Jove
Visualize
Contact Us

Related Experiment Videos

Recoverable one-dimensional encoding of three-dimensional protein structures.

Akira R Kinjo1, Ken Nishikawa

  • 1Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima 411-8540, Japan. akinjo@genes.nig.ac.jp

Bioinformatics (Oxford, England)
|February 22, 2005
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

Prevalence and Clinical Characteristics of Patients With Heart Failure With Preserved Ejection Fraction Who Meet the Obesity-Related Eligibility Criteria for Subcutaneous Incretin Receptor Agonists in Japan　- Insights From the PARACLETE Study.

Circulation journal : official journal of the Japanese Circulation Society·2026
Same author

Invasive Assessment of Coronary Microvascular Dysfunction in Patients With Wild-Type Transthyretin Amyloid Cardiomyopathy.

Journal of cardiac failure·2026
Same author

A novel risk score model for predicting mortality in heart failure with preserved ejection fraction: Insights from the CURE-HF Registry-ApHAC score.

PloS one·2025
Same author

Identification of Metabolomics Profile in Elderly Patients at the End Stage of Heart Failure.

Circulation journal : official journal of the Japanese Circulation Society·2025
Same author

Clinical Profile and Prognosis of Patients With Acute Decompensated Heart Failure Who Met the Obesity-Related Eligibility for Subcutaneous Semaglutide　- Findings From the CURE-HF Registry.

Circulation reports·2025
Same author

Clinical Utility of the HELT-E<sub>2</sub>S<sub>2</sub> Score for Risk Stratification in Patients with Acute Decompensated Heart Failure: Insights from the CURE-HF Registry.

Internal medicine (Tokyo, Japan)·2025
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

Researchers can now predict protein 3D structure using three types of 1D structures: secondary structure, contact number, and a novel residue-wise contact order. This method accurately reconstructs protein structures, advancing sequence-structure relationship understanding.

Area of Science:

  • * Structural Biology
  • * Computational Biology
  • * Biophysics

Background:

  • * One-dimensional (1D) protein structures, such as secondary structure and contact number, offer insights into how amino acid sequences encode three-dimensional (3D) protein structures.
  • * The sufficiency of 1D structural information for accurately reconstructing a protein's 3D native structure remains an open question in the field.

Purpose of the Study:

  • * To investigate if a combination of specific 1D structural features can reliably predict a protein's 3D structure.
  • * To introduce and validate a new 1D structural descriptor, residue-wise contact order, for protein structure prediction.

Main Methods:

  • * Utilized simulated annealing molecular dynamics simulations to search for protein structures consistent with provided 1D structural restraints.

Related Experiment Videos

  • * Applied the method to a dataset of 16 proteins spanning diverse structural classes and sizes (56–146 residues).

    • Main Results:

    • * Successfully recovered 3D protein structures with a coordinate Root Mean Square Deviation (RMSD) of less than 4 Å compared to native structures.
    • * Achieved an RMSD of less than 2 Å for the majority of the tested proteins, demonstrating high accuracy.
    • * Validated the predictive power of secondary structure, contact number, and the newly introduced residue-wise contact order.

    Conclusions:

    • * The combination of secondary structure, contact number, and residue-wise contact order provides sufficient information for accurate protein 3D structure prediction.
    • * This approach offers a novel pathway for protein structure prediction and deepens the understanding of the protein sequence-structure relationship.