Book of Abstracts: Albany 2011
June 14-18 2011
©Adenine Press (2010)
Modeling Three Dimensional Structures of Complete PKS Modules for Understanding Inter-Domain Interactions
Modular polyketide synthases (PKS) utilize multiple copies of distinct sets of catalytic domains, called modules for catalyzing biosynthesis of a variety of pharmaceutically important natural products (1). Even though bioinformatics analysis has played a major role in discovery of novel secondary metabolites and rational design of natural product analogs, most of these computational methods have used sequence information alone. However, recently available crystal structures of mammalian FAS and large polypeptide stretches from modular PKS indicate that, the polyketide biosynthesis is brought about by a tightly coupled network of catalytic and structural domains (2). Therefore, it is necessary to model three-dimensional structures of complete PKS modules for understanding role of inter domain interactions in substrate channeling.
Structure based sequence analysis on a data set of 662 KS, 541 AT, 308 DH, 99 ER, 450 KR and 562 ACP domains from 55 modular PKS clusters indicate that, except for the structural sub-domain of KR, all other domains show significant sequence similarity with available structural templates. Despite the high sequence divergence, the structural sub-domain of KR can be modeled using threading approach. The dimeric structure of complete PKS module could also be modeled based on the relative orientation of different domains in mechanistically analogous mammalian FAS structure (3). Modeling of a bi-modular PKS protein using this approach has provided valuable clues for recent discovery of a novel modularly iterative mechanism of mycoketide biosynthesis in Mycobacterium tuberculosis (4). Since the mammalian FAS structure lacks ACP domain, we have tried to predict its orientation with respect to other catalytic domains using protein-protein docking and molecular dynamics methods (5, 6). Long molecular dynamics simulations on the KS-AT di-domain structure indicate that, the extent of inter domain movement within a module is not large enough to bring them in proximity for acyl transfer. Thus, intrinsic flexibility of the linker regions preceding ACP might facilitate interaction of ACP with other catalytic domains. These results on inter domain interactions within PKS modules have interesting implications for design of domain swapping experiments for obtaining natural product analogs by biosynthetic engineering.
National Institute of Immunology