Kuroda Y
Protein Engineering Research Institute, Osaka, Japan.
Protein Eng. 1995 Feb;8(2):97-101. doi: 10.1093/protein/8.2.97.
This paper describes peptide analogs and the design strategy that were used to facilitate the final construction of a de novo-designed protein (ALIN) whose stable tertiary fold has been determined recently by NMR spectroscopy. Previous studies have suggested that the main problem in the de novo design of proteins is the attainment of a protein with a defined fold. To effectively overcome this mainchain multiconformation problem, three related steps, with experimental evaluation of the design hypotheses for each step, were pursued in the design process. Firstly, 15-residue sequences with experimentally verified high helicites were selected for the helical regions. Secondly, hydrophobic and electrostatic interhelical interactions as well as an interhelical disulfide bridge were designed to favor an antiparallel configuration of the helix axis. Finally, a loop with sufficient flexibility was inserted to stabilize the helices in the desired orientation. To assess the design strategy, peptides corresponding to each design step were synthesized and their structures verified experimentally by far-UV CD. As anticipated, ALIN was the most helical, and the SS-bridged dimeric peptides were more helical than their monomeric counterparts. The van't Hoff enthalpy change for ALIN computed from the CD denaturation curve and assuming a two-state model was 50 kJ/mol, a value close to that observed for helical coiled-coils. Overall, this report shows that small, simple proteins can be built using the current knowledge of protein structures.
本文描述了肽类似物以及用于最终构建一个从头设计的蛋白质(ALIN)的设计策略,该蛋白质稳定的三级结构最近已通过核磁共振光谱法确定。先前的研究表明,蛋白质从头设计中的主要问题是获得具有确定折叠的蛋白质。为了有效克服这个主链多构象问题,在设计过程中采取了三个相关步骤,并对每个步骤的设计假设进行了实验评估。首先,为螺旋区域选择了具有经实验验证的高螺旋度的15个残基序列。其次,设计疏水和静电螺旋间相互作用以及一个螺旋间二硫键,以有利于螺旋轴的反平行构象。最后,插入一个具有足够灵活性的环,以将螺旋稳定在所需的方向上。为了评估设计策略,合成了与每个设计步骤相对应的肽,并通过远紫外圆二色光谱对其结构进行了实验验证。正如预期的那样,ALIN的螺旋度最高,并且有二硫键桥连的二聚体肽比其单体对应物的螺旋度更高。根据圆二色变性曲线并假设为两态模型计算得出的ALIN的范特霍夫焓变为50 kJ/mol,该值接近于螺旋卷曲螺旋所观察到的值。总体而言,本报告表明,可以利用当前的蛋白质结构知识构建小型、简单的蛋白质。