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

[Computer simulation of protein molecular dynamics].

A G Grivtsov, G G Malenkov, L V Abaturov

    Molekuliarnaia Biologiia
    |May 1, 1983
    PubMed
    Summary

    Computer simulations reveal "anomalous" protein dynamics, showing structural drift in models. This deviation from experimental data suggests reduced conformational rigidity in simulated globular proteins, potentially due to missing water molecules.

    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

    [Protein conformational dynamics of crambin in crystal, solution and in the trajectories of molecular dynamics simulations].

    Biofizika·2014
    Same author

    Cyclodepsipeptides as chemical tools for studying ionic transport through membranes.

    The Journal of membrane biology·2013
    Same author

    [Structure of crambin in solution, crystal and in the trajectories of molecular dynamics simulations].

    Biofizika·2013
    Same author

    [Crystallographic and NMR spectroscopic protein structures: the inter-residue contacts].

    Molekuliarnaia biologiia·2012
    Same author

    [Hydrogen exchange and proteolytic degradation of ribonuclease A. The local splitting of the native structure and the conformation of loop segmentes].

    Biofizika·2012
    Same author

    [The mechanisms of the proteolytic degradation of native globular proteins. The role of local and global fluctuations of the native structure].

    Molekuliarnaia biologiia·2008

    Area of Science:

    • Biophysics
    • Computational Biology
    • Protein Science

    Background:

    • Computer simulations are crucial for understanding protein dynamics.
    • Previous studies have explored globular protein behavior computationally.

    Purpose of the Study:

    • To review computer simulation methods for globular protein dynamics.
    • To present key findings from simulations of pancreatic trypsin inhibitor and cytochrome c.
    • To discuss "anomalous" behaviors observed in simulated protein models.

    Main Methods:

    • Review of existing literature on protein dynamics simulations.
    • Analysis of simulation data for specific globular proteins (pancreatic trypsin inhibitor, cytochrome c).

    Main Results:

    • Simulated protein dynamics exhibit "anomalous" processes, including structural drift.
    • Simulated structures deviate from experimentally determined structures (e.g., X-ray crystallography).
    • This deviation is attributed to reduced conformational rigidity in model proteins compared to real ones.

    Conclusions:

    • The absence of hydrating water molecules may explain the reduced rigidity in simulated proteins.
    • Observed "anomalous" dynamics in simulations share similarities with phenomena in real proteins during function.
    • Further research is needed to incorporate hydration effects for more accurate protein dynamics simulations.

    Related Experiment Videos