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

Conformational filtering in polypeptides and proteins

S Vajda1

  • 1Department of Biomedical Engineering, Boston University, MA 02215.

Journal of Molecular Biology
|January 5, 1993
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

Atomically precise (catalytic) particles synthesized by a novel cluster deposition instrument.

The Journal of chemical physics·2014
Same author

Evolutionary origins of the estrogen signaling system: insights from amphioxus.

The Journal of steroid biochemistry and molecular biology·2011
Same author

Increased silver activity for direct propylene epoxidation via subnanometer size effects.

Science (New York, N.Y.)·2010
Same author

Technique of the analysis of variance.

Nature·2010
Same author

Consensus alignment for reliable framework prediction in homology modeling.

Bioinformatics (Oxford, England)·2003
Same author

Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins.

Journal of computational chemistry·2002
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
Same journal

Structural basis for the pro-amyloidogenic action and ligand binding of a novel W72R variant of human apolipoprotein A-I.

Journal of molecular biology·2026
Same journal

Cryo-EM Structure of the C. Elegans Septin Tetramer Reveals a Revised Architecture and Conserved Positional Orthology.

Journal of molecular biology·2026
See all related articles

This study introduces a novel conformational filtering method to predict protein structures by assigning ensembles of states to amino acid residues. The approach accurately predicts peptide conformers and protein structural variability, improving de novo structure prediction.

Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Predicting protein tertiary structure from sequence is a fundamental challenge in biology.
  • Peptides in solution exist as ensembles of rapidly interconverting conformers.
  • Traditional structure prediction methods often struggle with accuracy and computational cost.

Purpose of the Study:

  • To develop a novel method for assigning ensembles of conformational states to amino acid residues.
  • To improve de novo protein structure prediction by analyzing conformational ensembles.
  • To provide insights into protein structural variability and the influence of the environment.

Main Methods:

  • Utilizing conformational filters with varying approximations to estimate state probabilities.

Related Experiment Videos

  • Employing Markov chains with locally identifiable and transferable transition matrices.
  • Applying acceptance probabilities to retain true conformational states while reducing potential conformations.

    • Main Results:

    • The conformational filtering method successfully predicts ensembles of conformers for peptides in solution.
    • Transition matrices derived from crystal structures are transferable to solution structures of short peptides, agreeing with NMR data.
    • The method retains true conformational states for up to 87% of residues and quantifies conformational variability.

    Conclusions:

    • Conformational filtering offers an advantageous approach to de novo sequence analysis and structure prediction.
    • The method accurately models peptide ensembles and provides a measure of residue-level structural variability.
    • Understanding conformational variability aids in predicting how local structure is influenced by the broader protein environment.