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 and structural classes in proteins.

H Cid1, M Bunster, M Canales

  • 1Depto de Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile.

Protein Engineering
|July 1, 1992
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

Carbon Nanostructures Doped with Transition Metals for Pollutant Gas Adsorption Systems.

Molecules (Basel, Switzerland)·2021
Same author

Lessons learned for successful treatment of AML in the second wave of COVID-19 outbreak.

Leukemia & lymphoma·2021
Same author

Agreements and uncertainties in autologous haematopoietic stem cell mobilization and collection. A Spanish consensus document.

Bone marrow transplantation·2019
Same author

Brentuximab vedotin and ESHAP is highly effective as second-line therapy for Hodgkin lymphoma patients (long-term results of a trial by the Spanish GELTAMO Group).

Annals of oncology : official journal of the European Society for Medical Oncology·2019
Same author

Interaction of a Ti-doped semi-fullerene (TiC30) with molecules of CO and CO2.

Journal of molecular modeling·2016
Same author

A Long-term Remission of a Recurrent Acute Lymphoblastic Leukaemia with Donor Leukocyte Infusions after Allogeneic Peripheral Blood Stem Cell Transplantation.

Hematology (Amsterdam, Netherlands)·2016

This study analyzed amino acid hydrophobicity across 60 protein structures. Results indicate that averaging hydrophobicity coefficients should consider specific protein structural classes for improved accuracy in secondary structure predictions.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Hydrophobicity is a key property influencing protein folding and structure.
  • Existing hydrophobicity scales may not fully capture context-dependent variations.
  • Protein structures are diverse, falling into distinct classes based on secondary structure content.

Purpose of the Study:

  • To determine the bulk hydrophobic character of the 20 natural amino acid residues.
  • To compare these values with established hydrophobicity scales.
  • To investigate the influence of protein structural class on amino acid hydrophobicity.

Main Methods:

  • Analysis of a database comprising 60 protein structures.
  • Grouping proteins into four structural classes: alpha-alpha, beta-beta, alpha+beta, and alpha/beta.

Related Experiment Videos

  • Calculation and normalization of hydrophobicity coefficients (mean=0.0, std dev=1.0).
  • Comparison of derived coefficients with Ponnuswamy's original values.

    • Main Results:

    • Hydrophobic character was quantified for all 20 natural amino acids.
    • Most amino acid residues maintained their hydropathic character across different structural classes.
    • Variations in behavior suggest class-specific averaging is beneficial.

    Conclusions:

    • Averaging methods for hydrophobicity coefficients should account for protein structural class.
    • Incorporating structural class information can enhance the accuracy of secondary structure prediction methods.
    • Context-dependent hydrophobicity is crucial for understanding protein behavior.