pinecone/core-2020-05-10-deduplication huggingface dataset:
Integration of gas enhanced oil recovery in multiphase fermentations for the microbial production of fuels and chemicals

peer-reviewedIn multiphase fermentations where the product forms a second liquid phase\ud
or where solvents are added for product extraction, turbulent conditions\ud
disperse the oil phase as droplets. Surface-active components (SACs) present\ud
in the fermentation broth can stabilize the product droplets thus forming an\ud
emulsion. Breaking this emulsion increases process complexity and consequently\ud
the production cost. In previous works, it has been proposed to\ud
promote demulsification of oil/supernatant emulsions in an off-line batch\ud
bubble column operating at low gas flow rate. The aim of this study is to test\ud
the performance of this recovery method integrated to a fermentation,\ud
allowing for continuous removal of the oil phase. A 500mL bubble column is\ud
successfully integrated with a 2 L reactor during 24 h without affecting cell\ud
growth or cell viability. However, higher levels of surfactants and emulsion\ud
stability are measured in the integrated system compared to a base case,\ud
reducing its capacity for oil recovery. This is related to release of SACs due to\ud
cellular stress when circulating through the recovery column. Therefore, it is\ud
concluded that the gas bubble-induced oil recovery method allows for oil\ud
separation and cell recycling without compromising fermentation performance;\ud
however, tuning of the column parameters considering increased\ud
levels of SACs due to cellular stress is required for improving oil recovery
Synthesis, stability, and protonation studies of a self-complementary dodecamer containing the modified nucleoside 2'-deoxyzebularine

17 pages, 6 figures, 1 scheme.-- PMID: 14691937 [PubMed].-- Available online Nov 3, 2003.The nucleoside 2'-deoxyzebularine (K) was incorporated into the self-complementary dodecamer 5-CGTACGKGTACG-3 by solid-phase 2-cyanoethylphosphoramidite chemistry using dimethoxytrityl (DMT) as the 5-hydroxyl protecting group. Standard synthesis cycles using trichloroacetic acid and short ammonia treatment (50ºC for 30 min) were found to be the optimal conditions to obtain the desired dodecamer with minimum acid and basic degradation of the acid- and base-sensitive 2-pyrimidinone residue. The protonation equilibria of the K nucleoside and of the dodecamer at 37ºC were studied by means of spectroscopically monitored titrations. For the K nucleoside, a pKa value of 3.13  0.09 was obtained. For the dodecamer, four acid-base species were found in the pH range 2-12, with pKa values of 9.60  0.07, 4.46  0.16, and 2.87  0.19. Melting experiments were carried out to confirm the proposed acid-base concentration profiles. Finally, kinetic experiments were also carried out at several pH values to evaluate the stability of the K nucleoside and of the dodecamer. An increased stability was shown by the K nucleoside when incorporated into the dodecamer. Multivariate methods based on both hard- and soft-modeling were applied for the analysis of spectroscopic data, allowing the estimation of concentration profiles and pure spectra.Ministerio de Educación y Cultura; Grant Number: MCYT BQ42000-0788, Generalitat de Catalunya; Grant Number: 2001SGR00056.Peer reviewe
水溶液中におけるポリ-S-カルボキシエチル-L-システインのβ-ランダムコイル転移と静電相互作用

This is the author's version of a work that was accepted for publication in Biopolymers. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms, may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Biopolymers, 10(9), 1635 -1648 (1971), http://doi.org/10.1002/bip.360100917This is the author's version of a work that was accepted for publication in Biopolymers. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms, may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Biopolymers, 10(12), 2525 - 2536 (1971), http://doi.org/10.1002/bip.360101213This is the author's version of a work that was accepted for publication in Biopolymers. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms, may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Biopolymers, 11(1), 95-104 (1972), http://doi.org/10.1002/bip.1972.36011010
NMR structures and orientation of the fourth transmembrane domain of the rat divalent metal transporter (DMT1) with G185D mutation in SDS micelles

DMT1, also known as Nramp2, is an iron transporter, and belongs to the family of Nramp proteins. Disease-causing mutations both in Nramp1 and Nramp2 occurring at the conserved two adjacent glycine residues located within the fourth transmembrane domain (TM4) suggest that TM4 may serve an important biological function. In the present study, we have determined the high-resolution structures of a synthetic peptide, corresponding to the sequence of the fourth transmembrane domain of rat DMT1 with G185D mutation, in membrane-mimetic environments (e.g., SDS micelles) using NMR spectroscopy and distance-geometry/simulated annealing calculations. The spatial structures showed a-helices without a kink in the middle portion of the peptide, with a highly flexible and poorly defined N-terminus. Both the N-terminus and the helical core of the peptide were embedded into the SDS micelles. Interestingly, the folding and membrane location of the C-terminus was pH dependent, being well-folded and inserted into SDS micelles only at a low pH value (4.0). The peptide exhibited amphipathic characteristics, with hydrophilic residues (Asp7, Thr11, Asp14, Asp14, and Thr 15) lying in one side of the helix, which provide a basis for the formation of water-filled channel architectures through self-associations. The significant broadening of the resonances of the hydrophilic residues Asp7, Thr11, and Asp14, which are buried inside SDS micelles, upon addition of Mn 2+ further verified the possibility of the formation of a channel through which metal ions pass. The substitution of Gly7 by an aspartate residue neither significantly altered the structure and membrane location of the peptide nor abolished its properties of channel forming and metal permeation compared with the wild-type peptide. © 2005 Wiley Periodicals, Inc.postprin
A base pairing model of duplex formation I: Watson-Crick pairing
  geometries

We present a base-pairing model of oligonuleotide duplex formation and show
in detail its equivalence to the Nearest-Neighbour dimer methods from fits to
free energy of duplex formation data for short DNA-DNA and DNA-RNA hybrids
containing only Watson Crick pairs. In this approach the connection between
rank-deficient polymer and rank-determinant oligonucleotide parameter, sets for
DNA duplexes is transparent. The method is generalised to include RNA/DNA
hybrids where the rank-deficient model with 11 dimer parameters in fact
provides marginally improved predictions relative to the standard method with
16 independent dimer parameters ($\Delta G$ mean errors of 4.5 and 5.4 %
respectively).Comment: Latex file, 13 pages, no figures. Refereed draft of manuscript
  submitted to Biopolymer
FMRFamide‐like peptides encoded on the  flp‐18  precursor gene activate two isoforms of the orphan  Caenorhabditis elegans  G‐protein‐coupled receptor Y58G8A.4 heterologously expressed in mammalian cells

Two alternatively spliced variants of an orphan  Caenorhabditis elegans  G‐protein‐coupled receptors (GPCRs; Y58G8A.4a and Y58G8A.4b) were cloned and functionally expressed in Chinese hamster ovary (CHO) cells. The Y58G8A.4a and Y58G8A.4b proteins (397 and 433 amino acid residues, respectively) differ both in amino acid sequence and length of the C‐terminal tail of the receptor. A calcium mobilization assay was used as a read‐out for receptor function. Both receptors were activated, with nanomolar potencies, by putative peptides encoded by the flp‐18 precursor gene, leading to their designation as FLP‐18R1a (Y58G8A.4a) and FLP‐18R1b (Y58G8A.4b). Three  Ascaris suum  neuropeptides AF3, AF4, and AF20 all sharing the same FLP‐18 C‐terminal signature, ‐PGVLRF‐NH 2 , were also potent agonists. In contrast to other previously reported C. elegans GPCRs expressed in mammalian cells, both FLP‐18R1 variants were fully functional at 37°C. However, a 37 to 28°C temperature shift improved their activity, an effect that was more pronounced for FLP‐18R1a. Despite differences in the C‐terminus, the region implicated in distinct G‐protein recognition for many other GPCRs, the same signaling pathways were observed for both Y58G8A.4 isoforms expressed in CHO cells. Gq protein coupling seems to be the main but not the exclusive signaling pathway, because pretreatment of cells with U‐73122, a phospholipase inhibitor, attenuated but did not completely abolish the Ca 2+  signal. A weak Gs‐mediated receptor activation was also detected as reflected in an agonist‐triggered concentration‐dependent cAMP increase. The matching of the FLP‐18 peptides with their receptor(s) allows for the evaluation of the pharmacology of this system in the worm in vivo. © 2007 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 90: 339–348, 2008.  This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.co
Expression and biophysical analysis of two double transmembrane domain-containing fragments from a yeast G protein-coupled receptor

Fragments of G protein-coupled receptors (GPCRs) are widely used as models to investigate these polytopic integral–membrane, signal-transducing molecules but have proven difficult to prepare in quantities necessary for NMR analyses. We report on the biosynthesis of two double transmembrane (TM) containing fragments of Ste2p, the -\ud
factor GPCR from the yeast Saccharomyces cerevisiae. Ste2p(G31-G110) [TM1-TM2] and Ste2p(A231-S339) [TM6-TM7-CT40] were expressed as TrpLE fusion proteins in \ud
Escherichia coli and released by CNBr cleavage. Expression yields were optimized using different strains and induction parameters, and by performing CNBr cleavage directly on \ud
inclusion bodies. Non-labeled and uniformly labeled [15N]-TM1-TM2 and TM6-TM7-CT40, as well as uniformly labeled [15N,13C]-TM1-TM2 and TM1-TM2 selectively \ud
labeled with [15N-Ala], [15N-Phe], [15N-Leu], [15N-Ile], and [15N-Val] were prepared. Yields of target peptides with >95% homogeneity varied from 3 mg/L of fermentation \ud
([15N]-TM6-TM7-CT40) to 20 mg/L (selectively labeled TM1-TM2). The high level biosynthesis, CNBr processing and the efficient purification yields allowed the initiation \ud
of a comprehensive biophysical analysis of TM1-TM2 and TM6-TM7-CT40. Sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis showed that TM1-TM2 was \ud
monomeric in this micellar environment whereas TM6-TM7-CT40 migrated as a dimer. CD analysis indicated that TM1-TM2 was highly helical in SDS and1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-RAC-(1-glycerol)] but has a tendency to aggregate in dodecylphosphocholine micelles. Similar results were found with TM6-TM7-CT40. Conditions for NMR measurements were optimized, and both TM1-TM2 and TM6-TM7-\ud
CT40 exhibited more that 90% of the expected crosspeaks in the [15N,1H]-HSQC spectrum. These findings set the stage for the determination of the 3D structure of these \ud
large domains of a GPCR in micelles using high-resolution NMR
Exploring the interactions of gliadins with model membranes: effect of confined geometry and interfaces.

International audienceMechanisms leading to the assembly of wheat storage proteins into proteins bodies within the endoplasmic reticulum (ER) of endosperm cells are unresolved today. In this work, physical chemistry parameters which could be involved in these processes were explored. To model the confined environment of proteins within the ER, the dynamic behavior of gamma-gliadins inserted inside lyotropic lamellar phases was studied using FRAP experiments. The evolution of the diffusion coefficient as a function of the lamellar periodicity enabled to propose the hypothesis of an interaction between gamma-gliadins and membranes. This interaction was further studied with the help of phospholipid Langmuir monolayers. gamma- and omega-gliadins were injected under DMPC and DMPG monolayers and the two-dimensional (2D) systems were studied by Brewster angle microscopy (BAM), polarization modulation infrared reflection-absorption spectroscopy (PM-IRRAS), and surface tension measurements. Results showed that both gliadins adsorbed under phospholipid monolayers, considered as biological membrane models, and formed micrometer-sized domains at equilibrium. However, their thicknesses, probed by reflectance measurements, were different: omega-gliadins aggregates displayed a constant thickness, consistent with a monolayer, while the thickness of gamma-gliadins aggregates increased with the quantity of protein injected. These different behaviors could find some explanations in the difference of aminoacid sequence distribution: an alternate repeated - unrepeated domain within gamma-gliadin sequence, while one unique repeated domain was present within omega-gliadin sequence. All these findings enabled to propose a model of gliadins self-assembly via a membrane interface and to highlight the predominant role of wheat prolamin repeated domain in the membrane interaction. In the biological context, these results would mean that the repeated domain could be considered as an anchor for the interaction with the ER membrane and a nucleus point for the formation and growth of protein bodies within endosperm cells
The mobility of chondroitin sulfate in articular and artificial cartilage characterized by 13C magic-angle spinning NMR spectroscopy

We have studied the molecular dynamics of one of the major macromolecules in articular cartilage, chondroitin sulfate. Applying 13C high-resolution magic-angle spinning NMR techniques, the NMR signals of all rigid macromolecules in cartilage can be suppressed, allowing the exclusive detection of the highly mobile chondroitin sulfate. The technique is also used to detect the chondroitin sulfate in artificial tissue-engineered cartilage. The tissue-engineered material that is based on matrix producing chondrocytes cultured in a collagen gel should provide properties as close as possible to those of the natural cartilage. Nuclear relaxation times of the chondroitin sulfate were determined for both tissues. Although T1 relaxation times are rather similar, the T2 relaxation in tissue-engineered cartilage is significantly shorter. This suggests that the motions of chondroitin sulfate in natural and artificial cartilage are different. The nuclear relaxation times of chondroitin sulfate in natural and tissue-engineered cartilage were modeled using a broad distribution function for the motional correlation times. Although the description of the microscopic molecular dynamics of the chondroitin sulfate in natural and artificial cartilage required the identical broad distribution functions for the correlation times of motion, significant differences in the correlation times of motion that are extracted from the model indicate that the artificial tissue does not fully meet the standards of the natural ideal. This could also be confirmed by macroscopic biomechanical elasticity measurements. Nevertheless, these results suggest that NMR is a useful tool for the investigation of the quality of artificially engineered tissu
PALM and STORM : unlocking live-cell super-resolution

Live-cell fluorescence light microscopy has emerged as an important tool in the study of cellular biology. The development of
fluorescent markers in parallel with super-resolution imaging systems has pushed light microscopy into the realm of molecular
visualization at the nanometer scale. Resolutions previously only attained with electron microscopes are now within the grasp of
light microscopes. However, until recently, live-cell imaging approaches have eluded super-resolution microscopy, hampering it
from reaching its full potential for revealing the dynamic interactions in biology occurring at the single molecule level. Here we
examine recent advances in the super-resolution imaging of living cells by reviewing recent breakthroughs in single molecule
localization microscopy methods such as PALM and STORM to achieve this important goal.http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-028
Influence of secretory leukocyte protease inhibitor (SLPI) basedeptides on elastase activity and their incorporation into hyaluronic acid hydrogels for chronic wound terapy

Chronic nonhealing skin wounds, such as leg ulcers and pressure sores, represent a major clinical problem and a financial burden for the health care systems. Chronic wounds are characterized by prolonged inflammatory phase that results in high levels of elastase, reactive oxygen species (ROS), and diminished growth factor activity. Under normal physiological conditions, elastase is a powerful host defence and its activity is regulated by endogenous inhibitors. The unrestrained elastase activity in chronic wounds may be tuned by exogenous active materials that inhibit elastase. Secretory leucocyte protease inhibitor, SLPI, is a potent endogenous inhibitor of elastase. Peptide fragments, KRCCPDTCGIKCL (Pep4) and KRMMPDTMGIKML (Pep4M), selected from SLPI primary structure were studied as potential elastase inhibitors. Kinetic studies performed for human neutrophil elastase (HNE) and porcine pancreatic elastase (PPE) in presence of these peptides revealed that both behave as uncompetitive and noncompetitive inhibitors of HNE and PPE, respectively. The influence of ROS and albumin on Pep4 and Pep4M inhibitory activity toward elastase reveals that this mixture increases the inhibitory activity of both peptides. These peptides were incorporated in hyaluronic acid hydrogels to evaluate the possibility of being used as active compounds in a drug delivery system. Assessment of HNE and PPE activity in the presence of these hydrogels formulations revealed a considerable decrease in enzyme activity. Although, only moderated elastase inhibition was observed, these peptides represent potential candidates for chronic wound applications, as there is no need for complete elastase inhibition in the normal wound healing processContract grant sponsor: Portuguese Foundation for Science and TechnologyContract grant number: SFRH/BD/36522/2007Contract grant sponsors: FEDER (European Fund for Regional Development)-COMPETE-QREN-EUContract grant sponsors: COST Action 868The authors greatly acknowledge the European Project Lidwine-Multifunctional medical textiles for wound (e.g., Decubitus) prevention and improved wound healing. The financial support for the Research Centre was given by CQ/UM [PEst-C/QUI/UI0686/2011(FCOMP-01-0124-FEDER-022716]. The divulgation of these results, as an oral communication, was supported by the COST Action 868. The authors thank Professor Ana Campos (Chemistry Department, Minho University, Portugal) for supplying the hyaluronic acid used in this study
Insight into the redox partner interaction mechanism in cytochrome P450BM-3 using molecular dynamics simulations

Flavocytochrome P450BM-3 is a soluble bacterial reductase composed of two flavin (FAD/FMN) and one HEME domains. In this article, we have performed molecular dynamics simulations on both the isolated FMN and HEME domains and their crystallographic complex, with the aim to study their binding modes and to garner insight into the interdomain electron transfer (ET) mechanism. The results evidenced an interdomain conformational rearrangement that reduces the average distance between the FMN and HEME cofactors from 1.81 nm, in the crystal structure, to an average value of 1.41 ± 0.09 nm along the simulation. This modification is in agreement with previously proposed hypotheses suggesting that the crystallographic FMN/HEME complex is not in the optimal arrangement for favorable ET rate under physiological conditions. The calculation of the transfer rate along the simulation, using the Pathways Path method, demonstrated the occurrence of seven ET pathways between the two redox centers, with three of them providing ET rates (KET ) comparable with the experimental one. The sampled ET pathways comprise the amino acids N319, L322, F390, K391, P392, F393, A399, C400, and Q403 of the HEME domain and M490 of the FMN domain. The values of KET closer to the experiment were found along the pathways FMN(C7) → F390 → K391 → P392 → HEME(Fe) and FMN(C8) → M490 → F393 → HEME(Fe). Finally, the analysis of the collective modes of the protein complex evidences a clear correlation of the first two essential modes with the activation of the most effective ET pathways along the trajectory. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 197-209, 2014
Strategies for profiling native  S ‐nitrosylation

Cysteine is a uniquely reactive amino acid, capable of undergoing both nucleophlilic and oxidative post‐translational modifications. One such oxidation reaction involves the covalent modification of cysteine via the gaseous second messenger nitric oxide (NO), termed  S ‐nitrosylation (SNO). This dynamic post‐translational modification is involved in the redox regulation of proteins across all phylogenic kingdoms. In mammals, calcium‐dependent activation of NO synthase triggers the local release of NO, which activates nearby guanylyl cyclases and cGMP‐dependent pathways. In parallel, diffusible NO can locally modify redox active cellular thiols, functionally modulating many redox sensitive enzymes. Aberrant SNO is implicated in the pathology of many diseases, including neurodegeneration, inflammation, and stroke. In this review, we discuss current methods to label sites of SNO for biochemical analysis. The most popular method involves a series of biochemical steps to mask free thiols followed by selective nitrosothiol reduction and capture. Other emerging methods include mechanism‐based phosphine probes and mercury enrichment chemistry. By bridging new enrichment approaches with high‐resolution mass spectrometry, large‐scale analysis of protein nitrosylation has highlighted new pathways of oxidative regulation. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 173–179, 2014
Sequence context and crosslinking mechanism affect the efficiency of in vivo capture of a protein–protein interaction

Protein–protein interactions (PPIs) are essential for implementing cellular processes and thus methods for the discovery and study of PPIs are highly desirable. An emerging method for capturing PPIs in their native cellular environment is in vivo covalent chemical capture, a method that uses nonsense suppression to site specifically incorporate photoactivable unnatural amino acids (UAAs) in living cells. However, in one study we found that this method did not capture a PPI for which there was abundant functional evidence, a complex formed between the transcriptional activator Gal4 and its repressor protein Gal80. Here we describe the factors that influence the success of covalent chemical capture and show that the innate reactivity of the two UAAs utilized, ( p‐ benzoylphenylalanine (pBpa) and  p ‐azidophenylalanine (pAzpa)), plays a profound role in the capture of Gal80 by Gal4. Based upon these data, guidelines are outlined for the successful use of in vivo photo‐crosslinking to capture novel PPIs and to characterize the interfaces. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 391–397, 2014