Karunakar Reddy Pothula

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Electrophysiological measurements have shown that the channel protein OpdK, also known as OccK1, from Pseudomonas aeruginosa shows three conductance substates. Although several experimental studies have been performed, a description of the gating transitions at the molecular level remains elusive. In the present investigation, molecular dynamics simulations(More)
The OccK protein subfamily located in the outer membrane of Pseudomonas aeruginosa contains dynamic channels with several conformational states that range from open to closed forms. The molecular determinants of the OccK channels that contribute to the diverse gating have, however, remained elusive so far. Performing molecular dynamics (MD) simulations on(More)
The environmental coupling of the phycobiliprotein antenna complex PE555 and its excitonic energy transfer mechanisms are studied in detail. Molecular dynamics simulations were performed followed by calculations of the vertical transition energies along the classical ground-state trajectory. To this end, the distributions of energy levels for the PE555(More)
All-atom molecular dynamics simulations have a long history of applications studying ion and substrate permeation across biological and artificial pores. While offering unprecedented insights into the underpinning transport processes, MD simulations are limited in time-scales and ability to simulate physiological membrane potentials or asymmetric salt(More)
The human large intestine is populated by a high density of microorganisms, collectively termed the colonic microbiota, which has an important role in human health and nutrition. The survival of microbiota members from the dominant Gram-negative phylum Bacteroidetes depends on their ability to degrade dietary glycans that cannot be metabolized by the host.(More)
Channels in the outer membrane of Gram-negative bacteria provide essential pathways for the controlled and unidirectional transport of ions, nutrients and metabolites into the cell. At the same time the outer membrane serves as a physical barrier for the penetration of noxious substances such as antibiotics into the bacteria. Most antibiotics have to pass(More)
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