Journal of physical chemistry & biophysics最新文献

{"title":"Interaction of DNA with Globular Proteins of Different Structures in Thin Films on Substrates of Monocrystalline Silicon","authors":"L. Butusov, I. Nagovitsyn, V. V. Kurilkin, Chudinova Gk","doi":"10.4172/2161-0398.1000189","DOIUrl":"https://doi.org/10.4172/2161-0398.1000189","url":null,"abstract":"The two-component films of mixtures of DNA (from calf thymus) with different proteins: rabbit immunoglobulin (IgG), methemoglobin (MHB) and human serum albumin (HSA) were studied on single-crystal silicon substrates by the method of fluorescence spectroscopy. Registration of fluorescence spectra was performed by λex=260 and 280 nm in the range 340-380 nm. To prepare films the spincoating method was used. Solutions deposited on the substrate contained the small concentrations of proteins 10-9 - 10-15 M at the same quantity of DNA. \u0000Shape dependencies of the fluorescence intensity versus concentration differ markedly for each of the used proteins. The decreasing concentration of protein in the film is accompanied by a significant increase of the integrated fluorescence intensity (in comparison with the concentration of 10-9 M) for films of DNA-HSA in 2.5 and 5 times (10-13 and 10-15 M HSA), for films of DNA-IgG in 4.6 and 15.9 times (10-11 and 10-13 M IgG), for films of DNA-MHB in 3.4 times (10-11 M MHB). The single-component films of proteins was studied as control samples whose properties noticeably differ from the properties of DNA-protein systems. The specificity of the fluorescent characteristics of DNA-protein films for proteins of different structure and their different concentrations could be used as the basis for developing biosensor systems.","PeriodicalId":94103,"journal":{"name":"Journal of physical chemistry & biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88217452","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 Benchmark Study on the Properties of Unsubstituted and Some Substituted Polypyrroles","authors":"C. Ibeji, I. Adejoro, B. B. Adeleke","doi":"10.4172/2161-0398.1000193","DOIUrl":"https://doi.org/10.4172/2161-0398.1000193","url":null,"abstract":"The geometric, thermodynamic, electronic and absorption properties of Pyrrole and some of its derivatives have been carried out using CCSD/6-311++G(d,p)/STO-3G, TD-DFT and DFT/B3LYP/6-31G(d) from monomer to five repeating units. Substitution by a methyl group at C3 and functional groups at C4 cause small changes in atomic distances. The estimated inter-ring bond length based on Badger's rule of 1.41 A indicates that the average structure is about 30% quinoid. The geometries indicates that strong conjugate effects and effective aromatic structure are formed in the order Pyrrole>MPCam>MPC. The oligomers of simulated compounds have been extrapolated to polymer through second-degree polynomial-fit equation with r2 value ranging from 0.96-0.99. Calculated band gap of pyrrole, which is 2.9 eV, significantly correlates with the experimental value which ranges from 2.9-3.2 eV and this corresponds to π-π* transition energies. Natural bond orbitals of polypyrrole reveals that the wavefunctions contain dynamic correlations (single reference), closed shell character while substituted polypyrrole are multireference (static correlation), open shell character.","PeriodicalId":94103,"journal":{"name":"Journal of physical chemistry & biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77527541","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":"Study of Intermolecular Interaction of Hydroxypropyl-β-cyclodextrin Complexes through Phase Diagrams of the Fusion Entropy: Contrast between Nifedipine and Nicardipine Hydrochloride","authors":"Yingpeng Li, S. Goto, Yohsuke Shimada, Kazushi Komatsu, Y. Yokoyama, H. Terada, K. Makino","doi":"10.4172/2161-0398.1000187","DOIUrl":"https://doi.org/10.4172/2161-0398.1000187","url":null,"abstract":"In amorphous state, we examined the intermolecular interactions between the guest drugs nifedipine (NIF) and nicardipine hydrochloride (NIC), which are 1,4-dihydropyridine calcium channel blockers, and a host hydroxypropyl-β-cyclodextrin (HP- β-CD). Differential scanning calorimetry and powder X-ray diffraction showed that the interaction of NIC with HP-β-CD was remarkable stronger than that of NIF for both preparation methods. The structure of amorphous state complex of NIF/HP-β- CD presented as inclusion complex, and HP-β-CD in NIC/HP-β-CD complex was more like a surfactant which around NIC with its out-surface in any ratio. Fourier transform-infrared spectroscopy showed that the NIC/HP-β-CD complex contained multiple contact groups, whereas the NIF/HP-β-CD complex contained a single site bound to the HP-β-CD. Further, molecular dynamics simulation exhibited a much more vehemently reaction trend in NIC/HP-β-CD complex than that in NIF/HP-β-CD using compare the reaction constant. From the simulation images of NIF and NIC binding to HP-β-CD, we insure the different including situation in amorphous state of NIF/HP-β-CD and NIC/HP-β-CD. Consequently, we speculated that NIC binding to HP-β-CD with a different mechanism with NIF/ HP-β-CD complex. And this unique binding method may lead NIC has a higher potential energy changing in forming amorphous complexes.","PeriodicalId":94103,"journal":{"name":"Journal of physical chemistry & biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82303636","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":"The Viscous and External Forces Effect on the Thermal Denaturation of Peyrard-Bishop Model","authors":"W. Hidayat, A. Sulaiman, S. Viridi, F. P. Zen","doi":"10.4172/2161-0398.1000186","DOIUrl":"https://doi.org/10.4172/2161-0398.1000186","url":null,"abstract":"The viscous and the external forces effect on thermal DNA denaturation of Peyrard-Bishop model are investigated. The calculation of the partition function to determine the stretching of hydrogen bonds has been performed by path integral Monte-Carlo. The result shows that the interaction between the viscous potential and external forces prevent DNA to unzip perfectly but allows DNA to split at a certain distance from its original position. The increase of the viscosity coefficient will reduce the melting temperature. The result obtained also showed how at certain temperature external potential give dominant contribution in denaturation, higher even than the viscosity effect.","PeriodicalId":94103,"journal":{"name":"Journal of physical chemistry & biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79861418","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":"Environmentally affordable fluorescent nanotechnology for efficient lighting","authors":"Ching-Fuh Lin","doi":"10.4172/2161-0398.C1.013","DOIUrl":"https://doi.org/10.4172/2161-0398.C1.013","url":null,"abstract":"T energies involved in weak chiral interactions occurring between Odorant Binding Proteins (OBPs) and Carvone Enantiomers are evaluated, down to a few KJ/mol, by means of a water-gated organic field-effect transistor (WGOFET) whose Au-gate is modified with a porcine-OBP (pOBP) self-assembled monolayer. The output current measured is dependent on the concentration of the analytes and pM concentrations can be detected. The binding curves also are significantly different between the two enantiomers. The modelling of the two curves allows the energies associated with the OBPCarvone complexes formation to be independently extracted, from the very same set of data. From the dissociation constants the standard freeenergy, the complex formation at the electrode is derived, while the threshold voltage shifts gives information on the electrostatic component. This approach, representing a unique tool to quantitatively investigate low-energy bio-chemical interactions, is rather general as it relies on the relative dielectric constants of the protein-SAMs and of the organic semiconductors being much lower than that of water. The role of the OBPs in the olfaction system is still under debate and the detection of neutral odorant species at the pM level by means of a WGOFET adds relevant pieces of information to the understanding of the odor perception mechanism at the molecular level.","PeriodicalId":94103,"journal":{"name":"Journal of physical chemistry & biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72555226","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":"Nonlinear effects in optical fiber transmission systems","authors":"M. Ferreira","doi":"10.4172/2161-0398.C1.014","DOIUrl":"https://doi.org/10.4172/2161-0398.C1.014","url":null,"abstract":"T idea of making random lasers in one dimensional optical structures, such as optical fibers, has arisen great interests in the research world, because that the waveguide function provided by optical fibers help to reduce lasing threshold as well as to enhance emission directionality. Random distributed feedback fiber laser (RDF-FL) is a novel type of random laser reported by Turistsyn et al. based on a roll of single-mode fiber (SMF) in 2010. The SMF itself performs as the disorder medium, where Rayleigh backscattered (RS) radiation captured by fiber waveguide provides distributed feedback while the Raman pump provides optical amplification for generation of random lasing (RL). Compared with traditional random lasers, the RDF-FL shows relative stable output, single-transverse-mode profile, long-distance emission and wide wavelength tunability, which are of great interest in optical communication and optical sensing. To tune output wavelength of RDF-FLs, a passive component, i.e., a Fabry-Perot cavity combined with a LPFG based MZ interferometer, was designed to selectively feedback RS of a RDF-FL, and a novel all-fiber tunable multi-wavelength Raman fiber laser is achieved by us. To reduce the lasing threshold and design the output characteristics, a high nonlinear fiber, i.e., dispersion compensated fiber (DCF), with relative high Raman gain factor and RS was proposed to make RDF-FLs. Through combinations of SMF and DCF of varying length, the length and the lasing threshold of RDF-FL can be reduced remarkably when DCF is inserted at some position in the lasing cavity. Moreover, power distribution and spectrum of RDF-FL can be designed by controlling the length and the position of the DCF. Besides Raman gain, it is also possible to provide gain through active fibers, such as Er-doped fiber (EDF). In our studies, single-peak random lasing can be realized in a completely-opened cavity through pumping of both the EDF and the SMF. Combination of EDF and Raman amplifications helps to reduce the requirement of a unique pump for stable random lasing, as well as to reduce (increase) the threshold (output) power of RDF-FL. What’s more, random lasing with novel output characteristics, (i.e., stable single-peak random lasing and transitional variation between chaotic and stable states) are observed. In EDF, random distributed feedback can also be provided by inscription of randomly separated fiber Bragg gratings (FBGs), which usually generate unstable RL modes competition. In our case, a laterally-injected control light is used to induce local gain perturbation, providing additional seed light for certain random resonance modes. As a result, active mode selection of this type of RDF-FL is realized by changing locations of the laser cavity that is exposed to the control light.","PeriodicalId":94103,"journal":{"name":"Journal of physical chemistry & biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80730471","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":"X-ray Photoelectron Spectroscopy as an Effective Biomolecular Binding Site Probe","authors":"C. C. Chusuei","doi":"10.4172/2161-0398.1000e130","DOIUrl":"https://doi.org/10.4172/2161-0398.1000e130","url":null,"abstract":"X-ray photoelectron spectroscopy (XPS) is a versatile surface characterization tool capable of probing adsorbate structure at the topmost 100 Å layers of solid surfaces [1], and can serve as a useful biomolecular binding site probe. Although analysis is performed under conditions where equilibrium is interrupted at the solid-aqueous solution interface, insight into the biomolecular interactions at the interface can still be obtained. In particular, the technique is effective for quantifying the degree of Pb(II) binding to protein structures and antioxidants, important for understanding the metal ion’s interactions with protein structures [2], and developing therapeutic agents for lead poisoning [3], respectively. Also, XPS can effectively be used to measure the relative number of surface binding sites on metal oxide nanoparticulates to which extracellular material can attach, important for evaluating the cytotoxicity of various, 4th period transition metal oxide nanoparticles [4].","PeriodicalId":94103,"journal":{"name":"Journal of physical chemistry & biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73825865","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":"Applied Statistical Design of Experiments: Applications in Natural Sciences","authors":"I. Rauf","doi":"10.4172/2161-0398.1000E129","DOIUrl":"https://doi.org/10.4172/2161-0398.1000E129","url":null,"abstract":"Experiments are performed today in many scientific and engineering research fields to increase our understanding and knowledge of various scientific principles and processes. These experiments are often conducted in a series of trials or tests, which produce quantifiable outcomes. The quantitative as well as qualitative outcomes of these tests or trials are measured using scientific instruments as well as measurement equipment.","PeriodicalId":94103,"journal":{"name":"Journal of physical chemistry & biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88574038","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":"Fundamental Studies of Synthesizing Novel Calix[4]arene Derivative as Host for Treatment of Toxic Metal Cations (Hg2+, Cd2+, Pb2+ and Ag+)","authors":"Ahmed Yahya Issa Rubaye","doi":"10.4172/2161-0398.1000184","DOIUrl":"https://doi.org/10.4172/2161-0398.1000184","url":null,"abstract":"Novel calix[4]arene derivative containing mixed pendant arms in its lower rim, 25, 27- bis (diethylamino) ethoxy- 26, 28- (bis-methoxyethoxy) calix[4]arene, L3, has been synthesized to target the heavy metal cations. 1H NMR investigations seems to indicate that the receptor L3 interacts preferentially with Hg2+, Cd2+, Pb2+ and Ag+ in acetonitrile. Complexation studies in acetonitrile show that the lower rim groups of the receptor L3 are the active sites of its interaction with metal ions. These findings are corroborated by conductance measurements in acetonitrile, plots of molar conductance against the ligand/metal cation ratio reveal the formation of 1:1 complexes between this ligand with these cations. Standard thermodynamics parameters of complexation (log Ks, ΔHAiµ’ c, ΔSAiµ’ c, ΔGAiµ’ c) of L3 with Hg2+, Cd2+, Pb2+ and Ag+ in acetonitrile were determined using the Nano ITC (isothermal titration calorimetry). For all the systems investigated, the complexation process between these metal cations and the receptor L3 was enthalpically controlled. The enthalpic and entropic contributions to the Gibbs energy associated with these processes are analysed.","PeriodicalId":94103,"journal":{"name":"Journal of physical chemistry & biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88313244","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":"An Overview of Proteomics on Sepsis","authors":"M. Camprubí-Rimblas, A. Artigas, R. Guillamat-Prats","doi":"10.4172/2161-0398.1000183","DOIUrl":"https://doi.org/10.4172/2161-0398.1000183","url":null,"abstract":"Over the last years, proteomics has provided us a lot of information about the spectrum of all the proteins that are expressed by an organism in pathological and non-pathological processes. The advantage of studying the proteome over other omics (genomics, epigenetics, transcriptomics and metabolomics) is that proteins reflect the final effectors in all the complex network of replication, transcription and translation. Sepsis is a systemic inflammatory response caused by infection and that could produce multiple organ dysfunctions. The study of the secreted proteins would improve the knowledge of molecular mechanisms and pathways implicated in the septic process and consequently, data will allow us to find new therapeutic targets. The objective of this review is to summarize the proteomics updates of preclinical and clinical studies of sepsis in fields like pathophysiology, treatment, diagnosis or prognosis, providing new perspectives and directions of sepsis. Proteomics is a useful technique for the understanding of the pathophysiology of sepsis infection, the identification of new molecules for an early diagnosis and the prognosis, and the follow-up of treatment progress. The validation of new biomarkers needs a large cohort of patients and the use of other additional methods. Nevertheless, together with other techniques, proteomics has added important elements to the understanding of sepsis and other diseases. Despite current limitations, proteomic techniques improvement with bioinformatics tools might help results interpretation. Besides, the bettering in sensitivity and sensibility may facilitate further sepsis studies with these techniques.","PeriodicalId":94103,"journal":{"name":"Journal of physical chemistry & biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91136949","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}