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EmrE is a small multidrug resistance (SMR) pump of antiparallel topology that confers resistance to a broad range of polyaromatic cations in . Atomic-level understanding of conformational changes for the selectivity of substrate and transport of a diverse array of drugs through the smallest known efflux pumps is crucial to multi-drug resistance. Therefore, the present study aims to provide insights into conformational changes during the transport through EmrE transporter at different pH. Molecular dynamics simulations have been carried out on the complete structure of EmrE in the absence of substrate. Computational analyses such as secondary structure, principal component, dynamic cross-correlation matrix, and hydrogen bond calculations have been performed. Analysis of MD trajectories in this study revealed pH-dependent interactions that influenced the structural dynamics of EmrE. Notably, at high pH, Glu14 and Tyr60 in both monomers formed electrostatic interactions, while these interactions decreased significantly at a low pH. Interestingly, a kink at helix 3 (H3) and dual open conformation of EmrE at low pH were also observed in contrast to a closed state discerned towards the periplasmic side at high pH. Significant interactions between C-terminal residues and residues at the edge of H1 & Loop1 and H3 & Loop3 were identified, suggesting their role in stabilizing the closed conformation of EmrE at the periplasmic end under high pH conditions. The present study enhances our understanding of EmrE's conformational changes, shedding light on the pH-dependent mechanisms that are likely to impact its function in multi-drug resistance.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2023.2298386 | DOI Listing |
J Biomol Struct Dyn
December 2024
Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.
Nucleocapsid protein (N) of SARS-CoV-2 is a multivalent protein, which is responsible for viral replication, assembly, packaging and modulates host immune response. In this study, we report conformational measurements of N protein at different pH by observing transition in secondary and tertiary structural contents by biophysical and computational approaches. Spectroscopic measurements revealed that N protein loses its secondary and tertiary structure at extreme acidic pH while maintaining its native conformation at mild acidic and alkaline pH.
View Article and Find Full Text PDFACS Appl Mater Interfaces
December 2024
Group of Characterization of Materials, Departament de Física, Universitat Politècnica de Catalunya, Campus Diagonal-Besòs, Av. Eduard Maristany 10-14, Barcelona 08019, Spain.
Hybrid organic-inorganic perovskites (HOIP) have emerged in recent years as highly promising semiconducting materials for a wide range of optoelectronic and energy applications. Nevertheless, the rotational dynamics of the organic components and many-molecule interdependencies, which may strongly impact the functional properties of HOIP, are not yet fully understood. In this study, we quantitatively analyze the orientational disorder and molecular correlations in archetypal perovskite CHNHPbI (MAPI) by performing comprehensive molecular dynamics simulations and entropy calculations.
View Article and Find Full Text PDFInt J Biol Macromol
December 2024
School of Health Science and Engineering, Shanghai Engineering Research Center of Food Rapid Detection, University of Shanghai for Science and Technology, Shanghai 200093, China. Electronic address:
Aptamer conformations are susceptible to environmental conditions, which makes it difficult to achieve stable targets detection in complex environments with aptasensors. Imprinting strategy was proposed to immobilize the specific conformation of aptamers, aiming to enhance their recognition anti-interference. However, it is mechanistically unclear how the imprinted polymers affect aptamers' recognition, which limits application of the strategy.
View Article and Find Full Text PDFJ Biol Chem
December 2024
Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210. Electronic address:
Streptococcus pyogenes (Sp) Cas9 has been widely utilized to edit genomes across diverse species. To achieve high efficiency and specificity as a gene editing enzyme, Sp Cas9 undergoes a series of sequential conformational changes during substrate binding and catalysis. Here, we employed single molecule FRET techniques to investigate the effect of different KCl concentrations on conformational dynamics of Sp Cas9 in the presence or absence of a single-guide RNA (sgRNA).
View Article and Find Full Text PDFChem Asian J
December 2024
IIT Roorkee: Indian Institute of Technology Roorkee, Department of Chemistry, Room No D-307, Department of Chemistry, Indian Institute of Technology Roorkee, 247667, Roorkee, INDIA.
The extent of conformational alteration of the porphyrin macrocycle during the course of protonation was observed, both experimentally and theoretically. For synthesized β-substituted octaphenylporphyrin (OPP) ring systems this macrocyclic distortions have been investigated by spectroscopic and computational analysis. Protonation induced nonplanarity in macrocyclic system is experimentally observed in a single step during spectrophotometric titration.
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