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Related Concept Videos

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Related Experiment Video

Updated: Dec 27, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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SEQUENCE SLIDER: expanding polyalanine fragments for phasing with multiple side-chain hypotheses.

Rafael Junqueira Borges1, Kathrin Meindl1, Josep Triviño1

  • 1Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain.

Acta Crystallographica. Section D, Structural Biology
|March 6, 2020
PubMed
Summary

SEQUENCE SLIDER enhances fragment-based molecular replacement by extending initial fragments with side chains, improving macromolecular structure determination, especially in challenging low-resolution or low-fraction scenarios.

Keywords:
ARCIMBOLDOPhaserSEQUENCE SLIDERSHELXEfragment-based molecular replacementmolecular replacementphasingside-chain extension

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Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Fragment-based molecular replacement (MR) is a powerful technique for solving macromolecular structures.
  • Challenges arise at low resolution, with low solvent content, high beta-sheet composition, or low fragment accuracy.
  • Existing methods like ARCIMBOLDO struggle in these difficult scenarios.

Purpose of the Study:

  • To introduce SEQUENCE SLIDER, a novel method to overcome limitations in fragment-based MR.
  • To extend initial polyalanine fragments with side chains in a multisolution framework.
  • To improve the accuracy and success rate of macromolecular structure determination.

Main Methods:

  • SEQUENCE SLIDER extends initial fragments with side chains using a multisolution approach.
  • Fragment selection is guided by log-likelihood gain (LLG) calculated with Phaser.
  • Sequence assignment is based on secondary structure prediction or alignment with homologs.
  • Brute-force trial of sequence hypotheses through side-chain building and refinement.

Main Results:

  • SEQUENCE SLIDER successfully addressed challenging cases, including low-resolution data and low solvent content.
  • The method was validated on test cases and previously unknown structures.
  • Demonstrated success in solving the structures of MltC and a 638-residue pneumococcal lipoprotein.

Conclusions:

  • SEQUENCE SLIDER significantly enhances fragment-based MR, particularly for difficult datasets.
  • The method provides a robust framework for side-chain extension and sequence assignment.
  • Enables the determination of complex macromolecular structures previously intractable with standard methods.