The fuzzy oil drop model, based on hydrophobicity density distribution, generalizes the influence of water environment on protein structure and function

JOURNAL OF THEORETICAL BIOLOGY

卷:359

Article

Banach, Mateusz^1,2  Konieczny, Leszek³  Roterman, Irena¹ 

[1] Jagiellonian Univ, Coll Med, Dept Bioinformat & Telemed, Krakow, Poland

[2] Jagiellonian Univ, Fac Phys Astron & Appl Comp Sci, Krakow, Poland

[3] Jagiellonian Univ, Coll Med, Chair Med Chem, Krakow, Poland

关键词: Water environment;    Hydrophobic core;    Amyloidosis;    Thansthytetin;    Immunoglobulin-like fold;   

DOI  :  10.1016/j.jtbi.2014.05.007

来源: Elsevier

【 摘 要 】

In this paper we show that the fuzzy oil drop model represents a general framework for describing the generation of hydrophobic cores in proteins and thus provides insight into the influence of the water environment upon protein structure and stability. The model has been successfully applied in the study of a wide range of proteins, however this paper focuses specifically on domains representing immunoglobulin-like folds. Here we provide evidence that immunoglobulin-like domains, despite being structurally similar, differ with respect to their participation in the generation of hydrophobic core. It is shown that beta-structural fragments in beta-barrels participate in hydrophobic core formation in a highly differentiated manner. Quantitatively measured participation in core formation helps explain the variable stability of proteins and is shown to be related to their biological properties. This also includes the known tendency of immunoglobulin domains to form amyloids, as shown using transthyretin to reveal the clear relation between amyloidogenic properties and structural characteristics based on the fuzzy oil drop model. (C) 2014 The Authors. Published by Elsevier Ltd.

【 授权许可】

Free