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1.  Divalent cations activate TRPV1 through promoting conformational change of the extracellular region 
The Journal of General Physiology  2014;143(1):91-103.
Divalent cations Mg2+ and Ba2+ selectively and directly potentiate transient receptor potential vanilloid type 1 heat activation by lowering the activation threshold into the room temperature range. We found that Mg2+ potentiates channel activation only from the extracellular side; on the intracellular side, Mg2+ inhibits channel current. By dividing the extracellularly accessible region of the channel protein into small segments and perturbing the structure of each segment with sequence replacement mutations, we observed that the S1–S2 linker, the S3–S4 linker, and the pore turret are all required for Mg2+ potentiation. Sequence replacements at these regions substantially reduced or eliminated Mg2+-induced activation at room temperature while sparing capsaicin activation. Heat activation was affected by many, but not all, of these structural alternations. These observations indicate that extracellular linkers and the turret may interact with each other. Site-directed fluorescence resonance energy transfer measurements further revealed that, like heat, Mg2+ also induces structural changes in the pore turret. Interestingly, turret movement induced by Mg2+ precedes channel activation, suggesting that Mg2+-induced conformational change in the extracellular region most likely serves as the cause of channel activation instead of a coincidental or accommodating structural adjustment.
doi:10.1085/jgp.201311024
PMCID: PMC3874565  PMID: 24344245
2.  Divalent cations potentiate TRPV1 channel by lowering the heat activation threshold 
Transient receptor potential vanilloid type 1 (TRPV1) channel responds to a wide spectrum of physical and chemical stimuli. In doing so, it serves as a polymodal cellular sensor for temperature change and pain. Many chemicals are known to strongly potentiate TRPV1 activation, though how this is achieved remains unclear. In this study we investigated the molecular mechanism underlying the gating effects of divalent cations Mg2+ and Ba2+. Using a combination of fluorescence imaging and patch-clamp analysis, we found that these cations potentiate TRPV1 gating by most likely promoting the heat activation process. Mg2+ substantially lowers the activation threshold temperature; as a result, a significant fraction of channels are heat-activated at room temperature. Although Mg2+ also potentiates capsaicin- and voltage-dependent activation, these processes were found either to be not required (in the case of capsaicin) or insufficient (in the case of voltage) to mediate the activating effect. In support of a selective effect on heat activation, Mg2+ and Ba2+ cause a Ca2+-independent desensitization that specifically prevents heat-induced channel activation but does not prevent capsaicin-induced activation. These results can be satisfactorily explained within an allosteric gating framework in which divalent cations strongly promote the heat-dependent conformational change or its coupling to channel activation, which is further coupled to the voltage- and capsaicin-dependent processes.
doi:10.1085/jgp.201311025
PMCID: PMC3874569  PMID: 24344247
3.  Preparation, Characterization, In Vitro Release and Degradation of Cathelicidin-BF-30-PLGA Microspheres 
PLoS ONE  2014;9(6):e100809.
Cathelicidin-BF-30 (BF-30), a water-soluble peptide isolated from the snake venom of Bungarus fasciatus containing 30 amino acid residues, was incorporated in poly(D,L-lactide-co-glycolide) (PLGA) 75∶25 microspheres (MS) prepared by a water in oil in water W/O/W emulsification solvent extraction method. The aim of this work was to investigate the stability of BF-30 after encapsulation. D-trehalose was used as an excipient to stabilize the peptide. The MS obtained were mostly under 2 µm in size and the encapsulation efficiency was 88.50±1.29%. The secondary structure of the peptide released in vitro was determined to be nearly the same as the native peptide using Circular Dichroism (CD). The ability of BF-30 to inhibit the growth of Escherichia coli was also maintained. The cellular relative growth and hemolysis rates were 92.16±3.55% and 3.52±0.45% respectively.
doi:10.1371/journal.pone.0100809
PMCID: PMC4071013  PMID: 24963652
4.  Differences in Meiotic Recombination Rates in Childhood Acute Lymphoblastic Leukemia at an MHC Class II Hotspot Close to Disease Associated Haplotypes 
PLoS ONE  2014;9(6):e100480.
Childhood Acute Lymphoblastic Leukemia (ALL) is a malignant lymphoid disease of which B-cell precursor- (BCP) and T-cell- (T) ALL are subtypes. The role of alleles encoded by major histocompatibility loci (MHC) have been examined in a number of previous studies and results indicating weak, multi-allele associations between the HLA-DPB1 locus and BCP-ALL suggested a role for immunosusceptibility and possibly infection. Two independent SNP association studies of ALL identified loci approximately 37 kb from one another and flanking a strong meiotic recombination hotspot (DNA3), adjacent to HLA-DOA and centromeric of HLA-DPB1. To determine the relationship between this observation and HLA-DPB1 associations, we constructed high density SNP haplotypes of the 316 kb region from HLA-DMB to COL11A2 in childhood ALL and controls using a UK GWAS data subset and the software PHASE. Of four haplotype blocks identified, predicted haplotypes in Block 1 (centromeric of DNA3) differed significantly between BCP-ALL and controls (P = 0.002) and in Block 4 (including HLA-DPB1) between T-ALL and controls (P = 0.049). Of specific common (>5%) haplotypes in Block 1, two were less frequent in BCP-ALL, and in Block 4 a single haplotype was more frequent in T-ALL, compared to controls. Unexpectedly, we also observed apparent differences in ancestral meiotic recombination rates at DNA3, with BCP-ALL showing increased and T-ALL decreased levels compared to controls. In silico analysis using LDsplit sotware indicated that recombination rates at DNA3 are influenced by flanking loci, including SNPs identified in childhood ALL association studies. The observed differences in rates of meiotic recombination at this hotspot, and potentially others, may be a characteristic of childhood leukemia and contribute to disease susceptibility, alternatively they may reflect interactions between ALL-associated haplotypes in this region.
doi:10.1371/journal.pone.0100480
PMCID: PMC4069019  PMID: 24959916
5.  Molecular Interactions of Alzheimer Amyloid-β Oligomer with Neutral and Negatively Charged Lipid Bilayers 
Interaction of p3 (Aβ17-42) peptides with cell membrane is crucial for the understanding of amyloid toxicity associated with Alzheimer’s disease (AD). Such p3-membrane interactions are considered to induce the disruption of membrane permeability and integrity, but the exact mechanisms of how p3 aggregates, particularly small p3 oligomers, induce receptor-independent membrane disruption are not yet completely understood. Here, we investigate the adsorption, orientation, and surface interaction of the p3 pentamer with lipid bilayers composed of both pure zwitterionic POPC (palmitoyl-oleyl-phosphatidylcholine) and mixed anionic POPC/POPG (palmitoyl-oleyl-phosphatidylglycerol) (3:1) lipids using explicit-solvent molecular dynamics (MD) simulations. MD simulation results show that the p3 pentamer has much stronger interactions with mixed POPC/POPG lipids than pure POPC lipids, consistent with experimental observation that Aβ adsorption and fibrililation are enhanced on anionic lipid bilayers. Although electrostatic interactions are main attractive forces to drive the p3 to adsorb on the bilayer surface, the adsorption of the p3 pentamer on the lipid bilayer with a preferential C-terminal β-strands facing toward the bilayer surface is a net outcome of different competitions between p3 peptides-lipid bilayer and ions-p3-bilayer interactions. More importantly, Ca2+ ions are found to form ionic bridges to associate negatively charged residues of p3 with anionic headgroups of the lipid bilayer, resulting in Aβ–Ca2+–PO4− complexes. Intensive Ca2+ bound to lipid bilayer and Ca2+ ionic bridges may lead to the alternation of Ca2+ hemostasis responsible for neuronal dysfunction and death. This work provides insights into the mutual structure, dynamics, and interactions of both Aβ peptides and lipid bilayer at the atomic level, which expand our understanding of the complex behavior of amyloid-induced membrane disruption.
doi:10.1039/c3cp44448a
PMCID: PMC3711658  PMID: 23493873
6.  Tanshinones Inhibit Amyloid Aggregation by Amyloid-β Peptide, Disaggregate Amyloid Fibrils, and Protect Cultured Cells 
ACS Chemical Neuroscience  2013;4(6):1004-1015.
The misfolding and aggregation of amyloid-β (Aβ) peptides into amyloid fibrils is regarded as one of the causative events in the pathogenesis of Alzheimer’s disease (AD). Tanshinones extracted from Chinese herb Danshen (Salvia Miltiorrhiza Bunge) were traditionally used as anti-inflammation and cerebrovascular drugs due to their antioxidation and antiacetylcholinesterase effects. A number of studies have suggested that tanshinones could protect neuronal cells. In this work, we examine the inhibitory activity of tanshinone I (TS1) and tanshinone IIA (TS2), the two major components in the Danshen herb, on the aggregation and toxicity of Aβ1–42 using atomic force microscopy (AFM), thioflavin-T (ThT) fluorescence assay, cell viability assay, and molecular dynamics (MD) simulations. AFM and ThT results show that both TS1 and TS2 exhibit different inhibitory abilities to prevent unseeded amyloid fibril formation and to disaggregate preformed amyloid fibrils, in which TS1 shows better inhibitory potency than TS2. Live/dead assay further confirms that introduction of a very small amount of tanshinones enables protection of cultured SH-SY5Y cells against Aβ-induced cell toxicity. Comparative MD simulation results reveal a general tanshinone binding mode to prevent Aβ peptide association, showing that both TS1 and TS2 preferentially bind to a hydrophobic β-sheet groove formed by the C-terminal residues of I31-M35 and M35-V39 and several aromatic residues. Meanwhile, the differences in binding distribution, residues, sites, population, and affinity between TS1-Aβ and TS2-Aβ systems also interpret different inhibitory effects on Aβ aggregation as observed by in vitro experiments. More importantly, due to nonspecific binding mode of tanshinones, it is expected that tanshinones would have a general inhibitory efficacy of a wide range of amyloid peptides. These findings suggest that tanshinones, particularly TS1 compound, offer promising lead compounds with dual protective role in anti-inflammation and antiaggregation for further development of Aβ inhibitors to prevent and disaggregate amyloid formation.
doi:10.1021/cn400051e
PMCID: PMC3756451  PMID: 23506133
Aβ; amyloid; tanshinone; Alzheimer’s disease
7.  Structural insights into the role of the Smoothened cysteine-rich domain in Hedgehog signalling 
Nature communications  2013;4:2965.
Smoothened (Smo) is a member of the Frizzled (FzD) class of G-protein-coupled-receptors (GPCRs), and functions as the key transducer in the Hedgehog (Hh) signalling pathway. Smo has an extracellular cysteine-rich domain (CRD), indispensable for its function and downstream Hh signalling. Despite its essential role, the functional contribution of the CRD to Smo signalling has not been clearly elucidated. However, given that the FzD CRD binds to the endogenous Wnt ligand, it has been proposed that the Smo CRD may bind its own endogenous ligand. Here we present the NMR solution structure of the Drosophila Smo CRD, and describe interactions between the glucocorticoid budesonide (Bud) and the Smo CRDs from both Drosophila and human. Our results highlight a function of the Smo CRD, demonstrating its role in binding to small molecule modulators.
doi:10.1038/ncomms3965
PMCID: PMC3890372  PMID: 24351982
8.  Standardized Metadata for Human Pathogen/Vector Genomic Sequences 
PLoS ONE  2014;9(6):e99979.
High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium’s minimal information (MIxS) and NCBI’s BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant.
doi:10.1371/journal.pone.0099979
PMCID: PMC4061050  PMID: 24936976
9.  Phosphorylation of Paxillin LD4 Destabilizes Helix Formation and Inhibits Binding to Focal Adhesion Kinase† 
Biochemistry  2007;47(2):548-554.
Cell migration is a dynamic process that requires the coordinated formation and disassembly of focal adhesions (FAs). Several proteins such as paxillin, focal adhesion kinase (FAK), and G protein–coupled receptor kinase–interacting protein 1 (GIT1) are known to play a regulatory role in FA disassembly and turnover. However, the mechanisms by which this occurs remain to be elucidated. Paxillin has been shown to bind the C-terminal domain of FAK in FAs, and an increasing number of studies have linked paxillin association with GIT1 during focal adhesion disassembly. It has been reported recently that phosphorylation of serine 273 in the LD4 motif of paxillin leads to an increased association with Git1 and focal adhesion turnover. In the present study, we examined the effects of phosphorylation of the LD4 peptide on its binding affinity to the C-terminal domain of FAK. We show that phosphorylation of LD4 results in a reduction of binding affinity to FAK. This reduction in binding affinity is not due to the introduction of electrostatic repulsion or steric effects, but rather by a destabilization of the helical propensity of the LD4 motif. These results further our understanding of the focal adhesion turnover mechanism as well as identify a novel process by which phosphorylation can modulate intracellular signaling.
doi:10.1021/bi702103n
PMCID: PMC4054611  PMID: 18092823
10.  Therapeutic use of PDZ protein-protein interaction antagonism 
Drug news & perspectives  2008;21(3):137-141.
PDZ domains are important interaction modules in many intracellular pathways and abnormal activations of many of those pathways lead to diseases, including several types of cancer. The domains are characterized by the ability to recognize the extreme COOH-terminus of target proteins, such as G protein-coupled receptors and ion channels. Because PDZ protein-protein interaction is a key factor in the function of cellular pathways and signal transmission in those pathways, developing small-molecule inhibitors to compete with PDZ targets is very attractive in dissecting molecular mechanisms and formulating pharmaceutical agents. Moreover, there is a growing interest in developing small-molecule drugs to block signaling within cells. The modulation of PDZ-involved interactions in cells might be an approach to target the G protein-coupled receptors and ion channels, which are among the most important classes of drug targets in the pharmaceutical industry today. Here, we review recent progress in the development of small-molecule PDZ inhibitors, and especially focus on two PDZ domain-containing target proteins, postsynaptic density 95 and dishevelled.
PMCID: PMC4055467  PMID: 18560611
11.  In Vitro Biocompatibility and Endothelialization of Novel Magnesium-Rare Earth Alloys for Improved Stent Applications 
PLoS ONE  2014;9(6):e98674.
Magnesium (Mg) based alloys are the most advanced cardiovascular stent materials. This new generation of stent scaffold is currently under clinical evaluation with encouraging outcomes. All these Mg alloys contain a certain amount of rare earth (RE) elements though the exact composition is not yet disclosed. RE alloying can usually enhance the mechanical strength of different metal alloys but their toxicity might be an issue for medical applications. It is still unclear how RE elements will affect the magnesium (Mg) alloys intended for stent materials as a whole. In this study, we evaluated MgZnCaY-1RE, MgZnCaY-2RE, MgYZr-1RE, and MgZnYZr-1RE alloys for cardiovascular stents applications regarding their mechanical strength, corrosion resistance, hemolysis, platelet adhesion/activation, and endothelial biocompatibility. The mechanical properties of all alloys were significantly improved. Potentiodynamic polarization showed that the corrosion resistance of four alloys was at least 3–10 times higher than that of pure Mg control. Hemolysis test revealed that all the materials were non-hemolytic while little to moderate platelet adhesion was found on all materials surface. No significant cytotoxicity was observed in human aorta endothelial cells cultured with magnesium alloy extract solution for up to seven days. Direct endothelialization test showed that all the alloys possess significantly better capability to sustain endothelial cell attachment and growth. The results demonstrated the promising potential of these alloys for stent material applications in the future.
doi:10.1371/journal.pone.0098674
PMCID: PMC4055625  PMID: 24921251
12.  Binding Modes of Three Inhibitors 8CA, F8A and I4A to A-FABP Studied Based on Molecular Dynamics Simulation 
PLoS ONE  2014;9(6):e99862.
Adipocyte fatty-acid binding protein (A-FABP) is an important target of drug designs treating some diseases related to lipid-mediated biology. Molecular dynamics (MD) simulations coupled with solvated interaction energy method (SIE) were carried out to study the binding modes of three inhibitors 8CA, F8A and I4A to A-FABP. The rank of our predicted binding affinities is in accordance with experimental data. The results show that the substitution in the position 5 of N-benzyl and the seven-membered ring of N-benzyl-indole carboxylic acids strengthen the I4A binding, while the substitution in the position 2 of N-benzyl weakens the F8A binding. Computational alanine scanning and dynamics analyses were performed and the results suggest that the polar interactions of the positively charged residue R126 with the three inhibitors provide a significant contribution to inhibitor bindings. This polar interaction induces the disappearance of the correlated motion of the C terminus of A-FABP relative to the N terminus and favors the stability of the binding complex. This study is helpful for the rational design of potent inhibitors within the fields of metabolic disease, inflammation and atherosclerosis.
doi:10.1371/journal.pone.0099862
PMCID: PMC4053400  PMID: 24918907
13.  Molecular Dynamics Simulation Study of Conformational Changes of Transcription Factor TFIIS during RNA Polymerase II Transcriptional Arrest and Reactivation 
PLoS ONE  2014;9(5):e97975.
Transcription factor IIS (TFIIS) is a protein known for catalyzing the cleavage reaction of the 3′-end of backtracked RNA transcript, allowing RNA polymerase II (Pol II) to reactivate the transcription process from the arrested state. Recent structural studies have provided a molecular basis of protein-protein interaction between TFIIS and Pol II. However, the detailed dynamic conformational changes of TFIIS upon binding to Pol II and the related thermodynamic information are largely unknown. Here we use computational approaches to investigate the conformational space of TFIIS in the Pol II-bound and Pol II-free (unbound) states. Our results reveal two distinct conformations of TFIIS: the closed and the open forms. The closed form is dominant in the Pol II-free (unbound) state of TFIIS, whereas the open form is favorable in the Pol II-bound state. Furthermore, we discuss the free energy difference involved in the conformational changes between the two forms in the presence or absence of Pol II. Additionally, our analysis indicates that hydrophobic interactions and the protein-protein interactions between TFIIS and Pol II are crucial for inducing the conformational changes of TFIIS. Our results provide novel insights into the functional interplay between Pol II and TFIIS as well as mechanism of reactivation of Pol II transcription by TFIIS.
doi:10.1371/journal.pone.0097975
PMCID: PMC4026522  PMID: 24842057
14.  Temperature-dependent Activation of Neurons by Continuous Near-infrared Laser 
Optical control of neuronal activity has a number of advantages over electrical methods and can be conveniently applied to intact individual neurons in vivo. In this study, we demonstrated an experimental approach in which a focused continuous near-infrared (CNI) laser beam was used to activate single rat hippocampal neurons by transiently elevating the local temperature. Reversible changes in the amplitude and kinetics of neuronal voltage-gated Na and K channel currents were recorded following irradiation with a single-mode 980 nm CNI-laser. Using single-channel recordings under controlled temperatures as a means of calibration, it was estimated that temperature at the neuron rose by 14°C in 500 ms. Computer simulation confirmed that small temperature changes of about 5°C were sufficient to produce significant changes in neuronal excitability. The method should be broadly applicable to studies of neuronal activity under physiological conditions, in particular studies of temperature-sensing neurons expressing thermoTRP channels.
doi:10.1007/s12013-008-9035-2
PMCID: PMC4019448  PMID: 19034696
Voltage-dependent ion channels; Activation; Inactivation; Action potential; Laser; Temperature
15.  Glucose Biosensor Based on a Glassy Carbon Electrode Modified with Polythionine and Multiwalled Carbon Nanotubes 
PLoS ONE  2014;9(5):e95030.
A novel glucose biosensor was fabricated. The first layer of the biosensor was polythionine, which was formed by the electrochemical polymerisation of the thionine monomer on a glassy carbon electrode. The remaining layers were coated with chitosan-MWCNTs, GOx, and the chitosan-PTFE film in sequence. The MWCNTs embedded in FAD were like “conductive wires” connecting FAD with electrode, reduced the distance between them and were propitious to fast direct electron transfer. Combining with good electrical conductivity of PTH and MWCNTs, the current response was enlarged. The sensor was a parallel multi-component reaction system (PMRS) and excellent electrocatalytic performance for glucose could be obtained without a mediator. The glucose sensor had a working voltage of −0.42 V, an optimum working temperature of 25°C, an optimum working pH of 7.0, and the best percentage of polytetrafluoroethylene emulsion (PTFE) in the outer composite film was 2%. Under the optimised conditions, the biosensor displayed a high sensitivity of 2.80 µA mM−1 cm−2 and a low detection limit of 5 µM (S/N = 3), with a response time of less than 15 s and a linear range of 0.04 mM to 2.5 mM. Furthermore, the fabricated biosensor had a good selectivity, reproducibility, and long-term stability, indicating that the novel CTS+PTFE/GOx/MWCNTs/PTH composite is a promising material for immobilization of biomolecules and fabrication of third generation biosensors.
doi:10.1371/journal.pone.0095030
PMCID: PMC4015890  PMID: 24816121
16.  Molecular Insights into the Reversible Formation of Tau Protein Fibrils 
We computationally and experimentally showed that tau protein fibrils can be formed at high temperature. When cooled, the fibrils dissociate back to monomers. Heparin promotes tau fibril formation and prevents its reversion. Our results revealed the physicochemical mechanism of reversible formation of tau fibrils.
doi:10.1039/c3cc00241a
PMCID: PMC3637047  PMID: 23527380
17.  Fabrication of Anti-Aging TiO2 Nanotubes on Biomedical Ti Alloys 
PLoS ONE  2014;9(5):e96213.
The primary objective of this study was to fabricate a TiO2 nanotubular surface, which could maintain hydrophilicity over time (resist aging). In order to achieve non-aging hydrophilic surfaces, anodization and annealing conditions were optimized. This is the first study to show that anodization and annealing condition affect the stability of surface hydrophilicity. Our results indicate that maintenance of hydrophilicity of the obtained TiO2 nanotubes was affected by anodization voltage and annealing temperature. Annealing sharply decreased the water contact angle (WCA) of the as-synthesized TiO2 nanotubular surface, which was correlated to improved hydrophilicity. TiO2 nanotubular surfaces are transformed to hydrophilic surfaces after annealing, regardless of annealing and anodization conditions; however, WCA measurements during aging demonstrate that surface hydrophilicity of non-anodized and 20 V anodized samples decreased after only 11 days of aging, while the 60 V anodized samples maintained their hydrophilicity over the same time period. The nanotubes obtained by 60 V anodization followed by 600 °C annealing maintained their hydrophilicity significantly longer than nanotubes which were obtained by 60 V anodization followed by 300 °C annealing.
doi:10.1371/journal.pone.0096213
PMCID: PMC4008568  PMID: 24788345
18.  Syn-Lethality: An Integrative Knowledge Base of Synthetic Lethality towards Discovery of Selective Anticancer Therapies 
BioMed Research International  2014;2014:196034.
Synthetic lethality (SL) is a novel strategy for anticancer therapies, whereby mutations of two genes will kill a cell but mutation of a single gene will not. Therefore, a cancer-specific mutation combined with a drug-induced mutation, if they have SL interactions, will selectively kill cancer cells. While numerous SL interactions have been identified in yeast, only a few have been known in human. There is a pressing need to systematically discover and understand SL interactions specific to human cancer. In this paper, we present Syn-Lethality, the first integrative knowledge base of SL that is dedicated to human cancer. It integrates experimentally discovered and verified human SL gene pairs into a network, associated with annotations of gene function, pathway, and molecular mechanisms. It also includes yeast SL genes from high-throughput screenings which are mapped to orthologous human genes. Such an integrative knowledge base, organized as a relational database with user interface for searching and network visualization, will greatly expedite the discovery of novel anticancer drug targets based on synthetic lethality interactions. The database can be downloaded as a stand-alone Java application.
doi:10.1155/2014/196034
PMCID: PMC4016865  PMID: 24864230
19.  Gel Formation in Protein Amyloid Aggregation: A Physical Mechanism for Cytotoxicity 
PLoS ONE  2014;9(4):e94789.
Amyloid fibers are associated with disease but have little chemical reactivity. We investigated the formation and structure of amyloids to identify potential mechanisms for their pathogenic effects. We incubated lysozyme 20 mg/ml at 55C and pH 2.5 in a glycine-HCl buffer and prepared slides on mica substrates for examination by atomic force microscopy. Structures observed early in the aggregation process included monomers, small colloidal aggregates, and amyloid fibers. Amyloid fibers were observed to further self-assemble by two mechanisms. Two or more fibers may merge together laterally to form a single fiber bundle, usually in the form of a helix. Alternatively, fibers may become bound at points where they cross, ultimately forming an apparently irreversible macromolecular network. As the fibers assemble into a continuous network, the colloidal suspension undergoes a transition from a Newtonian fluid into a viscoelastic gel. Addition of salt did not affect fiber formation but inhibits transition of fibers from linear to helical conformation, and accelerates gel formation. Based on our observations, we considered the effects of gel formation on biological transport. Analysis of network geometry indicates that amyloid gels will have negligible effects on diffusion of small molecules, but they prevent movement of colloidal-sized structures. Consequently gel formation within neurons could completely block movement of transport vesicles in neuronal processes. Forced convection of extracellular fluid is essential for the transport of nutrients and metabolic wastes in the brain. Amyloid gel in the extracellular space can essentially halt this convection because of its low permeability. These effects may provide a physical mechanism for the cytotoxicity of chemically inactive amyloid fibers in neurodegenerative disease.
doi:10.1371/journal.pone.0094789
PMCID: PMC3989237  PMID: 24740416
20.  Exploring the Influence of EGCG on the β-Sheet-Rich Oligomers of Human Islet Amyloid Polypeptide (hIAPP1–37) and Identifying Its Possible Binding Sites from Molecular Dynamics Simulation 
PLoS ONE  2014;9(4):e94796.
EGCG possesses the ability of disaggregating the existing amyloid fibrils which were associated with many age-related degenerative diseases. However, the molecular mechanism of EGCG to disaggregate these fibrils is poorly known. In this work, to study the influence of EGCG on the full-length human islet amyloid polypeptide 1–37 (hIAPP1–37) oligomers, molecular dynamics simulations of hIAPP1–37 pentamer and decamer with EGCG were performed, respectively. The obtained results indicate that EGCG indeed destabilized the hIAPP1–37 oligomers. The nematic order parameter and secondary structure calculations coupled with the free-energy landscape indicate that EGCG broke the initial ordered pattern of two polymers, greatly reduced their β-sheet content and enlarged their conformational space. On this basis, three possible target sites were identified with the binding capacity order of S1>S2>S3. After a deeper analysis of each site, we found that S1 was the most possible site on which residues B-Ile26/Ala25, A-Phe23, B/C-Leu27 and E-Tyr37 played an important role for their binding. The proposal of this molecular mechanism can not only provide a prospective interaction figure between EGCG and β-sheet-rich fibrils of hIAPP1–37, but also is useful for further discovering other potential inhibitors.
doi:10.1371/journal.pone.0094796
PMCID: PMC3989243  PMID: 24739876
21.  Characteristic Variation of α-Fetoprotein DNA Nanometer-Range Irradiated by Iodine-125 
Abstract
To obtain the characteristic variation of structure and functional groups of α-fetoprotein (AFP) DNA irradiated by iodine-125(125I), the AFP antisense oligonucleotide labeled with various radioactivity dose 125I was mixed with the AFP DNA in a simulated polymerase chain reaction temperature condition. After the mixtures were irradiated by the 125I from 2 to 72 hours, the mutation of the biogenic conformation and functional groups of the irradiated DNA were investigated using laser Raman spectroscopy. The shifted peak and the decreased intensity of the characteristic Raman spectra were found, which demonstrated that the structure of the phosphodiester linkage was broke, the pyridine and purine bases in DNA emerged and damaged. The model of gene conformation changed from form B to form C spectrum after the nanometer-range irradiation with 125I from 2 to 24 hours. The damage of local pyridine and purine bases gradually increased along with the accumulation of irradiation, and the bases and ribosome were finally dissociated and stacked.
doi:10.1089/cbr.2012.1231
PMCID: PMC3615693  PMID: 23573955
gene therapy; irradiation; radionuclide; Raman spectroscopy
22.  Domain–domain interactions in ion channels 
The Journal of General Physiology  2013;142(4):347-350.
doi:10.1085/jgp.201311090
PMCID: PMC3787767  PMID: 24043858
23.  Quantitative and Semi-quantitative Measures of Regional Pulmonary Parenchymal Perfusion by Magnetic Resonance Imaging and their Relationships to Global Lung Perfusion and Lung Diffusing Capacity – The MESA COPD Study 
Investigative radiology  2013;48(4):223-230.
Objectives
To evaluate quantitative and semi-quantitative measures of regional pulmonary parenchymal perfusion in patients with COPD in relationship to global lung perfusion (GLP) and lung diffusing capacity (DLCO).
Materials and Methods
One hundred and forty three participants in the MESA COPD Study were examined by dynamic contrast-enhanced pulmonary perfusion MRI at 1.5 T. Pulmonary blood flow (PBF) was calculated on a pixel-by-pixel basis by using a dual-bolus technique and the Fermi function model. Semi-quantitative parameters for regional lung perfusion were calculated from signal-intensity time curves in the lung parenchyma. Intra- and inter-observer coefficients of variation (CV) and correlations between quantitative and semi-quantitative MRI parameters and with GLP and DLCO were determined.
Results
Quantitative and semi-quantitative parameters of pulmonary parenchymal perfusion were reproducible with CVs for all <10%. Furthermore, these MRI parameters were correlated with GLP and DLCO and there was good agreement between PBF and GLP. Quantitative and semi-quantitative MRI parameters were closely correlated (e.g., r=0.86 for maximum signal increase with PBF). In participants without COPD, the physiological distribution of pulmonary perfusion could be determined by regional MRI measurements.
Conclusion
Regional pulmonary parenchymal perfusion can reliably be quantified from dynamic contrast-enhanced MRI. MRI-derived quantitative and semi-quantitative perfusion measures correlate with GLP and DLCO.
doi:10.1097/RLI.0b013e318281057d
PMCID: PMC3952075  PMID: 23385398
Pulmonary perfusion; chronic obstructive pulmonary disease (COPD); dynamic contrast-enhanced MRI; quantitative perfusion maps; diffusing lung capacity
24.  Effects of Dextrose and Lipopolysaccharide on the Corrosion Behavior of a Ti-6Al-4V Alloy with a Smooth Surface or Treated with Double-Acid-Etching 
PLoS ONE  2014;9(3):e93377.
Diabetes and infections are associated with a high risk of implant failure. However, the effects of such conditions on the electrochemical stability of titanium materials remain unclear. This study evaluated the corrosion behavior of a Ti-6Al-4V alloy, with a smooth surface or conditioned by double-acid-etching, in simulated body fluid with different concentrations of dextrose and lipopolysaccharide. For the electrochemical assay, the open-circuit-potential, electrochemical impedance spectroscopy, and potentiodynamic test were used. The disc surfaces were characterized by scanning electron microscopy and atomic force microscopy. Their surface roughness and Vickers microhardness were also tested. The quantitative data were analyzed by Pearson's correlation and independent t-tests (α = 0.05). In the corrosion parameters, there was a strong lipopolysaccharide correlation with the Ipass (passivation current density), Cdl (double-layer capacitance), and Rp (polarization resistance) values (p<0.05) for the Ti-6Al-4V alloy with surface treatment by double-acid-etching. The combination of dextrose and lipopolysaccharide was correlated with the Icorr (corrosion current density) and Ipass (p<0.05). The acid-treated groups showed a significant increase in Cdl values and reduced Rp values (p<0.05, t-test). According to the topography, there was an increase in surface roughness (R2 = 0.726, p<0.0001 for the smooth surface; R2 = 0.405, p = 0.036 for the double-acid-etching-treated surface). The microhardness of the smooth Ti-6Al-4V alloy decreased (p<0.05) and that of the treated Ti-6Al-4V alloy increased (p<0.0001). Atomic force microscopy showed changes in the microstructure of the Ti-6Al-4V alloy by increasing the surface thickness mainly in the group associated with dextrose and lipopolysaccharide. The combination of dextrose and lipopolysaccharide affected the corrosion behavior of the Ti-6Al-4V alloy surface treated with double-acid-etching. However, no dose-response corrosion behavior could be observed. These results suggest a greater susceptibility to corrosion of titanium implants in diabetic patients with associated infections.
doi:10.1371/journal.pone.0093377
PMCID: PMC3966875  PMID: 24671257
25.  Human coronary plaque wall thickness correlated positively with flow shear stress and negatively with plaque wall stress: an IVUS-based fluid-structure interaction multi-patient study 
Background
Atherosclerotic plaque progression and rupture are believed to be associated with mechanical stress conditions. In this paper, patient-specific in vivo intravascular ultrasound (IVUS) coronary plaque image data were used to construct computational models with fluid-structure interaction (FSI) and cyclic bending to investigate correlations between plaque wall thickness and both flow shear stress and plaque wall stress conditions.
Methods
IVUS data were acquired from 10 patients after voluntary informed consent. The X-ray angiogram was obtained prior to the pullback of the IVUS catheter to determine the location of the coronary artery stenosis, vessel curvature and cardiac motion. Cyclic bending was specified in the model representing the effect by heart contraction. 3D anisotropic FSI models were constructed and solved to obtain flow shear stress (FSS) and plaque wall stress (PWS) values. FSS and PWS values were obtained for statistical analysis. Correlations with p < 0.05 were deemed significant.
Results
Nine out of the 10 patients showed positive correlation between wall thickness and flow shear stress. The mean Pearson correlation r-value was 0.278 ± 0.181. Similarly, 9 out of the 10 patients showed negative correlation between wall thickness and plaque wall stress. The mean Pearson correlation r-value was -0.530 ± 0.210.
Conclusion
Our results showed that plaque vessel wall thickness correlated positively with FSS and negatively with PWS. The patient-specific IVUS-based modeling approach has the potential to be used to investigate and identify possible mechanisms governing plaque progression and rupture and assist in diagnosis and intervention procedures. This represents a new direction of research. Further investigations using more patient follow-up data are warranted.
doi:10.1186/1475-925X-13-32
PMCID: PMC3977946  PMID: 24669780
Coronary; Fluid-structure interaction; Plaque rupture; Plaque progression; IVUS

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