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Combining Wet and Dry Lab Techniques to Guide the Crystallization of Large Coiled-coil Containing Proteins

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Published on: January 6, 2017

Predicting helix orientation for coiled-coil dimers.

James R Apgar¹, Karl N Gutwin, Amy E Keating

¹MIT Department of Chemistry, Cambridge, Massachusetts 02139, USA.

|May 29, 2008

Summary

This summary is machine-generated.

Predicting protein structure, specifically alpha-helical coiled coil orientation, remains challenging. Computational models and sequence-based methods achieved similar accuracy, correctly identifying about 81% of parallel versus antiparallel dimers.

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Area of Science:

Structural biology
Computational biology
Protein structure prediction

Background:

Alpha-helical coiled coils are common protein motifs formed by two or more alpha helices in a supercoiled bundle.
Variations in stoichiometry, helix orientation, and alignment make coiled coils difficult for computational fold recognition.
Subtle sequence differences encode crucial structural details, posing a challenge for predicting protein structure and interactions.

Purpose of the Study:

To evaluate computational models for recognizing the correct orientation (parallel vs. antiparallel) of dimeric alpha-helical coiled coils.
To compare the performance of structure-based energy functions and sequence-based approaches in predicting coiled coil structure.
To investigate the energetic contributions and sequence-dependent factors influencing coiled coil orientation.

Main Methods:

Generated numerous parallel and antiparallel structural models for 131 known coiled coil structures.
Assessed the accuracy of five different energy functions in identifying the correct fold orientation.
Developed and tested three sequence-based prediction methods incorporating implicit structural information.

Main Results:

Both the best structure-based and sequence-based methods achieved comparable accuracy, correctly categorizing approximately 81% of dimeric coiled coils.
Steric compatibility was identified as a significant factor for some coiled coil structures.
For many cases, the correct orientation was determined by subtle energy differences across multiple residues and energy components.

Conclusions:

Predicting the precise orientation of alpha-helical coiled coils is a complex problem in protein structure prediction.
Computational approaches, both structure-based and sequence-based, show promise but require further refinement.
Understanding subtle energetic and sequence-based determinants is crucial for improving the accuracy of coiled coil structure prediction.