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

Molecular dynamics and protein function.

M Karplus1, J Kuriyan

  • 1Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA. marci@tammy.harvard.edu

Proceedings of the National Academy of Sciences of the United States of America
|May 5, 2005
PubMed
Summary
This summary is machine-generated.

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

All-atom empirical potential for molecular modeling and dynamics studies of proteins.

The journal of physical chemistry. B·2014
Same author

A conformational transition in the myosin VI converter contributes to the variable step size.

Biophysical journal·2011
Same author

Calculation of free-energy differences by confinement simulations. Application to peptide conformers.

The journal of physical chemistry. B·2009
Same author

CHARMM: the biomolecular simulation program.

Journal of computational chemistry·2009
Same author

Allosteric communication in myosin V: from small conformational changes to large directed movements.

PLoS computational biology·2008
Same author

Heat capacity and compactness of denatured proteins.

Biophysical chemistry·2006
Same journal

The TaMYB55-TaSnRK1α1-TabZIP9 module confers heat stress tolerance in wheat.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same journal

Superstatistics approach to turbulent circulation fluctuations.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same journal

A molecular timescale for evolution of cobamide biosynthesis.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same journal

Pierre Chambon, a pioneer of molecular biology and gene regulation in eukaryotes.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same journal

Granulosa cell glycogen fuels the avascular corpus luteum.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same journal

Synthetic essentiality of TRAIL/TNFSF10 in VHL-deficient renal cell carcinoma.

Proceedings of the National Academy of Sciences of the United States of America·2026
See all related articles

Molecular dynamics simulations help understand biological macromolecules like proteins. These simulations explore protein folding, enzymatic catalysis, and molecular motors, advancing structural biology.

Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Understanding biological macromolecules requires knowledge of their structure and dynamics.
  • Molecular dynamics (MD) simulations are powerful computational tools for exploring molecular conformational landscapes.
  • Advancements in computational power and simulation methodologies enhance MD's applicability in structural biology.

Purpose of the Study:

  • To survey the application of MD simulations in understanding biological mechanisms.
  • To highlight contributions of simulations to protein folding and enzymatic catalysis.
  • To present specific examples of MD simulations applied to biological systems like F(1) ATPase and Src proteins.

Main Methods:

  • Molecular dynamics simulations

Related Experiment Videos

  • Computational exploration of conformational energy landscapes
  • Analysis of simulation data for mechanistic insights

    • Main Results:

    • Simulations have elucidated mechanisms in protein folding and enzymatic catalysis.
    • MD simulations provide insights into the function of the F(1) ATPase molecular motor.
    • Applications to Src family signaling proteins demonstrate simulation utility in studying specific biological systems.

    Conclusions:

    • MD simulations are crucial for understanding the structure-dynamics-function relationship of macromolecules.
    • The continued development of computational methods promises further breakthroughs in structural biology.
    • Simulations offer a powerful approach to dissecting complex biological processes at the molecular level.