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1.
Mar Drugs ; 21(6)2023 Jun 01.
Article in English | MEDLINE | ID: mdl-37367665

ABSTRACT

Agarobiose (AB; d-galactose-ß-1,4-AHG), produced by one-step acid hydrolysis of agarose of red seaweed, is considered a promising cosmetic ingredient due to its skin-moisturizing activity. In this study, the use of AB as a cosmetic ingredient was found to be hampered due to its instability at high temperature and alkaline pH. Therefore, to increase the chemical stability of AB, we devised a novel process to synthesize ethyl-agarobioside (ethyl-AB) from the acid-catalyzed alcoholysis of agarose. This process mimics the generation of ethyl α-glucoside and glyceryl α-glucoside by alcoholysis in the presence of ethanol and glycerol during the traditional Japanese sake-brewing process. Ethyl-AB also showed in vitro skin-moisturizing activity similar to that of AB, but showed higher thermal and pH stability than AB. This is the first report of ethyl-AB, a novel compound produced from red seaweed, as a functional cosmetic ingredient with high chemical stability.


Subject(s)
Alcoholic Beverages , Seaweed , Sepharose/chemistry , Fermentation , Seaweed/chemistry , Glucosides
2.
Chemistry ; 29(27): e202300330, 2023 May 11.
Article in English | MEDLINE | ID: mdl-36746778

ABSTRACT

The efficient utilization of lignin, the direct source of renewable aromatics, into value-added renewable chemicals is an important step towards sustainable biorefinery practices. Nevertheless, owing to the random heterogeneous structure and limited solubility, lignin utilization has been primarily limited to burning for energy. The catalytic depolymerization of lignin has been proposed and demonstrated as a viable route to sustainable biorefinery, however, low yields and poor selectivity of products, high char formation, and limited to no recycling of transition-metal-based catalyst involved in lignin depolymerization demands attention to enable practical-scale lignocellulosic biorefineries. In this study, we demonstrate the catalytic depolymerization of ionic liquid-based biorefinery poplar lignin into guaiacols over a reusable zirconium phosphate supported palladium catalyst. The essence of the study lies in the high conversion (>80 %), minimum char formation (7-16 %), high yields of guaiacols (up to 200 mg / g of lignin), and catalyst reusability. Both solid residue, liquid stream, and gaseous products were thoroughly characterized using ICP-OES, PXRD, CHN analysis, GC-MS, GPC, and 2D NMR to understand the hydrogenolysis pathway.

3.
Elife ; 112022 03 11.
Article in English | MEDLINE | ID: mdl-35272765

ABSTRACT

Cancer mutations in Ras occur predominantly at three hotspots: Gly 12, Gly 13, and Gln 61. Previously, we reported that deep mutagenesis of H-Ras using a bacterial assay identified many other activating mutations (Bandaru et al., 2017). We now show that the results of saturation mutagenesis of H-Ras in mammalian Ba/F3 cells correlate well with the results of bacterial experiments in which H-Ras or K-Ras are co-expressed with a GTPase-activating protein (GAP). The prominent cancer hotspots are not dominant in the Ba/F3 data. We used the bacterial system to mutagenize Ras constructs of different stabilities and discovered a feature that distinguishes the cancer hotspots. While mutations at the cancer hotspots activate Ras regardless of construct stability, mutations at lower-frequency sites (e.g. at Val 14 or Asp 119) can be activating or deleterious, depending on the stability of the Ras construct. We characterized the dynamics of three non-hotspot activating Ras mutants by using NMR to monitor hydrogen-deuterium exchange (HDX). These mutations result in global increases in HDX rates, consistent with destabilization of Ras. An explanation for these observations is that mutations that destabilize Ras increase nucleotide dissociation rates, enabling activation by spontaneous nucleotide exchange. A further stability decrease can lead to insufficient levels of folded Ras - and subsequent loss of function. In contrast, the cancer hotspot mutations are mechanism-based activators of Ras that interfere directly with the action of GAPs. Our results demonstrate the importance of GAP surveillance and protein stability in determining the sensitivity of Ras to mutational activation.


Subject(s)
GTPase-Activating Proteins , Neoplasms , Animals , Mammals , Mutagenesis , Mutation , Nucleotides , ras GTPase-Activating Proteins
4.
Nat Chem Biol ; 18(2): 171-179, 2022 02.
Article in English | MEDLINE | ID: mdl-34937913

ABSTRACT

FeII/α-ketoglutarate (FeII/αKG)-dependent enzymes offer a promising biocatalytic platform for halogenation chemistry owing to their ability to functionalize unactivated C-H bonds. However, relatively few radical halogenases have been identified to date, limiting their synthetic utility. Here, we report a strategy to expand the palette of enzymatic halogenation by engineering a reaction pathway rather than substrate selectivity. This approach could allow us to tap the broader class of FeII/αKG-dependent hydroxylases as catalysts by their conversion to halogenases. Toward this goal, we discovered active halogenases from a DNA shuffle library generated from a halogenase-hydroxylase pair using a high-throughput in vivo fluorescent screen coupled to an alkyne-producing biosynthetic pathway. Insights from sequencing halogenation-active variants along with the crystal structure of the hydroxylase enabled engineering of a hydroxylase to perform halogenation with comparable activity and higher selectivity than the wild-type halogenase, showcasing the potential of harnessing hydroxylases for biocatalytic halogenation.


Subject(s)
Halogens/metabolism , Mixed Function Oxygenases/chemistry , Mixed Function Oxygenases/metabolism , Catalytic Domain , Halogenation , Models, Molecular , Protein Conformation , Protein Engineering , Substrate Specificity
5.
RSC Chem Biol ; 2(5): 1462-1465, 2021 Oct 07.
Article in English | MEDLINE | ID: mdl-34704049

ABSTRACT

In nitrogenase biosynthesis, the iron-molybdenum cofactor (FeMo-co) is externally assembled at scaffold proteins and delivered to the NifDK nitrogenase component by the NafY metallochaperone. Here we have used nuclear magnetic resonance, molecular dynamics, and functional analysis to elucidate the environment and coordination of FeMo-co in NafY. H121 stands as the key FeMo-co ligand. Regions near FeMo-co diverge from H121 and include the η1, α1, α2 helical lobe and a narrow path between H121 and C196.

6.
Proc Natl Acad Sci U S A ; 118(12)2021 03 23.
Article in English | MEDLINE | ID: mdl-33723075

ABSTRACT

Ubiquitin is a common posttranslational modification canonically associated with targeting proteins to the 26S proteasome for degradation and also plays a role in numerous other nondegradative cellular processes. Ubiquitination at certain sites destabilizes the substrate protein, with consequences for proteasomal processing, while ubiquitination at other sites has little energetic effect. How this site specificity-and, by extension, the myriad effects of ubiquitination on substrate proteins-arises remains unknown. Here, we systematically characterize the atomic-level effects of ubiquitination at various sites on a model protein, barstar, using a combination of NMR, hydrogen-deuterium exchange mass spectrometry, and molecular dynamics simulation. We find that, regardless of the site of modification, ubiquitination does not induce large structural rearrangements in the substrate. Destabilizing modifications, however, increase fluctuations from the native state resulting in exposure of the substrate's C terminus. Both of the sites occur in regions of barstar with relatively high conformational flexibility. Nevertheless, destabilization appears to occur through different thermodynamic mechanisms, involving a reduction in entropy in one case and a loss in enthalpy in another. By contrast, ubiquitination at a nondestabilizing site protects the substrate C terminus through intermittent formation of a structural motif with the last three residues of ubiquitin. Thus, the biophysical effects of ubiquitination at a given site depend greatly on local context. Taken together, our results reveal how a single posttranslational modification can generate a broad array of distinct effects, providing a framework to guide the design of proteins and therapeutics with desired degradation and quality control properties.


Subject(s)
Ubiquitin/chemistry , Ubiquitin/metabolism , Hydrogen/chemistry , Mechanical Phenomena , Molecular Dynamics Simulation , Protein Conformation , Protein Processing, Post-Translational , Proteins/chemistry , Proteins/metabolism , Structure-Activity Relationship , Ubiquitination
7.
Green Chem ; 22(5): 1776-1785, 2020 Mar 07.
Article in English | MEDLINE | ID: mdl-33790689

ABSTRACT

Recently, the utilization of renewable biomass instead of fossil fuels for producing fuels and chemicals is receiving much attention due to the global climate change. Among renewable biomass, marine algae are gaining importance as third generation biomass feedstocks owing to their advantages over lignocellulose. Particularly, red macroalgae have higher carbohydrate contents and simpler carbohydrate compositions than other marine algae. In red macroalgal carbphydrates, 3,6-anhydro-L-galactose (AHG) is the main sugar composing agarose along with D-galactose. However, AHG is not a common sugar and is chemically unstable. Thus, not only AHG but also red macroalgal biomass itself cannot be efficiently converted or utilized. Here, we biologically upgraded AHG to a new platform chemical, its sugar alcohol form, 3,6-anhydro-l-galactitol (AHGol), an anhydrohexitol. To accomplish this, we devised an integrated process encompassing a chemical hydrolysis process for producing agarobiose (AB) from agarose and a biological process for converting AB to AHGol using metabolically engineered Saccharomyces cerevisiae to efficiently produce AHGol from agarose with high titers and yields. AHGol was also converted to an intermediate chemical for plastics, isosorbide. To our knowledge, this is the first demonstration of upgrading a red macroalgal biomass component to a platform chemical via a new biological route, by using an engineered microorganism.

8.
Nat Chem Biol ; 15(10): 1009-1016, 2019 10.
Article in English | MEDLINE | ID: mdl-31548692

ABSTRACT

The integration of synthetic and biological catalysis enables new approaches to the synthesis of small molecules by combining the high selectivity of enzymes with the reaction diversity offered by synthetic chemistry. While organohalogens are valued for their bioactivity and utility as synthetic building blocks, only a handful of enzymes that carry out the regioselective halogenation of unactivated [Formula: see text] bonds have previously been identified. In this context, we report the structural characterization of BesD, a recently discovered radical halogenase from the FeII/α-ketogluturate-dependent family that chlorinates the free amino acid lysine. We also identify and characterize additional halogenases that produce mono- and dichlorinated, as well as brominated and azidated, amino acids. The substrate selectivity of this new family of radical halogenases takes advantage of the central role of amino acids in metabolism and enables engineering of biosynthetic pathways to afford a wide variety of compound classes, including heterocycles, diamines, α-keto acids and peptides.


Subject(s)
Amino Acids/chemistry , Amino Acids/metabolism , Bacterial Proteins/metabolism , Protein Engineering , Streptomyces/enzymology , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Computational Biology , Gene Expression Regulation, Bacterial , Gene Expression Regulation, Enzymologic
9.
Biopolymers ; 110(6): e23267, 2019 Jun.
Article in English | MEDLINE | ID: mdl-30835821

ABSTRACT

Conformational control in peptoids, N-substituted glycines, is crucial for the design and synthesis of biologically-active compounds and atomically-defined nanomaterials. While there are a growing number of structural studies in solution, most have been performed with conformationally-constrained short sequences (e.g., sterically-hindered sidechains or macrocyclization). Thus, the inherent degree of heterogeneity of unconstrained peptoids in solution remains largely unstudied. Here, we explored the folding landscape of a series of simple peptoid tetramers in aqueous solution by NMR spectroscopy. By incorporating specific 13 C-probes into the backbone using bromoacetic acid-2-13 C as a submonomer, we developed a new technique for sequential backbone assignment of peptoids based on the 1,n-Adequate pulse sequence. Unexpectedly, two of the tetramers, containing an N-(2-aminoethyl)glycine residue (Nae), had preferred conformations. NMR and molecular dynamics studies on one of the tetramers showed that the preferred conformer (52%) had a trans-cis-trans configuration about the three amide bonds. Moreover, >80% of the ensemble contained a cis amide bond at the central amide. The backbone dihedral angles observed fall directly within the expected minima in the peptoid Ramachandran plot. Analysis of this compound against similar peptoid analogs suggests that the commonly used Nae monomer plays a key role in the stabilization of peptoid structure via a side-chain-to-main-chain interaction. This discovery may offer a simple, synthetically high-yielding approach to control peptoid structure, and suggests that peptoids have strong intrinsic conformational preferences in solution. These findings should facilitate the predictive design of folded peptoid structures, and accelerate application in areas ranging from drug discovery to biomimetic nanoscience.


Subject(s)
Peptoids/chemistry , Water/chemistry , Carbon Isotopes/chemistry , Isomerism , Molecular Dynamics Simulation , Nanostructures/chemistry , Nuclear Magnetic Resonance, Biomolecular , Peptoids/chemical synthesis , Protein Conformation , Protein Folding , Protein Multimerization , Quantum Theory
10.
J Am Chem Soc ; 140(24): 7471-7485, 2018 06 20.
Article in English | MEDLINE | ID: mdl-29771498

ABSTRACT

NsaS is one of four intramembrane histidine kinases (HKs) in Staphylococcus aureus that mediate the pathogen's response to membrane active antimicrobials and human innate immunity. We describe the first integrative structural study of NsaS using a combination of solution state NMR spectroscopy, chemical-cross-linking, molecular modeling and dynamics. Three key structural features emerge: First, NsaS has a short N-terminal amphiphilic helix that anchors its transmembrane (TM) bundle into the inner leaflet of the membrane such that it might sense neighboring proteins or membrane deformations. Second, the transmembrane domain of NsaS is a 4-helix bundle with significant dynamics and structural deformations at the membrane interface. Third, the intracellular linker connecting the TM domain to the cytoplasmic catalytic domains of NsaS is a marginally stable helical dimer, with one state likely to be a coiled-coil. Data from chemical shifts, heteronuclear NOE, H/D exchange measurements and molecular modeling suggest that this linker might adopt different conformations during antibiotic induced signaling.


Subject(s)
Bacterial Proteins/chemistry , Histidine Kinase/chemistry , Membrane Proteins/chemistry , Anti-Bacterial Agents/pharmacology , Bacitracin/pharmacology , Bacterial Proteins/genetics , Gene Knockout Techniques , Histidine Kinase/genetics , Hydrophobic and Hydrophilic Interactions , Magnetic Resonance Spectroscopy , Membrane Proteins/genetics , Microbial Sensitivity Tests , Molecular Dynamics Simulation , Nisin/pharmacology , Protein Conformation, alpha-Helical , Protein Domains , Staphylococcus aureus/drug effects , Staphylococcus aureus/enzymology , Staphylococcus aureus/genetics
11.
Proc Natl Acad Sci U S A ; 115(10): E2193-E2201, 2018 03 06.
Article in English | MEDLINE | ID: mdl-29453276

ABSTRACT

Fluorinated small molecules play an important role in the design of bioactive compounds for a broad range of applications. As such, there is strong interest in developing a deeper understanding of how fluorine affects the interaction of these ligands with their targets. Given the small number of fluorinated metabolites identified to date, insights into fluorine recognition have been provided almost entirely by synthetic systems. The fluoroacetyl-CoA thioesterase (FlK) from Streptomyces cattleya thus provides a unique opportunity to study an enzyme-ligand pair that has been evolutionarily optimized for a surprisingly high 106 selectivity for a single fluorine substituent. In these studies, we synthesize a series of analogs of fluoroacetyl-CoA and acetyl-CoA to generate nonhydrolyzable ester, amide, and ketone congeners of the thioester substrate to isolate the role of fluorine molecular recognition in FlK selectivity. Using a combination of thermodynamic, kinetic, and protein NMR experiments, we show that fluorine recognition is entropically driven by the interaction of the fluorine substituent with a key residue, Phe-36, on the lid structure that covers the active site, resulting in an ∼5- to 20-fold difference in binding (KD). Although the magnitude of discrimination is similar to that found in designed synthetic ligand-protein complexes where dipolar interactions control fluorine recognition, these studies show that hydrophobic and solvation effects serve as the major determinant of naturally evolved fluorine selectivity.


Subject(s)
Acetyl Coenzyme A/chemistry , Acetyl Coenzyme A/metabolism , Fluorine/chemistry , Fluorine/metabolism , Streptomyces/enzymology , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Catalytic Domain , Entropy , Nuclear Magnetic Resonance, Biomolecular , Phenylalanine/chemistry , Protein Binding , Substrate Specificity
12.
Protein Expr Purif ; 116: 82-9, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26231074

ABSTRACT

Alzheimer's disease (AD) is a progressive neurodegenerative disease affecting millions of people worldwide. AD is characterized by the presence of extracellular plaques composed of aggregated/oligomerized ß-amyloid peptides with Aß42 peptide representing a major isoform in the senile plaques. Given the pathological significance of Aß42 in the progression of AD, there is considerable interest in understanding the structural ensembles for soluble monomer and oligomeric forms of Aß42. This report describes an efficient method to express and purify high quality (15)N isotope-labeled Aß42 for structural studies by NMR. The protocol involves utilization of an auto induction system with (15)N isotope labeled medium, for high-level expression of Aß42 as a fusion with IFABP. After the over-expression of the (15)N isotope-labeled IFABP-Aß42 fusion protein in the inclusion bodies, pure (15)N isotope-labeled Aß42 peptide is obtained following a purification method that is streamlined and improved from the method originally developed for the isolation of unlabeled Aß42 peptide (Garai et al., 2009). We obtain a final yield of ∼ 6 mg/L culture for (15)N isotope-labeled Aß42 peptide. Mass spectrometry and (1)H-(15)N HSQC spectra of monomeric Aß42 peptide validate the uniform incorporation of the isotopic label. The method described here is equally applicable for the uniform isotope labeling with (15)N and (13)C in Aß42 peptide as well as its other variants including any Aß42 peptide mutants.


Subject(s)
Amyloid beta-Peptides/chemistry , Amyloid beta-Peptides/genetics , Escherichia coli/genetics , Peptide Fragments/chemistry , Peptide Fragments/genetics , Amyloid beta-Peptides/isolation & purification , Fatty Acid-Binding Proteins/chemistry , Fatty Acid-Binding Proteins/genetics , Fatty Acid-Binding Proteins/isolation & purification , Humans , Isotope Labeling , Nitrogen Isotopes/analysis , Nuclear Magnetic Resonance, Biomolecular , Peptide Fragments/isolation & purification , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/isolation & purification
13.
Environ Microbiol ; 17(5): 1677-88, 2015 May.
Article in English | MEDLINE | ID: mdl-25156229

ABSTRACT

The catabolic fate of the major monomeric sugar of red macroalgae, 3,6-anhydro-L-galactose (AHG), is completely unknown in any organisms. AHG is not catabolized by ordinary fermentative microorganisms, and it hampers the utilization of red macroalgae as renewable biomass for biofuel and chemical production. In this study, metabolite and transcriptomic analyses of Vibrio sp., a marine bacterium capable of catabolizing AHG as a sole carbon source, revealed two key metabolic intermediates of AHG, 3,6-anhydrogalactonate (AHGA) and 2-keto-3-deoxy-galactonate; the corresponding genes were verified in vitro enzymatic reactions using their recombinant proteins. Oxidation by an NADP(+) -dependent AHG dehydrogenase and isomerization by an AHGA cycloisomerase are the two key AHG metabolic processes. This newly discovered metabolic route was verified in vivo by demonstrating the growth of Escherichia coli harbouring the genes of these two enzymes on AHG as a sole carbon source. Also, the introduction of only these two enzymes into an ethanologenic E. coli strain increased the ethanol production in E. coli by fermenting both AHG and galactose in an agarose hydrolysate. These findings provide not only insights for the evolutionary adaptation of a central metabolic pathway to utilize uncommon substrates in microbes, but also a metabolic design principle for bioconversion of red macroalgal biomass into biofuels or industrial chemicals.


Subject(s)
Energy Metabolism/genetics , Escherichia coli/metabolism , Galactose/analogs & derivatives , Seaweed/metabolism , Vibrio/metabolism , Aquatic Organisms/enzymology , Aquatic Organisms/genetics , Aquatic Organisms/metabolism , Biofuels , Carbohydrate Metabolism , Escherichia coli/genetics , Fermentation/genetics , Galactose/metabolism , Gene Expression Profiling , Metabolic Networks and Pathways/genetics , Seaweed/enzymology , Vibrio/enzymology , Vibrio/genetics
14.
J Mol Biol ; 426(21): 3553-68, 2014 Oct 23.
Article in English | MEDLINE | ID: mdl-25158097

ABSTRACT

Transcription initiation by bacterial σ(54)-polymerase requires the action of a transcriptional activator protein. Activators bind sequence-specifically upstream of the transcription initiation site via a DNA-binding domain (DBD). The structurally characterized DBDs from activators all belong to the Fis (factor for inversion stimulation) family of helix-turn-helix DNA-binding proteins. We report here structures of the free and DNA-bound forms of the DBD of NtrC4 (4DBD) from Aquifex aeolicus, a member of the NtrC family of σ(54) activators. Two NtrC4-binding sites were identified upstream (-145 and -85bp) from the start of the lpxC gene, which is responsible for the first committed step in lipid A biosynthesis. This is the first experimental evidence for σ(54) regulation in lpxC expression. 4DBD was crystallized both without DNA and in complex with the -145-binding site. The structures, together with biochemical data, indicate that NtrC4 binds to DNA in a manner that is similar to that of its close homolog, Fis. The greater sequence specificity for the binding of 4DBD relative to Fis seems to arise from a larger number of base-specific contacts contributing to affinity than for Fis.


Subject(s)
Bacteria/enzymology , DNA/chemistry , Escherichia coli Proteins/chemistry , Factor For Inversion Stimulation Protein/chemistry , PII Nitrogen Regulatory Proteins/chemistry , RNA Polymerase Sigma 54/chemistry , Transcription Factors/chemistry , Bacterial Proteins/chemistry , Binding Sites , Crystallography, X-Ray , Deoxyribonuclease I/chemistry , Hydrogen Bonding , Magnetic Resonance Spectroscopy , Nucleic Acid Conformation , Protein Structure, Tertiary , Proteins/chemistry , Transcription, Genetic , Transcriptional Activation
15.
J Am Chem Soc ; 135(46): 17488-93, 2013 Nov 20.
Article in English | MEDLINE | ID: mdl-24195610

ABSTRACT

Hexavalent chromium [Cr(VI)] is a worldwide water contaminant that is currently without cost-effective and efficient remediation strategies. This is in part due to a lack of ligands that can bind it amid an excess of innocuous ions in aqueous solution. We present herein the design and application of a peptoid-based library of ligand candidates for toxic metal ions. A selective screening process was used to identify members of the library that can bind to Cr(VI) species at neutral pH and in the presence of a large excess of spectator ions. There were 11 sequences identified, and their affinities were compared using titrations monitored with UV-vis spectroscopy. To identify the interactions involved in coordination and specificity, we evaluated the effects of sequence substitutions and backbone variation in the highest affinity structure. Additional characterization of the complex formed between this sequence and Cr(VI) was performed using NMR spectroscopy. To evaluate the ability of the developed sequences to remediate contaminated solutions, the structures were synthesized on a solid-phase resin and incubated with environmental water samples that contained simulated levels of chromium contamination. The synthetic structures demonstrated the ability to reduce the amount of toxic chromium to levels within the range of the EPA contamination guidelines. In addition to providing some of the first selective ligands for Cr(VI), these studies highlight the promise of peptoid sequences as easily prepared components of environmental remediation materials.


Subject(s)
Chromium/chemistry , Combinatorial Chemistry Techniques , Organometallic Compounds/chemistry , Peptide Library , Peptides/chemistry , Hydrogen-Ion Concentration , Ligands , Magnetic Resonance Spectroscopy , Molecular Structure , Organometallic Compounds/chemical synthesis , Spectrophotometry, Ultraviolet
16.
Elife ; 2: e00813, 2013 Jul 30.
Article in English | MEDLINE | ID: mdl-23908768

ABSTRACT

RasGRP1 and SOS are Ras-specific nucleotide exchange factors that have distinct roles in lymphocyte development. RasGRP1 is important in some cancers and autoimmune diseases but, in contrast to SOS, its regulatory mechanisms are poorly understood. Activating signals lead to the membrane recruitment of RasGRP1 and Ras engagement, but it is unclear how interactions between RasGRP1 and Ras are suppressed in the absence of such signals. We present a crystal structure of a fragment of RasGRP1 in which the Ras-binding site is blocked by an interdomain linker and the membrane-interaction surface of RasGRP1 is hidden within a dimerization interface that may be stabilized by the C-terminal oligomerization domain. NMR data demonstrate that calcium binding to the regulatory module generates substantial conformational changes that are incompatible with the inactive assembly. These features allow RasGRP1 to be maintained in an inactive state that is poised for activation by calcium and membrane-localization signals. DOI:http://dx.doi.org/10.7554/eLife.00813.001.


Subject(s)
DNA-Binding Proteins/metabolism , Guanine Nucleotide Exchange Factors/metabolism , Amino Acid Sequence , Binding Sites , Calcium/metabolism , Crystallography, X-Ray , DNA-Binding Proteins/antagonists & inhibitors , DNA-Binding Proteins/chemistry , Guanine Nucleotide Exchange Factors/antagonists & inhibitors , Guanine Nucleotide Exchange Factors/chemistry , Humans , Models, Molecular , Molecular Sequence Data , Nuclear Magnetic Resonance, Biomolecular , Protein Conformation , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Sequence Homology, Amino Acid
17.
Biopolymers ; 99(12): 1082-96, 2013 Dec.
Article in English | MEDLINE | ID: mdl-23818155

ABSTRACT

We compare the structure, activity, and linkage of DNA-binding domains (DBDs) from σ(54) transcriptional activators and discuss how the properties of the DBDs and the linker to the neighboring domain are affected by the overall properties and requirements of the full proteins. These transcriptional activators bind upstream of specific promoters that utilize σ(54)-polymerase. Upon receiving a signal the activators assemble into hexamers, which then, through adenosine triphosphate (ATP) hydrolysis, drive a conformational change in polymerase that enables transcription initiation. We present structures of the DBDs of activators nitrogen regulatory protein C 1 (NtrC1) and Nif-like homolog 2 (Nlh2) from the thermophile Aquifex aeolicus. The structures of these domains and their relationship to other parts of the activators are discussed. These structures are compared with previously determined structures of the DBDs of NtrC4, NtrC, ZraR, and factor for inversion stimulation. The N-terminal linkers that connect the DBDs to the central domains in NtrC1 and Nlh2 were studied and found to be unstructured. Additionally, a crystal structure of full-length NtrC1 was solved, but density of the DBDs was extremely weak, further indicating that the linker between ATPase and DBDs functions as a flexible tether. Flexible linking of ATPase and DBDs is likely necessary to allow assembly of the active hexameric ATPase ring. The comparison of this set of activators also shows clearly that strong dimerization of the DBD only occurs when other domains do not dimerize strongly.


Subject(s)
Protein Structure, Tertiary , RNA Polymerase Sigma 54 , Amino Acid Motifs , Bacterial Proteins/metabolism , DNA , DNA-Binding Proteins/chemistry , Trans-Activators/chemistry , Transcription Factors
18.
Anesthesiology ; 119(5): 1120-36, 2013 Nov.
Article in English | MEDLINE | ID: mdl-23748856

ABSTRACT

BACKGROUND: Mild brain hypothermia (32°-34°C) after human neonatal asphyxia improves neurodevelopmental outcomes. Astrocytes but not neurons have pyruvate carboxylase and an acetate uptake transporter. C nuclear magnetic resonance spectroscopy of rodent brain extracts after administering [1-C]glucose and [1,2-C]acetate can distinguish metabolic differences between glia and neurons, and tricarboxylic acid cycle entry via pyruvate dehydrogenase and pyruvate carboxylase. METHODS: Neonatal rat cerebrocortical slices receiving a C-acetate/glucose mixture underwent a 45-min asphyxia simulation via oxygen-glucose-deprivation followed by 6 h of recovery. Protocols in three groups of N=3 experiments were identical except for temperature management. The three temperature groups were: normothermia (37°C), hypothermia (32°C for 3.75 h beginning at oxygen--glucose deprivation start), and delayed hypothermia (32°C for 3.75 h, beginning 15 min after oxygen-glucose deprivation start). Multivariate analysis of nuclear magnetic resonance metabolite quantifications included principal component analyses and the L1-penalized regularized regression algorithm known as the least absolute shrinkage and selection operator. RESULTS: The most significant metabolite difference (P<0.0056) was [2-C]glutamine's higher final/control ratio for the hypothermia group (1.75±0.12) compared with ratios for the delayed (1.12±0.12) and normothermia group (0.94±0.06), implying a higher pyruvate carboxylase/pyruvate dehydrogenase ratio for glutamine formation. Least Absolute Shrinkage and Selection Operator found the most important metabolites associated with adenosine triphosphate preservation: [3,4-C]glutamate-produced via pyruvate dehydrogenase entry, [2-C]taurine-an important osmolyte and antioxidant, and phosphocreatine. Final principal component analyses scores plots suggested separate cluster formation for the hypothermia group, but with insufficient data for statistical significance. CONCLUSIONS: Starting mild hypothermia simultaneously with oxygen-glucose deprivation, compared with delayed starting or no hypothermia, has higher pyruvate carboxylase throughput, suggesting that better glial integrity is one important neuroprotection mechanism of earlier hypothermia.


Subject(s)
Cerebral Cortex/physiology , Glucose/deficiency , Hypothermia, Induced , Hypoxia, Brain/metabolism , Acetates/metabolism , Adenosine Diphosphate/metabolism , Adenosine Triphosphate/metabolism , Animals , Biomarkers/metabolism , Body Temperature , Brain Chemistry , Female , Glial Fibrillary Acidic Protein/metabolism , Hypoxia, Brain/therapy , In Vitro Techniques , Magnetic Resonance Spectroscopy , Male , Metabolomics , Neuroglia/physiology , Neurons/physiology , Phosphocreatine/metabolism , Rats , Rats, Sprague-Dawley , Regression Analysis , Tricarboxylic Acids/metabolism
19.
Pediatr Res ; 74(2): 170-9, 2013 Aug.
Article in English | MEDLINE | ID: mdl-23708689

ABSTRACT

BACKGROUND: Mild brain hypothermia (31-34 °C) after neonatal hypoxia-ischemia (HI) improves neurodevelopmental outcomes in human and animal neonates. Using an asphyxia model with neonatal mice treated with mild hypothermia after HI, we investigated whether (1)H nuclear magnetic resonance (NMR) metabolomics of brain extracts could suggest biomarkers and distinguish different treatments and outcome groups. METHODS: At postnatal day 7 (P7), CD1 mice underwent right carotid artery occlusion, 30 min of HI (8% oxygen), and 3.5 h of either hypothermia (31 °C) or normothermia (37 °C). Whole brains were frozen immediately after HI, immediately after 3.5 h of hypothermia or normothermia treatments, and 24 h later. Perchloric acid extractions of 36 metabolites were quantified by 900 MHz (1)H NMR spectroscopy. Multivariate analyses included principal component analyses (PCA) and a novel regression algorithm. Histological injury was quantified after HI at 5 d. RESULTS: PCA scores plots separated normothermia/HI animals from hypothermia/HI and control animals, but more data are required for multivariate models to be predictive. Loadings plots identified 11 significant metabolites, whereas the regression algorithm identified 6. Histological injury scores were significantly reduced by hypothermia. CONCLUSION: Different treatment and outcome groups are identifiable by (1)H NMR metabolomics in a neonatal mouse model of mild hypothermia treatment of HI.


Subject(s)
Hypothermia, Induced/methods , Hypoxia-Ischemia, Brain/metabolism , Hypoxia-Ischemia, Brain/therapy , Metabolome/physiology , Animals , Animals, Newborn , Magnetic Resonance Spectroscopy , Metabolome/genetics , Metabolomics , Mice , Principal Component Analysis , Regression Analysis
20.
Cell ; 152(3): 543-56, 2013 Jan 31.
Article in English | MEDLINE | ID: mdl-23374349

ABSTRACT

How the epidermal growth factor receptor (EGFR) activates is incompletely understood. The intracellular portion of the receptor is intrinsically active in solution, and to study its regulation, we measured autophosphorylation as a function of EGFR surface density in cells. Without EGF, intact EGFR escapes inhibition only at high surface densities. Although the transmembrane helix and the intracellular module together suffice for constitutive activity even at low densities, the intracellular module is inactivated when tethered on its own to the plasma membrane, and fluorescence cross-correlation shows that it fails to dimerize. NMR and functional data indicate that activation requires an N-terminal interaction between the transmembrane helices, which promotes an antiparallel interaction between juxtamembrane segments and release of inhibition by the membrane. We conclude that EGF binding removes steric constraints in the extracellular module, promoting activation through N-terminal association of the transmembrane helices.


Subject(s)
Cell Membrane/metabolism , Epidermal Growth Factor/metabolism , ErbB Receptors/chemistry , Signal Transduction , Animals , COS Cells , Cell Membrane/chemistry , Chlorocebus aethiops , Dimerization , ErbB Receptors/metabolism , Humans , Models, Molecular
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