20 research outputs found
Unusual Constriction Zones in the Major Porins OmpU and OmpT from Vibrio cholerae
No full textThe outer membranes (OM) of many Gram-negative bacteria contain general porins, which form nonspecific, large-diameter channels for the diffusional uptake of small molecules required for cell growth and function. While the porins of Enterobacteriaceae (e.g., E. coli OmpF and OmpC) have been extensively characterized structurally and biochemically, much less is known about their counterparts in Vibrionaceae. Vibrio cholerae, the causative agent of cholera, has two major porins, OmpU and OmpT, for which no structural information is available despite their importance for the bacterium. Here we report high-resolution X-ray crystal structures of V. cholerae OmpU and OmpT complemented with molecular dynamics simulations. While similar overall to other general porins, the channels of OmpU and OmpT have unusual constrictions that create narrower barriers for small-molecule permeation and change the internal electric fields of the channels. Together with electrophysiological and in vitro transport data, our results illuminate small-molecule uptake within the Vibrionaceae. Pathania et al. describe the X-ray structures of the major Vibrio cholerae porins, OmpU and OmpT. The channels have narrow pore sizes and altered internal electric fields due to the presence of additional, unusual constriction elements. In addition, the interaction of deoxycholate and carbapenems with OmpU and OmpT are reported
Getting Drugs through Small Pores: Exploiting the Porins Pathway in Pseudomonas aeruginosa
No full textUnderstanding molecular properties of outer membrane channels of Gram-negative bacteria is of fundamental significance as they are the entry point of polar antibiotics into bacteria. Outer membrane proteomics revealed OccK8 (OprE) to be among the five most expressed substrate specific channels of the clinically important Pseudomonas aeruginosa. The high-resolution X-ray structure and electrophysiology highlighted a very narrow pore. However, experimental in vitro methods showed the transport of natural amino acids and antibiotics, among them ceftazidime. We used molecular dynamics simulations to reveal the importance of the physicochemical properties of ceftazidime in modulating the translocation through OccK8, proposing a structure–function relationship. As in general porins, the internal electric field favors the translocation of polar molecules by gainful energy compensation in the central constriction region. Importantly, the comparatively narrow OccK8 pore can undergo a substrate-induced expansion to accommodate relatively large-sized substrates
Characterisation of the major porins OmpU and OmpT of Vibrio cholerae
No full textPhD ThesisThe asymmetric outer membrane (OM) of a Gram-negative bacterium has many proteins embedded as β-barrel structures in it called outer membrane proteins (OMPs). The majority of these OMPs (porins) form non-selective channels across the OM to allow passive uptake of substrates. The treatment for infections caused by such bacteria mostly involves the administration of drugs/antibiotics, for which these porins play a very crucial role by providing an efficient (although not yet fully understood) route through their channel. The goal of this study is to study small-molecule permeation through the major porins, OmpU and OmpT, of Vibrio cholerae (the causative agent of cholera) for potential use of these proteins as the target for designing antibiotics or vaccines. Towards this project, we have succeeded in solving the 3D X-ray crystal structures of OmpU and OmpT as well as the structures of the major porins from Klebsiella pneumoniae (OmpK36) and Enterobacter cloacae (OmpE36, OmpE35).
The proteins (OmpU/T, OmpE35/E36 and OmpK36) show the typical arrangement of porins with three β-barrel monomers arranged into a trimer. Each monomer displays 16 antiparallel β-strands forming the hollow β-barrel formed by 8 long extracellular loops and 8 short periplasmic turns. The latching loop L2 stabilises the trimer while loop L3 departs from the β-barrel fold and constricts the pore half-way through the channel. An unusual feature is observed in the channels of OmpU and OmpT that distinguishes them from other typical porins. In OmpU, the first 10 residues of N-terminus insert into the barrel and constrict the pore. In contrast, the structure of OmpT reveals that the extracellular loop L8 folds inwards to constrict the lumen of the channel. Such constriction elements not only reduce the pore sizes of OmpU and OmpT but may also dramatically affect the internal electrostatics of these channels, which is very important for small-molecule permeation. In addition, we also performed single channel electrophysiology experiments with OmpU and OmpT which revealed interesting features with the addition of carbapenems.European Union’s Seventh Framework Programme (FP7/2007–2013) and European Federation of Pharmaceutical Industries and Associations companies in kind contribution. Therefore, a very special gratitude goes out to all down to EU Marie Curie network (ITN) for funding my PhD
How to get large drugs through small pores? Exploiting the porins pathway in Pseudomonas aeruginosa
No full textEvaluation of ready-to-eat cocoa based functional spreads.
No full textThis Dissertation / Report is the outcome of investigation carried out by the creator(s) / author(s) at the department/division of Central Food Technological Research Institute (CFTRI), Mysore mentioned below in this page
Dispersion relations and band gaps in wave number or frequency in the linear and nonlinear regimes for a coupled system with no paraxial approximation
No full text
Getting Drugs into Gram-Negative Bacteria: Rational Rules for Permeation through General Porins
No full textSmall, hydrophilic molecules, including most important antibiotics in clinical use, cross the Gram-negative outer membrane through the water-filled channels provided by porins. We have determined the X-ray crystal structures of the principal general porins from three species of Enterobacteriaceae, namely Enterobacter aerogenes, Enterobacter cloacae, and Klebsiella pneumoniae, and determined their antibiotic permeabilities as well as those of the orthologues from Escherichia coli. Starting from the structure of the porins and molecules, we propose a physical mechanism underlying transport and condense it in a computationally efficient scoring function. The scoring function shows good agreement with in vitro penetration data and will enable the screening of virtual databases to identify molecules with optimal permeability through porins and help to guide the optimization of antibiotics with poor permeation
Design of health monitoring models for power devices
No full textThis project highlights in a succinct manner various methods of failure for IGBT and a proposed method via Simplorer to find the Rth of a physical circuit system.
Insulated Gate Bipolar Transistors (IGBT) is amongst the most commonly used power electronic devices. They are widely used in the application of motor drivers, switching supplies, and other power conversion systems. Although they are fairly reliable, failures of IGBT still occur, leading to costly maintenance, inconvenient repairs, costly redundancy designs and at worst, catastrophic failures. By understanding the failure mechanisms in these IGBT and using real-time monitoring of their electrical and thermal characteristics, it may be possible to create health monitoring systems to predict impending failures of these devices. This can help the system controller to take evasive measures. In this project, the author has studied in detail, common failure mechanisms and so has come up with probable design health monitoring methods/models for IGBT.Bachelor of Engineerin
Raising against the trauma of parenting: A trans woman's existent experience in stuck in the middle with you
No full textAbstract
The term ‘Transgender’ is used to describe people who
hold a different gender identity than their birth sex.
Many transgenders are prescribed hormones and Sex
Reassignment Surgeries by their doctors to change their
bodies as part of the process of transition. Sometimes,
not everyone in the transgender community will take
these steps to live to their inner identity. A transsexual is
one who wishes to transition to the sex he/she
identifies. Jennifer Finney Boylan is a highly praised
trans woman author and professor. She is an activist,
and her involvement in social activities for LGBT
people, especially transgenders, are highly notable. The
work Stuck in the Middle with You: A Memoir of
Parenting in Three Genders is a memoir about Boylan,
and her transition from a man to a woman while being
married and raising a family. It explores how changes in
gender roles affect one’s viewpoint of our family as
parents. This paper deals with how Boylan’s memoir
reflects her role as a trans parent, and it also explores her
journey from being a dad to both mom and dad
