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1.  A Structural-informatics Approach for Tracing β-Sheets: Building Pseudo-Cα Traces for β-Strands in Intermediate-resolution Density Maps 
Journal of molecular biology  2004;339(1):117-130.
We report the development of two computational methods to assist density map interpretation at intermediate resolutions: sheettracer for building pseudo-Cα models of β-sheets, and a deconvolution method for enhancing features attributed to major secondary structural elements. Sheettracer is tightly coupled with sheetminer, which was developed to locate sheet densities in intermediate-resolution density maps. The results from sheetminer are used as inputs to sheettracer, which employs a multistep ad hoc morphological analysis of sheet densities to trace individual strands of β-sheets. The methods were tested on simulated density maps from 12 protein crystal structures that represent a reasonably complete sampling of sheet morphology. The sheet-tracing results were quantitatively assessed in terms of sensitivity, specificity and rms deviations. Furthermore, sheettracer and the deconvolution method were rigorously tested on experimental maps of the λ2 protein of reovirus at resolutions of 7.6 Å and 11.8 Å. Our results clearly demonstrate the capability of sheettracer in building pseudo-Cα models of β-sheets in intermediate-resolution density maps and the power of the deconvolution method in enhancing the performance of sheettracer. These computational methods, along with other related ones, should facilitate recognition and analysis of folding motifs from experimental data at intermediate resolutions.
doi:10.1016/j.jmb.2004.03.038
PMCID: PMC4148645  PMID: 15123425
macromolecular complexes; intermediate-resolution density maps; bioinformatics; secondary structural elements
2.  BRCAA1 monoclonal antibody conjugated fluorescent magnetic nanoparticles for in vivo targeted magnetofluorescent imaging of gastric cancer 
Background
Gastric cancer is 2th most common cancer in China, and is still the second most common cause of cancer-related death in the world. How to recognize early gastric cancer cells is still a great challenge for early diagnosis and therapy of patients with gastric cancer. This study is aimed to develop one kind of multifunctional nanoprobes for in vivo targeted magnetofluorescent imaging of gastric cancer.
Methods
BRCAA1 monoclonal antibody was prepared, was used as first antibody to stain 50 pairs of specimens of gastric cancer and control normal gastric mucous tissues, and conjugated with fluorescent magnetic nanoparticles with 50 nm in diameter, the resultant BRCAA1-conjugated fluorescent magnetic nanoprobes were characterized by transmission electron microscopy and photoluminescence spectrometry, as-prepared nanoprobes were incubated with gastric cancer MGC803 cells, and were injected into mice model loaded with gastric cancer of 5 mm in diameter via tail vein, and then were imaged by fluorescence optical imaging and magnetic resonance imaging, their biodistribution was investigated. The tissue slices were observed by fluorescent microscopy, and the important organs such as heart, lung, kidney, brain and liver were analyzed by hematoxylin and eosin (HE) stain method.
Results
BRCAA1 monoclonal antibody was successfully prepared, BRCAA1 protein exhibited over-expression in 64% gastric cancer tissues, no expression in control normal gastric mucous tissues, there exists statistical difference between two groups (P < 0.01). The BRCAA1-conjugated fluorescent magnetic nanoprobes exhibit very low-toxicity, lower magnetic intensity and lower fluorescent intensity with peak-blue-shift than pure FMNPs, could be endocytosed by gastric cancer MGC803 cells, could target in vivo gastric cancer tissues loaded by mice, and could be used to image gastric cancer tissues by fluorescent imaging and magnetic resonance imaging, and mainly distributed in local gastric cancer tissues within 12 h post-injection. HE stain analysis showed that no obvious damages were observed in important organs.
Conclusions
The high-performance BRCAA1 monoclonal antibody-conjugated fluorescent magnetic nanoparticles can target in vivo gastric cancer cells, can be used for simultaneous magnetofluorescent imaging, and may have great potential in applications such as dual-model imaging and local thermal therapy of early gastric cancer in near future.
doi:10.1186/1477-3155-9-23
PMCID: PMC3127991  PMID: 21612621
3.  Copper Selenide Nanosnakes: Bovine Serum Albumin-Assisted Room Temperature Controllable Synthesis and Characterization 
Nanoscale Research Letters  2010;5(6):949-956.
Herein we firstly reported a simple, environment-friendly, controllable synthetic method of CuSe nanosnakes at room temperature using copper salts and sodium selenosulfate as the reactants, and bovine serum albumin (BSA) as foaming agent. As the amounts of selenide ions (Se2−) released from Na2SeSO3 in the solution increased, the cubic and snake-like CuSe nanostructures were formed gradually, the cubic nanostructures were captured by the CuSe nanosnakes, the CuSe nanosnakes grew wider and longer as the reaction time increased. Finally, the cubic CuSe nanostructures were completely replaced by BSA–CuSe nanosnakes. The prepared BSA–CuSe nanosnakes exhibited enhanced biocompatibility than the CuSe nanocrystals, which highly suggest that as-prepared BSA–CuSe nanosnakes have great potentials in applications such as biomedical engineering.
Electronic supplementary material
The online version of this article (doi:10.1007/s11671-010-9587-0) contains supplementary material, which is available to authorized users.
doi:10.1007/s11671-010-9587-0
PMCID: PMC2894339  PMID: 20672034
Copper selenide; Nanosnakes; Bovine serum albumin; Synthesis; Characterization; Mechanism; Biocompatibility
4.  Copper Selenide Nanosnakes: Bovine Serum Albumin-Assisted Room Temperature Controllable Synthesis and Characterization 
Nanoscale Research Letters  2010;5(6):949-956.
Herein we firstly reported a simple, environment-friendly, controllable synthetic method of CuSe nanosnakes at room temperature using copper salts and sodium selenosulfate as the reactants, and bovine serum albumin (BSA) as foaming agent. As the amounts of selenide ions (Se2−) released from Na2SeSO3 in the solution increased, the cubic and snake-like CuSe nanostructures were formed gradually, the cubic nanostructures were captured by the CuSe nanosnakes, the CuSe nanosnakes grew wider and longer as the reaction time increased. Finally, the cubic CuSe nanostructures were completely replaced by BSA–CuSe nanosnakes. The prepared BSA–CuSe nanosnakes exhibited enhanced biocompatibility than the CuSe nanocrystals, which highly suggest that as-prepared BSA–CuSe nanosnakes have great potentials in applications such as biomedical engineering.
doi:10.1007/s11671-010-9587-0
PMCID: PMC2894339  PMID: 20672034
Copper selenide; Nanosnakes; Bovine serum albumin; Synthesis; Characterization; Mechanism; Biocompatibility
5.  Signaling pathways of PDZ2 domain: A molecular dynamics Interaction Correlation Analysis 
Proteins  2009;74(1):145-154.
PDZ domains are found in many signaling proteins. One of their functions is to provide scaffolds for forming membrane-associated protein complexes by binding to the carboxyl termini of its partners. PDZ domains are thought to play a signal transduction role by propagating the information that binding has occurred to remote sites. In the current study, a molecular dynamics simulation based approach, referred to an interaction correlation analysis, is applied to the PDZ2 domain to identity the possible signal transduction pathways. A residue correlation matrix is constructed from the interaction energy correlation between all residue pairs obtained from the molecular dynamics simulations. Two continuous interaction pathways, starting at the ligand binding pocket, are identified by a hierarchical clustering analysis of the residue correlation matrix. One pathway is mainly localized at the N terminal side of helix α1 and the adjacent C terminus of loop β1–β2. The other pathway is perpendicular to the central β sheet toward the side of PDZ2 domain opposite to the ligand binding pocket. The present results extend previous studies based on multiple sequence analysis, NMR and molecular dynamics simulations. Importantly, they reveal the energetic origin of the long-range coupling. The PDZ2 results, as well as the earlier rhodopsin analysis, show that the interaction correlation analysis is a robust approach for determining pathways of intramolecular signal transduction.
doi:10.1002/prot.22139
PMCID: PMC2605193  PMID: 18618698
PDZ2 domain; molecular dynamics simulation; signal transduction; allosteric effects; interaction correlation

Results 1-5 (5)