Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Sidechain rotational isomerization in proteins. Dynamic simulation with solvent surroundings.

I Ghosh, J A McCammon

    Biophysical Journal
    |April 1, 1987
    PubMed
    Summary

    Molecular dynamics simulations reveal solvent effects on tyrosine ring rotation in proteins. While simulations approach experimental values, further refinement is needed for precise free energy barrier calculations.

    Related Concept Videos

    You might also read

    Related Articles

    Articles linked to this work by shared authors, journal, and citation graph.

    Sort by
    Same author

    Robust Devaney chaos in the two-dimensional border-collision normal form.

    Chaos (Woodbury, N.Y.)·2022
    Same author

    RPYFMM: Parallel Adaptive Fast Multipole Method for Rotne-Prager-Yamakawa Tensor in Biomolecular Hydrodynamics Simulations.

    Computer physics communications·2018
    Same author

    Visible light C-H amidation of heteroarenes with benzoyl azides.

    Chemical science·2018
    Same author

    Multiple target-based pharmacophore design from active site structures.

    SAR and QSAR in environmental research·2017
    Same author

    Feasibility and efficacy of salvage radiotherapy with concurrent weekly topotecan in recurrent primitive neuroectodermal tumor.

    Indian journal of cancer·2016
    Same author

    Computing the Amino Acid Specificity of Fluctuations in Biomolecular Systems.

    Journal of chemical theory and computation·2015

    Area of Science:

    • Biophysics
    • Computational Chemistry
    • Protein Dynamics

    Background:

    • Tyrosine residues are crucial for protein function and stability.
    • Understanding rotational isomerization of aromatic amino acids is key to protein dynamics.
    • Bovine pancreatic trypsin inhibitor (BPTI) serves as a model protein system.

    Purpose of the Study:

    • To investigate the rotational isomerization of the tyrosine 35 ring in BPTI using molecular dynamics.
    • To assess the impact of explicit solvent models on simulation accuracy.
    • To determine the free energy barrier of tyrosine ring rotation and compare it with experimental data.

    Main Methods:

    • Employing molecular dynamics (MD) simulations.
    • Utilizing an explicit solvent model representing liquid water.

    Related Experiment Videos

  • Analyzing the free energy landscape of tyrosine 35 ring rotation.

    • Main Results:

    • Inclusion of solvent significantly improved agreement with experimental results.
    • The calculated free energy barrier (13 kcal/mol at 300K) was approximately 3 kcal/mol lower than experimental nuclear magnetic resonance (NMR) findings.
    • Frictional effects from solvent damping were found to be minimal for the tyrosine 35 ring.

    Conclusions:

    • Explicit solvent models are essential for accurate simulation of protein dynamics.
    • Further refinement of hydrogen atom models may resolve remaining discrepancies in free energy calculations.
    • The tyrosine 35 ring's rotational dynamics are minimally affected by solvent friction, despite partial surface exposure.