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

Hydrophobicity regained

P A Karplus1

  • 1Section of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, USA. pak4@cornell.edu

Protein Science : a Publication of the Protein Society
|June 1, 1997
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

Better models by discarding data?

Acta crystallographica. Section D, Biological crystallography·2013
Same author

Typical 2-Cys peroxiredoxins--structures, mechanisms and functions.

The FEBS journal·2009
Same author

Glutathione reductase of the malarial parasite Plasmodium falciparum: crystal structure and inhibitor development.

Journal of molecular biology·2003
Same author

Biochemical and crystallographic characterization of ferredoxin-NADP(+) reductase from nonphotosynthetic tissues.

Biochemistry·2001
Same author

Structure of intact AhpF reveals a mirrored thioredoxin-like active site and implies large domain rotations during catalysis.

Biochemistry·2001
Same author

Relatedness of baculovirus and gypsy retrotransposon envelope proteins.

BMC evolutionary biology·2001
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

Free energies of transfer (delta G0transfer) are commonly used to define amino acid hydrophobicity. However, these values are environment-dependent, challenging their use in predicting protein stability and ligand binding.

Area of Science:

  • Biochemistry
  • Physical Chemistry
  • Computational Biology

Background:

  • Hydrophobicity scales for amino acid side chains are crucial for understanding protein structure and function.
  • Free energies of transfer (delta G0transfer) between organic solvents and water are widely employed to quantify this hydrophobicity.
  • Existing scales often assume a universal applicability of delta G0transfer values, irrespective of the specific solvent environment.

Purpose of the Study:

  • To critically evaluate the reliability of delta G0transfer values in defining amino acid hydrophobicity.
  • To investigate the influence of the non-aqueous environment on the transfer free energies of polar side chains.
  • To propose a refined approach for establishing a more accurate hydrophobicity scale relevant to biological systems.

Main Methods:

Related Experiment Videos

  • Comparison of four established delta G0transfer scales for amino acid side chains.
  • Analysis of the solvent dependency of transfer free energies, particularly for hydrogen-bonding residues.
  • Re-evaluation of the fundamental concept of hydrophobicity in the context of solvation energetics.

Main Results:

  • delta G0transfer values for hydrogen-bonding amino acid side chains exhibit significant dependence on the specific non-aqueous solvent used.
  • This environmental sensitivity contradicts the assumption that delta G0transfer directly reflects intrinsic hydrophobicity or generic solvation energy.
  • The paradigm of equating delta G0transfer with hydrophobicity is flawed for polar groups.

Conclusions:

  • The environmental variability of delta G0transfer undermines its utility as a universal measure of amino acid hydrophobicity.
  • Current methods using delta G0transfer for estimating polar group burial energetics are unreliable.
  • A "pure" hydrophobicity scale, independent of specific solvent effects, is needed for accurate predictions in protein stability and ligand binding.