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

Correlating structure-dependent mutation matrices with physical-chemical properties

J M Koshi1, R A Goldstein

  • 1Biophysics Research Division, University of Michigan, Ann Arbor 48109-1055, USA.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|January 1, 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

HerpesDRG: a comprehensive resource for human herpesvirus antiviral drug resistance genotyping.

BMC bioinformatics·2024
Same author

Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation.

medRxiv : the preprint server for health sciences·2021
Same author

Effects of nuclear spin polarization on reaction dynamics in photosynthetic bacterial reaction centers.

Biophysical journal·2009
Same author

Ethical consideration of incidental findings on adult brain MRI in research.

Neurology·2004
Same author

Distribution of Indel lengths.

Proteins·2001
Same author

Evolution of functionality in lattice proteins.

Journal of molecular graphics & modelling·2001

Structure-dependent mutation matrices correlate with amino acid physical-chemical properties. Octanol transfer free energy (delta G) is a strong predictor, especially for buried and exposed residues, aiding stability and foldability studies.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Structure-dependent mutation matrices are crucial for understanding protein evolution and function.
  • Amino acid physical-chemical properties influence protein structure and stability.

Purpose of the Study:

  • To investigate the correlation between structure-dependent mutation matrices and physical-chemical properties of amino acids.
  • To determine which properties best explain observed mutation patterns in different residue environments.

Main Methods:

  • Analysis of mutation matrices derived from protein sequence data.
  • Correlation analysis with physical-chemical properties: delta G of transfer (octanol, cyclohexane), helical/sheet propensity, size, and charge.
  • Examination of correlations based on residue burial (buried vs. exposed).

Related Experiment Videos

Main Results:

  • High correlation found between mutation matrices and delta G of transfer to octanol, particularly for buried and exposed residues.
  • Correlations with amino acid size and charge were environment-dependent.
  • Low correlations observed for alpha-helical and beta-sheet propensities across most matrices.

Conclusions:

  • Octanol transfer free energy serves as a valuable proxy for predicting stability changes from buried residue substitutions and foldability from exposed residue variations.
  • Amino acid size and charge conservation are important in specific local environments.
  • Alpha-helix and beta-sheet propensity conservation are not primary drivers of mutation patterns in most contexts.