Konieczny Leszek, Brylinski Michal, Roterman Irena
Institute of Biochemistry, Collegium Medicum, Jagiellonian University, Kopernika 7, 31-034 Cracow, Poland.
In Silico Biol. 2006;6(1-2):15-22.
The model adopting the three-dimensional Gauss function to express the hydrophobicity distribution in proteins is presented in this paper. The tendency to create the hydrophobic center during protein folding is expressed in form of an external force field of the form of three-dimensional Gauss function which directs the folding polypeptide to locate the hydrophobic residues in a central part of the molecule and hydrophilic ones exposed toward the molecular surface. The decrease of the differences between hydrophobicity distribution as it appears at each step of the folding simulation and the expected hydrophobicity distribution (three-dimensional Gauss function) is the convergence criterion together with traditional non-bonding interaction optimization. The model was applied to fold the hypothetical membrane protein (target protein in CASP6) TA0354_69_121 from Thermoplasma acidophilum.
本文提出了一种采用三维高斯函数来表达蛋白质中疏水性分布的模型。在蛋白质折叠过程中形成疏水中心的趋势，是以三维高斯函数形式的外力场来表示的，该外力场引导折叠的多肽将疏水残基定位在分子的中心部分，而亲水残基则暴露于分子表面。在折叠模拟的每个步骤中出现的疏水性分布与预期疏水性分布（三维高斯函数）之间差异的减小，与传统的非键相互作用优化一起，作为收敛标准。该模型被应用于折叠来自嗜热栖热菌的假设膜蛋白（CASP6中的目标蛋白）TA0354_69_121。
