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Subunit secondary structure in filamentous viruses: predictions and observations
J Finer-Moore1, R M Stroud, B Prescott
1Department of Biochemistry and Biophysics, School of Medicine, University of California, San Francisco 94143.
Journal of Biomolecular Structure & Dynamics
|August 1, 1984
Summary
Protein secondary structure prediction reveals distinct conformations for filamentous bacteriophage coat proteins. Class I virions favor alpha-helices, while Class II virions show a propensity for beta-structures, suggesting varied disassembly mechanisms.
Area of Science:
- Structural biology
- Virology
- Biochemistry
Background:
- Filamentous bacteriophages are non-enveloped viruses with proteinaceous coats.
- Understanding coat protein structure is crucial for viral assembly and disassembly mechanisms.
Purpose of the Study:
- To predict the secondary structure of coat proteins from six filamentous bacteriophages using computational algorithms.
- To compare the predicted structures with experimental data and investigate differences between viral classes.
Main Methods:
- Application of the Garnier, Osguthorpe, and Robson algorithm for protein secondary structure prediction.
- Utilized the Chou and Fasman algorithm for qualitative comparison.
- Correlated predictions with experimental data from laser Raman spectroscopy and circular dichroism.
Main Results:
- The Garnier algorithm predicted a high percentage of alpha-helix for Class I virion subunits (fd, If1, IKe), aligning with experimental findings.
- Class II virion subunits (Pf1, Xf, Pf3) were consistently predicted to have a predominance of beta-structure, even when algorithms favored helix.
- Both predictive algorithms indicated a distinction between Class I and Class II subunits, with Class II showing less uniform alpha-helical conformation.
Conclusions:
- Predictive algorithms and experimental data highlight structural differences between Class I and Class II filamentous bacteriophage coat proteins.
- Class II subunits exhibit a greater tendency to adopt non-alpha-helical conformations.
- Results propose a model for viral disassembly involving the unraveling of coat protein helices at the N-terminus.