生物物理化学(英文)最新文献

{"title":"In Vitro Study of Iron Doped Hydroxyapatite","authors":"K. Ereiba, A. G. Mostafa, G. Gamal, A. Said","doi":"10.4236/JBPC.2013.44017","DOIUrl":"https://doi.org/10.4236/JBPC.2013.44017","url":null,"abstract":"The effect of iron substitution on the bioactivity of hydroxyapatite (HAp) under the physiological conditions was investigated. Five samples of iron doped hydroxyapatite (FeHAp) with different iron concentrations (0, 0.05, 0.1, 0.2, and 0.3 mol%) were synthesized by wet chemical method. The formation of bone-like apatite layer on the surface of the samples was detected using X-ray diffraction (XRD), Fourier transforms infrared (FTIR) and scanning electron microscope techniques. The changes of the pH of SBF medium were measured at pre-determined time intervals using a pH meter. The dissolution of calcium, phosphorus and iron ions in SBF medium was determined by single beam scanning spectrophotometer. XRD and FTIR results exhibit the formation of carbonate apatite layer on the surface of the immersed samples, which increase with the increase of iron content. SEM results showed agglomeration of small crystals on the surface of the immersed samples. The solubility and dissolution tests revealed that iron doped HAp samples had a higher solubility and dissolution rate than pure sample, which indicated that iron increased the bioactivity of HAp in vitro.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70902659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dopamine cannot promote oligomerization of unoxidized α-synuclein","authors":"S. Shimotakahara, M. Matsui, C. Sakuma, Teruaki Takahashi, T. Fujimoto, K. Furihata, M. Kojima, Shohei Seino, T. Machinami, Y. Shibusawa, K. Uéda, M. Tashiro","doi":"10.4236/JBPC.2013.43015","DOIUrl":"https://doi.org/10.4236/JBPC.2013.43015","url":null,"abstract":"α-Synuclein is the major component of the filamentous Lewy bodies and Lewy neurites that define neuropathological features of Parkinson’s disease and dementia with Lewy bodies. To investigate the oligomerization process of α-synuclein in association with dopamine (DA), the structural propensities to form oligomers were studied using NMR and other biophysical techniques. The1H-15N HSQC spectra indicated that both N- and C-termini interacted with DA. Although interactions with DA were also observed in the presence of glutathione by ESI-MS, the significant suppression of oligomerization was observed in the size exclusion chromatography, suggesting that oxidations of α-synuclein are required for its oligomerization.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70902642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Suprafibrillar structures of collagen, evidence for local organization and auxetic behaviour in architectures","authors":"K. Patten, T. Wess","doi":"10.4236/JBPC.2013.43014","DOIUrl":"https://doi.org/10.4236/JBPC.2013.43014","url":null,"abstract":"The suprafibrillar organisation of collagen rich tissues is the keystone to the diversity of resultant structures made from relatively similar materials. The local organisation between fibrils may be essential to suprafibril structures that are critical to functionality such as transparency in cornea, where specific lateral relationships between fibrils dictate optical properties. Here we show that corneal X-ray diffraction combined with mechanical strains to disrupt a specific suprafibrillar relationship between fibrils evidence and a coherent staggered axial relationship between collagen fibrils. The data also shows evidence for auxetic behavior of the collagen fibrils and reveals a 120 nm diffraction feature previously unreported in collagen tissues. The results show that suprafibrillar organisation can be an essential component in tissue architecture that has hitherto been ignored, but now must be considered in mechanical and structural models.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70902573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A conformational B-Z DNA study monitored with phosphatemethylated DNA as a model for epigenetic dynamics focused on 5-(hydroxy)methylcytosine","authors":"H. Buck","doi":"10.4236/JBPC.2013.42005","DOIUrl":"https://doi.org/10.4236/JBPC.2013.42005","url":null,"abstract":"This study was directed on the B- into Z-DNA isomerization with alternating CG sequences monitored \u0000with artificial DNA model-systems based on methylation of the phosphate backbone. \u0000The chemical concept for this transition wherein shielding of the oxygen anions \u0000of the backbone phosphates plays an essential role, resulted in the preparation of the phosphatemethylated d(CpG). Even on this primitive level of only two base pair long, the B-Z conformational \u0000aspects of this self-complementary duplex could be described in solution \u0000with nuclear magnetic resonance (NMR) and circular dichroism (CD) measurements. \u0000The exclusivity of this choice became clear after synthesizing phosphatemethylated \u0000DNA with longer alternating CG fragments. It could be shown that conflicting \u0000conformational effects of the CG and GC fragments resulted in an overall B \u0000structure of the phosphatemethylated \u0000tetramer d(CPGPCPG). From our model \u0000considerations, it is clear that the internal stress introduced by the \u0000alternating CG sequences will be promoted by a complete shielding of the \u0000phosphate backbone. Elimination of this effect may be realized by a site-specific phosphate shielding. The role of the anti-syn isomerization of G in \u0000the CG fragments is clarified by methylation of the phosphate group. This anti-syn transition is absent in \u0000corresponding methylphosphonates, suggesting an exclusive role for \u0000base-backbone coordination via hydrogen bonding. In addition, we propose that \u0000the B- into Z-DNA interconversion may offer a mechanistic view for differences \u0000in dynamics between cytosine and its epigenetic derivative 5-methylcytosine. \u0000This mechanism has been extended to the demethylation of 5-methylcytosine and \u0000the exchange of information \u0000between the new epigenetic base, 5-hydroxymethylcytosine and the DNA backbone \u0000via an intramolecular phosphorylation. The role of 5-hydroxymethylcytosine in \u0000Alzheimer disease has been briefly discussed. In our opinion, this study \u0000can be considered as a new dynamic concept for epigenetics based on the \u0000dynamics of the B-Z transition in natural and phosphatemethylated DNA.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70902622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selection of highly efficient small interference RNA (SiRNA) targeting mammalian genes","authors":"A. El-Lakkani, Wissam H. Abd Elgawad, E. Sayed","doi":"10.4236/JBPC.2013.42010","DOIUrl":"https://doi.org/10.4236/JBPC.2013.42010","url":null,"abstract":"RNAi is the method of \u0000silencing the expression of targeted genes. \u0000RNAi applications include gene function analysis and target validation. \u0000Designing highly efficient small interference \u0000RNA (siRNA) sequence with maximum target specificity for mammalian RNAi \u0000is one of important topics in recent years. In this work, a statistical \u0000analysis of the information for a large number (3734) of siRNA presented in the \u0000database available on the internet is done. \u0000This is to improve the design of efficient siRNA molecules. The (3734) \u0000siRNAs are classified according to their efficiency \u0000to three groups (high efficient, moderate efficient and low efficient). \u0000Thirteen properties (positional and thermodynamics) are identified in the high \u0000efficient group in the primary statistical study. In the final statistical \u0000study, the average weight of each identified \u0000property is calculated. A very good linear correlation was found between \u0000the average percentage efficiency and the \u0000weighted score of siRNA properties. It is found that the most important \u0000feature of highly efficient siRNA is the difference in binding energy between \u0000the 5’ end and the 3’ end of the anti-sense strand. The (RISC) activation step \u0000is a critical step in RNAi process where the efficiency of this process depends \u0000on the instability of the 5’ end of the anti-sense strand.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70902426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spin nature of genetic code","authors":"A. A. Tulub, V. E. Stefanov","doi":"10.4236/JBPC.2013.42007","DOIUrl":"https://doi.org/10.4236/JBPC.2013.42007","url":null,"abstract":"Nature has \u0000developed codon as a tool to manipulate a two-electron spin symmetry \u0000(short-living electrons, forming a radical pair, arise from the Mg-bound \u0000nucleosidetriphosphate cleavage at the triplet/singlet (T/S) crossing), which \u0000permits or forbids further nucleotide synthesis (DNA/RNA) and the synthesis of proteins. The thesis is \u0000confirmed by conducting DFT:B3LYP (6-311G** basis set) computations (T/S potential energy surfaces) with the model \u0000system composed of the template (C-G-C-G-A \u0000nucleotide sequence) and the growing chain (G-C-G nucleotide sequence, \u0000DNA or RNA). The origin of codon is in hyperfine interaction between a single \u0000electron, transferred onto the template, and three 31P nuclei \u0000built into the phosphorus fragments of nucleotides. The nuclei, together with \u0000the polynucleotide structure, form a spiral twist that is homeomorphic to a \u0000triangle patch on the Poincare sphere. Each triangle has unique angle values \u0000depending on the nucleotide nature and their position in the codon. The patch \u0000tracing produces the Berry phase changing the electron spin orientation from “up” to “down”. The Berry phase accumulation proceeds around the (T/S) \u0000conical intersections (CIs). The CIs are a \u0000result of complementary recognition between nucleotide bases at \u0000distances exceeding the commonly accepted Watson-Crick pairing by 0.17 A. Upon \u0000changing spin symmetry, the DNA or RNA chain is allowed to elongate by \u0000attaching a newly coming nucleotide. Without complementary recognition between \u0000the bases, the chain stops its elongation. The Berry phase accumulation along \u0000the patch tracing explains the effect of \u0000Crick’s wobbling when the second nucleotide plays a primary role in \u0000recognition. The data is directly linked to creation \u0000of a quantum computing device.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70902692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improvements in the score matrix calculation method using parallel score estimating algorithm","authors":"G. F. D. Zafalon, E. A. Marucci, J. C. Momente, J. Amazonas, L. Sato, J. M. Machado","doi":"10.4236/JBPC.2013.42006","DOIUrl":"https://doi.org/10.4236/JBPC.2013.42006","url":null,"abstract":"The \u0000increasing amount of sequences stored in genomic databases has become unfeasible \u0000to the sequential analysis. Then, the parallel computing brought its power to \u0000the Bioinformatics through parallel algorithms to align and analyze the \u0000sequences, providing improvements mainly in the running time of these \u0000algorithms. In many situations, the parallel strategy contributes to reducing \u0000the computational complexity of the big problems. This work shows some results \u0000obtained by an implementation of a parallel score estimating technique for \u0000the score matrix calculation stage, which is the first stage of a progressive \u0000multiple sequence alignment. The performance and quality of the parallel \u0000score estimating are compared with the results of a dynamic programming \u0000approach also implemented in parallel. This comparison shows a significant reduction \u0000of running time. Moreover, the quality of the \u0000final alignment, using the new strategy, is analyzed and compared with \u0000the quality of the approach with dynamic programming.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70902820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differential protein expression between EBV-positive and negative epithelial cells","authors":"Haibo Yu, Lian Zhao, Yanying QiJia, L. Zuo, Zhengyuan Yu, W. Xiong, Xiaoling Li, Shou-rong Sheng, Zhaojian Gong, Jianhong Lu, Guiyuan Li","doi":"10.4236/JBPC.2013.42011","DOIUrl":"https://doi.org/10.4236/JBPC.2013.42011","url":null,"abstract":"Epstein \u0000Barr virus infection is believed to play a role in the development of \u0000nasopharyngeal carcinoma. In order to investigate the function of EBV in \u0000epithelial cell, proteomic methods were used to find and identify the differential \u0000proteins and expected to elucidate the mechanism of EBV. Altered protein \u0000expressions were found between 293 cell (HEK293) and EBV infected cell (293-EBV). \u0000In this study, we separated differential expressed proteins using 2D-DIGE \u0000method while matrix-assisted laser desorption/ionization tandem time of flight \u0000mass spectrometry (MALDI-TOF-MS) method was used to identify proteins. The \u0000results showed that 14 proteins were up regulated and 3 proteins were down regulated in 293-EBV cells. Bioinformatic analysis showed that these proteins are involved \u0000in cell proliferation, metastasis, apoptosis, \u0000metabolism, and signal transduction. Western blotting analysis was \u0000further carried out to verify the MS results. Thus, EBV may exert its \u0000functions by mediating differential expression of these proteins.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70902479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fermented papaya preparation halts the progression of non-alcoholic steatohepatitis in rats","authors":"S. Murakami, F. Takayama, T. Egashira, Mitsuko Imao, A. Mori","doi":"10.4236/JBPC.2013.42012","DOIUrl":"https://doi.org/10.4236/JBPC.2013.42012","url":null,"abstract":"Non-alcoholic \u0000steatohepatitis (NASH) can progress to cirrhosis or hepatocellular carcinoma. \u0000Oxidative stress is implicated in NASH progression. Fermented papaya \u0000preparation (FPP) has oxygen radical scavenging activity and is effective in \u0000oxidative stress-related diseases. We investigated the effects of FPP on NASH \u0000progression using a rat NASH model. Plasma biochemical parameters and lipid \u0000peroxidation in the liver were elevated in NASH rats. Histologically, the liver \u0000of NASH rats showed liver fibrosis, mitochondrial dysfunction and over-expression \u0000of microsomal CYP2E1. Myeloperoxidase activity and nuclear factor-kappaB activation \u0000were also markedly increased in NASH. Oral administration of FPP ameliorated \u0000these changes in NASH rats. These results suggest that FPP halts NASH \u0000progression through its anti-oxidative and antiinflammatory properties.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70902525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Validation of the CHARMM27 force field for nucleic acids using 2D nuclear overhauser effect spectroscopy","authors":"Kirill Zinovjev, E. Liepinsh","doi":"10.4236/JBPC.2013.42008","DOIUrl":"https://doi.org/10.4236/JBPC.2013.42008","url":null,"abstract":"Nuclear \u0000magnetic resonance spectroscopy offers a powerful method for validation of molecular dynamics simulations as it provides information on the molecular \u0000structure and dynamics in solution. We performed 10 ns MD simulations using the \u0000CHARMM27 force field of four palindromic oligonucleotides and compared the results with experimental NOESY data using the full relaxation matrix formalism. \u0000The correlation coefficients between theoretical and experimental data for \u0000the four molecular species under study ranged from 0.82 to 0.98 confirming \u0000the high quality of the selected force field and providing a valid basis for \u0000the identification of force field imperfections. Hence, we observed an unsatisfactory treatment of deoxyribose conformational equilibrium, which resulted in \u0000the overrepresentation of the \u0000energetically favorable C3'-endo conformation in the MD trajectory. \u0000Our developed approach for force field validation based on NMR NOESY spectral data is applicable to a wide range \u0000of molecular systems and appropriate force fields.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70902752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}