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Vitro Methods (vitro + methods)
Selected AbstractsGene expression changes in human cells after exposure to mobile phone microwavesPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 17 2006Daniel Remondini Abstract Possible biological effects of mobile phone microwaves were investigated in,vitro. In this study, which was part of the 5FP EU project REFLEX (Risk Evaluation of Potential Environmental Hazards From Low-Energy Electromagnetic Field Exposure Using Sensitive in,vitro Methods), six human cell types, immortalized cell lines and primary cells, were exposed to 900 and 1800,MHz. RNA was isolated from exposed and sham-exposed cells and labeled for transcriptome analysis on whole-genome cDNA arrays. The results were evaluated statistically using bioinformatics techniques and examined for biological relevance with the help of different databases. NB69 neuroblastoma cells, T,lymphocytes, and CHME5 microglial cells did not show significant changes in gene expression. In EA.hy926 endothelial cells, U937,lymphoblastoma cells, and HL-60 leukemia cells we found between 12 and 34,up- or down-regulated genes. Analysis of the affected gene families does not point towards a stress response. However, following microwave exposure, some but not all human cells might react with an increase in expression of genes encoding ribosomal proteins and therefore up-regulating the cellular metabolism. [source] Dendritic cells: biology of the skinCONTACT DERMATITIS, Issue 1 2009Mascha J. Toebak Allergic contact dermatitis results from a T-cell-mediated, delayed-type hypersensitivity immune response induced by allergens. Skin dendritic cells (DCs) play a central role in the initiation of allergic skin responses. Following encounter with an allergen, DCs become activated and undergo maturation and differentiate into immunostimulatory DCs and are able to present antigens effectively to T cells. The frequency of allergic skin disorders has increased in the past decades. Therefore, the identification of potential sensitizing chemicals is important for skin safety. Traditionally, predictive testing for allergenicity has been conducted in animal models. For regulatory reasons, animal use for sensitization testing of compounds for cosmetic purposes is shortly to be prohibited in Europe. Therefore, new non-animal-based test methods need to be developed. Several DC-based assays have been described to discriminate allergens from irritants. Unfortunately, current in vitro methods are not sufficiently resilient to identify allergens and therefore need refinement. Here, we review the immunobiology of skin DCs (Langerhans' cells and dermal dendritic cells) and their role in allergic and irritant contact dermatitis and then explore the possible use of DC-based models for discriminating between allergens and irritants. [source] L1, ,1 integrin, and cadherins mediate axonal regeneration in the embryonic spinal cordDEVELOPMENTAL NEUROBIOLOGY, Issue 14 2006Murray Blackmore Abstract Embryonic birds and mammals are capable of axon regeneration after spinal cord injury, but this ability is lost during a discrete developmental transition. We recently showed that changes within maturing neurons, as opposed to changes solely in the spinal cord environment, significantly restrict axon regeneration during development. The developmental changes within neurons that limit axon regeneration remain unclear. One gap in knowledge is the identity of the adhesive receptors that embryonic neurons use to extend axons in the spinal cord. Here we test the roles of L1/NgCAM, ,1 integrin, and cadherins, using a coculture system in which embryonic chick brainstem neurons regenerate axons into an explant of embryonic spinal cord. By in vivo and in vitro methods, we found that brainstem neurons reduce axonal expression of L1 as they mature. Disrupting either L1 or ,1 integrin function individually in our coculture system partially inhibited growth of brainstem axons in spinal cords, while disrupting cadherin function alone had no effect. However, when all three adhesive receptors were blocked simultaneously, axon growth in the spinal cord was reduced by 90%. Using immunohistochemistry and in situ hybridization we show that during the period when neurons lose their regenerative capacity they reduce expression of mRNA for N-cadherin, and reduce axonal L1/NgCAM protein through a post-transcriptional mechanism. These data show that embryonic neurons use L1/NgCAM, ,1 integrin, and cadherin receptors for axon regeneration in the embryonic spinal cord, and raise the possibility that a reduced expression of these essential receptors may contribute to the low-regenerative capacity of older neurons. © 2006 Wiley Periodicals, Inc. J Neurobiol, 2006 [source] Effect of cyclosporin A in Lewis rats in vivo and HeLa cells in vitroJOURNAL OF APPLIED TOXICOLOGY, Issue 3 2002Andrea Sovcikova Abstract The aim of this study was to compare the effect of cyclosporin A (CsA) in inbred Lewis rats with published assessment of immunotoxicity in ,classical' outbred Wistar rats. A second purpose was to consider the contribution of a panel of in vitro assays in cell cultures when added to an immunotoxicity study in vivo. The in vivo effect of CsA was investigated in a 28-day subacute immunotoxicity study in male Lewis rats at three different concentrations: 1.25, 5 and 20 mg kg,1. The highest dose of CsA exceeded the maximum tolerated dose. A drop in body, spleen and popliteal lymph node weight of exposed animals displayed symptoms of toxicity. At a high toxic dose, haematological changes showed a decrease in the leucocyte count and in the percentage of lymphocytes, and an increase in the percentage of polymorphonuclear leucocytes. The haematocrit was significantly dose-dependently suppressed in all rats exposed to CsA. A similar dose-dependent depression of the mean cell volume of erythrocytes was found in rats given high and middle doses of CsA. The phagocytic activity of polymorphonuclear leucocytes and monocytes also was significantly dose-dependently suppressed. No significant changes in primary antibody response to sheep erythrocytes or in vitro proliferative response of spleen lymphocytes to mitogens were found in those rats. A battery of in vitro cytotoxicity methods was selected for the evaluation of metabolic and functional activity of subcellular organelles (mitochondria, lysosomes) and for the detection of drug-induced superoxide-mediated damage in HeLa cells. This cell line was chosen because it has a lower activity of superoxide dismutase (SOD) than normal cells and is sufficiently sensitive for the detection of the induction of oxygen radicals. The in vitro results indicated a direct relationship between CsA cytotoxicity and a change in the mitochondrial enzyme activity, as well as an induction of superoxide production. The results of the study indicated that a combination of selected in vivo and in vitro methods is an inexpensive way to obtain more complex information on cell status affected by xenobiotics. Copyright © 2002 John Wiley & Sons, Ltd. [source] Antioxidant activity of peptide fractions derived from cottonseed protein hydrolysateJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 11 2010Dandan Gao Abstract BACKGROUND: Cottonseed protein is widely regarded as a potential source of nutrients for humans and animals, but it is mainly used as forage in China. In the present study, Neutrase was employed to hydrolyse cottonseed protein to produce a hydrolysate with antioxidant activity suitable for conversion to high-value products. The antioxidant potential of the cottonseed protein hydrolysate (CPH) and its fractions was investigated using different in vitro methods. Furthermore, the amino acid composition of the CPH fractions was determined to evaluate the relationship between antioxidant activity and amino acid composition. RESULTS: The CPH prepared using Neutrase was separated into four fractions (I, II, III and IV) by gel filtration on Sephadex G-25. All fractions were effective antioxidants, with fraction III (0.8,1.2 kDa) showing the strongest activity. The amino acid analysis showed that fraction III also had the highest total amino acid content (616.8 g kg,1 protein) and was rich in Phe, His, Pro, Met, Ile and Cys compared with the other fractions. CONCLUSION: The results showed that the hydrolysate derived from cottonseed protein, particularly fraction III, could be a natural antioxidant source suitable for use as a food additive. Copyright © 2010 Society of Chemical Industry [source] Comparison of in vitro starch digestibility methods for predicting the glycaemic index of grain foodsJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 4 2008Kirsty A Germaine Abstract BACKGROUND:In vitro starch digestibility tests are useful for the prediction of glycaemic index (GI). However, there are no internationally recognised methods and no one method has been found to be suitable for all food types. This study compared six in vitro methods, using four grain foods, including those with a varied particle size and soluble fibre content. Method variations included using chewing or mincing, mincing with or without amylase and incubation in a restricted versus non-restricted system. Hydrolysis index (HI) values, calculated from the starch digestibility curves and GI prediction equations were used to compare the in vitro results to GI. RESULTS: HI values for five of the six methods ranked all foods in the same order as the GI values. Using a GI prediction equation (predicted GIHI) the mincing (without amylase) non-restricted method had the smallest standard error of prediction between the predicted GIHI and GI values. This method was then validated using 14 grain foods and demonstrated a significant correlation (r = 0.93, P < 0.01) between the in vitro starch digestibility and reported GI responses. CONCLUSIONS: The non-restricted mincing method showed good potential as a new in vitro starch digestibility method for predicting GI in grain foods. Copyright © 2007 Society of Chemical Industry [source] Principles of pharmacodynamics and their applications in veterinary pharmacologyJOURNAL OF VETERINARY PHARMACOLOGY & THERAPEUTICS, Issue 6 2004P. LEES Pharmacodynamics (PDs) is the science of drug action on the body or on microorganisms and other parasites within or on the body. It may be studied at many organizational levels , sub-molecular, molecular, cellular, tissue/organ and whole body , using in vivo, ex vivo and in vitro methods and utilizing a wide range of techniques. A few drugs owe their PD properties to some physico-chemical property or action and, in such cases, detailed molecular drug structure plays little or no role in the response elicited. For the great majority of drugs, however, action on the body is crucially dependent on chemical structure, so that a very small change, e.g. substitution of a proton by a methyl group, can markedly alter the potency of the drug, even to the point of loss of activity. In the late 19th century and first half of the 20th century recognition of these facts by Langley, Ehrlich, Dale, Clarke and others provided the foundation for the receptor site hypothesis of drug action. According to these early ideas the drug, in order to elicit its effect, had to first combine with a specific ,target molecule' on either the cell surface or an intracellular organelle. It was soon realized that the ,right' chemical structure was required for drug,target site interaction (and the subsequent pharmacological response). In addition, from this requirement, for specificity of chemical structure requirement, developed not only the modern science of pharmacology but also that of toxicology. In relation to drug actions on microbes and parasites, for example, the early work of Ehrlich led to the introduction of molecules selectively toxic for them and relatively safe for the animal host. In the whole animal drugs may act on many target molecules in many tissues. These actions may lead to primary responses which, in turn, may induce secondary responses, that may either enhance or diminish the primary response. Therefore, it is common to investigate drug pharmacodynamics (PDs) in the first instance at molecular, cellular and tissue levels in vitro, so that the primary effects can be better understood without interference from the complexities involved in whole animal studies. When a drug, hormone or neurotransmitter combines with a target molecule, it is described as a ligand. Ligands are classified into two groups, agonists (which initiate a chain of reactions leading, usually via the release or formation of secondary messengers, to the response) and antagonists (which fail to initiate the transduction pathways but nevertheless compete with agonists for occupancy of receptor sites and thereby inhibit their actions). The parameters which characterize drug receptor interaction are affinity, efficacy, potency and sensitivity, each of which can be elucidated quantitatively for a particular drug acting on a particular receptor in a particular tissue. The most fundamental objective of PDs is to use the derived numerical values for these parameters to classify and sub-classify receptors and to compare and classify drugs on the basis of their affinity, efficacy, potency and sensitivity. This review introduces and summarizes the principles of PDs and illustrates them with examples drawn from both basic and veterinary pharmacology. Drugs acting on adrenoceptors and cardiovascular, non-steroidal anti-inflammatory and antimicrobial drugs are considered briefly to provide a foundation for subsequent reviews in this issue which deal with pharmacokinetic (PK),PD modelling and integration of these drug classes. Drug action on receptors has many features in common with enzyme kinetics and gas adsorption onto surfaces, as defined by Michaelis,Menten and Langmuir absorption equations, respectively. These and other derived equations are outlined in this review. There is, however, no single theory which adequately explains all aspects of drug,receptor interaction. The early ,occupation' and ,rate' theories each explain some, but not all, experimental observations. From these basic theories the operational model and the two-state theory have been developed. For a discussion of more advanced theories see Kenakin (1997). [source] Panose, a new prebiotic candidateLETTERS IN APPLIED MICROBIOLOGY, Issue 6 2009H. Mäkeläinen Abstract Aims:, To investigate the prebiotic potential of two novel candidates, sophorose and panose, with in vitro methods. Methods and Results:, The growth of single microbial strains was first assessed for both substrates in pure cultures, and panose was further analysed in the simulated colon model with mixed human faecal culture. Quantitative PCR and flow cytometry were used to determine the microbial group and strain densities after the simulated colonic fermentation of panose, and chromatographic methods were utilized to analyse metabolite concentrations. In pure cultures, sophorose and panose were both fermented only by few beneficial strains, and in the colon simulator, panose gave a significant increase in the numbers of Bifidobacterium and Bifidobacterium lactis, concomitantly decreasing Bacteroides group. Butyrate and acetate production was significantly increased together with decreased markers of protein fermentation as a result of panose fermentation. Conclusions:, Panose had bifidogenic activities in vitro, and these potential beneficial effects should be further assessed in vitro and in vivo. Significance and Impact of the Study:, The current study has provided the first data on pure panose fermentation by the endogenous microbiota and extends our knowledge of the selective fermentation of oligosaccharides by the intestinal microbes. [source] Effectiveness of dentine bonding agents against cariogenic bacteria in vitro: a comparison of two methodsMOLECULAR ORAL MICROBIOLOGY, Issue 3 2003O. A. Schmidlin Data obtained from studies on the antimicrobial properties of bonding agents are the subject of controversy, probably because of methodological differences. This study compared two commonly used in vitro methods, the disc agar diffusion test and the well agar diffusion test. Agar plates were seeded with Streptococcus sobrinus, Lactobacillus gasseri, or Actinomyces naeslundii. For the well diffusion test, wells cut out of the agar were filled with the test material, and for the disc method, discs impregnated with the test material were applied to the agar; the discs and wells were both 9 mm in diameter. After incubation, measurements of the zones of inhibition showed little agreement between the two methods when bonding agents were tested; the mean differences (± sdiff) in the zones of inhibition between the methods were 0.7 ± 3.4 mm (P = 0.40, one sample t -test against zero), 4.9 ± 4.4 mm (P = 0.97), and 0.8 ± 4.3 mm (P = 0.47) for S. sobrinus, L. gasseri, and A. naeslundii, respectively. Mean differences were less contrasting when chlorhexidine and pure components were tested (P < 0.05 for S. sobrinus and L. gasseri). These results indicate the need for a gold standard method to evaluate the antimicrobial properties of bonding agents. [source] In Vitro Sunscreen Transmittance Measurement with Concomitant Evaluation of Photostability: Evolution of a MethodPHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2009Robert M. Sayre The recent paper by Miura et al. (Photochem. Photobiol. 84[6], 1569,1575) offers a re-examination of extant in vitro methods for dynamically measuring sunscreen photodegradation under continuous irradiation in situ. We commend the authors' efforts toward developing an improved system for accurate in vitro sunscreen assessment. This work describes an alternate derivative apparatus incorporating an improved detector which may prove an exceptionally valuable contribution toward that goal. Unfortunately their report suffers from insufficient detail in instrumentation description and lacks requisite calibration procedures. Their utilization of a solar simulator filtered for conventional in vivo sun protection factor (SPF) testing poses transmittance measurement limitations at short wavelengths that are not adequately addressed and is also deficient, relative to sunlight, in longer UVA wavelengths shown to contribute to sunscreen photoinstability. We concur that the in vitro sunscreen testing should utilize continuous or multiple irradiation doses and should ideally use the same 2 mg cm,2 product application amount as does the human SPF test. We encourage their proposal that methodology, which simultaneously measures sunscreen spectral transmittance and photodegradation under continuous irradiation to an accumulated erythemic endpoint, as we previously described, be developed into a consensus test standard. [source] 004 Validation of in vivo and in vitro methods to measure UVA protectiveness of sunscreenPHOTODERMATOLOGY, PHOTOIMMUNOLOGY & PHOTOMEDICINE, Issue 2 2002C. Cole Standard methods for measuring the sunburning protection of sunscreens (SPF) are globally established. In vivo methods of determining UVA protectiveness of sunscreens have been reduced to either a Persistent Pigment Darkening (PPD) or Protection Factor A (PFA-either persistent pigment darkening or erythema endpoints) test protocols. Both of these techniques require human exposure to UVA radiation that can be time consuming and do not benefit the human subject. Validated methodologies that would minimize the UVA exposure, or could be performed in vitro would simplify the determination of UVA protectiveness and assist product optimization. Diffuse reflectance spectroscopy of sunscreens on human skin was utilized to evaluate a series of seven model sunscreen systems that were previously evaluated in vivo by both PPD and PFA testing. Correlation of the values found with this technique correlated highly with the in vivo test results, with 1:1 correspondence of protection values. Separately, an in vitro test model was assessed on these same model sunscreens. Sunscreen was applied to roughened surface quartz plates, and the absorbance of the sunscreens was measured before and after UV exposure. The absorbance was mathematically forced to fit the in vivo SPF value and the UVA protectiveness was calculated using both erythema and pigment darkening action spectra. The in vitro predictions of UVA was highly correlated with the in vivo PPD and PFA values. It was determined that preirradiation of the sunscreen samples is needed to accurately predict the protection provided by sunscreens that are not photostable. Both of these techniques provide new ways to accurately predict sunscreen UVA protectiveness. [source] Preparation and characterization of biocompatible spongy cryogels of poly(vinyl alcohol),gelatin and study of water sorption behaviourPOLYMER INTERNATIONAL, Issue 9 2005Dr AK Bajpai Abstract Porous biocompatible spongy hydrogels of poly(vinyl alcohol) (PVA),gelatin were prepared by the freezing,thawing method and characterized by infrared and differential scanning calorimetry. The prepared so-called ,cryogels' were evaluated for their water-uptake potential and the influence of various factors, such as the chemical architecture of the spongy hydrogels, pH and the temperature of the swelling bath, on the degree of water sorption by the cryogels was investigated. It was found that the water sorption capacity constantly decreased with increasing concentration of PVA while initially an increase and thereafter a decrease in swelling was obtained with increasing amounts of gelatin in the cryogel. The water sorption capacity decreased with an increase in the number of freeze,thaw cycles. The hydrogels were also swollen in salt solutions and various simulated biological fluids and a fall in swelling ratio was noticed. The effect of the drying temperature of the cryogel on its water sorption capacity was also investigated, and a decrease in swelling was obtained with increasing temperature of drying. The biocompatibility of the prepared materials was assessed by in vitro methods of blood-clot formation, platelet adhesion, and per cent haemolysis. It was noticed that with increasing concentration of PVA and gelatin the biocompatibility increased, while a reduced biocompatibility was noted with an increasing number of freeze,thaw cycles. Copyright © 2005 Society of Chemical Industry [source] Lactic acid bacteria vs. pathogens in the gastrointestinal tract of fish: a reviewAQUACULTURE RESEARCH, Issue 4 2010Einar Ringø Abstract Intensive fish production worldwide has increased the risk of infectious diseases. However, before any infection can be established, pathogens must penetrate the primary barrier. In fish, the three major routes of infection are the skin, gills and gastrointestinal (GI) tract. The GI tract is essentially a muscular tube lined by a mucous membrane of columnar epithelial cells that exhibit a regional variation in structure and function. In the last two decades, our understanding of the endocytosis and translocation of bacteria across this mucosa, and the sorts of cell damage caused by pathogenic bacteria, has increased. Electron microscopy has made a valuable contribution to this knowledge. In the fish-farming industry, severe economic losses are caused by furunculosis (agent, Aeromonas salmonicida spp. salmonicida) and vibriosis [agent, Vibrio (Listonella) anguillarum]. This article provides an overview of the GI tract of fish from an electron microscopical perspective focusing on cellular damage (specific attack on tight junctions and desmosomes) caused by pathogenic bacteria, and interactions between the ,good' intestinal bacteria [e.g. lactic acid bacteria (LAB)] and pathogens. Using different in vitro methods, several studies have demonstrated that co-incubation of Atlantic salmon (Salmo salar L.) foregut (proximal intestine) with LAB and pathogens can have beneficial effects, the cell damage caused by the pathogens being prevented, to some extent, by the LAB. However, there is uncertainty over whether or not similar effects are observed in other species such as Atlantic cod (Gadus morhua L.). When discussing cellular damage in the GI tract of fish caused by pathogenic bacteria, several important questions arise including: (1) Do different pathogenic bacteria use different mechanisms to infect the gut? (2) Does the gradual development of the GI tract from larva to adult affect infection? (3) Are there different infection patterns between different fish species? The present article addresses these and other questions. [source] Aberrant hypertrophy in Smad3-deficient murine chondrocytes is rescued by restoring transforming growth factor ,,activated kinase 1/activating transcription factor 2 signaling: A potential clinical implication for osteoarthritisARTHRITIS & RHEUMATISM, Issue 8 2010Tian-Fang Li Objective To investigate the biologic significance of Smad3 in the progression of osteoarthritis (OA), the crosstalk between Smad3 and activating transcription factor 2 (ATF-2) in the transforming growth factor , (TGF,) signaling pathway, and the effects of ATF-2 overexpression and p38 activation in chondrocyte differentiation. Methods Joint disease in Smad3-knockout (Smad3,/,) mice was examined by microfocal computed tomography and histologic analysis. Numerous in vitro methods including immunostaining, real-time polymerase chain reaction, Western blotting, an ATF-2 DNA-binding assay, and a p38 kinase activity assay were used to study the various signaling responses and protein interactions underlying the altered chondrocyte phenotype in Smad3,/, mice. Results In Smad3,/, mice, an end-stage OA phenotype gradually developed. TGF,-activated kinase 1 (TAK1)/ATF-2 signaling was disrupted in Smad3,/, mouse chondrocytes at the level of p38 MAP kinase (MAPK) activation, resulting in reduced ATF-2 phosphorylation and transcriptional activity. Reintroduction of Smad3 into Smad3,/, cells restored the normal p38 response to TGF,. Phosphorylated p38 formed a complex with Smad3 by binding to a portion of Smad3 containing both the MAD homology 1 and linker domains. Additionally, Smad3 inhibited the dephosphorylation of p38 by MAPK phosphatase 1 (MKP-1). Both ATF-2 overexpression and p38 activation repressed type X collagen expression in wild-type and Smad3,/, chondrocytes. P38 was detected in articular cartilage and perichondrium; articular and sternal chondrocytes expressed p38 isoforms ,, ,, and ,, but not ,. Conclusion Smad3 is involved in both the onset and progression of OA. Loss of Smad3 abrogates TAK1/ATF-2 signaling, most likely by disrupting the Smad3,phosphorylated p38 complex, thereby promoting p38 dephosphorylation and inactivation by MKP-1. ATF-2 and p38 activation inhibit chondrocyte hypertrophy. Modulation of p38 isoform activity may provide a new therapeutic approach for OA. [source] Calcium sensing and cell signaling processes in the local regulation of osteoclastic bone resorptionBIOLOGICAL REVIEWS, Issue 1 2004Mone Zaidi ABSTRACT The skeletal matrix in terrestrial vertebrates undergoes continual cycles of removal and replacement in the processes of bone growth, repair and remodeling. The osteoclast is uniquely important in bone resorption and thus is implicated in the pathogenesis of clinically important bone and joint diseases. Activated osteoclasts form a resorptive hemivacuole with the bone surface into which they release both acid and osteoclastic lysosomal hydrolases. This article reviews cell physiological studies of the local mechanisms that regulate the resorptive process. These used in vitro methods for the isolation, culture and direct study of the properties of neonatal rat osteoclasts. They demonstrated that both local microvascular agents and products of the bone resorptive process such as ambient Ca2+ could complement longer-range systemic regulatory mechanisms such as those that might be exerted through calcitonin (CT). Thus elevated extracellular [Ca2+], or applications of surrogate divalent cation agonists for Ca2+, inhibited bone resorptive activity and produced parallel increases in cytosolic [Ca2+], cell retraction and longer-term inhibition of enzyme release in isolated rat osteoclasts. These changes showed specificity, inactivation, and voltage-dependent properties that implicated a cell surface Ca2+ receptor (CaR) sensitive to millimolar extracellular [Ca2+]. Pharmacological, biophysical and immunochemical evidence implicated a ryanodine-receptor (RyR) type II isoform in this process and localized it to a unique, surface membrane site, with an outward-facing channel-forming domain. Such a surface RyR might function either directly or indirectly in the process of extracellular [Ca2+] sensing and in turn be modulated by cyclic adenosine diphosphate ribose (cADPr) produced by the ADP-ribosyl cyclase, CD38. The review finishes by speculating about possible detailed models for these transduction events and their possible interactions with other systemic mechanisms involved in Ca2+ homeostasis as well as the possible role of the RyR-based signaling mechanisms in longer-term cell regulatory processes. [source] Minimum sequence requirements for the binding of paromomycin to the rRNA decoding site ABIOPOLYMERS, Issue 2 2007Peter C. Anderson Abstract We have recently introduced a computational methodology that combines molecular dynamics (MD) simulations, free-energy calculations, and in vitro binding assays to predict the minimum RNA structural requirements for selective, high-affinity RNA binding to small-molecule ligands. Here, we show that this methodology can be applied to the conformationally flexible aminoglycoside antibiotic paromomycin. A RNA consisting of an 11-mer:10-mer duplex that contains one 16S ribosome RNA decoding A-site bound to paromomycin was simulated for 4 ns. The methodology predicts that the 11-mer:10-mer duplex binds to paromomycin with high affinity, whereas smaller RNA duplexes lose complex stability and the ability to bind paromomycin. The predicted high-affinity binding to paromomycin of the 11-mer:10-mer duplex was confirmed experimentally (EC50 = 0.28 ,M), as well as the inability of smaller complexes to bind. Our simulations show good agreement with experiment for dynamic and structural properties of the isolated A-site, including hydrogen-bonding networks and RNA structural rearrangements upon ligand binding. The results suggest that MD simulations can supplement in vitro methods as a tool for predicting minimum RNA-binding motifs for both small, rigid ligands, and large, flexible ligands when structural information is available. © 2007 Wiley Periodicals, Inc. Biopolymers 86: 95,111, 2007. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] | ||||||||||||||||