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

Does secondary structure determine tertiary structure in proteins?

Haipeng Gong1, George D Rose

  • 1Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218-2608, USA.

Proteins
|August 17, 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

A dataset of 1.2 million molecules with DFT-level quantum chemical annotations for molecular representation learning.

Communications chemistry·2026
Same author

The master molecule that built biology: How water shaped the chemistry of life.

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

Development and internal validation of a kinetic heterogeneity-based nomogram by dynamic contrast-enhanced magnetic resonance imaging to differentiate benign and malignant breast BI-RADS 4 lesions.

Gland surgery·2026
Same author

Preoperative Prediction of Perineural Invasion and Survival in Gastric Cancer Using Extracellular Volume Fraction and Dual-Energy CT Quantitative Parameters: A Dual-Center Study.

Academic radiology·2026
Same author

Vitamin B6 preserves the stemness-like phenotypes and antitumor ability of CD8<sup>+</sup> T cells.

Developmental cell·2025
Same author

50 years in the shadow of the Ramachandran plot.

Protein science : a publication of the Protein Society·2025
Same journal

Engineered HSP90-MP65 Bivalent Fusion Antigen: A Novel Vaccine Candidate Against Invasive Candidiasis.

Proteins·2026
Same journal

Physics-Based Energy Functions for Computational Protein Design.

Proteins·2026
Same journal

Impact of Stabilizing Osmolytes on the Conformational Dynamics of Human and Rat Islet Amyloid Polypeptides.

Proteins·2026
Same journal

Stabilization of Bone Morphogenetic Protein-2 at Physiological pH: Contrasting Roles of CHAPS and Arginine in Aggregation Inhibition.

Proteins·2026
Same journal

Structural Insights Into the Function of Leishmania major Adenylosuccinate Lyase.

Proteins·2026
Same journal

Generalizing the Gaussian Network Model: Spanning-Tree Thermodynamics Shows Entropy-Driven KRAS Activation.

Proteins·2026
See all related articles

Approximate protein backbone structures, represented as sequences of mesostates, can accurately identify protein families, superfamilies, and tertiary folds. This coarse-grained approach simplifies structural analysis for protein identification.

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Accurate protein tertiary fold identification is crucial for understanding protein function.
  • Current methods often require detailed atomic coordinates, which may not always be available.

Purpose of the Study:

  • To determine if approximate protein backbone structure is sufficient for identifying protein family, superfamily, and tertiary fold.
  • To develop a coarse-grained method for protein structure representation and comparison.

Main Methods:

  • Extracted backbone dihedral angles from 2,439 known protein structures.
  • Mapped these angles into 36 labeled mesostates (60° x 60° bins).
  • Represented protein conformation as a linear sequence of mesostates for alignment using sequence-comparison methods.

Related Experiment Videos

Main Results:

  • The mesostate sequence successfully approximated protein conformation.
  • This coarse-grained representation allowed for the recognition of protein family, superfamily, and fold with good fidelity.
  • Demonstrated the efficacy of sequence-comparison methods on mesostate sequences.

Conclusions:

  • Highly approximate knowledge of protein backbone structure is sufficient for accurate protein identification at family, superfamily, and fold levels.
  • The mesostate sequence approach offers a viable, simplified alternative for protein structural analysis and classification.