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Alignment of Synchronized Time-Series Data Using the Characterizing Loss of Cell Cycle Synchrony Model for Cross-Experiment Comparisons

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The meaning of alignment: lessons from structural diversity.

Walter Pirovano¹, K Anton Feenstra, Jaap Heringa

¹Centre for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, De Boelelaan 1081A, 1081HV Amsterdam, the Netherlands. pirovano@few.vu.nl

BMC Bioinformatics

|December 25, 2008

Summary

Protein structural diversity significantly impacts sequence alignments, revealing inconsistencies even with minor structural changes. This highlights the need for better methods to handle ambiguous alignment regions in protein analysis.

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Published on: July 14, 2015

Area of Science:

Structural biology
Bioinformatics
Computational biology

Background:

Protein structural alignment is crucial for understanding protein function, evolution, and classification.
Current methods often overlook protein structural diversity, producing single alignments.
This limitation affects the accuracy of sequence alignment benchmarks and functional interpretations.

Purpose of the Study:

To investigate the impact of protein structural diversity on structural alignment.
To analyze alignment inconsistencies arising from subtle structural variations.
To develop improved methods for representing and visualizing protein alignments.

Main Methods:

Utilized alternative protein crystal structures and simulation snapshots.
Generated and analyzed multiple structural alignments from diverse conformations.
Examined specific examples like the GroES 'mobile loop' to illustrate alignment variability.

Main Results:

Protein structural diversity significantly affects structural alignment outcomes.
Even small spatial divergences (sub-Angstrom) can lead to contradictory sequence alignments.
Alignment inconsistencies challenge the straightforward biological interpretation of protein structures.

Conclusions:

Comprehensive handling of ambiguous alignment regions is essential for advancing structural alignment applications.
New visualization methods and an online database (http://www.ibi.vu.nl/databases/stralivari) have been developed to address these inconsistencies.
Accurate protein structural alignment requires accounting for conformational flexibility and diversity.