From Globular Proteins to Amyloids

From Globular Proteins to Amyloids
Copyright
Contributors
Preface
	References
Introduction
	References
1 . Description of the fuzzy oil drop model
	Amyloids as seen from the perspective of the FOD model
	References
2 . Folding with active participation of water
	References
3 . Information encoded in protein structure
	References
4 . Globular or ribbon-like micelle
	Effect of the aqueous environment on intramolecular processes
	The effect of proteins influence on the water structuralization
	Amyloid structures
	The protein is an intelligent micelle
	References
5 . Proteins structured as spherical micelles
	Type III antifreeze proteins
	Titin
	Ultrafast-folding proteins
	Stabilization in the presence of disulfide bonds
	Proteins consistent with the theoretical model—spherical micelles
	Counter-example—prefoldin
	References
6 . Local discordance
6.A . The active site in a single-chain enzyme
	Lysozyme
	Ribonuclease
	References
6.B . Protein-protein interaction encoded as an exposure of hydrophobic residues on the surface
	Individual chains
	DNA binding
	References
6.C . Ligand binding cavity encoded as a local hydrophobicity deficiency
	References
7 . Solenoid – An amyloid under control
	Antifreeze proteins represented by protein extracted from Flavobacterum frigoris PS1 found in the Antarctic region
	Lyase family represented by pectate lyase
	“Perfect” solenoid
	Flattened double-walled solenoid
	Conclusions and discussion
	References
8 . Composite structures
	Single-chian enzyme consisting of three domains
		Analysis of the molecule as a whole
		Domains treated as independent structural units
	Homodimer enzyme
		Analysis of chains and domains regarded as standalone structures
		Domains
	Conclusions and discussion
	References
9 . Non-amyloid structure of the Aβ(1–42) polypeptide in presence of a permanent chaperone
9.A . Complexes Aβ(1–42) polypeptide with non-protein molecules
	Structural characteristics of Aβ(1–42) fragments in complex with selected compounds
	Assessment of the hydrophobic core structure in non-amyloid forms of Aβ(1–42)
		Analysis of the 11–16 fragment
		Analysis of the 16–22 fragment
		Analysis of the 22–28 fragment
		Unusual structure observed in 1HZ3 – 10-35 fragment of Aβ(1–42) forming a random coil, together with an external factor (tr ...
		Common characteristics of all discussed proteins
		Comprehensive analysis
	Conclusions and discussion
	References
9.B . Structure of selected fragments of Aβ(1–42) in complex with other proteins
	Non-amyloid conformations of Aβ(1–42) fragments
	Aβ(17–27) and Aβ(16–28) in complex with lipocain
	Aβ(16–40) in complex with phage-display selected affibody protein Z(Aβ3)
	Aβ(1–40) in complex with polyphenol ε-viniferin glucoside (EVG)
	Aβ(1–21) in complex with the JEF ligand
	Aβ(18–41) fragment inserted as the antigen receptor variable domain in shark immunoglobulin
	Discussion and conclusions
	References
10 . Amyloids identification based on fuzzy oil drop model
	References
10.A . Amyloid as a ribbon-like micelle
	Amyloid Aβ(1–40) peptide with the Osaka mutation (E22Δ)
	Aβ(11–42) amyloid
	Prion amyloid
	In silico experiment
	References
10.B . Analysis of alternative conformations of the Aβ(1–40) amyloid protein
	Alternative structural forms of polypeptide Aβ(1–40) polypeptide which includes the Osaka mutation
	Values of RD and correlation coefficients may be calculated for the entire protein (polypeptide), but also for selected fra ...
	Comparative analysis of protein structures generated using folding simulation software
	References
10.C . Specificity of amino acid sequence and its role in secondary and supersecondary structure generation
	Short fragments of polypeptide playing the ole of linkers between β-strands belonging to β-sheets
		Short peptides
	Alternative structures solve the problem of minimization of the hydrophobic area on the surface generating the ribbon-like  ...
	References
11 . Anti-amyloid drug design
	References
12 . The hypothetical amyloid transformation of transthyretin
	References
. Summary: protein is an intelligent micelle
	Influence of protein on water environment
	Influence of water environment on amyloid transformation
	Protein is an intelligent micelle
	References
Index
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W