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

Alignment of beta-barrels in (beta/alpha)8 proteins using hydrogen-bonding pattern

Y Sergeev1, B Lee

  • 1Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892.

Journal of Molecular Biology
|November 25, 1994
PubMed
Summary

A new method aligns beta-sheet residues in (beta/alpha)8-barrel proteins using a 2D numbering scheme. Optimal alignment requires allowing cyclic permutation of beta-strands for rotational symmetry.

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

Control of the characteristics of a long-period grating by cladding etching.

Applied optics·2008
Same author

Simultaneous measurement of strain and temperature by use of a single fiber Bragg grating written in an erbium:ytterbium-doped fiber.

Applied optics·2008
Same author

Simultaneous measurement of strain and temperature by use of a single-fiber Bragg grating and an erbium-doped fiber amplifier.

Applied optics·2008
Same author

Fiber Bragg grating temperature sensor with controllable sensitivity.

Applied optics·2008
Same author

Angular and Speckle Multiplexing of Photorefractive Holograms by use of Fiber Speckle Patterns.

Applied optics·2008
Same author

Recirculating fiber delay-line filter with a fiber bragg grating.

Applied optics·2008

Area of Science:

  • Structural bioinformatics
  • Protein structure analysis
  • Computational biology

Background:

  • The (beta/alpha)8-barrel fold is a common protein structural motif.
  • Multiple sequence alignment is crucial for understanding protein evolution and function.
  • Aligning structurally similar but sequentially divergent proteins remains a challenge.

Purpose of the Study:

  • To develop and apply a novel multiple alignment procedure for (beta/alpha)8-barrel proteins.
  • To investigate the impact of beta-strand numbering preservation versus cyclic permutation on alignment quality.
  • To achieve optimal rotational alignment of beta-barrel structures.

Main Methods:

  • A two-dimensional numbering scheme based on beta-sheet topology (covalent and hydrogen bonding).

Related Experiment Videos

  • Two scoring functions: sequence/topological similarity and root-mean-square deviation (RMSD).
  • Application to ten known (beta/alpha)8-barrel protein structures, generating two types of alignments.

    • Main Results:

    • Alignments preserving beta-strand numbering reflect only the layer structure.
    • Allowing cyclic permutation of beta-strands is necessary for optimal rotational alignment.
    • Specific proteins like enolase and xylose isomerase require beta-strand permutation for optimal alignment with others.

    Conclusions:

    • The developed procedure effectively aligns (beta/alpha)8-barrel proteins.
    • Cyclic permutation of beta-strands is essential for accurate rotational alignment of these structures.
    • This method aids in comparative analysis and understanding of protein families with this fold.