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

Specific correlations between relative synonymous codon usage and protein secondary structure

M Oresic1, D Shalloway

  • 1Section of Biochemistry Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA.

Journal of Molecular Biology
|July 29, 1998
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

The Hepato-Exposome Axis: How Endocrine Disruptors Hijack Liver Receptors to Drive MASLD.

Journal of hepatology·2026
Same author

Pharmacometabolomic profiles in type 2 diabetic subjects treated with liraglutide or glimepiride.

Cardiovascular diabetology·2021
Same author

Technological readiness and implementation of genomic-driven precision medicine for complex diseases.

Journal of internal medicine·2021
Same author

Identification of a plasma signature of psychotic disorder in children and adolescents from the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort.

Translational psychiatry·2017
Same author

Sphingolipids and glycerophospholipids - The "ying and yang" of lipotoxicity in metabolic diseases.

Progress in lipid research·2017
Same author

Serum metabolite profile associates with the development of metabolic co-morbidities in first-episode psychosis.

Translational psychiatry·2016
Same journal

Tesorai Search: cloud-based database search engine boosts identifications for mass spectrometry proteomics with a pretrained peptide-spectrum deep-learning model.

Journal of molecular biology·2026
Same journal

Characterization of diverse functions of NRF1 nuclear localization sequence.

Journal of molecular biology·2026
Same journal

UPF3A and UPF3B shape the transcriptome cooperatively yet oppose cell function.

Journal of molecular biology·2026
Same journal

Antibody-secreting cells integrate efficient NMD with non‑canonical UPR signaling to maintain proteostasis and support massive immunoglobulin synthesis.

Journal of molecular biology·2026
Same journal

Small molecule stabilization of diverse amyloidogenic immunoglobulin light chains revealed by hydrogen-deuterium exchange mass spectrometry.

Journal of molecular biology·2026
Same journal

UPF1 at Work: Structural and Mechanistic Insights Into a Master Regulator of Nonsense-Mediated mRNA Decay.

Journal of molecular biology·2026
See all related articles

Species-specific codon usage correlates with protein secondary structures in humans and E. coli. These findings suggest unique translational mechanisms and implications for gene expression and protein folding.

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Structural Biology

Background:

  • Codon usage bias is known to influence protein expression levels.
  • The relationship between synonymous codon usage and protein structure is less understood.
  • Previous studies have not fully explained species-specific codon-structure correlations.

Purpose of the Study:

  • To investigate species-specific correlations between synonymous codon usage and protein secondary structure units.
  • To explore the potential functional and evolutionary implications of these correlations.
  • To determine if these correlations are influenced by factors like codon context or expression levels.

Main Methods:

  • Comparative analysis of three-dimensional protein structures and mRNA sequences from human and Escherichia coli.

Related Experiment Videos

  • Statistical analysis to identify significant correlations between specific codons and secondary structure elements (alpha-helices and beta-sheets).
  • Evaluation of potential confounding factors such as codon context, gene expression, GC/AU content, and positional effects.

    • Main Results:

    • Significant species-specific correlations were found between synonymous codon usage and protein secondary structures.
    • In E. coli, the Asn (AAC) codon correlates with the C-termini of beta-sheet segments, potentially for translational accuracy.
    • In humans, the Asp (GAU) codon correlates with the N-termini of alpha-helices, possibly for cotranslational folding.

    Conclusions:

    • Species-specific codon-structure correlations suggest differences in translational mechanisms between kingdoms.
    • These findings may aid in identifying key residues for secondary structure formation and improving secondary structure prediction algorithms.
    • The correlations have potential implications for optimizing recombinant gene expression in different organisms.