Studies on periplasmic chaperone lola and outer membrane protein lolb in escherichia coli An analysis of lipoprotein interactions leading to identification of inhibitors a molecular dynamics and in silico study

Abstract

The crystal structures of LolA and LolB have been solved and extensive studies have been performed on these biomolecules Takeda et al 2003 Despite the fact that crystal structures of the closed and open conformations of LolA and LolB are well characterized the studies on the complete dynamics of protein movement are still lacking In order to understand the importance of closing and opening of the lid in these molecules amino acid residues expected to be involved in these structures are the focus of our analysis Molecular dynamics simulation studies have the potential to discover novel binding sites including pockets that are not present in the existing crystal structures Simulation may also allow refinement of low resolution structural models of proteins thus enabling structure based drug design We have employed MD simulation studies to identify novel conformations and characterize the important residues involved in critical protein function Changes in conformational distribution were also studied as a result of in silico point mutation performed on the original protein structures Inhibitory drug molecules may also be employed to locate effective binding sites in specific conformations Further it is well established that lipoproteins are involved in various envelope activities their structures and functions must be clarified in order to understand how bacterial envelopes are formed and maintained It is not very well known as to how lipoprotein binding affects the primary structure of the protein Our investigations also involve the study of protein lipoprotein interactions such as LolA PAL and LolB PAL through simulation newline