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

Heterogeneity of packing: structural approach

N Kurochkina1, G Privalov

  • 1Applied Thermodynamics, Hunt Valley, Maryland 21031-0157, USA. Kurochkina@aol.com

Protein Science : a Publication of the Protein Society
|May 6, 1998
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

Specific sequence combinations at parallel and antiparallel helix-helix interfaces.

Journal of theoretical biology·2008
Same author

Amino acid composition of parallel helix-helix interfaces.

Journal of theoretical biology·2007
Same author

Conversion of fibrinogen to fibrin: mechanism of exposure of tPA- and plasminogen-binding sites.

Biochemistry·2000
Same author

Stabilization of a recombinant Fv fragment by base-loop interconnection and V(H)-V(L) permutation.

Journal of molecular biology·1997
Same author

Protein folding by a biased Monte Carlo procedure in the dihedral angle space.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology·1996
Same author

Precise scanning calorimeter for studying thermal properties of biological macromolecules in dilute solution.

Analytical biochemistry·1995
Same journal

Macromolecular crowding inhibits degradation of alpha-synuclein amyloid fibrils induced by cathepsins and MMP9.

Protein science : a publication of the Protein Society·2026
Same journal

Sequence-encoded differences in the conformational ensembles of CITED transcriptional activation domains impact coactivator binding.

Protein science : a publication of the Protein Society·2026
Same journal

The phospholipid biosynthesis enzyme PlsB contains three distinct domains for membrane association, lysophosphatidic acid synthesis, and dimerization.

Protein science : a publication of the Protein Society·2026
Same journal

Structural basis of ligand selectivity in FAD/NAD(P)H-dependent dehydrogenases: insights from trypanothione reductase and type II NADH dehydrogenase.

Protein science : a publication of the Protein Society·2026
Same journal

Achieving protease substrate-specific inhibition by mAb dual functional selections.

Protein science : a publication of the Protein Society·2026
Same journal

How important are quantum mechanical effects in controlling biological functions: Enzymes, electron transfer and bird navigation.

Protein science : a publication of the Protein Society·2026
See all related articles

Protein packing density is not uniform, with distinct low- and high-density regions. These regions are influenced by backbone and side-chain atomic groups, revealing insights into protein structure and dynamics.

Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Biology

Background:

  • Protein internal structure exhibits heterogeneity in atomic packing.
  • Understanding packing density variations is crucial for protein function and dynamics.

Purpose of the Study:

  • To analyze the heterogeneity of protein packing density.
  • To identify factors contributing to low- and high-density regions within proteins.
  • To investigate the spatial distribution of cavities and their relation to packing density.

Main Methods:

  • Statistical analysis of protein packing density distribution.
  • Examination of atomic group contributions to density variations.
  • Analysis of low-density regions around peptide groups in various protein packing types (alpha-alpha, alpha-beta, beta-beta).

Related Experiment Videos

Main Results:

  • Protein packing density shows two preferred ranges: 0.55-0.65 (low-density) and 0.75-0.8 (high-density).
  • High-density regions are mainly from the hydrogen-bonded backbone, while low-density regions involve polar/charged and apolar side chains.
  • Cavities are consistently found in the grooves between associated secondary structure elements, explaining low density near peptide and side-chain end groups.

Conclusions:

  • Protein packing density is a complex interplay of backbone and side-chain contributions.
  • The presence of cavities significantly influences local packing density, particularly around peptide groups and side-chain termini.
  • The proposed model aids in understanding protein internal motions, signal transduction, and diffusion within the protein matrix.