Molecular dynamics investigation of the active site dynamics of mycobacterial cyclopropane synthase during various stages of the cyclopropanation process.
Mycobacterial cyclopropane synthase 1 (CmaA1) is one of the most important drug targets in anti tuberculosis drug discovery as it is responsible for cis-cyclopropanation at the distal position of unsaturated mycolates, which is an essential step for the pathogenicity, persistence and drug resistance. Five representative models of CmaA1 which correspond to different stages in the cyclopropanation process have been studied using molecular dynamics (MD) simulations. The MD simulations and structural analyses provide a detailed account of the structural changes in the active sites of CmaA1. CmaA1 has two distinct binding sites, i.e., cofactor binding site (CBS) and acyl substrate binding site (ASBS). The apo state of CmaA1 corresponds to a closed conformation where the CBS is inaccessible due to the existence of H-bond between Pro202 of loop10 (L10) and Asn11 of N-terminal α1 helix. However, cofactor binding leads to the breaking of this H-bond and thus the H-bond is absent in the holo form. The hydrophobic side chains orient towards the inner side of the ASBS upon cofactor binding to create a hydrophobic environment for the substrate. The cofactor and substrate tend to come close to each other facilitated by opening of L10 to exchange the methyl group from the cofactor to the substrate. The MD study also revealed that the system tends to regain the apo conformation within 40ns after releasing the product.
Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information and Technology, Hyderabad, India; Centre for Molecular Modelling, Indian Institute of Chemical Technology, Hyderabad, India.
Chinmayee
C
Choudhury
Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information and Technology, Hyderabad, India. Electronic address: deva@iiit.ac.in.
U
U
Deva Priyakumar
Centre for Molecular Modelling, Indian Institute of Chemical Technology, Hyderabad, India. Electronic address: gnsastry@gmail.com.
G Narahari
GN
Sastry
D000595:Amino Acid Sequence; D001059:Apoproteins / Q000737:chemistry* / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D020134:Catalytic Domain; D003067:Coenzymes / Q000737:chemistry* / Q000378:metabolism; D018360:Crystallography, X-Ray; D003521:Cyclopropanes / Q000737:chemistry / Q000378:metabolism; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D007527:Isoenzymes / Q000737:chemistry / Q000378:metabolism; D008780:Methyltransferases / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009169:Mycobacterium tuberculosis / Q000737:chemistry* / Q000201:enzymology; D009171:Mycolic Acids / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
D001059:Apoproteins; D001426:Bacterial Proteins; D003067:Coenzymes; D003521:Cyclopropanes; D007527:Isoenzymes; D009171:Mycolic Acids; C030797:cyclopropane; D008780:Methyltransferases; C019964:cyclopropane synthetase
Active site dynamics; Cofactor binding site; Cyclopropane synthase; MD simulations; Mycobacterium tuberculosis