a median of 11.5 (IQR, 6-28) and 19 (IQR, 5-41) months post-transplantation, respectively. The median age at transplant of the non-atopic children was 72 months, higher than patients with atopy (p < 0.001). Food allergy and atopic skin disease symptoms were present in 40% and 56% of cases, respectively. Asthma, allergic rhinitis, or both were found in 66% of cases. The onset of symptoms of food allergy and eczema (median, 12 months post-transplantation) preceded symptoms of allergic rhinitis and asthma. (median of 27 and 30 months post-transplantation, respectively). Atopy occurs in ∼14% of pediatric liver transplant recipients, with manifestations including food allergy, eczema, allergic rhinitis, and asthma.
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Affiliation(s)
- P Shroff
- Section of Allergy, Immunology, and Rheumatology, Department of Internal Medicine, Baylor College of Medicine, Houston, TX, USA
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31
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Fairbanks SL, Young JM, Nelson JW, Davis CM, Koerner IP, Alkayed NJ. Mechanism of the sex difference in neuronal ischemic cell death. Neuroscience 2012; 219:183-91. [PMID: 22641086 DOI: 10.1016/j.neuroscience.2012.05.048] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 05/15/2012] [Accepted: 05/17/2012] [Indexed: 12/20/2022]
Abstract
BACKGROUND Stroke risk and outcome are different in men and women. We hypothesized that this is partly due to an inherent difference in susceptibility to ischemia between neurons from male vs. female brains. We tested whether neurons from male rodents are more susceptible to in-vitro ischemia than cells from females, and if this is related to increased expression of soluble epoxide hydrolase (sEH). sEH contributes to neuronal cell death by inactivating neuroprotective epoxyeicosatrienoic acids (EETs). METHODS Rodent cortical neurons were cultured, and exposed to oxygen-glucose deprivation (OGD); then cell death was measured. EETs levels were determined by LC-MS/MS. Expression of sEH-encoding ephx2 was determined by qRT-PCR. Western blotting, immunocytochemistry, and hydrolase activity assay assessed protein expression and activity. RESULTS Cell death after OGD was higher in neurons from males vs. females, which correlated with higher ephx2 mRNA and stronger sEH immunoreactivity. However, EETs levels were similar in both sexes and pharmacological inhibition of the hydrolase domain of sEH did not abolish the sex difference in cell death. Genetic knockout of sEH in mice abolished the sex difference observed in neurons isolated from these mice after OGD. CONCLUSIONS Cultured cortical neurons from females are more resistant to ischemia than neurons from males. Neurons from females have less sEH activity compared to neurons from males at baseline, although sEH levels were not measured after OGD. While pharmacological inhibition of the hydrolase domain of sEH does not affect cell death, knockout of the gene encoding sEH eradicates the sex difference seen in wild-type neurons, suggesting a role for further study of the lesser-known phosphatase domain of sEH and its role in sexual dimorphism in neuronal sensitivity to ischemia.
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Affiliation(s)
- S L Fairbanks
- Department of Anesthesiology and Perioperative Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239-3098, USA
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32
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Schroers R, Davis CM, Wagner HJ, Chen SY. Lentiviral transduction of human T-lymphocytes with a RANTES intrakine inhibits human immunodeficiency virus type 1 infection. Gene Ther 2002; 9:889-97. [PMID: 12080383 DOI: 10.1038/sj.gt.3301711] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2001] [Accepted: 02/11/2002] [Indexed: 11/09/2022]
Abstract
Intrakines, modified intracellular chemokines, offer a novel strategy to prevent cellular entry of HIV-1 by blocking the surface expression of HIV-1 co-receptors. To investigate potential clinical applications of the RANTES-intrakine, we explored the use of HIV-1-based lentiviral vectors for therapeutic gene transfer into T-lymphocytes. RANTES-intrakine genes can be efficiently transduced into primary human T-lymphocytes by lentiviral vectors, especially when human T-lymphocytes were stimulated with CD3 and CD28 antibodies. The transduced T cells showed decreased surface expression of the chemokine receptor CCR-5, as well as CCR-1 and CCR-3. This lentivirus-mediated approach to intrakine gene transfer protected human T-lymphocytes from infection by a variety of R5-tropic HIV-1 strains. A quantitative real-time PCR assay, developed to monitor cells for HIV entry and persistence, revealed persistent low copy numbers of proviral HIV DNA in RANTES intrakine-transduced T-lymphocytes during 3-week culture, suggesting that viruses produced from infected untransduced cell populations were unable to infect the surrounding transduced T-lymphocytes. We conclude that targeting HIV-1 co-receptors to block virus entry with lentiviral vectors is an attractive approach to the control of HIV-1 infection.
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Affiliation(s)
- R Schroers
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
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33
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Davis CM, Doerger C, Rowland J, Sauber C, Eaton T. MYOFASCIAL RELEASE AS COMPLEMENTARY IN PHYSICAL THERAPY FOR TWO ELDERLY PATIENTS WITH OSTEOPOROSIS AND KYPHOSCOLIOSIS ~ TWO CASE STUDIES. J Geriatr Phys Ther 2002. [DOI: 10.1519/00139143-200225030-00027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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34
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Ravishankar JP, Davis CM, Davis DJ, MacDonald E, Makselan SD, Millward L, Money NP. Mechanics of solid tissue invasion by the mammalian pathogen Pythium insidiosum. Fungal Genet Biol 2001; 34:167-75. [PMID: 11728155 DOI: 10.1006/fgbi.2001.1304] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The relative significance of mechanical penetration versus the action of substrate-degrading enzymes during solid tissue invasion has not been established for any fungal disease. Pythium insidiosum is an oomycete fungus (or stramenopile) that causes a rare, but potentially lethal infection in humans and other mammalian hosts. Experiments with miniature strain gauges showed that single hyphal apices of this pathogen exert forces of up to 6.9 microN, corresponding to maximum pressures of 0.3 microN microm(-2) or MPa. Samples of cutaneous and subcutaneous tissue from fresh human cadavers displayed a mean strength (resistance to needle puncture) of 24 microN microm(-2), and a mean pressure of 30 microN microm(-2) was necessary to penetrate skin strips from slaughtered horses. These experiments demonstrate that P. insidiosum does not exert sufficient pressure to penetrate undamaged skin by mechanics alone, but must effect a decisive reduction in tissue strength by proteinase secretion.
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Affiliation(s)
- J P Ravishankar
- Department of Botany, Miami University, Oxford, Ohio 45056, USA
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35
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Davis CM, Caseby NG. Prevalence and incidence studies of pressure ulcers in two long-term care facilities in Canada. Ostomy Wound Manage 2001; 47:28-34. [PMID: 11890073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
A study was initiated to determine the prevalence and incidence of pressure ulcers in two long-term care facilities in Canada, one with 95 residents and the other with 92 residents. The prevalence study was conducted at both facilities on a single day. The incidence study was completed after 41 and 42 days, respectively, at each facility. Data were collected on demographics, medical information, and possible contributing factors. Each resident was assessed for the presence of a pressure ulcer. Each ulcer was staged and anatomical location was noted. The prevalence of pressure ulcers in the two long-term care facilities was 36.8% and 53.2%, respectively. The incidence of pressure ulcers in the two long-term care facilities was 11.7% and 11.6%, respectively. In conclusion, the pressure ulcer prevalence is higher than published figures for the long-term care setting. However, a pressure ulcer incidence of less than 12% in each facility suggests an equal and acceptable level of nursing care in both facilities. The disparity of pressure ulcer prevalence between the two facilities may be explained by a difference of case mix.
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Affiliation(s)
- C M Davis
- Rothbart Pain Management Clinic, North York, Ontario, Canada.
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Ullrich RL, Davis CM. Radiation-induced cytogenetic instability in vivo. Radiat Res 1999; 152:170-3. [PMID: 10409326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Radiation-induced cytogenetic instability has been well documented in a number of laboratories, and we have hypothesized that such instability is the initiating event in the process leading to radiation-induced cancer. To date most studies of radiation-induced instability have used systems in which cells are rapidly dividing. For this phenomenon to have significance for radiation carcinogenesis, it must be established that instability can be induced in vivo in less rapidly dividing fully differentiated tissues known to be at risk. In the present study, we have examined the kinetics of radiation-induced cytogenetic instability in mammary epithelial cells after irradiation in vivo. Having established that instability could arise in vivo in intact mammary tissue, we subsequently demonstrated a dose-response relationship both in vitro and in vivo and demonstrated a lower frequency of instability after fractionated exposures.
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Affiliation(s)
- R L Ullrich
- Department of Radiation Oncology and Human Biological Chemistry and Genetics, University of Texas Medical Branch, Galveston, Texas 77555, USA
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Davis CM, Curley CM. Disparities of health in African Americans. Nurs Clin North Am 1999; 34:345-57. [PMID: 10318728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
As a cohort of the vulnerable populations, African Americans have the poorest health status indicators of all ethnic groups. Using a vulnerable populations theoretical framework, the reasons for the disparities are discussed.
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Affiliation(s)
- C M Davis
- Lecturer, Department of Nursing, California State University San Bernardino, San Bernardino, California, USA
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Recchia PA, Davis CM, Lilburn TG, Beatty JT, Parkes-Loach PS, Hunter CN, Loach PA. Isolation of the PufX protein from Rhodobacter capsulatus and Rhodobacter sphaeroides: evidence for its interaction with the alpha-polypeptide of the core light-harvesting complex. Biochemistry 1998; 37:11055-63. [PMID: 9693001 DOI: 10.1021/bi980657l] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Using mutant strains of Rhodobacter capsulatus and Rhodobacter sphaeroides in which the pufX gene had been deleted, it was possible to identify by HPLC membrane protein components present in pufX+ cells but absent in pufX- cells. In parallel preparations, membrane proteins soluble in chloroform/methanol containing ammonium acetate were first extracted from lyophilized membrane fractions of the pufX+ cells and separated from pigments and larger protein material by gel-filtration chromatography. Protein-containing fractions were examined by HPLC, and several peaks were collected from pufX+ material that were not present in pufX- material. From N-terminal amino acid sequencing, the PufX protein of Rb. capsulatus was identified, and from positive interaction with a PufX protein antibody, the Rb. sphaeroides PufX protein was identified. Although overall yields were very small, sufficient quantities of these proteins were isolated to evaluate their effect on the reconstitution of the core light-havesting antenna (LH1) and its subunit complex. From the behavior of the PufX protein and the alpha-polypeptide of LH1 on HPLC, qualitative evidence was obtained that the two proteins have a high affinity for each other. In reconstitution assays with bacteriochlorophyll (Bchl) and the LH1 alpha- and beta-polypeptides of Rb. capsulatus, the PufX protein of Rb. capsulatus was inhibitory to LH1 formation at low concentration. A similar inhibition was exhibited by Rb. sphaeroides PufX protein for reconstitution of LH1 with Bchl and the LH1 alpha- and beta-polypeptides of Rb. sphaeroides. In both cases, the ratios of concentrations of the PufX protein to the alpha-polypeptide causing 50% inhibition were approximately 0.5. Formation of the heterologous (alpha beta) subunit-type complex formed with Bchl and the alpha- and beta-polypeptides of LH1 of Rb. capsulatus was also inhibited by low concentrations of the Rb. capsulatus PufX protein (approximately 50% inhibition at PufX:alpha-polypeptide ratios = 0.5). However, neither PufX protein inhibited formation of a homologous (beta beta) subunit-type complex, which indicates that the PufX proteins do not interact with the beta-polypeptides.
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Affiliation(s)
- P A Recchia
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois 60208-3500, USA
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Gago LA, Moore EE, Partrick DA, Sauaia A, Davis CM, Toal TR, Silliman CC. Secretory phospholipase A2 cleavage of intravasated bone marrow primes human neutrophils. J Trauma 1998; 44:660-4. [PMID: 9555838 DOI: 10.1097/00005373-199804000-00017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Recent clinical reports suggest that early femoral intramedullary rod (IMR) fixation in patients with multiple injuries increases the risk of adult respiratory distress syndrome (ARDS). We have shown that lipid-mediated neutrophil (PMN) priming and elevated circulating levels of secretory phospholipase A2 (sPLA2) within the first 24 hours after injury correlate with the development of ARDS. We thus hypothesized that circulating lipid products, generated by sPLA2 cleavage of intravasated bone marrow, prime PMNs for enhanced superoxide anion (O2-) production. METHODS Isolated PMNs from healthy volunteers were incubated for 5 minutes with buffer or sPLA2-lysed bone marrow (100 U/mL) collected from trauma patients. After formyl-methionyleucylphenylalanine (fMLP) activation, O2- production was quantified by the superoxide dismutase-inhibitable reduction of cytochrome c. Blood samples were also drawn from five injured patients before and 24 hours after femoral IMR fixation. PMNs were isolated and assessed for in vivo priming. RESULTS PMNs incubated with sPLA2-lysed bone marrow were primed for more than 3.5 times greater fMLP-induced O2- production. Furthermore, in patients with femoral fractures, PMN O2- release in response to fMLP after IMR fixation was more than 2.5 times higher than before fixation. CONCLUSION Collectively, the findings suggest that bone marrow released from acute fracture sites may become a lipid substrate for the elevated sPLA2 levels found in injured patients. The resultant priming of PMNs may thus render the injured patient at risk for ARDS. Although clearly hypothetical at present, we submit that these observations warrant further investigation because of their clinical implications.
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Affiliation(s)
- L A Gago
- Department of Surgery, Denver Health Medical Center, Colorado 80204, USA
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Davis CM, Ambros-Ingerson J, Granger R, Wu J, Zabaneh R, Abdelnaby M, Lynch G. Triazolam impairs delayed recall but not acquisition of various everyday memory tasks in humans. Exp Neurol 1997; 148:124-34. [PMID: 9398455 DOI: 10.1006/exnr.1997.6631] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A double-blind test battery was administered to 24 human subjects (8 control, 16 drug) to assess the effects of 0.125 mg triazolam (oral) on memory encoding and retention across delay intervals ranging from seconds to 1 week after presentation. Although the drug reduced immediate psychomotor performance, it did not impair recall of previously learned information, nor did it significantly impair encoding of new information. The drug enhanced immediate recall of the location and identity of playing cards, without affecting 4-h delayed recall. The drug treatment impaired correct recall of object names after a delay of 20 min. At 4 h delay, the drug impaired olfactory recognition and free-recall of object names. At both 1 day and 1 week delay, the drug impaired recall of biographical information and correct identification of picture-photographer pair associations. The drug also impaired the daily improvement of the drug group as compared with the control group in a geometric puzzle solving task. The time course of these memory impairments compares well with the known effects of triazolam on long-term potentiation (LTP), a candidate biological mechanism underlying telencephalic memory formation and expression.
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Affiliation(s)
- C M Davis
- Center for the Neurobiology of Learning and Memory, University of California, Irvine 92697-3800, USA
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Medder J, Susman JL, Gilbert C, Crabtree BF, McIlvain HE, McVea K, Davis CM, Hawver M. Dissemination and implementation of Put Prevention into Family Practice. Am J Prev Med 1997; 13:345-51. [PMID: 9315265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
INTRODUCTION The Put Prevention into Practice (PPIP) program was developed and disseminated to address patient, clinician, and office barriers that result in less than optimal delivery of preventive services in the United States. METHODS To study the dissemination of PPIP by the American Academy of Family Physicians (AAFP), pre- and post-dissemination surveys of knowledge about PPIP and purchase order data were obtained from the AAFP. In addition, a mail questionnaire was sent to a random sample of purchasers to study their use of PPIP. RESULTS After two years of active promotion, 27% of AAFP members had heard about PPIP, and PPIP components were purchased by 2,004 individuals during its inital dissemination. Flow sheets, health guides, exam room wall charts, and the Clinician's Handbook of Preventive Services were the PPIP items most frequently purchased and used. Excluding the Clinician's Handbook of Preventive Services, 58% of purchasers used one or more parts of the kit with an average of less than four items used per purchaser. CONCLUSIONS Initial dissemination and implementation of PPIP among family physicians was limited; continued promotion will likely improve dissemination of PPIP. However, this study, and others suggest that the simple availability of a kit of materials is not sufficient to enhance the delivery of preventive services as envisioned by clinicians or policy makers. Additional strategies for dissemination and implementation of preventive services will be required, such as providing external consultation services to practices, incorporation of preventive services into HMO organizations, and training of residents in strategies for change in their future practices.
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Affiliation(s)
- J Medder
- Department of Family Medicine, University of Nebraska Medical Center, Omaha 68198-3075, USA.
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Davis CM, Moskovitz B, Nguyen MA, Tran BB, Arai A, Lynch G, Granger R. A profile of the behavioral changes produced by facilitation of AMPA-type glutamate receptors. Psychopharmacology (Berl) 1997; 133:161-7. [PMID: 9342782 DOI: 10.1007/s002130050386] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A newly developed group of benzoylpiperidine drugs that enhance AMPA-receptor-gated currents ("ampakines") has been shown to improve memory encoding in rats across a variety of experimental paradigms. The present experiments were intended to i) provide a partial profile of the behavioral changes produced by ampakines, ii) test if two ampakines (BDP-12 and BDP-20) that differ significantly in their effects on AMPA receptor kinetics produce similar behavioral profiles, and iii) determine if physiological potency is reflected in behavioral potency. BDP-20 reduced two measures of exploratory activity in aged rats but increased speed of performance in a radial maze; the drug also caused substantially improved retention of spatial information. These results are similar to those obtained with BDP-12, an analog that differs from BDP-20 in its effects on ligand binding to the AMPA receptor and on the physiological responses of the receptors to glutamate. BDP-20 was approximately ten-fold more potent in behavioral effects than BDP-12, which agrees with the relative potencies of the two drugs as assessed with excised patches and excitatory synaptic responses. These findings indicate that ampakines, though differing in their effects on AMPA-receptor-mediated responses, have similar effects at the behavioral level.
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Affiliation(s)
- C M Davis
- Center for the Neurobiology of Learning and Memory, University of California, Irvine 92697-3800, USA
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Caron SL, Carter DB, Davis CM, Macklin E. Evaluating the Effectiveness of Workshop Interventions on Contraceptive Use Among First-Year College Students. ACTA ACUST UNITED AC 1997; 9:99-120. [PMID: 12293611 DOI: 10.1300/j056v09n03_06] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Lynch G, Granger R, Ambros-Ingerson J, Davis CM, Kessler M, Schehr R. Evidence that a positive modulator of AMPA-type glutamate receptors improves delayed recall in aged humans. Exp Neurol 1997; 145:89-92. [PMID: 9184112 DOI: 10.1006/exnr.1997.6447] [Citation(s) in RCA: 122] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Elderly subjects (65-76 years) were tested for recall of nonsense syllables prior to and after oral administration of 1-(quinoxalin-6 ylcarbonyl)piperidine (CX516), a centrally active drug that enhances currents mediated by AMPA-type glutamate receptors. A significant and positive drug effect was found for delayed (5 min) recall at 75 min posttreatment; average scores for the highest dose group were more than twofold greater than for the placebo group. The drug had no evident influence on heart rate or self-assessment of several psychological variables.
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Affiliation(s)
- G Lynch
- Cortex Pharmaceuticals, Inc., Irvine, California 92718, USA
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Abstract
A possible new mechanism for the amplification of insulin receptor tyrosine kinase activity in response to insulin has been identified. The chromium-containing oligopeptide low molecular weight chromium-binding substance (LMWCr) does not effect the tyrosine protein kinase activity of rat adipocytic membrane fragments in the absence of insulin; however, insulin-stimulated kinase activity in the membrane fragments is increased up to 8-fold by the oligopeptide. Using isolated rat insulin receptor, LMWCr has been shown to bind to insulin-activated insulin receptor with a dissociation constant of circa 250 pM, resulting in the increase of its tyrosine protein kinase activity. The ability of LMWCr to stimulate insulin receptor tyrosine kinase activity is dependent on its chromium content. The results appear to explain the previously poorly understood relationship between chromium and adult-onset diabetes and cardiovascular disease.
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Affiliation(s)
- C M Davis
- Department of Chemistry, University of Alabama, Tuscaloosa 35487-0336, USA
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Davis CM, Bustamante PL, Todd JB, Parkes-Loach PS, McGlynn P, Olsen JD, McMaster L, Hunter CN, Loach PA. Evaluation of structure-function relationships in the core light-harvesting complex of photosynthetic bacteria by reconstitution with mutant polypeptides. Biochemistry 1997; 36:3671-9. [PMID: 9132020 DOI: 10.1021/bi962386p] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Seven mutant LH1 polypeptides of Rhodobactor sphaeroides have been isolated, and their behaviors in in vitro reconstitution of LH1 and its subunit complex have been characterized. Two mutants were selected to address the increased stability of the subunit complex of Rb. sphaeroides compared with that of Rhodobacter capsulatus. We found that this difference can be largely ascribed to the existence of Tyr at position +4 in the beta-polypeptide (the numbering system used assigns position 0 to the His which provides the coordinating ligand to bacteriochlorophyll) of the former bacterium compared to Met in that position in the latter. The amount of energy involved in the increased interaction was 1.6 kcal/mol, which would be consistent with a hydrogen bond involving Tyr. Mutation of the His at position 0 to Asn allows an estimate of the binding energy for subunit formation contributed by coordination of the imidazole group of His to the Mg atom of bacteriochlorophyll of >4.5 kcal/mol per BChl. Finally, an evaluation of the role of amino acids in the C-terminal region of the alpha-polypeptide was begun. Reconstitution of a mutant alpha-polypeptide in which Trp at position +11 was changed to Phe resulted in optimal formation of an LH1-type complex whose lambda(max) was blue-shifted to 853 nm, the same as observed in the intact bacterium harboring this mutation. These results provide further confirmation that the environment of BChl in reconstituted LH1 complexes is the same as in vivo and support the assignment of this residue to a role in hydrogen bonding with the C3(1) carbonyl group of BChl. Two other mutants of the alpha-polypeptide in which 5 and 14 amino acids in the C-terminus were deleted were also examined. These were of interest because the latter mutant, unlike the former, resulted in a low level of expression of LH1 in intact cells. However, with both of these mutant polypeptides, reconstitution appeared identical to that of the native system. In the case of the mutant shortened by 14 amino acids, a small blue-shift in lambda(max) to 861 nm was observed, again reproducing the blue-shift exhibited by the intact cells. Thus, these results suggest that the lowered levels of in vivo expression observed in these two mutants are due to reduced incorporation of the alpha-polypeptide into the membrane or its increased degradation, rather than to decreased stabilization of the LH1 complex.
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Affiliation(s)
- C M Davis
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois 60208-3500, USA
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Abstract
Low-molecular-weight chromium-binding substance (LMWCr), the only known naturally occurring Cr-containing polypeptide from mammals and candidate for the biologically active form of chromium, has been isolated for the first time in yields sufficient for spectroscopic studies capable of providing structural and mechanistic data on a molecular level. The results of paramagnetic 1H NMR, electron paramagnetic resonance, and electronic spectroscopic studies indicate that the four chromic ions per polypeptide are probably arranged in an integer-spin tetranuclear assembly, although an alternate possibility, the presence of two dinuclear assemblies, could not be ruled out. This assembly (or assemblies) is bridged by anionic ligands and supported by carboxylates provided by the polypeptide.
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Affiliation(s)
- C M Davis
- Department of Chemistry, University of Alabama, Tuscaloosa, Alabama, 35487-0336, USA
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Davis CM, McLaughlin TM, Watson TJ, Buckley RH, Schiff SE, Hale LP, Haynes BF, Markert ML. Normalization of the peripheral blood T cell receptor V beta repertoire after cultured postnatal human thymic transplantation in DiGeorge syndrome. J Clin Immunol 1997; 17:167-75. [PMID: 9083893 DOI: 10.1023/a:1027382600143] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Complete DiGeorge syndrome is an immunodeficiency disease characterized by thymic aplasia and the absence of functioning peripheral T cells. A patient with this syndrome was transplanted with cultured postnatal human thymic tissue. Within 5 weeks of transplantation, flow cytometry, T cell receptor V beta sequence analysis, and cell function studies showed the presence of oligoclonal populations of nonfunctional clonally expanded peripheral T cells that were derived from pretransplantation T cells present in the skin. However, at 3 months posttransplantation, a biopsy of the transplanted thymus showed normal intrathymic T cell maturation of host T cells with normal TCR V beta expression on thymocytes. By 9 months postransplantation, peripheral T cell function was restored and the TCR V beta repertoire became polyclonal, coincident with the appearance of normal T cell function. These data suggest that the transplanted thymus was responsible for the establishment of a new T cell repertoire via thymopoiesis in the chimeric thymic graft.
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Affiliation(s)
- C M Davis
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina 27710, USA
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Fletcher JM, Page JB, Francis DJ, Copeland K, Naus MJ, Davis CM, Morris R, Krauskopf D, Satz P. Cognitive correlates of long-term cannabis use in Costa Rican men. Arch Gen Psychiatry 1996; 53:1051-7. [PMID: 8911228 DOI: 10.1001/archpsyc.1996.01830110089011] [Citation(s) in RCA: 121] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND Cognitive correlates of long-term cannabis use have been elusive. We tested the hypothesis that long-term cannabis use is associated with deficits in short term memory, working memory, and attention in a literate, westernized culture (Costa Rica) in which the effects of cannabis use can be isolated. METHODS Two cohorts of long-term cannabis users and nonusers were studied. Within each cohort, users and nonusers were comparable in age and socioeconomic status. Polydrug users and users who tested positive for the use of cannabis at the time of cognitive assessment after a 72-hour abstention period were excluded. The older cohort (whose age was approximately 45 years) had consumed cannabis for an average of 34 years, and comprised 17 users and 30 nonusers, who had been recruited in San José, Costa Rica, and had been observed since 1973. The younger cohort (whose age was approximately 28 years) had consumed cannabis for an average of 8 years, and comprised 37 users and 49 nonusers. Short-term memory, working memory, and attentional skills were measured in each subject. RESULTS Older long-term users performed worse than older nonusers on 2 short-term memory tests involving learning lists of words. In addition, older long-term users performed worse than older nonusers on selective and divided attention tasks associated with working memory. No notable differences were apparent between younger users and nonusers. CONCLUSION Long-term cannabis use was associated with disruption of short-term memory, working memory, and attentional skills in older long-term cannabis users.
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Affiliation(s)
- J M Fletcher
- Department of Pediatrics, University of Texas-Houston Medical School, USA
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McVea K, Crabtree BF, Medder JD, Susman JL, Lukas L, McIlvain HE, Davis CM, Gilbert CS, Hawver M. An ounce of prevention? Evaluation of the 'Put Prevention into Practice' program. J Fam Pract 1996; 43:361-369. [PMID: 8874371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
BACKGROUND The "Put Prevention into Practice" (PPIP) program was designed to enhance the capacity of health care providers to deliver clinical preventive services. This study was designed to evaluate the program's effectiveness when applied to family physicians in private practice settings. METHODS Eight Midwestern practices that had purchased PPIP kits were identified and agreed to participate in the study. A comparative case study approach encompassing a variety of data collection techniques was used. These techniques included participant observation of clinic operations and patient encounters, semistructured and key informant interviews with physicians and staff members, chart reviews, and structured postpatient encounter and office environment checklists. Content analysis of the qualitative data and construction of the individual cases were done by consensus of the research team. RESULTS PPIP materials are not being used, even by the clinics that ordered them. Physicians already providing quality preventive services prefer their existing materials to those in the PPIP kit. Sites that are underutilizing preventive services are unable or unwilling to independently implement the PPIP program. CONCLUSIONS Development of technical support may facilitate implementation of PPIP materials into those practices most deficient in providing preventive services. Given the diversity of practice environments it is unlikely that a "one size fits all" approach will ever be able to address the needs of all providers.
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Affiliation(s)
- K McVea
- Department of Family Medicine, University of Nebraska Medical Center, Omaha 68198-3075, USA.
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