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Function: require_once
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Filename: controllers/Detail.php
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Function: _error_handler
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Filename: controllers/Detail.php
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File: /var/www/html/application/controllers/Detail.php
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Function: _error_handler
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Filename: helpers/my_audit_helper.php
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Pleotropic drug resistant protein 5 (Pdr5p) is a plasma membrane ATP-binding cassette (ABC) transporter and the major drug efflux pump in Saccharomyces cerevisiae. The Pdr5p family of fungal transporters possesses a number of structural features significantly different from other modeled or crystallized ABC transporters, which include a reverse topology, an atypical ATP-binding site, a very low sequence similarity in the transmembrane section and long linkers between domains. These features present a considerable hurdle in molecular modeling studies of these important transporters. Here, we report the creation of an atomic model of Pdr5p based on a combination of homology modeling and ab initio methods, incorporating information from consensus transmembrane segment prediction, residue lipophilicity, and sequence entropy. Reported mutations in the transmembrane substrate-binding pocket that altered drug-resistance were used to validate the model, and one mutation that changed the communication pattern between transmembrane and nucleotide-binding domains was used in model improvement. The predictive power of the model was demonstrated experimentally by the increased sensitivity of yeast mutants to clotrimazole having alanine substitutions for Thr1213 and Gln1253, which are predicted to be in the substrate-binding pocket, without reducing the amount of Pdr5p in the plasma membrane. The quality and reliability of our model are discussed in the context of various approaches used for modeling different parts of the structure.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3026082 | PMC |
http://dx.doi.org/10.1016/j.jsb.2010.10.012 | DOI Listing |
ACS Chem Neurosci
December 2024
Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80210, United States.
The formation of Lewy bodies (LB) is a pathological hallmark for synucleinopathies, which is an umbrella term for many diseases, including Parkinson's disease, Lewy body dementia, and multiple system atrophy. One of the main components of LB is the aggregates of phosphorylated modification of α-Synuclein at residue 129 (αS-129), a neuronal protein expressed in the dopaminergic neurons in the brain. There are equivocal results about the role of αS-129, suggesting its involvement in both potentiating pathology and a functional role to rescue pathology.
View Article and Find Full Text PDFJ Phys Chem B
December 2024
Department of Chemistry, Eszterházy Károly Catholic University, Leányka utca 12, H-3300 Eger, Hungary.
In this work, we carry out a systematic computer simulation investigation of the single particle dynamics at the free surface of imidazolium-based room temperature ionic liquids by applying intrinsic surface analysis. Besides assessing the effect of the potential model and temperature, we focus in particular on the effect of changing the anion type, and, hence, their shape and size. Further, we also address the role of the length of the cation alkyl chains, known to protrude into the vapor phase, on the surface dynamics of the ions.
View Article and Find Full Text PDFACS Nano
December 2024
School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore.
Induction of systemic acquired resistance (SAR) in plants to control bacterial diseases has become an effective solution to the problems of agrochemical resistance and ecological environment damage caused by long-term and large-scale use of traditional bactericides. However, current SAR-inducing compounds are often unable to rapidly eliminate pathogenic bacteria in infected plant tissues to prevent further spread of the disease, severely restraining the potential for extensive application in agriculture. Herein, we address the limitations by developing a series of visible-light-absorbing aggregation-induced emission photosensitizers suitable for agricultural use.
View Article and Find Full Text PDFBiochemistry
December 2024
Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States.
The effects of guanidinium hydrochloride (GdmCl) on two intrinsically disordered proteins (IDPs) are investigated using simulations of the self-organized polymer-IDP (SOP-IDP) model. The impact of GdmCl is taken into account using the molecular transfer model (MTM). We show that due to the dramatic reduction in the stiffness of the highly charged Prothymosin-α (ProTα) with increasing concentration of GdmCl ([GdmCl]), the radius of gyration () decreases sharply until about 1.
View Article and Find Full Text PDFZebrafish
December 2024
Department of Medicine, Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK.
Zebrafish larvae are used to model the pathogenesis of multiple bacteria. This transparent model offers the unique advantage of allowing quantification of fluorescent bacterial burdens (fluorescent pixel counts [FPC]) by facile microscopical methods, replacing enumeration of bacteria using time-intensive plating of lysates on bacteriological media. Accurate FPC measurements require laborious manual image processing to mark the outside borders of the animals so as to delineate the bacteria inside the animals from those in the culture medium that they are in.
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