Development of a Structural Bioinformatics-Based Three-Dimensional Domain Swapping Protein Engineering Platform
|關鍵字:||蛋白質立體域交換現象;蛋白質工程;three-dimensional domain swapping;protein engineering|
|摘要:||蛋白質立體域交換現象(3D domain swapping)是蛋白質形成四級結構的一種機制。其定義
現象的蛋白質的兩個域的片段稱為hinge loop。研究 hinge loop 有助深入了解此現象，
Three-dimensional domain swapping (DS), a structural phenomenon first clearly described in the mid 1990s, is a mechanism for protein oligomerization defined as two or more proteins exchanging part of their identical domain to form intertwined oligomers. Studying DS can help reveal the functional regulation, molecular evolution and structural dynamics of proteins, and help find applications in creating artificial biopolymers and treating deposition diseases like the Alzheimer’s disease and bovine spongiform encephalopathy. Despite the increasing interest in DS, related bioinformatics methods are rarely available and there is still a lack of a comprehensive database for studying DS. The domains of a DS protein are connected by a hinge loop. Hinge loops have been proposed to be the causes and/or the results of DS; however, precise methods for their identification are not readily available. We have previously developed a rapid protein structural similarity search method called SARST and an accurate method ADiDoS for the detection of DS relationship between proteins. In this proposal, we have determined to improve and combine them into the first database searching system for DS-related proteins. This searching system, named DSSARST (3D Domain Swapping Search Aided by Ramachandran Sequential Transformation), will enable large-scale studies on this interesting phenomenon and facilitate its application in biotechnology. By utilizing DSSARST, we will then establish the first DS protein database, which is going to provide plenty information for researchers and us to elucidate the mechanisms of DS and the properties of the hinge loop. Results of these studies will further enabled us to develop prediction systems determining whether and how a protein can be artificially engineered to become a domain-swapped oligomer or monomer and thus acquires improved functionality. We will finally apply our prediction systems and use wet-lab procedures, including mutagenesis, protein expression and purification, and structural determination with nuclear magnetic resonance (NMR) spectroscopy, to engineer several important enzymes used to produce biofuels. The research interests of the applicants, Dr. Wei-Cheng Lo and Dr. Shih-Che Sue, mainly focus on structural biology and protein engineering. Lo had received solid biochemistry wet-lab trainings in college and greatly expanded his capability of doing computational biology researches in his doctoral days. Dr. Sue is an experimental structural biologist with many experiences in cooperating with computational biologists. They have collaborated for three years in an Interdiscipline Project funded by the National Science Council. Because of their pleasant experiences in previous collaborations and their complementary professional backgrounds, they are supposed fully capable of accomplishing the proposed research project, which shall be greatly helpful for moving DS related researches and bioengineering fields forward.