Simulating Protein Folding in Variable Environmental Conditions

I. Definition of the amyloid
Irena Roterman and Leszek Konieczny
Introduction
I.1. Secondary structure criteria: β-structure, presence of L- and
R-helical conformations, H-bonds system, configuration of Phi and Psi angles
I.2. Tertiary structure criterion: planar (2D) structure
I.3. Quaternary structure―structure of the fibril―dominance of hydrogen
bonds in ensuring stability of the fibril
Conclusions
References
II. Introduction to the model
Irena Roterman, Katarzyna Stapor, Piotr Fabian, Dawid Dułak and
Leszek Konieczny
II.1. Secondary structure―Partial unfolding model
II.2. Tertiary structure―Fuzzy oil drop model (FOD-M): Assessment of
non-bonding stabilization; size and shape of the protein
II.3. Quaternary structure - capability for association - structure of the fibril
on the basis of the FOD-M model
References
III. Environment-dependent structural factors
Irena Roterman, Leszek Konieczny and Katarzyna Stapor
III.1. Micelle-like structures: 0.0 < K < 0.4
III.2. Analysis of prion proteins
III.3. Enzymes — Tracing biological activity
III.4. Membrane proteins
III.5. Chaperone and chaperonins
III.6. Funnel model
References
IV. Three scenarios for amyloid transformation
Irena Roterman, Leszek Konieczny, Piotr Fabian and Katarzyna Stapor
IV.1. Transthyretin, VL domain of IgG―Increase of hydrophobicity disorder as
a result of amyloid transformation
IV.2. α-synuclein―Decrease in hydrophobicity disorder as a result of amyloid
transformation
IV.3. Functional amyloid―Endorphin
IV.4. Funnel model for amyloid transformation
References
Further reading
V. Proposed computational procedure for protein and amyloid
structure prediction
Irena Roterman, Leszek Konieczny, Dawid Du1ak and Katarzyna Stapor
V.1. In silico protein folding
V.2. Protein transformation to amyloid form―In silico procedure
V.3. Partial unfolding of native structure
References
VI. Other models
Irena Roterman, Leszek Konieczny, Piotr Fabian and Katarzyna Stapor
VI.1. Miscellaneous models
VI.2. Solenoids as examples of how the propagation of a fibrillar
structure can be arrested- computer aided drug design method limiting
the propagation of the fibril
VI.3. Prospective research
References
Suggested Readings