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Related Concept Videos

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving01:29

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
Fischer Projections02:18

Fischer Projections

Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...

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Related Experiment Video

Updated: May 20, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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Published on: July 16, 2017

LeuT conformational sampling utilizing accelerated molecular dynamics and principal component analysis.

James R Thomas, Patrick C Gedeon, Barry J Grant

    Biophysical Journal
    |July 26, 2012
    PubMed
    Summary

    This study used molecular dynamics simulations to reveal novel conformations of monoamine transporters (MATs), uncovering how sodium ions stabilize key transport states. These findings advance our understanding of neurotransmitter transport mechanisms.

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    Area of Science:

    • Biochemistry
    • Neuroscience
    • Structural Biology

    Background:

    • Monoamine transporters (MATs) are crucial for regulating neurotransmission by transporting dopamine, norepinephrine, and serotonin.
    • The precise conformational mechanisms governing MAT function remain poorly understood, hindering therapeutic development.

    Purpose of the Study:

    • To elucidate the conformational dynamics of monoamine transporters (MATs) during the substrate transport cycle.
    • To identify key structural states and the role of ions in stabilizing these conformations.

    Main Methods:

    • Performed seven accelerated molecular dynamics simulations (250 ns each) of the leucine transporter as a model for MATs.
    • Varied the presence of substrate and sodium ions to sample different states of the transport cycle.
    • Utilized principal component analysis on transmembrane helices 1b and 6a to analyze simulation trajectories.

    Main Results:

    • Identified seven unique conformations, including two matching known crystallographic structures and one resembling an open inward state.
    • Discovered four novel conformations potentially critical for the MAT transport cycle.
    • Demonstrated that sodium ions are essential for stabilizing the locked-occluded and open-inward conformations.

    Conclusions:

    • The study provides unprecedented insights into the dynamic conformational landscape of monoamine transporters.
    • Sodium ion binding is a critical determinant for achieving specific functional states, such as occluded and open-inward.
    • These findings offer a foundation for understanding transporter function and designing targeted therapeutics.