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Zhaohui Li

Publications and source records attributed to Zhaohui Li.

At least 19 recordsLinked to original sources
PubMed2007

Strategies for high-throughput comparative modeling: applications to leverage analysis in structural genomics and protein family organization.

The technological breakthroughs in structural genomics were designed to facilitate the solution of a sufficient number of structures, so that as many protein sequences as possible can be structurally characterized with the aid of comparative modeling. The leverage of a solved structure is the number and quality of the models that can be produced using the structure as a template for modeling and may be viewed as the "currency" with which the success of a structural genomics endeavor can be measured. Moreover, the models obtained in this way should be valuable to all biologists. To this end, at the Northeast Structural Genomics Consortium (NESG), a modular computational pipeline for automated high-throughput leverage analysis was devised and used to assess the leverage of the 186 unique NESG structures solved during the first phase of the Protein Structure Initiative (January 2000 to July 2005). Here, the results of this analysis are presented. The number of sequences in the nonredundant protein sequence database covered by quality models produced by the pipeline is approximately 39,000, so that the average leverage is approximately 210 models per structure. Interestingly, only 7900 of these models fulfill the stringent modeling criterion of being at least 30% sequence-identical to the corresponding NESG structures. This study shows how high-throughput modeling increases the efficiency of structure determination efforts by providing enhanced coverage of protein structure space. In addition, the approach is useful in refining the boundaries of structural domains within larger protein sequences, subclassifying sequence diverse protein families, and defining structure-based strategies specific to a particular family.

Computational Biology↗
PubMed2006

Mutant caveolin-3 induces persistent late sodium current and is associated with long-QT syndrome.

BACKGROUND: Congenital long-QT syndrome (LQTS) is a primary arrhythmogenic syndrome stemming from perturbed cardiac repolarization. LQTS, which affects approximately 1 in 3000 persons, is 1 of the most common causes of autopsy-negative sudden death in the young. Since the sentinel discovery of cardiac channel gene mutations in LQTS in 1995, hundreds of mutations in 8 LQTS susceptibility genes have been identified. All 8 LQTS genotypes represent primary cardiac channel defects (ie, ion channelopathy) except LQT4, which is a functional channelopathy because of mutations in ankyrin-B. Approximately 25% of LQTS remains unexplained pathogenetically. We have pursued a "final common pathway" hypothesis to elicit novel LQTS-susceptibility genes. With the recent observation that the LQT3-associated, SCN5A-encoded cardiac sodium channel localizes in caveolae, which are known membrane microdomains whose major component in the striated muscle is caveolin-3, we hypothesized that mutations in caveolin-3 may represent a novel pathogenetic mechanism for LQTS. METHODS AND RESULTS: Using polymerase chain reaction, denaturing high-performance liquid chromatography, and direct DNA sequencing, we performed open reading frame/splice site mutational analysis on CAV3 in 905 unrelated patients referred for LQTS genetic testing. CAV3 mutations were engineered by site-directed mutagenesis and the molecular phenotype determined by transient heterologous expression into cell lines that stably express the cardiac sodium channel hNa(v)1.5. We identified 4 novel mutations in CAV3-encoded caveolin-3 that were absent in >1000 control alleles. Electrophysiological analysis of sodium current in HEK293 cells stably expressing hNa(v)1.5 and transiently transfected with wild-type and mutant caveolin-3 demonstrated that mutant caveolin-3 results in a 2- to 3-fold increase in late sodium current compared with wild-type caveolin-3. Our observations are similar to the increased late sodium current associated with LQT3-associated SCN5A mutations. CONCLUSIONS: The present study reports the first CAV3 mutations in subjects with LQTS, and we provide functional data demonstrating a gain-of-function increase in late sodium current.

Amino Acid Sequence↗
PubMed2006

A shift in pathway of iron-mediated perchloroethylene reduction in the presence of sorbed surfactant--a column study.

Surface modification of zero-valent iron (ZVI) to enhance its reduction rates for chlorinated ethanes and ethenes has recently attracted great attention. In this research, the enhancement of perchloroethylene (PCE) reduction by ZVI in the presence of sorbed micelles of the cationic surfactant hexadecyltrimethylammonium (HDTMA) was examined in a series of laboratory column tests with varying flow rates and input PCE concentrations. Model simulations using HYDRUS-1D showed that the overall pseudo first-order rate constants for PCE reduction by ZVI increased by a factor of four in the presence of sorbed HDTMA admicelles. The increase in reduction rate was attributed to a higher distribution coefficient (K(d)) for contaminant sorption on surfactant-modified ZVI (SM-ZVI) compared to untreated ZVI. Modeling results also showed that in the presence of HDTMA admicelles 58-100% of PCE reduction occurred via hydrogenolysis. In contrast, only 12-25% PCE underwent hydrogenolysis when HDTMA was absent. The significant increase in TCE production during PCE reduction by SM-ZVI verified a shift in reaction pathway previously observed in batch studies, most likely from beta-elimination to hydrogenolysis. Although this shift in reaction pathway resulted in a higher accumulation of TCE, the combined concentrations of chlorinated hydrocarbons in the effluent were 1.5-5 times lower when SM-ZVI rather than unmodified ZVI was used.

Adsorption↗
PubMed2006

Hyperhomocysteinemia decreases circulating high-density lipoprotein by inhibiting apolipoprotein A-I Protein synthesis and enhancing HDL cholesterol clearance.

We previously reported that hyperhomocysteinemia (HHcy), an independent risk factor of coronary artery disease (CAD), is associated with increased atherosclerosis and decreased plasma high-density lipoprotein cholesterol (HDL-C) in cystathionine beta-synthase-/apolipoprotein E-deficient (CBS(-/-)/apoE(-/-)) mice. We observed that plasma homocysteine (Hcy) concentrations are negatively correlated with HDL-C and apolipoprotein A1 (apoA-I) in patients with CAD. We found the loss of large HDL particles, increased HDL-free cholesterol, and decreased HDL protein in CBS(-/-)/apoE(-/-) mice, and attenuated cholesterol efflux from cholesterol-loaded macrophages to plasma in CBS(-/-)/apoE(-/-) mice. ApoA-I protein was reduced in the plasma and liver, but hepatic apoA-I mRNA was unchanged in CBS(-/-)/apoE(-/-) mice. Moreover, Hcy (0.5 to 2 mmol/L) reduced the levels of apoA-I protein but not mRNA and inhibited apoA-1 protein synthesis in mouse primary hepatocytes. Further, plasma lecithin:cholesterol acyltransferase (LCAT) substrate reactivity was decreased, LCAT specific activity increased, and plasma LCAT protein levels unchanged in apoE(-/-)/CBS(-/-) mice. Finally, the clearance of plasma HDL cholesteryl ester, but not HDL protein, was faster in CBS(-/-)/apoE(-/-) mice, correlated with increased scavenger receptor B1, and unchanged ATP-binding cassette transporter A1 protein expression in the liver. These findings indicate that HHcy inhibits reverse cholesterol transport by reducing circulating HDL via inhibiting apoA-I protein synthesis and enhancing HDL-C clearance.

Aged↗
PubMed2006

The role of electrostatics in protein-membrane interactions.

Many experimental, structural and computational studies have established the importance of nonspecific electrostatics as a driving force for peripheral membrane association. Here we focus on this component of protein/membrane interactions by using examples ranging from phosphoinositide signaling to retroviral assembly. We stress the utility of the collaboration of experiment and theory in identifying and quantifying the role of electrostatics not only in contributing to membrane association, but also in affecting subcellular targeting, in the control of membrane binding, and in the organization of proteins and lipids at membrane surfaces.

Animals↗
PubMed2006

Immunofluorescent labeling of cancer cells with quantum dots synthesized in aqueous solution.

Thioglycolic-acid-stabilized CdTe quantum dots, synthesized directly in aqueous solution, are successfully conjugated with biotin and polyethylene glycol. Using these conjugates, we report the development of this kind of water-soluble quantum dot for immunofluorescent labeling of cancer cells. The results show that these conjugates have very low nonspecific binding and good stability against photobleaching, enabling them to be applied in many biological fields, such as cellular labeling, intracellular tracking, and other imaging applications.

Cell Line, Tumor↗
PubMed2006

[Application of portable esophageal dilator in treatment of esophageal stenosis at home].

OBJECTIVE: To explore an economical protocol for esophageal stenosis treatment at home and evaluate the effects of portable esophageal dilator. METHOD: Sixty-seven patients with esophageal stenosis were treated at home by themselves with portable esophageal dilator, which was designed by Prof Wang HT, one of the authors. Twenty-nine cases of esophageal stenosis were caused by chemical damage, 23 cases by esophageal tumor, 13 postoperation cases with hypopharyngeal and upper esophageal tumor and two cases by laryngeal thyroid gland recurrent tumor. Stricture happened at esophageal entrance and upper segment in 15 cases, at middle in 32 cases, both at middle and upper in 17 cases and at whole length of esophagus in three cases. Stricture was not complete atresia and dilators could insert into esophagus in all patients. RESULT: Significant effects were found in 43 patients and good effects in 24 patients. Seven deaths were caused by remote metastasis of recurrent cancer resulting in multiple organ failure or large blood vessels bleeding resulting of tumor erosion. Follow-up visit ranged from the shortest period of four months to the longest period of five years and 1 month, 9.8 months on average. CONCLUSION: Family portable dilator and self-catering dilation is an effective and safe method for treating esophageal stenosis. It is so simple, convenient, painless with low expense that it is especially useful in countryside hospitals and undeveloped rural areas.

Adolescent↗
PubMed2005

Hyperhomocysteinemia inhibits post-injury reendothelialization in mice.

OBJECTIVE: Hyperhomocysteinemia (HHcy) is a risk factor for cardiovascular disease and has been reported to inhibit endothelial cell (EC) growth. Notwithstanding, precisely how HHcy regulates EC growth in vivo remains unknown. In this study, we established a mouse model of endothelial injury and reendothelialization and examined the role and mechanism of HHcy in endothelial repair. METHODS AND RESULTS: A mouse model of carotid artery air-dry endothelium denudation and reendothelialization was established and used to evaluate post-injury endothelial repair in mice with the gene deletion of cystathionine-beta-synthase (CBS). Moderate and severe HHcy were induced in CBS+/+ and CBS-/+ mice through a high-methionine diet. Post-injury reendothelialization, which correlated with increased post-injury neointima formation, was impaired in severe HHcy mice. To elucidate the underlying mechanism, we examined circulating endothelial progenitor cells (EPC) in HHcy mice and studied the effect of homocysteine (Hcy) on proliferation, migration, and adhesion of human umbilical vein endothelial cells (HUVEC). The peripheral EPC population was not significantly altered in HHcy mice. Hcy had a profound inhibitory effect on EC proliferation and migration at physiologically relevant concentrations and inhibited EC adhesion at concentrations of 200 microM and higher. CONCLUSION: We have established a convenient and accurate mouse model of carotid injury in which the reendothelialization process can be precisely quantified. In addition, we have observed impaired reendothelialization and increased neointimal formation in severe HHcy mice. The capacity of Hcy to inhibit proliferation and migration of EC may be responsible for impaired reendothelialization and contribute to arteriosclerosis in HHcy.

Animals↗
PubMed2005

HLA polymorphisms are associated with Helicobacter pylori infected gastric cancer in a high risk population, China.

Helicobacter pylori is one of the most common bacterial infections associated with an increased risk of gastric cancer, but its association with host factors, particularly polymorphisms of the immune response genes, such as human leukocyte antigen (HLA) genes, is still unclear. To investigate the role of HLA polymorphisms in the risk of gastric cancer among subjects with H. pylori infection, a case-control study involving 52 gastric cancer patients and 139 non-cancer controls was conducted in Linqu County, China, an area with a high incidence of gastric cancer. Polymorphisms of HLA class I and class II alleles were determined by PCR with sequence-specific primers (PCR-SSP). The information about H. pylori infection was obtained from previous records. Among 48 class I and 19 class II HLA alleles detected in this study, two alleles, CW*03 and DRB1*01, were found to be distributed significantly differently between patients and controls [odds ratio(OR)=1.95, 95% confidence interval (CI)=1.13-3.35, P=0.017 and OR=4.39, 95% CI=1.39-13.84, P=0.012, respectively). The OR of gastric cancer risk in individuals carrying CW*03/CW*03 or CW*03/CW*N was 2.06, 95% CI=1.05-4.02, P=0.035, while the OR was 3.49, 95% CI=1.0-12.4, P=0.04 for DRB1*01/DRB1*01 or DRB1*01/DRB1*N carriers. The analysis of the interaction between H. pylori infection and HLA risk genotypes of CW*03 or DRB1*01 revealed that the effect of CW*03 and DRB1*01 genotypes on gastric cancer risk was manifested stronger in H. pylori-positive individuals (OR=5.30, 95% CI=1.73-16.29, P=0.004 and OR=13.38, 95% CI=2.52-70.98, P=0.002, respectively) than in H. pylori-negative ones (OR=1.25, 95% CI=0.25-6.12, P=0.785 and OR=2.26, 95% CI=0.18-28.88, P=0.531, respectively). The combined effect of the two risk HLA genotypes on gastric cancer risk was also analysed. The result showed that the individuals carrying both the CW*03 and DRB1*01 alleles could only be found in cancer patients (5/52), and not in controls (0/139), further suggesting that CW*03 and DRB1*01 are risk alleles advancing the progression of tumorigenesis. These observations demonstrate that host HLA genotypes may play an important role in the risk of gastric cancer, especially among persons with H. pylori infection.

China↗
PubMed2005

NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure.

The 150-residue protein TM1509 is encoded in gene YF09_THEMA of Thermotoga maritima. TM1509 has so far no functional annotation and belongs to protein family UPF0054 (PFAM accession number: PF02130) which contains at least 146 members. The NMR structure of TM1509 reveals an alpha+beta fold comprising a four stranded beta-sheet with topology A( upward arrow), B( upward arrow), D( upward arrow), C( downward arrow) as well as five alpha-helices I-V. The structures of most members of family PF02130 can be reliably constructed using the TM1509 NMR structure, demonstrating high leverage for exploration of fold space. A multiple sequence alignment of TM1509 with homologues of family UPF0054 shows that three polypeptide segments, as well as a putative zinc-binding consensus motif HGXLHLXGYDH located at the C-terminal end of alpha-helix IV, are highly conserved. The spatial arrangement of the three His residues of this UPF0054 consensus motif is similar to the arrangement found for the His residues in the HEXXHXXGXXH zinc-binding consensus motif of matrix metallo-proteases (MMPs). Moreover, the other conserved polypeptide segments form a large cavity which encloses the putative Zn-binding pocket and might confer specificity during catalysis. However, TM1509 and the other members of the UPF0054 family do not have the crucial Glu residue in position 2 of the MMP consensus motif. Intriguingly, the TM1509 structure indicates that the Asp in the UPF0054 consensus motif (Asp 111 in TM1509) may overtake the catalytic role of the Glu. This suggests that protein family UPF0054 might contain members of a hitherto uncharacterized class of metalloproteases.

Amino Acid Sequence↗
PubMed2005

Retroviral matrix domains share electrostatic homology: models for membrane binding function throughout the viral life cycle.

The matrix domain (MA) of Gag polyproteins performs multiple functions throughout the retroviral life cycle. MA structures have an electropositive surface patch that is implicated in membrane association. Here, we use computational methods to demonstrate that electrostatic control of membrane binding is a central characteristic of all retroviruses. We are able to explain a wide range of experimental observations and provide a level of quantitative and molecular detail that has been inaccessible to experiment. We further predict that MA may exist in a variety of oligomerization states and propose mechanistic models for the effects of phosphoinositides and phosphorylation. The calculations provide a conceptual model for how non-myristoylated and myristoylated MAs behave similarly in assembly and disassembly. Hence, they provide a unified quantitative picture of the structural and energetic origins of the entire range of MA function and thus enhance, extend, and integrate previous observations on individual stages of the process.

Cell Membrane↗
PubMed2005

High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases.

The structural biology of proteins mediating iron-sulfur (Fe-S) cluster assembly is central for understanding several important biological processes. Here we present the NMR structure of the 16-kDa protein YgdK from Escherichia coli, which shares 35% sequence identity with the E. coli protein SufE. The SufE X-ray crystal structure was solved in parallel with the YdgK NMR structure in the Northeast Structural Genomics (NESG) consortium. Both proteins are (1) key components for Fe-S metabolism, (2) exhibit the same distinct fold, and (3) belong to a family of at least 70 prokaryotic and eukaryotic sequence homologs. Accurate homology models were calculated for the YgdK/SufE family based on YgdK NMR and SufE crystal structure. Both structural templates contributed equally, exemplifying synergy of NMR and X-ray crystallography. SufE acts as an enhancer of the cysteine desulfurase activity of SufS by SufE-SufS complex formation. A homology model of CsdA, a desulfurase encoded in the same operon as YgdK, was modeled using the X-ray structure of SufS as a template. Protein surface and electrostatic complementarities strongly suggest that YgdK and CsdA likewise form a functional two-component desulfurase complex. Moreover, structural features of YgdK and SufS, which can be linked to their interaction with desulfurases, are conserved in all homology models. It thus appears very likely that all members of the YgdK/SufE family act as enhancers of Suf-S-like desulfurases. The present study exemplifies that "refined" selection of two (or more) targets enables high-quality homology modeling of large protein families.

Animals↗
PubMed2004

Surfactant-enhanced oxidation of trichloroethylene by permanganate--proof of concept.

Oxidative dechlorination of chlorinated solvents by permanganate is an emerging technology for remediation of groundwater contaminated with dissolved chlorinated contaminants. In this study, the enhancement of trichloroethylene (TCE) degradation by permanganate in aqueous solution in the presence of surfactant was evaluated through a continuous stir batch reactor system with the presence of permanganate as the limiting reagent and free phase TCE. The TCE degradation was determined by continuous monitoring the amount of chloride produced, which was then reverted to the rate of permanganate consumption. It was found that the chloride production, an indication of TCE degradation, followed a pseudo-first-order reaction kinetics with respect to KMnO(4) in the presence of free phase TCE. When no surfactants were present, the observed pseudo-first-order rate constant (k(obs)) was 0.08-0.19 min(-1) and the half-life (t(1/2)) was 4-9 min for MnO(4)(-). When the surfactant concentration was less than its critical micelle concentration (CMC), the k(obs) values increased to 0.42-0.46 min(-1) and the t(1/2) reduced to 1.5-1.7 min for MnO(4)(-). As the surfactant concentration was greater than the CMC, the k(obs) values increased to 0.56-0.58 min(-1) and the t(1/2) reduced to 1.2-1.3 min. The preliminary results showed that combination of permanganate with a proper type of surfactant can speed up contaminant removal.

Chlorides↗
PubMed2004

The NMR solution structure of the 30S ribosomal protein S27e encoded in gene RS27_ARCFU of Archaeoglobus fulgidis reveals a novel protein fold.

The Archaeoglobus fulgidis gene RS27_ARCFU encodes the 30S ribosomal protein S27e. Here, we present the high-quality NMR solution structure of this archaeal protein, which comprises a C4 zinc finger motif of the CX(2)CX(14-16)CX(2)C class. S27e was selected as a target of the Northeast Structural Genomics Consortium (target ID: GR2), and its three-dimensional structure is the first representative of a family of more than 116 homologous proteins occurring in eukaryotic and archaeal cells. As a salient feature of its molecular architecture, S27e exhibits a beta-sandwich consisting of two three-stranded sheets with topology B(decreasing), A(increasing), F(decreasing), and C(increasing), D(decreasing), E(increasing). Due to the uniqueness of the arrangement of the strands, the resulting fold was found to be novel. Residues that are highly conserved among the S27 proteins allowed identification of a structural motif of putative functional importance; a conserved hydrophobic patch may well play a pivotal role for functioning of S27 proteins, be it in archaeal or eukaryotic cells. The structure of human S27, which possesses a 26-residue amino-terminal extension when compared with the archaeal S27e, was modeled on the basis of two structural templates, S27e for the carboxy-terminal core and the amino-terminal segment of the archaeal ribosomal protein L37Ae for the extension. Remarkably, the electrostatic surface properties of archaeal and human proteins are predicted to be entirely different, pointing at either functional variations among archaeal and eukaryotic S27 proteins, or, assuming that the function remained invariant, to a concerted evolutionary change of the surface potential of proteins interacting with S27.

Amino Acid Sequence↗
PubMed2003

Interpolymetallic assembly of d8-d10 sulfide aggregates from [Pt2(PPh3)4(mu-S)2] and group 12 metals.

A series of heterometallic Pt-M (M=Zn and Cd) sulfide aggregates with growing nuclearities (Pt2M), (Pt4M), and (Pt4M2), viz., [ZnPt2Cl2(PPh3)4(mu3-S)2] (2), [CdPt2Cl2(PPh3)4(mu3-S)2] (3), [Pt2(PPh3)4(mu3-S)2]2[ZnSO4]2 (4), [Pt2(PPh3)4(mu3-S)2]2[CdSO4]2.H2O (5), [CdPt4(PPh3)8(mu3-S)4][ClO4]2 (7), and [ZnPt4(PPh3)8(mu3-S)4][ClO4]2 (8), have been prepared from Pt2(PPh3)4(mu-S)2 (1) with appropriate zinc and cadmium substrates. The structures have been determined by single-crystal X-ray diffraction. The supporting anions play an active role in the structural assembly process. An unexpected disintegration complex [Pt2(S2CH2)Cl(PPh3)4][PF6] (6) has also been isolated and characterized by single-crystal X-ray diffraction. The mechanism of the formation of 6 is proposed.

Journal Article↗
PubMed2003

Molecular quantum cellular automata cells. Electric field driven switching of a silicon surface bound array of vertically oriented two-dot molecular quantum cellular automata.

The amine functionality of the linker on the dinuclear complex [trans-Ru(dppm)(2)(Ctbd1;CFc)(NCCH(2)CH(2)NH(2))][PF(6)] reacts with Si-Cl bonds of a chlorinated, highly B doped Si (111) surface to yield Si-N surface-complex bonds. The surface bound complex is constrained to a near vertical orientation by the chain length of the linker as confirmed by variable angle XPS. Oxidation of the dinuclear complex with ferrocenium ion or electrochemically generates a stable, biased Fe(III)-Ru(II) mixed-valence complex on the surface. Characterization of the array of surface bound complexes with spectroscopic as well as electrochemical techniques confirms the presence of strongly bound, chemically robust, mixed-valence complexes. Capping the flat array of complexes with a minimally perturbing mercury electrode permits the equalization of the Fe and Ru energy wells by an applied electric field. The differential capacitance of oxidized and unoxidized bound complexes is compared as a function of voltage applied between the Hg gate and the Si. The results show that electron exchange between the Fe and Ru sites of the array of dinuclear mixed-valence complexes at energy equalization generates a fluctuating dipole that produces a maximum in the capacitance versus voltage curve for each complex-counterion combination present. Passage through the capacitance maximum corresponds to switching of the molecular quantum cellular automata (QCA) cell array by the electric field from the Fe(III)-Ru(II) configuration to the Fe(II)-Ru(III) configuration, thereby confirming that molecules possess an essential property necessary for their use as elements of a QCA device.

Journal Article↗