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

Packing at the protein-water interface

M Gerstein1, C Chothia

  • 1Department of Structural Biology, Stanford University, CA 94305, USA.

Proceedings of the National Academy of Sciences of the United States of America
|September 17, 1996
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

What is bioinformatics? An introduction and overview.

Yearbook of medical informatics·2016
Same author

Novel transcribed regions in the human genome.

Cold Spring Harbor symposia on quantitative biology·2007
Same author

The geometry of the ribosomal polypeptide exit tunnel.

Journal of molecular biology·2006
Same author

Remodeling of hippocampal GABAergic system in adult offspring after maternal hypoxia and magnesium sulfate load: immunohistochemical study.

Experimental neurology·2005
Same author

Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly.

Journal of molecular biology·2005
Same author

Identification of novel functional elements in the human genome.

Cold Spring Harbor symposia on quantitative biology·2004
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

Protein surface atoms occupy larger volumes due to voids, indicating less efficient packing compared to the protein core. Water molecules near the surface show reduced volumes, compensating for this effect.

Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Biology

Background:

  • Protein surfaces are hydrated, influencing protein structure and function.
  • The packing efficiency of atoms at the protein-water interface is not well understood.

Purpose of the Study:

  • To quantify the packing efficiency at the protein-water interface.
  • To investigate the relationship between atomic volume, location, and surface curvature.
  • To determine how water molecules adapt to the protein surface.

Main Methods:

  • Analysis of 22 crystal structures.
  • Calculation of atomic volumes for surface and core atoms.
  • Assessment of water molecule volumes near the protein surface.

Related Experiment Videos

Main Results:

  • Protein surface atoms occupy ~7% larger volumes than core atoms, indicating looser packing.
  • Atomic volumes correlate with structural location and surface exposure, not chemical type.
  • Concave surface regions exhibit looser packing than convex regions, linked to hydration.
  • Water molecules near the surface occupy up to 20% smaller volumes than bulk water.

Conclusions:

  • Protein surface atom packing is less efficient due to voids, influenced by surface curvature.
  • Water molecules near the protein surface adapt their volume based on contact extent.
  • These findings provide insights into protein hydration and structural dynamics.