Solvent‐induced organization: A physical model of folding myoglobin

@article{Callaway1994SolventinducedOA,
  title={Solvent‐induced organization: A physical model of folding myoglobin},
  author={David J. E. Callaway},
  journal={Proteins: Structure},
  year={1994},
  volume={20}
}
The essential features of the in vitro refolding of myoglobin are expressed in a solvable physical model. Alpha helices are taken as the fundamental collective coordinates of the system, while the refolding is assumed to be mainly driven by solvent‐induced hydrophobic forces. A quantitative model of these forces is developed and compared with experimental and theoretical results. The model is then tested by being employed in a simulation scheme designed to mimic solvent effects. Realistic… 
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15 Citations
Background Citations
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Methods Citations
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15 Citations

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References

SHOWING 1-10 OF 64 REFERENCES

Diffusion‐collision model for the folding kinetics of myoglobin

The diffusion‐collision model has been used to analyze the folding kinetics of myoglobins and significant differences in the contributing intermediates are found in the native state and to the midpoint of the folding transitions.

A model of myoglobin self-organization.

Mechanism of protein folding: I. General considerations and refolding of myoglobin

To explain the rapidity of the process of protein folding, we cite two aspects of hydrophobic interaction: its long‐range nature and the specificity of pairing after the formation of secondary…

Structural characterization of a partly folded apomyoglobin intermediate.

A structural model is presented for the partly folded intermediate of native myoglobin in which a compact subdomain retains structure while the remainder of the protein is essentially unfolded.

Temperature dependence of the structure and dynamics of myoglobin. A simulation approach.

Folding and stability of helical proteins: carp myogen.

Cold denaturation of myoglobin.

Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin.

Hydrogen exchange pulse labeling and stopped-flow circular dichroism were used to establish that the structure of the earliest detectable intermediate formed during refolding of apomyoglobin…

Probing the stability of a partly folded apomyoglobin intermediate by site-directed mutagenesis.

It is suggested that I is stabilized by relatively nonspecific hydrophobic interactions that allow it to adapt easily to mutation, and appears to conform to the "molten globule" model, with the caveat that only part of the polypeptide chain appears to participate in the globule.

Protein folding: evaluation of some simple rules for the assembly of helices into tertiary structures with myoglobin as an example.

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