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Mechanistic models, a category encompassing both physiological and compartmental modeling, differ from empirical models' approaches to incorporating known factors about the systems being modeled. Empirical models describe data with minimal assumptions, while mechanistic models aim to provide a robust description of available data by specifying assumptions and integrating known factors about the system. Compartmental analysis is a key example of a mechanistic model in pharmacokinetics and...
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ATP-binding cassette or ABC transporter is the largest superfamily of integral membrane proteins. The transporters have transmembrane-binding domains (TMDs) and nucleotide-binding domains (NBDs). The TMDs are specific to their substrates, whereas the NBDs are similar to engines that complete ATP hydrolysis to complete the substrate transport. They can be full transporters consisting of two TMDs and NBDs, half transporters with one TMD and NBD, while some encoded with a single TMD or NBD are...
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Ras-related nuclear protein or Ran is a small G protein that cycles between its GTP and GDP bound states. Ran specific regulators, a Ran GTPase Activating Protein or RanGAP present in the cytosol and a Ran guanine nucleotide exchange factor or RanGEF present inside the nucleus regulate GTP/GDP exchange. A high concentration of GTP inside the cells, in addition to this asymmetric distribution of  Ran-specific regulators, leads to a higher RanGTP concentration inside the nucleus. This...
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Mechanistic models are utilized in individual analysis using single-source data, but imperfections arise due to data collection errors, preventing perfect prediction of observed data. The mathematical equation involves known values (Xi), observed concentrations (Ci), measurement errors (εi), model parameters (ϕj), and the related function (ƒi) for i number of values. Different least-squares metrics quantify differences between predicted and observed values. The ordinary least...
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Studying dynamics without explicit dynamics: A structure-based study of the export mechanism by AcrB.

Méliné Simsir1, Isabelle Broutin2, Isabelle Mus-Veteau1

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Resistance-nodulation-cell division (RND) proteins are key drug transporters.
  • AcrB is a major multidrug efflux pump in gram-negative bacteria, contributing to antibiotic resistance.
  • Its large size and complex mechanism hinder detailed dynamical studies.

Purpose of the Study:

  • To develop a novel strategy for exploring the dynamics of large molecular machines like AcrB.
  • To refine the understanding of AcrB's functional rotation mechanism and its associated states (A, B, E).
  • To identify key subdomains and interfaces involved in AcrB's drug efflux process.

Main Methods:

  • Utilizing information from numerous existing crystal structures of AcrB.
  • Analyzing the dynamics and interactions of systematically considered subdomains.
  • Tracking the evolution of intramonomer and intermonomer interfaces throughout the functional cycle.

Main Results:

  • Identified specific subdomains driving dynamic events in AcrB.
  • Refined the functional states (A, B, E) of the rotation mechanism.
  • Characterized the dynamic changes at protein interfaces during drug efflux.
  • Demonstrated the applicability of this strategy to other large molecular machines.

Conclusions:

  • The AcrB efflux mechanism serves as a relevant model within the HAE1 family.
  • This approach enables targeted simulations and the identification of potential drug efflux inhibitors.
  • Complex molecular dynamics can be inferred from static structural data.