生物物理化学(英文)最新文献

{"title":"More Stable, More Estrogenic: The SERM-ERα LBD Complex","authors":"Li Gao, Yaoquan Tu, L. Eriksson","doi":"10.4236/JBPC.2011.23029","DOIUrl":"https://doi.org/10.4236/JBPC.2011.23029","url":null,"abstract":"Many synthetic selective estrogen receptor modulators (SERMs) have been cocrystallized with the human estrogen receptor α ligand binding domain (ERα LBD). Despite stabilizing the same canonical inactive conformation of the LBD, most SERMs display different ligand-dependent pharmacological profiles. We show here that increased partial agonism of SERMs is associated with increased conformational stability of the SERM-LBD complexes, by investigation of dihydrobenzoxathiin-based SERMs using molecular modelling techniques. Analyses of tamoxifen (TAM) and 4-hydroxytamoxifen (OHT) in complex with the LBD furthermore indicates that the conversion of TAM to OHT increases both the affinity to ERα and the partial agonism of the anti-cancer drug, which provides a plausible explanation of the counterintuitive results of TAM therapy.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":"2011 1","pages":"233-243"},"PeriodicalIF":0.0,"publicationDate":"2011-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70899714","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":"Modulation of CNS excitability by water movement. The D2O effects on the non-linear neuron-glial dynamics","authors":"Vera Maura, F. D. Lima, W. Hanke, São João del Rei","doi":"10.4236/JBPC.2011.23040","DOIUrl":"https://doi.org/10.4236/JBPC.2011.23040","url":null,"abstract":"Macroscopic spatiotemporal patterns arising in grey matter may explain the clinical manifestations of several functional neurological syndromes (migraine aura, epilepsies). Detailed descriptions of these patterns in central grey matter and their physicochemical or pharmacological manipulations can be useful in many scientific fields ranging from drug design to functional brain imaging. These evanescent dynamic structures are electrochemical in nature and show macroscopic tissue polarization due to coupled and macroscopic flow of ions and water across, along and between neuronal and glial membranes. So far the importance of the water flow in the CNS functional syndromes has been examined by manipulations of water channels aquaporines (AQP). In this paper we show the result of substituting H2O for D2O in retinal spreading depression experiments. This inverts the present logic by changing the flow in the water channels in intact tissue and observing the evolution of electrochemical patterns and recording the optical profiles of excitation waves in isolated chick retinas. D2O flow through AQPs is ~20% slower than that of H2O. The slower flux disturbs the tight coupling between ion and water flows across membranes and slowdown the Na-KATPase rate of change with metabolic consequences for the tissue. The whole tissue excitability shifts in a non-stationary manner toward a non-excitable state.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":"02 1","pages":"353-360"},"PeriodicalIF":0.0,"publicationDate":"2011-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70899750","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":"Fluorescence quenching of tryptophan and tryptophanyl dipeptides in solution","authors":"A. Osysko, P. L. Muiño","doi":"10.4236/JBPC.2011.23036","DOIUrl":"https://doi.org/10.4236/JBPC.2011.23036","url":null,"abstract":"We report measurements of fluorescence quantum yields of tryptophan, tryptophanylaspartate and tryptophanylarginine in several solvents as well as in aqueous solutions over a wide range of pH. We aim to test a computational model developed by Callis and coworkers of fluorescence quantum yield, which postulates that quenching in tryptophan arises from energy loss due to an electron transfer from the aromatic system of tryptophan to one of the amides in the protein backbone. Since the electron transfer state is expected to be high in energy, normally this would not be a possible outcome, but because of its large dipole, such a state should be more accessible in polar solvents. In addition, conditions of low (high) pH, which result in a net positive (negative) charge for the terminal amine (carboxyl) should result in an increase (decrease) of electron transfer rates and low (high) quantum yields. The observed results confirm the predictions of the model.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":"46 11 1","pages":"316-321"},"PeriodicalIF":0.0,"publicationDate":"2011-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4236/JBPC.2011.23036","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70899615","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":"Effect of disulfide bridges deletion on the conformation of the androctonin, polyphemusin-I, and thanatin antimicrobial peptides: molecular dynamics simulation studies","authors":"C. J. Moreira, Fuzo Carlos Alessando, De Leo","doi":"10.4236/JBPC.2011.23030","DOIUrl":"https://doi.org/10.4236/JBPC.2011.23030","url":null,"abstract":"In this work, the role of the disulfide bridges in the maintenance of the secondary structure of the antimicrobial peptides androctonin, poly-phemusin-I, and thanatin is analyzed on the basis of their structural characteristics and of three of their respective mutants, andry4, poly4, and thany2, in which all the cysteine residues have been replaced with tyrosine residues. The absence of the disulfide bridges in andry4, poly4, and thany2 seems to be compensated by an overall enforcement of the original hydrogen bonds and by extra attractive interactions between the aromatic rings of the tyrosine residues. In spite of the mutations, the original β-hairpin structures are maintained in the three mutants, but the best conformational similarities are found for the androctonin/andry4 pair.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":"2011 1","pages":"244-257"},"PeriodicalIF":0.0,"publicationDate":"2011-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70899380","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":"Computational modeling studies on anti-HIV-1 non-nucleoside reverse transcriptase inhibition by dihydroalkoxybenzyloxopyrimidines analogues: an electrotopological atomistic approach","authors":"N. Sapre, Tarang Bhati, Swagata Gupta, N. Pancholi, U. Raghuvanshi, D. Dubey, Vandana Rajopadhyay, N. Sapre","doi":"10.4236/JBPC.2011.23041","DOIUrl":"https://doi.org/10.4236/JBPC.2011.23041","url":null,"abstract":"For the first time we report quantitative structure activity relationship (QSAR) studies based on Kier-Hall Electrotopological State (E-State) Indices for Dihydroalkoxybenzyloxopyrimidines (DABO) derivatives acting as NNRTIs of HIV-1. A dataset of 74 compounds was compiled from published studies and randomly subdivided into training and test sets. To understand the pharmacophoric effect, Kier-Hall Electrotopological State descriptors namely SN1, SN3, SF, SAr, SS, SO, SNO2, SCl, SY (Y = S-alkyl and NH-alkyl), SX (X = Me) and biological activity were used as independent and dependent variable respectively. Statistical results were highly encouraging for the training set multiple linear regression [(MLR): r2 = 0.961, F = 100.41 and q2 = 0.926, neural networks (NN): r2 = 0.966, F = 115.594, degrees of freedom = 40 and k-nearest neighbour (k-NN): r2 = 0.770, q2 = 0.757, degrees of freedom = 40]. Results of validation using a test set showed the same trend as training set (NN > MLR > kNN). The above results suggest that of various functional groups present in DABO such as SN3, SO, SCl, SAr and SNO2 contribute more significantly towards activity. On the other hand SN1, SS, and SF do not play any role in enhancing the activity. The substitution of S-alkyl and NH-alkyl at C2 position is essential though it does not contribute much towards the activity. The substitution of methyl group at C5 position is unfavorable and exhibit negative impact on inhibitory activity. Therefore, it seems reasonable to choose E-state indices as suitable and significant descriptors for exploring the relationship between the pIC50 and the pharmacological properties of the compounds.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":"2011 1","pages":"361-372"},"PeriodicalIF":0.0,"publicationDate":"2011-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70899481","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":"Suppression of immunity by some pesticides, xenobiotics, and industrial chemicals. In vitro model","authors":"I. Brondz, Anton Brondz","doi":"10.4236/JBPC.2011.23028","DOIUrl":"https://doi.org/10.4236/JBPC.2011.23028","url":null,"abstract":"In recent years, attention has focused on suppression of immunity in immunocompromised patients. The definition of immunocompromise is impairment of the immune system caused by a disease or treatment. In addition to disease and treatment, other factors such as exposure to pesticides or toxic chemicals can damage the immune system. An in vitro test was used to assess the ability of monochloroacetic acid (MCA) (CAS number 79-11-8), dichloroacetic acid (DCA) (CAS number 79-43-6), trichloroacetic acid (TCA) (CAS number 76-03-9), and 2,2- dichloropropionic acid sodium salt (2,2-DCPANa, Dalapon) (CAS number 127-20-8) to suppress bacteriolysis by hen egg white lysozyme (HEWL). The system for bacteriolysis of Gram-negative bacteria Actinobacillus, Haemophilus, and Pasteurella in Tris-maleate buffer supplemented with EDTA and HEWL developed by Brondz et al. [1–4] was used to monitor bacteriolysis of Gram-negative bacteria in the Actinobacillus–Haemophilus–Pasteurella group. The halogenated acetic acid DCA is produced as a toxic artifact of the degradation of TCA and by disinfection of drinking and pool water and industrial waste. Nearly all humans consume DCA in drinking water during their lifetime; the concentration of DCA in drinking water can be higher than that associated with the upper-bound excess life-time cancer risk of 10–4 (40μg/L) [5]. Lysozyme found in tears, saliva, nasal secretions, and excretions from all mucous membranes can break down the cell walls of bacteria and destabilize bacterial membranes. Lysozyme is involved in innate (nonspecific) immunity; the innate immune system is the first line of defense against invading organisms. Actinobacillus actinomy- \u0000cetemcomitans (ATCC29522), a Gram-negative bacterium whose primary ecological niche is the respiratory tract and oral cavity, provided the peptidoglycan substrate for HEWL. The optical density (OD) of a standardized suspension of A. actinomycetemcomitans decreased from 100% (OD 0.6 at 540 nm) to 23.5% after exposure to EDTA/HEWL for 50 min. After 50 min of exposure to 10.0 mg/mL of MCA, DCA, TCA, or 2,2-DCPANa as a supplement, EDTA/HEWL-induced lysis of A. actinomycetemcomitans decreased to 66.3%, 66.8%, 65.7%, and 73.6%, respectively. The aim of the presented study was the development of a model for measuring possible immunotoxic effects of chemicals, degradation products, xenobiotics and metabolites by these chemicals on the immune system. The method used is an in vitro bacteriolysis of Gram- negative bacterium induced by HEWL, described previously [1-4]. In the present study, several halogenated acids, MCA, DCA, and TCA, and the Na salt of 2,2-DCPA, exhibited immunosuppressive activity. The ability of MCA, DCA, TCA, and 2,2-DCPANa (Dalapon) to suppress HEWL induced bacteriolysis was demonstrated in vitro. document.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":"2011 1","pages":"226-232"},"PeriodicalIF":0.0,"publicationDate":"2011-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70899677","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 predictive kinetic model for inhibitory effect of nitrite on myeloperoxidase catalytic activity towards oxidation of chloride","authors":"Y. Tahboub, M. Fares","doi":"10.4236/JBPC.2011.23024","DOIUrl":"https://doi.org/10.4236/JBPC.2011.23024","url":null,"abstract":"Myeloperoxidase (MPO) is a neutrophil enzyme that employs hydrogen peroxide (H2O2) to catalyze the oxidation of chloride (Cl–) to hypochlorous acid (HOCl). Accepted mechanism is based on rapid reaction of native MPO with H2O2to produce Compound I (MPO-I) which oxidizes Cl– through a 2e– transition generating MPO and HOCl. MPO-I also reacts with H2O2 to generate Compound II (MPO-II) which is inactive in 2e oxidation of Cl–. Nitrite ( NO2-) inhibits the 2e oxidation of Cl– by reaction with MPO-I through 1e transition generating MPO-II and nitrite radical. H2O2 consumption during steady- state catalysis was monitored amperometrically by a carbon fiber based H2O2-biosensor at 25oC. Results demonstrated that in absence of NO2- reactions were monophasic and rapid (complete H2O2 consumption occurs in 2- increases, reactions change to biphasic (rapid step followed by a slow step) and both steps have been inhibited by NO2- . A predictive kinetic model describing the inhibittory effect of NO2- was developed and applied to experimental results The model is based on the assumption that MPO–I cannot be detected during steady-state catalysis. Calculated rate constants are in agreement with those obtained from pre-steady state kinetic methods.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":"2 1","pages":"202-207"},"PeriodicalIF":0.0,"publicationDate":"2011-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70899133","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":"Novel histone deacetylase inhibitor exhibits antitumor activity via apoptosis induction in oral squamous cell carcinoma","authors":"O. Takahashi, T. Okinaga, Kenjiro Iwanaga, M. Habu, W. Ariyoshi, K. Tominaga, N. Nishino, T. Nishihara","doi":"10.4236/JBPC.2011.23026","DOIUrl":"https://doi.org/10.4236/JBPC.2011.23026","url":null,"abstract":"Epigenetic modifications such as histone deacetylation are commonly related to tumor development and histone deacetylase (HDAC) inhibitors have been shown to be potential drugs for cancer treatment. In the present study, we investigated the effects of a novel HDAC inhibitor, Ky-2, on oral squamous carcinoma cells in vitro. Cell viability was significantly reduced by treatment with Ky-2 at 25 nM, while it also led to augmentation of the proportion of cells in the sub-G1 phase and DNA fragmentation. In addition, immunoblot analysis revealed that Ky-2 enhanced the expression of apoptosis-related proteins. Our results showed that a low concentration of Ky-2 induced apoptosis in oral squamous carcinoma cells via activation of apoptotic cascades.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":"32 1","pages":"215-221"},"PeriodicalIF":0.0,"publicationDate":"2011-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70899492","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":"Coarse-grained simulations of branched bilayer membranes: effects of cholesterol-dependent phase separation on curvature-driven lipid sorting","authors":"M. Nishizawa, K. Nishizawa","doi":"10.4236/JBPC.2011.23032","DOIUrl":"https://doi.org/10.4236/JBPC.2011.23032","url":null,"abstract":"Our recent coarse-grained (CG) molecular dynamics (MD) simulations of membranes with a hemifused-ribbon (λ-shaped) geometry showed curvature-driven demixing leading to enrich ment in dioleoyl-phosphatidylethanolamine (DOPE) in a negatively-curved region (at C = –0.8 nm–1) of a DOPE/dipalmitoyl-phosphati-dylcholine (DPPC) membrane. Here we extend the analysis with respect to lipid composition and simulation time. Simulations of 12 – 20 μs effective time show that, compared with DOPE of the DOPE/DPPC system, a DPPC/dilinoleyl-PC [di(18:2)PC] membrane showed a similar degree of enrichment of di(18:2)PC in the curved region with C=–0.8 nm–1. For the latter mixture, even weak negative curvatures (C=–0.5 – 0.6 nm–1) caused significant degrees of di(18:2)PC enrichment. In agreement with recent studies of a planar bilayer, a ternary DPPC/ di(18:2)PC/cholesterol 0.42:0.28:0.3 mixture phase-separated into nanoscale raft-like liquid-ordered (Lo) and non-raft liquid-disordered (Ld) phases on a sub-microsecond time scale. The Lo domains were preferentially localized at planar portions, whereas the Ld domains were positioned mainly in curved regions of the membrane. Unlike binary dioleoylphosphatidylcho-line (DOPC)/cholesterol and DPPC/cholesterol mixtures, which showed only a slight enrich ment of cholesterol in the curved region, the ternary mixtures showed considerable migra tion of cholesterol and DPPC from the curved to the planar region. A pronounced degree of lipid segregation due to the preferential distribution of the Ld and Lo domains in the curved and planar regions, respectively, was observed even when the curvature of the fused monolayers \u0000(originally ‘cis’ leaflets) was weakened (C= –0.5 nm-1). Overall, the results are consistent with theoretical predictions based on spontaneous curvature of the constituent lipids and the difference in rigidity between the Ld and Lo domains, whereas lipid-lipid interactions, such as PE-PE or DPPC-cholesterol, as well as propensity for interleaflet colocalization (registration) of the Lo and Ld domains appear to significantly amplify curvature-induced lipid demixing in the λ system. Intriguingly, for the DPPC/ di(18:2)PC/cholesterol ternary mixtures, a Lo/Ld domain boundary often moved to the branched point of the membrane, suggesting enhanced flexibility at the domain boundary. We hypothesize that curvature-driven lipid sorting and energetically favored localization of domain boundaries at sharp bends in the membranes may collaborate to assist intracellular lipid sorting.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":"2 1","pages":"268-284"},"PeriodicalIF":0.0,"publicationDate":"2011-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70899508","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":"Kinetic and binding equilibrium studies of dihydroflavonol 4-reductase from Vitis vinifera and its unusually strong substrate inhibition","authors":"N. Trabelsi, B. d'Estaintot, G. Sigaud, B. Gallois, J. Chaudière","doi":"10.4236/JBPC.2011.23038","DOIUrl":"https://doi.org/10.4236/JBPC.2011.23038","url":null,"abstract":"Dihydroflavonol 4-reductase (DFR), a member of the short-chain dehydrogenase family, catalyzes the last common step in the biosynthesis of flavan-3-ols and condensed tannins. Initial rates of DFR were measured by monitoring the 340-nm absorbance decrease resulting from the joint consumption of dihydroquercetin (DHQ) and NADPH, as a function of pH, temperature and ionic strength. At pH 6.5 and 30o C, substrate inhibition was observed above 30 µM DHQ. At lower/non-inhibitory DHQ concentrations, NADP+ behaves as a competitive inhibitor with respect to NADPH and as a mixed inhibitor with respect to DHQ, which supports a sequential ordered mechanism, with NADPH binding first and NADP+ released last. Binding-equilib-rium data obtained by means of the chromatographic method of Hummel and Dreyer at pH 7.5 and by isothermal calorimetric titration at pH 6.5 led to the conclusion that ligands of the apoenzyme included NADPH, NADP+ and DHQ. The mechanism which best accounts for substrate inhibition at pH 6.5 in the absence of product involves the formation of a binary non-productive E.DHQ complex. Thus, a productive ternary complex cannot be formed when DHQ binds first. This mechanism of inhibition may prevent the accumulation of unstable leucoanthocyanidins within cells.","PeriodicalId":62927,"journal":{"name":"生物物理化学(英文)","volume":"02 1","pages":"332-344"},"PeriodicalIF":0.0,"publicationDate":"2011-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4236/JBPC.2011.23038","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70899691","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}