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Hui Lu

Publications and source records attributed to Hui Lu.

At least 37 records · Page 2Linked to original sources
PubMed2004

Functional TIM10 chaperone assembly is redox-regulated in vivo.

The TIM10 chaperone facilitates the insertion of hydrophobic proteins at the mitochondrial inner membrane. Here we report the novel molecular mechanism of TIM10 assembly. This process crucially depends on oxidative folding in mitochondria and involves: (i) import of the subunits in a Cys-reduced and unfolded state; (ii) folding to an assembly-competent structure maintained by intramolecular disulfide bonding of their four conserved cysteines; and (iii) assembly of the oxidized zinc-devoid subunits to the functional complex. We show that intramolecular disulfide bonding occurs in vivo, whereas intermolecular disulfides observed in vitro are abortive intermediates in the assembly pathway. This novel mechanism of compartment-specific redox-regulated assembly is crucial for the formation of a functional TIM10 chaperone.

Cell Compartmentation↗
PubMed2004

The structural basis of the TIM10 chaperone assembly.

Tim9 and Tim10 are essential components of the "small Tim" family of proteins that facilitate insertion of polytopic proteins at the inner mitochondrial membrane. The small Tims are themselves imported from the cytosol and are organized in specific translocation assemblies in the intermembrane space. Their conformational properties and how these influence the mechanism of assembly remain poorly understood. Moreover, the three-dimensional structure of the TIM10 complex is unknown. We have characterized the structural properties of these proteins in their free and assembled states using NMR, circular dichroism, and small angle x-ray scattering. We show that the free proteins are largely unfolded in their reduced assembly-incompetent state and molten globules in their oxidized assembly-competent state. Tim10 appears less structured than Tim9 in their respective free oxidized forms and undergoes a larger structural change than Tim9 upon complexation. The NMR data here demonstrates unequivocally that only the oxidized states of the Tim9 and Tim10 proteins are capable of forming a complex. Zinc binding stabilizes the reduced state against proteolysis without significantly affecting the secondary structure. Solution x-ray scattering was used to obtain a molecular envelope for the subunits individually and for their fully functional TIM10 complex. Ab initio shape reconstructions based on the scattering data has allowed us to obtain the first low resolution three-dimensional structure of the TIM10 complex. This is a novel structure that displays extensive surface hydrophobicity. The structure also provides an explanation for the escorting function of this non-ATP-powered chaperone particle.

Hydrophobic and Hydrophilic Interactions↗
PubMed2004

Towards the elucidation of shrinkage stress development and relaxation in dental composites.

OBJECTIVE: Although various photo-curing techniques aiming to partially relieve the shrinkage stress by flow have been proposed and investigated, the direct monitoring and observation of stress relaxation behavior received little attention. In this study, the elucidation of stress relaxation behavior and its impact on the overall stress development were investigated. METHODS: A novel experimental set-up capable of real-time, simultaneous shrinkage stress and double bond conversion measurements on the same sample was utilized. The coupled shrinkage stress and conversion for specimens of a barium glass filled Bis-GMA/TEGDMA composite were continuously monitored during and after irradiation for various intervals (2, 3, 6, 10 and 60s). RESULTS: Specimens irradiated for 60s reached the highest conversion (67.9+/-1.2%) and shrinkage stress (2.9+/-0.1 MPa). Shrinkage stress relaxation phenomena were only observed prior to vitrification, which only applied to specimens partially cured for 2 or 3 s; specimens irradiated for 2 s exhibit the largest capability to relieve stress (approximately 40%). However, to achieve this a much longer post-cure stress relaxation time is required as compared to clinically practical time scales. For specimens irradiated for 6, 10 or 60 s, the majority of the shrinkage stress is developed during and after the vitrification stage, and no appreciable stress relaxation can be observed. SIGNIFICANCE: Although stress relaxation prior to vitrification stage has been observed, this study revealed that it did not provide a significant benefit towards the reduction of overall shrinkage stress since, to achieve clinically relevant conversion, the majority of the shrinkage stress is developed during and after the vitrification stage, which does not permit stress relaxation on the time scales used in this study.

Bisphenol A-Glycidyl Methacrylate↗
PubMed2004

[Effect of kidney-warming and astringent therapy on plasma endothelin and interleukin-2 receptor in patients with nephrotic syndrome].

OBJECTIVE: To explore the effect and mechanism of kidney-warming and astringent therapy in treating nephrotic syndrome patients with deficiency of spleen and kidney yang and overflow of water, and to observe the change of plasma endothelin and interleukin-2 receptor after treatment. METHODS: Forty-four patients were randomly divided into conventional steroid treated group (control group, 20 cases) and conventional steroid plus kidney-warming and astringent therapy treated group (treatment group, 24 cases). The levels of plasma endothelin (ET) and soluble interleukin-2 receptor (sIL-2) were observed. RESULTS: Before treatment, plasma ET and sIL-2 in the patients were significantly higher than those in healthy people (P<0.01). After treatment, the ET and sIL-2 levels were obviously improved in both treated groups (P<0.05) and the improvement in the treatment group was more obvious. The difference between the two treated groups after treatment was significant (P<0.05). CONCLUSION: Conventional treatment plus kidney-warming and astringent therapy can effectively improve the levels of plasma ET and sIL-2 in treating nephrotic syndrome patients with deficiency of spleen and kidney yang and overflow of water, and hence alleviate the damage of renal tissue.

Adrenal Cortex Hormones↗
PubMed2004

[Effects of nonnutritive sucking on gastric emptying and gastroesophageal reflux in premature infants].

OBJECTIVE: Although nonnutritive sucking (NNS) during tube feeding has some benefits on the physiology and development of premature infants, the effect on gastrointestinal function remains controversial. The aim of the study was to evaluate the effects of NNS on the gastric emptying and gastroesophageal reflux (GER) in premature infants. METHODS: Thirty eight healthy appropriate-for-gestational-age premature infants (birth weight ranged from 1050 g to 1790 g, gestational age ranged from 28 weeks to 35 weeks) accepting intermittent nasogastric feeding (INGF) were randomized into NNS group and N-NNS group according to INGF with and without NNS and fed with the same milk formula. Group NNS (n = 18) received oral stimulation by means of a pacifier immediately before feeding, during feeding and then after feeding for 5 min. Group N-NNS (n = 20) served as control and received INGF alone. The following data were collected and recorded, the fluid intake (including both intravenous and oral), milk intake, caloric intake, time of caloric intake reaching 418.4 kJ/(kg x d) by enteral feeding and relevant condition to feeding. Gastric emptying was measured when oral intake reaching above 8 ml/kg while concurrently measuring 24 hour esophageal pH. Real time ultrasonic images of the gastric antrum were obtained and the antral cross sectional area (ACSA) was measured and the half emptying time (50% DeltaACSA) was calculated. Using 24-hour intraesophageal pH monitoring for evaluation of GER, the five parameters of esophageal pH were recorded: number of reflux episodes during 24 hours, reflux index, number of episodes lasting > 5 min, the duration of longest episode and the total time of pH < 4.0. RESULTS: Within two weeks after feeding, there was no significant difference in the fluid intake, caloric intake between the two groups (P > 0.05). Gastric emptying was measured on day 13.26, milk intake had no difference between the two groups and there was no difference in prefeed ACSA. The half gastric emptying time in NNS group was significantly shorter than that in N-NNS group [(58.33 +/- 22.94) min vs. (73.75 +/- 17.76) min, P < 0.05]. Thirty-two of the 38 infants developed GER, the morbidity was 84.2%; the number of reflux episodes during 24 hours was significantly fewer in NNS group than that in N-NNS group [9 (2 - 31) vs. 14 (5 - 31), P < 0.05]; the total time pH < 4.0 and reflux index was lower in NNS than that in N-NNS, but the difference was not statistically significant. The time of reaching 418.4 kJ/(kg x d) by enteral feeding in NNS group was significantly shorter than that in N-NNS group [(12.36 +/- 4.29) d vs. (15.50 +/- 4.58) d, P < 0.05]. The incidence of feeding intolerance such as vomiting and abdominal distension was lower in NNS group than that in N-NNS group, but the difference was not statistically significant (P > 0.05). However, the morbidity of gastric residue in NNS was significantly lower than that in N-NNS (16.7% vs 50.0%, respectively, P < 0.05). CONCLUSION: NNS used during intermittent nasogastric tube feeding is an easy and safe intervention. NNS can improve gastric emptying and decrease the number of reflux episodes, has a positive improving effect on the development of gastrointestinal motility, is beneficial to premature infants for establishing postnatal enteral nutrition.

Enteral Nutrition↗
PubMed2003

The mechanical stability of ubiquitin is linkage dependent.

Ubiquitin chains are formed through the action of a set of enzymes that covalently link ubiquitin either through peptide bonds or through isopeptide bonds between their C terminus and any of four lysine residues. These naturally occurring polyproteins allow one to study the mechanical stability of a protein, when force is applied through different linkages. Here we used single-molecule force spectroscopy techniques to examine the mechanical stability of N-C-linked and Lys48-C-linked ubiquitin chains. We combined these experiments with steered molecular dynamics (SMD) simulations and found that the mechanical stability and unfolding pathway of ubiquitin strongly depend on the linkage through which the mechanical force is applied to the protein. Hence, a protein that is otherwise very stable may be easily unfolded by a relatively weak mechanical force applied through the right linkage. This may be a widespread mechanism in biological systems.

Humans↗
PubMed2003

Juxtaposition of the two distal CX3C motifs via intrachain disulfide bonding is essential for the folding of Tim10.

The TIM10 complex, composed of the homologous proteins Tim10 and Tim9, chaperones hydrophobic proteins inserted at the mitochondrial inner membrane. A salient feature of the TIM10 complex subunits is their conserved "twin CX3C" motif. Systematic mutational analysis of all cysteines of Tim10 showed that their underlying molecular defect is impaired folding (demonstrated by circular dichroism, aberrant homo-oligomer formation, and thiol trapping assays). As a result of defective folding, clear functional consequences were manifested in (i) complex formation with Tim9, (ii) chaperone activity, and (iii) import into tim9ts mitochondria lacking both endogenous Tim9 and Tim10. The organization of the four cysteines in intrachain disulfides was determined by trypsin digestion and mass spectrometry. The two distal CX3C motifs are juxtaposed in the folded structure and disulfide-bonded to each other rather than within each other, with an inner cysteine pair connecting Cys44 with Cys61 and an outer pair between Cys40 and Cys65. These cysteine pairs are not equally important for folding and assembly; mutations of the inner Cys are severely affected and form wrong, non-native disulfides, in contrast to mutations of the outer Cys that can still maintain the native inner disulfide pair and display weaker functional defects. Taken together these data reveal this specific intramolecular disulfide bonding as the crucial mechanism for Tim10 folding and show that the inner cysteine pair has a more prominent role in this process.

Amino Acid Motifs↗
PubMed2003

Application of statistical potentials to protein structure refinement from low resolution ab initio models.

Recently ab initio protein structure prediction methods have advanced sufficiently so that they often assemble the correct low resolution structure of the protein. To enhance the speed of conformational search, many ab initio prediction programs adopt a reduced protein representation. However, for drug design purposes, better quality structures are probably needed. To achieve this refinement, it is natural to use a more detailed heavy atom representation. Here, as opposed to costly implicit or explicit solvent molecular dynamics simulations, knowledge-based heavy atom pair potentials were employed. By way of illustration, we tried to improve the quality of the predicted structures obtained from the ab initio prediction program TOUCHSTONE by three methods: local constraint refinement, reduced predicted tertiary contact refinement, and statistical pair potential guided molecular dynamics. Sixty-seven predicted structures from 30 small proteins (less than 150 residues in length) representing different structural classes (alpha, beta, alpha;/beta) were examined. In 33 cases, the root mean square deviation (RMSD) from native structures improved by more than 0.3 A; in 19 cases, the improvement was more than 0.5 A, and sometimes as large as 1 A. In only seven (four) cases did the refinement procedure increase the RMSD by more than 0.3 (0.5) A. For the remaining structures, the refinement procedures changed the structures by less than 0.3 A. While modest, the performance of the current refinement methods is better than the published refinement results obtained using standard molecular dynamics.

Computer Simulation↗
PubMed2003

Development of unified statistical potentials describing protein-protein interactions.

A residue-based and a heavy atom-based statistical pair potential are developed for use in assessing the strength of protein-protein interactions. To ensure the quality of the potentials, a nonredundant, high-quality dimer database is constructed. The protein complexes in this dataset are checked by a literature search to confirm that they form multimers, and the pairwise amino acid preference to interact across a protein-protein interface is analyzed and pair potentials constructed. The performance of the residue-based potentials is evaluated by using four jackknife tests and by assessing the potentials' ability to select true protein-protein interfaces from false ones. Compared to potentials developed for monomeric protein structure prediction, the interdomain potential performs much better at distinguishing protein-protein interactions. The potential developed from homodimer interfaces is almost the same as that developed from heterodimer interfaces with a correlation coefficient of 0.92. The residue-based potential is well suited for genomic scale protein interaction prediction and analysis, such as in a recently developed threading-based algorithm, MULTIPROSPECTOR. However, the more time-consuming atom-based potential performs better in identifying near-native structures from docking generated decoys.

Algorithms↗
PubMed2003

Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome.

MULTIPROSPECTOR, a multimeric threading algorithm for the prediction of protein-protein interactions, is applied to the genome of Saccharomyces cerevisiae. Each possible pairwise interaction among more than 6000 encoded proteins is evaluated against a dimer database of 768 complex structures by using a confidence estimate of the fold assignment and the magnitude of the statistical interfacial potentials. In total, 7321 interactions between pairs of different proteins are predicted, based on 304 complex structures. Quality estimation based on the coincidence of subcellular localizations and biological functions of the predicted interactors shows that our approach ranks third when compared with all other large-scale methods. Unlike other in silico methods, MULTIPROSPECTOR is able to identify the residues that participate directly in the interaction. Three hundred seventy-four of our predictions can be found by at least one of the other studies, which is compatible with the overlap between two different other methods. From the analysis of the mRNA abundance data, our method does not bias towards proteins with high abundance. Finally, several relevant predictions involved in various functions are presented. In summary, we provide a novel approach to predict protein-protein interactions on a genomic scale that is a useful complement to experimental methods.

DNA, Fungal↗
PubMed2003

[Quantitative detection of intrahepatic hepatitis B virus DNA in patients with chronic hepatitis B].

OBJECTIVE: To study the relationships between intrahepatic HBV DNA level and serum HBV DNA level, between intrahepatic HBV DNA level and hepatitis B e antigen (HBeAg) level in patients with chronic hepatitis B (CHB), and assess the valuation of pretreatment liver HBV DNA level in antivirus therapy. METHODS: Liver specimens taken from 41 HBeAg-positive CHB patients before antivirus treatment were divided into two parts, one for histological examination, and the other for intrahepatic HBV DNA quantified detection by PCR-fluorescence. At the same time, serum levels of HBV DNA and HBeAg were detected. The patients were classified into two groups according to the pretreatment intrahepatic HBV DNA level (< or = 10(4)fg/cm(3) in group A, >10(4)fg/cm(3) in group B) and accepted interferon alpha-1b (3MU every day for 26 weeks) in combination with lamivudine (100mg per day for 52 weeks). During the treatment, the serum levels of alanine aminotransferase (ALT), HBV DNA and HBeAg seroconversion rate were monitored. RESULTS: (1) The level of liver HBV DNA was much higher than that of serum HBV DNA (4.081 +/-1.127 vs 3.163 +/-1.010, t = 2.218, P < 0.05). Liver HBV DNA level had positive correlation to serum HBV DNA level (r = 0.840, t = 4.322, P < 0.001) and serum HBeAg level (r = 0.459, t = 3.056, P < 0.005). (2) Intrahepatic HBV DNA level was negative correlation to the severity of liver damage (chi(2) = 3.874, P < 0.05). (3) Serum HBV DNA level in all the patients reduced remarkedly after therapy, especially in group A. At the end of 52 weeks, the rates of HBeAg and anti-HBe seroconversion in group A were higher than those in group B (68.4% vs 36.4%, chi(2) = 4.194, P < 0.05; 73.7% vs 40.9%, chi(2) = 4.447, P<0.05). CONCLUSIONS: Intrahepatic HBV DNA is a more valuable marker than serum HBV DNA or HBeAg to assess HBV replication, and can reflect the status of body immunity indirectly. It may be a useful indicator for the efficacy of antivirus treatment.

Adolescent↗
PubMed2003

[Effects of intermittent nasogastric feeding with nonnutritive sucking on nutrient and gastrointestinal tract transit time in premature infants].

OBJECTIVE: To evaluate the effects of nonnutritive sucking (NNS) on the nutrient intake, physical growth, feeding-related complications and whole gastrointestinal transit time (WGTT) in premature infants. METHODS: Thirty eight healthy appropriate for gestational age premature infants (birth weights ranged from 1 050 g to 1 790 g) accepting intermittent nasogastric feeding (INGF) were randomized into NNS group and N-NNS group according to INGF with and without NNS and fed with the same milk formula. The following data were collected and recorded, the physical growth parameters (e.g, body weight, length and head circumference) and the birth-weight regaining time, the fluid intake (including both intravenous and oral), caloric intake, time of reaching 418.4 kJ/(kg.d) by enteral feeding, time of putting nasogastric tube, stool frequency and characters, and relevant complications. WGTT were monitored. RESULTS: The birth-weight regaining time in NNS group was significantly shorter than that in N-NNS group [(8.8 +/- 3.7) d vs (11.1 +/- 3.0) d, P < 0.05]. Within two weeks after feeding, there was no significant difference in the increase of body weight, length and head circumference between the two groups (P > 0.05). The time of reaching 418.4 kJ/(kg.d) by enteral feeding in NNS group was significantly shorter than that in N-NNS group [(12.3 +/- 5.1) d vs (15.7 +/- 5.2) d, P < 0.05]; the times of putting nasogastric tube were respectively (13 +/- 10) d and (17 +/- 12) d, but the difference was not significant (P > 0.05). The morbidity of such complications as vomiting and abdominal distension was lower in NNS group than that in N-NNS group, but the difference was not statistically significant (P > 0.05). However, the morbidity of gastric residue in NNS was significantly lower than that in N-NNS (P < 0.05). WGTT of the second week in NNS group was significantly shorter than that in N-NNS [(33 +/- 13) h vs (45 +/- 20) h, P < 0.05]. Stool frequencies of the second week in NNS group were significantly more than those in N-NNS group [(2.26 +/- 0.17) times/d vs (1.79 +/- 0.58) times/d, P < 0.05]. However, there were no significantly differences in WGTT and stool frequencies of the first week between the two groups (P > 0.05). CONCLUSION: NNS was recommended as a beneficial intervention for premature infants during intermittent nasogastric tube feeding.

Enteral Nutrition↗
PubMed2002

MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading.

In this postgenomic era, the ability to identify protein-protein interactions on a genomic scale is very important to assist in the assignment of physiological function. Because of the increasing number of solved structures involving protein complexes, the time is ripe to extend threading to the prediction of quaternary structure. In this spirit, a multimeric threading approach has been developed. The approach is comprised of two phases. In the first phase, traditional threading on a single chain is applied to generate a set of potential structures for the query sequences. In particular, we use our recently developed threading algorithm, PROSPECTOR. Then, for those proteins whose template structures are part of a known complex, we rethread on both partners in the complex and now include a protein-protein interfacial energy. To perform this analysis, a database of multimeric protein structures has been constructed, the necessary interfacial pairwise potentials have been derived, and a set of empirical indicators to identify true multimers based on the threading Z-score and the magnitude of the interfacial energy have been established. The algorithm has been tested on a benchmark set comprised of 40 homodimers, 15 heterodimers, and 69 monomers that were scanned against a protein library of 2478 structures that comprise a representative set of structures in the Protein Data Bank. Of these, the method correctly recognized and assigned 36 homodimers, 15 heterodimers, and 65 monomers. This protocol was applied to identify partners and assign quaternary structures of proteins found in the yeast database of interacting proteins. Our multimeric threading algorithm correctly predicts 144 interacting proteins, compared to the 56 (26) cases assigned by PSI-BLAST using a (less) permissive E-value of 1 (0.01). Next, all possible pairs of yeast proteins have been examined. Predictions (n = 2865) of protein-protein interactions are made; 1138 of these 2865 interactions have counterparts in the Database of Interacting Proteins. In contrast, PSI-BLAST made 1781 predictions, and 1215 have counterparts in DIP. An estimation of the false-negative rate for yeast-predicted interactions has also been provided. Thus, a promising approach to help assist in the assignment of protein-protein interactions on a genomic scale has been developed.

Algorithms↗
PubMed2002

[Properties of whole-cell potassium currents in mechanically dissociated Drosophila larval central neurons].

By electrophysiological methods, cultured Drosophila embryonic and larval central neurons have been widely used to study ion channels, neurotransmitter release and intracellular message regulation. Voltage-activated K(+) channels play a crucial role in repolarizing the membrane following action potentials, stabilizing membrane potentials and shaping firing patterns of cells. In this study, a mechanical vibration-isolation system was used to produce a sufficient number of acutely dissociated larval central neurons, of which the majority were type II neurons (2~5 microm in diameter). Using patch clamp technique, the whole-cell K(+) currents in type II neurons were characterized by containing a transient 4-AP-sensitive current (I(A)) and a more slowly inactivating, TEA-sensitive component (I(K)). According to their kinetic properties, five types of whole-cell K(+) currents were identified. Type A current exhibited primarily fast transient K(+) currents that activated and inactivated rapidly. The majority of the neurons, however, slowly inactivated K(+) currents with variable inactivation time course (type B current). Type C current, being present in a small number of the cells, was mainly composed of noninactivating components. Some of the neurons expressed both transient and slow inactivating components, but the slowly inactivating components could reach more than 50% of the peak current (type D current). Type E current showed distinct voltage-dependent activation properties, characterized by its bell-shaped activation curve. Type E current was inhibited by application of Ca(2+)-free solution or 0.1 mmol/L Cd(2+). Moreover, this novel current ran down much more rapidly than other types. These results indicate that different K(+) channels, which have different kinetic and pharmacological properties, underlie the whole-cell K(+) currents in type II neurons of Drosophila larval central nervous system.

Action Potentials↗