28 results on '"Liu PB"'
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2. Ag@Mg 12 @Ag 20 : a three-layer matryoshka structure with S 6 symmetry.
- Author
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Liu PB, Guo JJ, Chen YS, Zhao HY, Wang J, and Liu Y
- Abstract
The C
60 fullerene, renowned for its soccer ball-like high-symmetry configuration, has attracted extensive interest. As research on C60 progresses, the synthesis of diverse C60 derivatives and the exploration of embedding varying numbers of atoms within the carbon cage, ranging from singular atoms to entire molecules, have emerged. This trend has prompted investigations into potential high-symmetry structures formed by incorporating main group or transition metal elements. This study presents a detailed analysis of a three-layer Ag@Mg12 @Ag20 structure, featuring a Mg12 icosahedron enclosed within an Ag20 dodecahedron with a singular Ag atom at its core. Employing density-functional theory, the structure underwent comprehensive scrutiny, including energy minimization resulting in the adoption of a S6 symmetry, and subsequent evaluation of stability via vibrational frequency analysis and molecular dynamics simulations. The electronic structures and bonding characteristics of this three-layer Ag@Mg12 @Ag20 architecture were explored through electron density analysis, density of states, and adaptive natural density partitioning analysis. Considering structural stability, the proposed three-layer Ag@Mg12 @Ag20 structure exhibits promise as a novel constituent in the construction of other nano-materials., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)- Published
- 2024
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3. The perceptual distinctiveness of the [n-l] contrast in different vowel and tonal contexts.
- Author
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Liu PB and Li M
- Subjects
- Humans, Male, Language, Female, Speech Acoustics, Adult, Young Adult, Speech Perception physiology, Phonetics
- Abstract
This study investigates the relative perceptual distinction of the [n] vs [l] contrast in different vowel contexts ([_a] vs [_i]) and tonal contexts (high-initial such as HH, HL, vs low-initial such as LL, LH). The results of two speeded AX discrimination experiments indicated that a [n-l] contrast is perceptually more distinct in the [_a] context and with a high-initial tone. The results are consistent with the typology of the [n] vs [l] contrast across Chinese dialects, which is more frequently observed in the [_a] context and with a high-initial tone, supporting a connection between phonological typology and perceptual distinctiveness., (© 2024 Acoustical Society of America.)
- Published
- 2024
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4. Probing amino acid side chains of the integral membrane protein PagP by solution NMR: Side chain immobilization facilitates association of secondary structures.
- Author
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Goel S, Feisal MR, Danmaliki GI, Yu S, Liu PB, Bishop RE, West FG, and Hwang PM
- Subjects
- Magnetic Resonance Spectroscopy, Escherichia coli metabolism, Bacterial Outer Membrane Proteins chemistry, Hydrogen, Acyltransferases chemistry, Amino Acids metabolism, Escherichia coli Proteins chemistry
- Abstract
Solution NMR spectroscopy of large protein systems is hampered by rapid signal decay, so most multidimensional studies focus on long-lived
1 H-13 C magnetization in methyl groups and/or backbone amide1 H-15 N magnetization in an otherwise perdeuterated environment. Herein we demonstrate that it is possible to biosynthetically incorporate additional1 H-12 C groups that possess long-lived magnetization using cost-effective partially deuterated or unlabeled amino acid precursors added to Escherichia coli growth media. This approach is applied to the outer membrane enzyme PagP in membrane-mimetic dodecylphosphocholine micelles. We were able to obtain chemical shift assignments for a majority of side chain1 H positions in PagP using nuclear Overhauser enhancements (NOEs) to connect them to previously assigned backbone1 H-15 N groups and newly assigned1 H-13 C methyl groups. Side chain methyl-to-aromatic NOEs were particularly important for confirming that the amphipathic α-helix of PagP packs against its eight-stranded β-barrel, as indicated by previous X-ray crystal structures. Interestingly, aromatic NOEs suggest that some aromatic residues in PagP that are buried in the membrane bilayer are highly mobile in the micellar environment, like Phe138 and Phe159. In contrast, Tyr87 in the middle of the bilayer is quite rigid, held in place by a hydrogen bonded network extending to the surface that resembles a classic catalytic triad: Tyr87-His67-Asp61. This hydrogen bonded arrangement of residues is not known to have any catalytic activity, but we postulate that its role is to immobilize Tyr87 to facilitate packing of the amphipathic α-helix against the β-barrel., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Peter Hwang reports financial support was provided by NSERC., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)- Published
- 2024
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5. Novel Isomer of Volleyballene Sc 20 C 60 .
- Author
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Liu PB, Guo JJ, Zhao HY, Ma HM, Wang J, and Liu Y
- Abstract
The Stone-Wales defect is a well-known and significant defective structure in carbon materials, impacting their mechanical, chemical, and electronic properties. Recently, a novel metal-carbon nanomaterial named Volleyballene was discovered, characterized by a C-C bond bridging two carbon pentagons. Using first-principles calculations, a stable Stone-Wales-defective counterpart of Volleyballene, exhibiting T
h symmetry, has been proposed by rotating the C-C bond by 90°. Although its binding energy per atom is slightly higher than that of Volleyballene (Δ Eb = 0.009 eV/atom), implying marginally lower structural stability, it can maintain its bond structure until the effective temperature reaches about 1500 K, indicating greater thermodynamic stability. Additionally, its highest vibration frequency is 1346.2 cm-1 , indicating a strong chemical bond strength. A theoretical analysis of the Sc20 C60 + Sc20 C60 binary systems highlights that the stable building block may be applied in potential nanoassemblies.- Published
- 2023
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6. Bartonella Prevalence and Genome Sequences in Rodents in Some Regions of Xinjiang, China.
- Author
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Xu AL, Chen YF, Mu L, Liu PB, Wang J, Li RX, and Li DM
- Subjects
- Animals, Humans, Rodentia, Phylogeny, Prevalence, China epidemiology, Bartonella genetics, Bartonella Infections epidemiology, Bartonella Infections veterinary
- Abstract
In this study, we investigated Bartonella infection and its genetic diversity in rodents in Beitun, Xinjiang Uygur Autonomous Region, China. Small mammals were captured using snap traps at four sampling sites in 2018. Spleen and liver tissues were collected and cultured to isolate Bartonella strains. Whole-genome sequencing was performed on the strains identified as Bartonella by gltA gene PCR, and the average nucleotide identity (ANI) of the genomes was calculated by using FastANI v1.33. Phylogenetic trees were constructed for the samples positive for Bartonella spp. by the gltA PCR assay based on 1,290-bp gltA genes, 2,903-bp rpoB genes, and core-genome single nucleotide polymorphisms (SNPs). Among 66 rodents, 11 were positive for Bartonella , with an infection rate of 16.67%. The rodent infection rates in different tissues (χ
2 = 2.133; P = 0.242), species (χ2 = 9.631; P = 0.141), and habitats (χ2 = 4.309; P = 0.312) did not show statistical differences. Bartonella spp. isolated from the rodents were phylogenetically divided into six clades (two different Bartonella species were detected in two rodents). By comparing phylogenetic trees based on gltA genes, rpoB genes, and SNPs, we found that the topological structures of several evolutionary trees are different. However, the Bartonella strains isolated in this study were clustered into six clusters in different phylogenetic trees. Broad distributions and high genetic diversity of Bartonella strains were observed among rodents in Beitun, Xinjiang. IMPORTANCE Rodent-borne Bartonella species have been associated with zoonotic diseases. Bartonella species such as Bartonella elizabethae, Bartonella grahamii, and Bartonella tribocorum can cause disease in humans. Humans can be infected by blood-sucking arthropods through the scratches and bites of an infected reservoir host or via contact with infectious rodents. Xinjiang is one of the provinces with the most abundant species of Bartonella in China, but there are few reports about the prevalence of Bartonella in the Beitun area. This research aims to investigate the occurrence and prevalence of Bartonella infection in rodents at these sampling sites and provide a basis for the prevention and control of rodent Bartonella species in Beitun and the surrounding areas of Xinjiang.- Published
- 2023
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7. Small Molecule RPI-194 Stabilizes Activated Troponin to Increase the Calcium Sensitivity of Striated Muscle Contraction.
- Author
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Mahmud Z, Tikunova S, Belevych N, Wagg CS, Zhabyeyev P, Liu PB, Rasicci DV, Yengo CM, Oudit GY, Lopaschuk GD, Reiser PJ, Davis JP, and Hwang PM
- Abstract
Small molecule cardiac troponin activators could potentially enhance cardiac muscle contraction in the treatment of systolic heart failure. We designed a small molecule, RPI-194, to bind cardiac/slow skeletal muscle troponin (Cardiac muscle and slow skeletal muscle share a common isoform of the troponin C subunit.) Using solution NMR and stopped flow fluorescence spectroscopy, we determined that RPI-194 binds to cardiac troponin with a dissociation constant K
D of 6-24 μM, stabilizing the activated complex between troponin C and the switch region of troponin I. The interaction between RPI-194 and troponin C is weak (KD 311 μM) in the absence of the switch region. RPI-194 acts as a calcium sensitizer, shifting the pCa50 of isometric contraction from 6.28 to 6.99 in mouse slow skeletal muscle fibers and from 5.68 to 5.96 in skinned cardiac trabeculae at 100 μM concentration. There is also some cross-reactivity with fast skeletal muscle fibers (pCa50 increases from 6.27 to 6.52). In the slack test performed on the same skinned skeletal muscle fibers, RPI-194 slowed the velocity of unloaded shortening at saturating calcium concentrations, suggesting that it slows the rate of actin-myosin cross-bridge cycling under these conditions. However, RPI-194 had no effect on the ATPase activity of purified actin-myosin. In isolated unloaded mouse cardiomyocytes, RPI-194 markedly decreased the velocity and amplitude of contractions. In contrast, cardiac function was preserved in mouse isolated perfused working hearts. In summary, the novel troponin activator RPI-194 acts as a calcium sensitizer in all striated muscle types. Surprisingly, it also slows the velocity of unloaded contraction, but the cause and significance of this is uncertain at this time. RPI-194 represents a new class of non-specific troponin activator that could potentially be used either to enhance cardiac muscle contractility in the setting of systolic heart failure or to enhance skeletal muscle contraction in neuromuscular disorders., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Mahmud, Tikunova, Belevych, Wagg, Zhabyeyev, Liu, Rasicci, Yengo, Oudit, Lopaschuk, Reiser, Davis and Hwang.)- Published
- 2022
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8. Reduced Inter-Voxel White Matter Integrity in Subjective Cognitive Decline: Diffusion Tensor Imaging With Tract-Based Spatial Statistics Analysis.
- Author
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Chao YP, Liu PB, Wang PN, and Cheng CH
- Abstract
Subjective cognitive decline (SCD), a self-reported worsening in cognition concurrent with normal performance on standardized neuropsychological tests, has gained much attention due to its high risks in the development of mild cognitive impairments or Alzheimer's disease. The existing cross-sectional diffusion tensor imaging (DTI) studies in SCD have shown extremely controversial findings. Furthermore, all of these studies investigated diffusion properties within the voxel, such as fractional anisotropy, mean diffusivity, or axial diffusivity (DA). However, it remains unclear whether individuals with SCD demonstrate alterations of diffusion profile between voxels and their neighbors, as indexed by local diffusion homogeneity (LDH). We selected 30 healthy controls (HCs) and 23 SCD subjects to acquire their whole-brain DTI. Diffusion images were compared using the tract-based spatial statistics method. Diffusion indices with significant between-group tract clusters were extracted from each individual for further region-of-interest (ROI)-based comparisons. Our results showed that subjects with SCD demonstrated reduced LDH in the left superior frontal gyrus (SFG) and DA in the right anterior cingulate cortex compared with the HC group. In contrast, the SCD group showed higher LDH values in the left lingual gyrus (LG) compared with the HC group. Notably, LDH in the left SFG was significantly and negatively correlated with LDH in the left LG. In conclusion, white matter (WM) integrity in the left SFG, right ACC, and left LG is altered in SCD, suggesting that individuals with SCD exhibit detectable changes in WM tracts before they demonstrate objective cognitive deficits., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Chao, Liu, Wang and Cheng.)
- Published
- 2022
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9. Dilated Cardiomyopathy Mutations and Phosphorylation disrupt the Active Orientation of Cardiac Troponin C.
- Author
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Mahmud Z, Dhami PS, Rans C, Liu PB, and Hwang PM
- Subjects
- Calcium metabolism, Cardiomyopathy, Dilated metabolism, Humans, Magnetic Resonance Spectroscopy, Models, Molecular, Multiprotein Complexes chemistry, Multiprotein Complexes metabolism, Phosphorylation, Protein Binding, Protein Domains, Tropomyosin chemistry, Tropomyosin metabolism, Troponin C chemistry, Troponin C metabolism, Troponin I chemistry, Troponin I metabolism, Troponin T chemistry, Troponin T metabolism, Cardiomyopathy, Dilated genetics, Mutation, Myocardium metabolism, Troponin C genetics
- Abstract
Cardiac troponin (cTn) is made up of three subunits, cTnC, cTnI, and cTnT. The regulatory N-terminal domain of cTnC (cNTnC) controls cardiac muscle contraction in a calcium-dependent manner. We show that calcium-saturated cNTnC can adopt two different orientations, with the "active" orientation consistent with the 2020 cryo-EM structure of the activated cardiac thin filament by Yamada et al. Using solution NMR
15 N R2 relaxation analysis, we demonstrate that the two domains of cTnC tumble independently (average R2 10 s-1 ), being connected by a flexible linker. However, upon addition of cTnI1-77 , the complex tumbles as a rigid unit (R2 30 s-1 ). cTnI phosphomimetic mutants S22D/S23D, S41D/S43D and dilated cardiomyopathy- (DCM-)associated mutations cTnI K35Q, cTnC D75Y, and cTnC G159D destabilize the active orientation of cNTnC, with intermediate15 N R2 rates (R2 17-23 s-1 ). The active orientation of cNTnC is stabilized by the flexible tails of cTnI, cTnI1-37 and cTnI135-209 . Surprisingly, when cTnC is incorporated into complexes lacking these tails (cTnC-cTnI38-134 , cTnC-cTnT223-288 , or cTnC-cTnI38-134 -cTnT223-288 ), the cNTnC domain is still immobilized, revealing a new interaction between cNTnC and the IT-arm that stabilizes a "dormant" orientation. We propose that the calcium sensitivity of the cardiac troponin complex is regulated by an equilibrium between active and dormant orientations, which can be shifted through post-translational modifications or DCM-associated mutations., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 The Author(s). Published by Elsevier Ltd.. All rights reserved.)- Published
- 2021
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10. CoMo-bimetallic N-doped porous carbon materials embedded with highly dispersed Pt nanoparticles as pH-universal hydrogen evolution reaction electrocatalysts.
- Author
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Huang WH, Li XM, Yu DY, Yang XF, Wang LF, Liu PB, and Zhang J
- Abstract
The hydrogen evolution reaction is a key half reaction for water electrolysis and is of great significance. Pt-based nanomaterials are promising candidates for HER electrocatalysts. However, the high price of platinum and poor durability impede their practical applications. Herein, a new CoMo-bimetallic hybrid zeolite imidazolate framework is employed to load Pt nanoparticles in a highly dispersed manner as a precursor to synthesize an efficient pH-universal HER electrocatalyst (PtCoMo@NC), which displays overpotentials of 26, 51, and 66 mV at a current density of 10 mA cm
-2 in acidic, basic, and neutral media, respectively. The strong synergistic effect of highly dispersed multi-type catalytic species, including cobalt, molybdenum carbide, and platinum (4.7%) promotes the catalytic activity in the HER process. Meanwhile, the aggregation of Pt nanoparticles is greatly restrained by the carbon matrix so that a brilliant long-time durability of 12 hours and a negligible current decrease in the LSV curve after 10 000 CV cycles are achieved.- Published
- 2020
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11. Structure and proteolytic susceptibility of the inhibitory C-terminal tail of cardiac troponin I.
- Author
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Mahmud Z, Zahran S, Liu PB, Reiz B, Chan BYH, Roczkowsky A, McCartney CE, Davies PL, Li L, Schulz R, and Hwang PM
- Subjects
- Actins chemistry, Actins metabolism, Animals, Calpain metabolism, Cattle, Chromatography, Liquid, Heart, Humans, Mass Spectrometry, Matrix Metalloproteinase 2 metabolism, Nuclear Magnetic Resonance, Biomolecular, Protein Conformation, Proteolysis, Recombinant Proteins chemistry, Recombinant Proteins isolation & purification, Recombinant Proteins metabolism, Troponin I chemistry, Troponin I isolation & purification, Troponin I metabolism
- Abstract
Background: Cardiac troponin I (cTnI) has two flexible tails that control the cardiac cycle. The C-terminal tail, cTnI
135-209 , binds actin to shut off cardiac muscle contraction, whereas the competing calcium-dependent binding of the switch region, cTnI146-158 , by cardiac troponin C (cTnC) triggers contraction. The N-terminal tail, cTnI1-37 , regulates the calcium affinity of cTnC. cTnI is known to be susceptible to proteolytic cleavage by matrix metalloproteinase-2 (MMP-2) and calpain, two intracellular proteases implicated in ischemia-reperfusion injury., Methods: Soluble fragments of cTnI containing its N- and C-terminal tails, cTnI1-77 and cTnI135-209 , were highly expressed and purified from E. coli. We performed in vitro proteolysis studies of both constructs using liquid chromatography-mass spectrometry and solution NMR studies of the C-terminal tail., Results: cTnI135-209 is intrinsically disordered, though it contains three regions with helical propensity (including the switch region) that acquire more structure upon actin binding. We identified three precise MMP-2 cleavage sites at cTnI P17-I18, A156-L157, and G199-M200. In contrast, calpain-2 has numerous cleavage sites throughout Y25-T30 and A152-A160. The critical cTnI switch region is targeted by both proteases., Conclusions: Both N-terminal and C-terminal tails of cTnI are susceptible to cleavage by MMP-2 and calpain-2. Binding to cTnC or actin confers some protection to proteolysis, which can be understood in terms of their interactions as probed by NMR studies., General Significance: cTnI is an important marker of intracellular proteolysis in cardiomyocytes, given its many protease-specific cut sites, high natural abundance, indispensable functional role, and clinical use as gold standard biomarker of myocardial injury., (Copyright © 2019 Elsevier B.V. All rights reserved.)- Published
- 2019
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12. The calcium sensitizer drug MCI-154 binds the structural C-terminal domain of cardiac troponin C.
- Author
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Li MX, Gelozia S, Danmaliki GI, Wen Y, Liu PB, Lemieux MJ, West FG, Sykes BD, and Hwang PM
- Abstract
The compound MCI-154 was previously shown to increase the calcium sensitivity of cardiac muscle contraction. Using solution NMR spectroscopy, we demonstrate that MCI-154 interacts with the calcium-sensing subunit of the cardiac troponin complex, cardiac troponin C (cTnC). Surprisingly, however, it binds only to the structural C-terminal domain of cTnC (cCTnC), and not to the regulatory N-terminal domain (cNTnC) that determines the calcium sensitivity of cardiac muscle. Physiologically, cTnC is always bound to cardiac troponin I (cTnI), so we examined its interaction with MCI-154 in the presence of two soluble constructs, cTnI
1-77 and cTnI135-209 , which contain all of the segments of cTnI known to interact with cTnC. Neither the cTnC-cTnI1-77 complex nor the cTnC-cTnI135-209 complex binds to MCI-154. Since residues 39-60 of cTnI are known to bind tightly to the cCTnC domain to form a structured core that is invariant throughout the cardiac cycle, we conclude that MCI-154 does not bind to cTnC when it is part of the intact cardiac troponin complex. Thus, MCI-154 likely exerts its calcium sensitizing effect by interacting with a target other than cardiac troponin.- Published
- 2018
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13. Stereoselective Deuteration in Aspartate, Asparagine, Lysine, and Methionine Amino Acid Residues Using Fumarate as a Carbon Source for Escherichia coli in D 2 O.
- Author
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Danmaliki GI, Liu PB, and Hwang PM
- Subjects
- Asparagine chemistry, Aspartic Acid chemistry, Culture Media, Humans, Lysine chemistry, Methionine chemistry, Models, Molecular, Mutant Proteins genetics, Mutant Proteins metabolism, NIMA-Interacting Peptidylprolyl Isomerase genetics, Stereoisomerism, Amino Acids chemistry, Carbon chemistry, Deuterium chemistry, Escherichia coli metabolism, Fumarates chemistry, NIMA-Interacting Peptidylprolyl Isomerase metabolism
- Abstract
Perdeuteration with selective
1 H,13 C-enrichment of methyl groups has enabled solution NMR studies of large (>30 kDa) protein systems. However, we propose that for all non-methyl positions, only magnetization originating from1 H-12 C groups is sufficiently long-lived, and it can be transferred via through-space NOEs to slowly relaxing1 H-15 N or1 H-13 C methyl groups to achieve multidimensional solution NMR. We demonstrate stereoselective1 H,12 C-labeling by adding relatively inexpensive unlabeled carbon sources to Escherichia coli growth media in D2 O. Using our model system, a mutant WW domain from human Pin1, we compare deuteration patterns in 19 amino acids (all except cysteine). Protein grown using glucose as the sole carbon source had high levels of protonation in aromatic rings and the Hβ positions of serine and tryptophan. In contrast, using our FROMP media (fumarate, rhamnose, oxalate, malonate, pyruvate), stereoselective protonation of Hβ2 with deuteration at Hα and Hβ3 was achieved in Asp, Asn, Lys, and Met residues. In solution NMR, stereospecific chemical shift assignments for Hβ are typically obtained in conjunction with χ1 dihedral angle determinations using 3-bond J-coupling (3 JN-Hβ ,3 JCO-Hβ ,3 JHα-Hβ ) experiments. However, due to motional averaging, the assumption of a pure rotameric state can yield incorrect χ1 dihedral angles with incorrect stereospecific assignments. This was the case for three residues in the Pin1 WW domain (Lys28, Met30, and Asn44). Thus, stereoselective1 H,12 C-labeling will be useful not only for NMR studies of large protein systems, but also for determining side chain rotamers and dynamics in any protein system.- Published
- 2017
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14. Combining a PagP fusion protein system with nickel ion-catalyzed cleavage to produce intrinsically disordered proteins in E. coli.
- Author
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Zahran S, Pan JS, Liu PB, and Hwang PM
- Subjects
- Acyltransferases chemistry, Acyltransferases isolation & purification, Acyltransferases metabolism, Amino Acid Sequence, Catalysis, Escherichia coli chemistry, Escherichia coli metabolism, Escherichia coli Proteins chemistry, Escherichia coli Proteins isolation & purification, Escherichia coli Proteins metabolism, Gene Expression, Hydrolysis, Inclusion Bodies chemistry, Inclusion Bodies metabolism, Intrinsically Disordered Proteins chemistry, Intrinsically Disordered Proteins isolation & purification, Intrinsically Disordered Proteins metabolism, Molecular Sequence Data, Plasmids chemistry, Plasmids genetics, Plasmids metabolism, Recombinant Fusion Proteins chemistry, Recombinant Fusion Proteins genetics, Recombinant Fusion Proteins isolation & purification, Recombinant Fusion Proteins metabolism, Acyltransferases genetics, Escherichia coli genetics, Escherichia coli Proteins genetics, Inclusion Bodies genetics, Intrinsically Disordered Proteins genetics, Nickel metabolism
- Abstract
Many proteins contain intrinsically disordered regions that are highly solvent-exposed and susceptible to post-translational modifications. Studying these protein segments is critical to understanding their physiologic regulation, but proteolytic degradation can make them difficult to express and purify. We have designed a new protein expression vector that fuses the target protein to the N-terminus of the integral membrane protein, PagP. The two proteins are connected by a short linker containing the sequence SRHW, previously shown to be optimal for nickel ion-catalyzed cleavage. The methodology is demonstrated for an intrinsically disordered segment of cardiac troponin I. cTnI[135-209]-SRHW-PagP-His6 fusion protein was overexpressed in Escherichia coli, accumulating in insoluble inclusion bodies. The protein was solubilized, purified using nickel affinity chromatography, and then cleaved with 0.5mM NiSO4 at pH 9.0 and 45 °C, all in 6M guanidine-HCl. Nickel ion-catalyzed peptide bond hydrolysis is an effective chemical cleavage technique under denaturing conditions that preclude the use of proteases. Moreover, nickel-catalyzed cleavage is more specific than the most commonly used agent, cyanogen bromide, which cleaves C-terminal to methionine residues. We were able to produce 15 mg of purified cTnI[135-209] from 1L of M9 minimal media using this protocol. The methodology is more generally applicable to the production of intrinsically disordered protein segments., (Copyright © 2015 Elsevier Inc. All rights reserved.)
- Published
- 2015
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15. Metabolomic prediction of fetal congenital heart defect in the first trimester.
- Author
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Bahado-Singh RO, Ertl R, Mandal R, Bjorndahl TC, Syngelaki A, Han B, Dong E, Liu PB, Alpay-Savasan Z, Wishart DS, and Nicolaides KH
- Subjects
- Adult, Chromatography, Liquid, Female, Humans, Logistic Models, Magnetic Resonance Spectroscopy, Pregnancy, Pregnancy Trimester, First, Tandem Mass Spectrometry, Heart Defects, Congenital diagnosis, Metabolomics methods
- Abstract
Objective: The objective of the study was to identify metabolomic markers in maternal first-trimester serum for the detection of fetal congenital heart defects (CHDs)., Study Design: Mass spectrometry (direct injection/liquid chromatography and tandem mass spectrometry) and nuclear magnetic resonance spectrometry-based metabolomic analyses were performed between 11 weeks' and 13 weeks 6 days' gestation on maternal serum. A total of 27 CHD cases and 59 controls were compared. There were no known or suspected chromosomal or syndromic abnormalities indicated., Results: A total of 174 metabolites were identified and quantified using the 2 analytical methods. There were 14 overlapping metabolites between platforms. We identified 123 metabolites that demonstrated significant differences on a univariate analysis in maternal first-trimester serum in CHD vs normal cases. There was a significant disturbance in acylcarnitine, sphingomyelin, and other metabolite levels in CHD pregnancies. Predictive algorithms were developed for CHD detection. High sensitivity (0.929; 95% confidence interval [CI], 0.92-1.00) and specificity (0.932; 95% CI, 0.78-1.00) for CHD detection were achieved (area under the curve, 0.992; 95% CI, 0.973-1.0)., Conclusion: In the first such report, we demonstrated the feasibility of the use of metabolomic developing biomarkers for the first-trimester prediction of CHD. Abnormal lipid metabolism appeared to be a significant feature of CHD pregnancies., (Copyright © 2014 Mosby, Inc. All rights reserved.)
- Published
- 2014
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16. Excellent electromagnetic absorption properties of poly(3,4-ethylenedioxythiophene)-reduced graphene oxide-Co3O4 composites prepared by a hydrothermal method.
- Author
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Liu PB, Huang Y, and Sun X
- Abstract
The ternary composites of poly(3,4-ethylenedioxythiophene)-reduced graphene oxide-Co3O4 (PEDOT-RGO-Co3O4) were synthesized and the electromagnetic absorption property of the composites was investigated. The structure of the composites was characterized with Fourier-transform infrared spectra, X-ray diffraction, Raman spectroscopy, X-ray photoelectron spectroscopy, and transmission electron microscope. The electromagnetic parameters indicate the enhanced electromagnetic absorption property of the composites was attributed to the better impedance matching. On the basis of the above characterization, an electromagnetic complementary theory was proposed to explain the impedance matching. It can be found that the maximum reflection loss of PEDOT-RGO-Co3O4 can reach -51.1 dB at 10.7 GHz, and the bandwidth exceeding -10 dB is 3.1 GHz with absorber thickness of 2.0 mm. Therefore, the PEDOT-RGO-Co3O4 composites, with such excellent electromagnetic absorption properties and wide absorption bandwidth, can be used as a new kind of candidate for microwave absorbing materials.
- Published
- 2013
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17. [Groundwater organic pollution source identification technology system research and application].
- Author
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Wang XH, Wei JH, Cheng ZN, Liu PB, Ji YQ, and Zhang G
- Subjects
- China, Industrial Waste adverse effects, Industrial Waste analysis, Models, Theoretical, Pesticides adverse effects, Pesticides analysis, Risk Assessment, Environmental Monitoring, Groundwater analysis, Organic Chemicals analysis, Water Pollutants, Chemical analysis
- Abstract
Groundwater organic pollutions are found in large amount of locations, and the pollutions are widely spread once onset; which is hard to identify and control. The key process to control and govern groundwater pollution is how to control the sources of pollution and reduce the danger to groundwater. This paper introduced typical contaminated sites as an example; then carried out the source identification studies and established groundwater organic pollution source identification system, finally applied the system to the identification of typical contaminated sites. First, grasp the basis of the contaminated sites of geological and hydrogeological conditions; determine the contaminated sites characteristics of pollutants as carbon tetrachloride, from the large numbers of groundwater analysis and test data; then find the solute transport model of contaminated sites and compound-specific isotope techniques. At last, through groundwater solute transport model and compound-specific isotope technology, determine the distribution of the typical site of organic sources of pollution and pollution status; invest identified potential sources of pollution and sample the soil to analysis. It turns out that the results of two identified historical pollution sources and pollutant concentration distribution are reliable. The results provided the basis for treatment of groundwater pollution.
- Published
- 2013
18. [Effects of ulinastatin on coagulation in children after cardiopulmonary bypass].
- Author
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Huang P, Liu PB, Luo JW, Chen RW, Wang JH, and Zeng DB
- Subjects
- Cardiac Surgical Procedures, Female, Humans, Infant, Male, Partial Thromboplastin Time, Prothrombin Time, Blood Coagulation drug effects, Cardiopulmonary Bypass, Glycoproteins pharmacology, Trypsin Inhibitors pharmacology
- Abstract
Objective: To study the effects of ulinastatin on coagulation in children who underwent open-heart surgery with cardiopulmonary bypass (CPB)., Methods: Fifty children who underwent open-heart surgery for ventricular septal defect were randomly divided into two groups: ulinastatin treatment and control. Before CPB, ulinastatin (1.0×10(4) U/kg) was added to CPB priming fluid only in the ulinastatin treatment group. Activated partial thromboplasin time (APTT), prothrombin time (PT), thrombin time (TT), fibrinogen and international normalized ratio (INR) were measured both before and at 1 hr, 6 hrs and 24 hrs after CPB., Results: The PT in the ulinastatin group was more prolonged than in the control group at 1 hr after CPB (18.7 ± 0.7 s vs 15.5 ± 0.5 s) and 6 hrs after CPB (17.5 ± 0.6 s vs 15.0 ± 0.6 s). The APTT in the ulinatatin group was also significantly more prolonged than in the control group at 6 hrs after CPB (38.7 ± 3.1 s vs 35.3 ± 3.1 s) and 24 hrs after CPB (34.2 ± 3.0 s vs 31.1 ± 2.6 s)., Conclusions: Ulinastatin may prolong PT and APTT after CPB, and thus affects coagulation in children.
- Published
- 2012
19. [In situ experimental research on natural attenuation of oil pollutants in a gas station].
- Author
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Jia H, Wu XF, Hu LM, and Liu PB
- Subjects
- Biodegradation, Environmental, Carbon Dioxide analysis, China, Oxygen analysis, Environmental Monitoring methods, Petroleum analysis, Soil Pollutants analysis, Volatile Organic Compounds analysis
- Abstract
The natural attenuation rules of oil pollutants are investigated by carrying out a field experiment in a gas station in Beijing, using a set of soil gas sampling and monitoring device designed independently. The samples of soil gas were collected in the field and tested to examine the content of O2, CO2 and VOCs in the unsaturated zone. The results show that after 381 days' natural attenuation, the concentration of the contaminants at the polluted point deceased by 99.2%, while the ratio of BTEX to TVOC decreased from 17.0% to 12.1%. Moreover, the content of O2 decreased while that of CO2 grew as the soil depth increases at G3 point. Further theoretical analysis indicated that: (1) The test results of first-step experiment show that there was a certain level of contamination in G3 area. And after 381 days' natural attenuation, the content of the BTEX at G3 point fell below the environmental standard level, which means the control measures could be removed. (2) The origin of the contamination was proved as short-term sources, and no long-term sources of leakage existed. (3) An effective removal of contaminants in the soil was found under the influence of the natural attenuation. This method could be applied in long-term monitoring for similar contaminated sites. (4) The test of O2and CO2 contents was proved to be an effective approach to determine if the aerobic degradation happens.
- Published
- 2012
20. [Research of the natural attenuation capacity of oil pollutants based on in-situ experiment].
- Author
-
Jia H, Wu XF, Hu LM, and Liu PB
- Subjects
- Benzene analysis, Biodegradation, Environmental, China, Xylenes analysis, Environmental Monitoring methods, Petroleum analysis, Soil Pollutants analysis, Volatile Organic Compounds analysis
- Abstract
Based on the results of the in-situ experiment carried out in a Beijing gas station, the ways of natural attenuation were evaluated as both aerobic and anaerobic biodegradation via oxygen and carbon equilibrium calculation. And the research got the rates of the natural attenuation and half-life of the oil pollutants byusing the first-order decay model. Based on the analysis, the capability of monitored natural attenuation and the environmental quality were evaluated. The results show that the actual oxygen consumption of contaminated site is less than that needed theoretically in aerobic degradation of all pollutants, while the amount of CO2 detected is far less than that in the aerobic degradation by theoretical formation. And the half-life of petroleum contaminants in contaminated site is about 50 days. The analysis indicated that: (1) The ways of natural attenuation were proved as both aerobic and anaerobic biodegradation; (2) The contamination of the BTEX tested by the fist-step experiment fell below the environmental standard level after about 250 days' natural attenuation, which means the environmental risk in this gas station had been eliminated and the control measures could be removed.
- Published
- 2011
21. [Effects of mechanical ventilation on plasma IL-6, IL-10 and TNF-alpha in children after cardiopulmonary bypass].
- Author
-
Huang P, Zhou WW, and Liu PB
- Subjects
- Female, Humans, Infant, Male, Tumor Necrosis Factor-alpha, Cardiopulmonary Bypass, Interleukin-10 blood, Interleukin-6 blood, Respiration, Artificial
- Abstract
Objective: To study the effects of different models of mechanical ventilation on inflammatory cytokines, IL-6, IL-10 and TNF-alpha, in children after cardiopulmonary bypass (CPB)., Methods: Sixty patients who underwent CPB were randomly divided into group A and group B. After CPB, group A was ventilated with high tidal volume (VT, 10-12 mL/kg) /low positive end-expiratory pressure (PEEP, 3-5 cm H2O), while group B was ventilated with low VT (6-8 mL/kg) /high PEEP (6-9 cm H2O). Plasma levels of IL-6, IL-10 and TNF-alpha were measured before operation, at the end of the operation, and 1 and 6 hrs after operation., Results: Serum levels of IL-6, IL-10 and TNF-alpha in both groups increased significantly at the end of the operation and reached a peak by 1 hr after operation. Group B showed lower serum levels of IL-6, IL-10 and TNF-alpha than group A 1 and 6 hrs after operation., Conclusions: Mechanical ventilation with low VT /high PEEP may more effectively inhibit the release of inflammatory cytokines than that with high VT /low PEEP in children after CPB.
- Published
- 2008
22. [Physicochemical properties of Guanting Reservoir sediment and its land application].
- Author
-
Su DC, Hu YF, Song CW, Wu FL, and Liu PB
- Subjects
- China, Environmental Monitoring, Water Pollution, Chemical analysis, Agriculture methods, Geologic Sediments chemistry, Water Pollution, Chemical prevention & control, Water Supply analysis
- Abstract
Surface sediment of Guanting Reservoir was dredged up and dewatered in field, and pollutant and physicochemical characterizations were mensurated. The stabilization and agricultural land use of the sediment was also studied in the field. Results showed that the sediments have a higher clay content, bulk density (1.89 g x cm(-3)) and lower porosity (23.8%), higher deoxidize material and available nitrogen, phosphorus concentration. Heavy metal and organochlorinated pesticides concentration was lower than the class II of national standard for soil. Stabilized the sediment with sand soil and straw could improve the physical property and decrease the concentration of deoxidize material and available nitrogen, phosphorus. Stabilized sediment could be a suitable medium for alfalfa, tree and corn growth and used for agricultural land.
- Published
- 2007
23. Gene expression profile of multiple myeloma cell line treated by realgar.
- Author
-
Wang MC, Liu SX, and Liu PB
- Subjects
- Humans, Microarray Analysis, Multiple Myeloma genetics, Multiple Myeloma metabolism, RNA, Messenger genetics, RNA, Messenger metabolism, Reverse Transcriptase Polymerase Chain Reaction, Tumor Cells, Cultured, Arsenicals therapeutic use, Gene Expression Profiling, Gene Expression Regulation, Neoplastic drug effects, Multiple Myeloma drug therapy, Oligonucleotide Array Sequence Analysis, Sulfides therapeutic use
- Abstract
In order to elucidate the molecular mechanism of Realgar treatment for multiple myeloma (MM), cDNA microaaray was used to compare the gene expression profiles of MM cell line RPMI8226 at 72 hrs pre- and post-Realgar treatment on three separate days. 54 up-regulated and 60 down-regulated genes were identified by cDNA microarray. Further analysis screened out 17 up-regulated and 3 down-regulated genes with Z-score greater than 2 or less than -2, which can be considered the significantly altered genes after Realgar treatment in this study. CCL2, CCL3, BTG1,TNFAIP3, TNFAIP8, SLC38A2, IGFBP4 were important up-regulated genes and they were associated with a variety of cell life functions such as cell growth, cell-cell signaling, regulation of apoptosis and cell homeostasis based on biological process of gene. There are only 3 significantly down-regulated genes (Z-score <-2.0) involved in muscle contract. Several of these genes have been previously identified in relation to MM in published papers. Subsequent validation of selected genes (CCL2, TNFAIP3 and BTG1) by reverse transcription polymerase chain reaction was consistent with our microarray analysis. CCL2 may be involved in MM pathobiology by tumor growth suppression. BTG1 could be used as a potential treatment-related biomarker for monitoring the therapy effect and the remission status of leukemia patients.
- Published
- 2006
24. [Changes of gene expression profile of multiple myeloma cell line RPMI 8226 treated by arsenic trioxide].
- Author
-
Wang MC, Liu SX, and Liu PB
- Subjects
- Apoptosis drug effects, Arsenic Trioxide, Humans, Oligonucleotide Array Sequence Analysis, Tumor Cells, Cultured, Antineoplastic Agents pharmacology, Arsenicals pharmacology, Gene Expression Profiling, Multiple Myeloma pathology, Oxides pharmacology
- Abstract
Objective: To compare the changes of gene expression profiles of multiple myeloma cell line RPMI 8226 before and after 24-hour intervention of arsenic trioxide., Methods: The responses of the RPMI 8226 cells to arsenic trioxide were determined with cDNA microarray which included 4,096 different human genes., Results: Of these 4,096 genes, the expressions of 273 genes were altered significantly at mRNA level. The expressions of 121 genes were up-regulated while the expressions of 152 genes were down-regulated., Conclusion: The effect of arsenic trioxide on RPMI 8226 cells is related to changing the expression levels of a number of genes. ZFYVE16, ALK1 and TXNIP genes may play important roles in apoptosis and differentiation of RPMI 8226 cells.
- Published
- 2006
25. [Effect of realgar on the gene expression profile of multiple myeloma cell line RPMI 8226].
- Author
-
Wang MC, Liu SX, and Liu PB
- Subjects
- Humans, Oligonucleotide Array Sequence Analysis, Tumor Cells, Cultured, Arsenicals pharmacology, Gene Expression Profiling, Multiple Myeloma pathology, Sulfides pharmacology
- Abstract
Objective: To explore the effect of realgar on the gene expression profiles of multiple myeloma cell line RPMI 8226 by apply cDNA microarray., Methods: The gene expression of RPMI 8226 cells before and after 48 hours of realgar treatment was determined with a cDNA microarray representing 4096 human genes., Results: At the mRNA level, 164 genes were differentially altered; 53 genes were up-regulated; and 111 genes were down-regulated., Conclusion: The realgar treatment to RPMI 8226 cell line may induce a number of gene changes. Many genes may be involved in the pathogenesis of multiple myeloma. BTG1, ALK1, and TXNIP genes may play an important role in the apoptosis and differentiation of RPMI 8226 cells.
- Published
- 2006
26. [Gene expression profiles on three kinds of genotype hepatitis C virus core protein in Huh-7 cell line with microarray analysis].
- Author
-
Dou J, Wang J, Liu PB, and Zhang XJ
- Subjects
- Carcinoma, Hepatocellular pathology, Carcinoma, Hepatocellular virology, Cell Line, Tumor, Gene Expression Regulation, Viral, Genotype, Humans, Liver Neoplasms pathology, Liver Neoplasms virology, Gene Expression Profiling, Hepacivirus genetics, Oligonucleotide Array Sequence Analysis methods, Viral Core Proteins genetics
- Abstract
Objective: To analyze three kinds of genotype hepatitis C virus (HCV) core protein expressed in human hepatoma (Huh-7) cell line and to recognize HCV core proteins biological function and its pathogenic mechanism., Methods: The Huh-7 cell expressed three kinds of core proteins were established respectively. Affymetrix human gene chip was used for identifying the gene expression dependently on Affymetrix's protocol. All genes changed by 3 or 1.5 folds between the transfected cells and a control cells were further analyzed, and annotated by using NetAffx analysis through Affymetrix website and were categorized based on their biological processes., Results: The HCV-1b core protein caused 16 genes up/down-regulated expression, of which the immune response genes of PF4V1 and SPP1 were up-regulated 3.4 or 4.4 folds respectively. The HCV-2a core protein had caused the immune response gene CXCL5 and apoptosis gene BTF a down-regulated expression of 3.4 and 3.1 folds respectively, but caused the apoptosis genes of HRK and LZTS1 an up-regulated expression of 3.2 and 3.4 folds respectively. As compared with HCV 1b or 2a core protein, HCV-4b core protein caused 111 genes expression changing and it had more obvious effects on gene expression. If we applied 1.5 fold change for a comparison gene expression, a few of the same gene expression profiles might be caused by these two core proteins., Conclusion: The three kinds of HCV core protein should have its own expression character and be mainly shown in immune responses, signal transduction, apoptosis, etc. It should be helpful for our recognizing the HCV core protein biological function and its pathogenic mechanism.
- Published
- 2006
27. [Performance of treatment wetland systems for surface water quality improvement].
- Author
-
Liu H, Dai ML, Liu XY, Ouyang W, and Liu PB
- Subjects
- Biodegradation, Environmental, Seasons, Typhaceae metabolism, Plants metabolism, Water Pollutants, Chemical analysis, Water Purification methods, Water Supply analysis
- Abstract
Intercropped with Phragmites communis and Typha angustifolia, subsurface flow constructed wetland systems (CWs) with the surface area of 3 x 20m x 2m were established beside Guanting Reservoir, an important source water base of Beijing. The treatment performance of the systems with different season were studied, the impacts of influent concentration, hydraulic loading rate and water temperature on contaminations removal were analyzed. The result showed that the subsurface flow CWs had the better decontamination effect to micro-pollution surface water. The relationship between the concentrations of CODMn and NH4+ -N in inflow and outflow followed the linear equation. The removal rates of total nitrogen (TN) and total phosphorus (TP) in the systems were 20%-60% and 30%-45%, respectively. The removal rates of contaminations were reduced with the decrease of water temperature and the increase of hydraulic loading rate, the removal rates of CODMn, N4+ -N and TN showed the positive correlation with their inflow concentration, but the removal rate of TP showed the negative correlation with its inflow concentration. Operation and management considerations of the subsurface flow CWs in winter were investigated in this study.
- Published
- 2004
28. Response of seedlings of a dwarf and a normal strain of watermelon to gibberellins.
- Author
-
Loy JB and Liu PB
- Abstract
Hypocotyl and root elongation in a dwarf and a normal strain of watermelon (Citrullus lanatus [Thunb.] Matsu.) in the absence or presence of different gibberellins was investigated in seedlings grown under gold fluorescent light or in darkness. The normal strain, "Sugar Baby," responded only slightly to the gibberellic acids employed. At appropriate concentrations all of the gibberellic acids were capable of normalizing growth in the monorecessive dwarf strain, WB-2, in darkness or in light. Gibberellins A(4+7) and A(7) were effective in stimulating hypocotyl elongation at concentrations 10 to 15 times lower than that needed for a response to GA(1) or GA(3). Dark-grown dwarfs responded to about a 3-fold lower concentration of GA(4+7) than those grown in light.In contrast to hypocotyl elongation, root elongation was greater in the dwarf than in the normal strain. Concentrations of gibberellic acids which enhanced hypocotyl elongation of WB-2 plants, inhibited root growth proportionately.Anatomically, the response of the dwarf strain to GA(4+7) was primarily in terms of increased cell division. Dark-enhanced elongation of both SB and WB-2 was due almost solely to increased cell elongation. The results suggest that, at least in some species, a major component of dark-enhanced growth (or light-inhibited growth) is physiologically distinct from gibberellic acid-stimulated elongation.
- Published
- 1974
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