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Pharmaceuticals 2017, 10(4), 89;

Propagation of Fibrillar Structural Forms in Proteins Stopped by Naturally Occurring Short Polypeptide Chain Fragments

Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, 31-530 Krakow, Poland
Chair of Medical Biochemistry, Medical College, Jagiellonian University, 31-034 Krakow, Poland
Author to whom correspondence should be addressed.
Received: 22 September 2017 / Revised: 2 November 2017 / Accepted: 13 November 2017 / Published: 16 November 2017
(This article belongs to the Special Issue Chemoinformatics and Drug Design)
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Amyloids characterized by unbounded growth of fibrillar structures cause many pathological processes. Such unbounded propagation is due to the presence of a propagating hydrophobicity field around the fibril’s main axis, preventing its closure (unlike in globular proteins). Interestingly, similar fragments, commonly referred to as solenoids, are present in many naturally occurring proteins, where their propagation is arrested by suitably located “stopper” fragments. In this work, we analyze the distribution of hydrophobicity in solenoids and in their corresponding “stoppers” from the point of view of the fuzzy oil drop model (called FOD in this paper). This model characterizes the unique linear propagation of local hydrophobicity in the solenoid fragment and allows us to pinpoint “stopper” sequences, where local hydrophobicity quite closely resembles conditions encountered in globular proteins. Consequently, such fragments perform their function by mediating entropically advantageous contact with the water environment. We discuss examples of amyloid-like structures in solenoids, with particular attention to “stop” segments present in properly folded proteins found in living organisms. View Full-Text
Keywords: amyloid; hydrophobicity; fibrillation; solenoid amyloid; hydrophobicity; fibrillation; solenoid

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Roterman, I.; Banach, M.; Konieczny, L. Propagation of Fibrillar Structural Forms in Proteins Stopped by Naturally Occurring Short Polypeptide Chain Fragments. Pharmaceuticals 2017, 10, 89.

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