Carnitine palmitoyl transferase I: Conformational changes induced by long-chain fatty acyl CoA ligands

Author(s)

Lopes, Vitor Galvao ; de Britto Chaves Filho, Adriano ; Yoshinaga, Macros Yukio ; Hirata, Mario Hiroyuki ; Ferreira, Glaucio Monteiro

• Document type: Journal article
• Source: JOURNAL OF MOLECULAR GRAPHICS & MODELLING; v. 112, p. 7-pg., 2022-05-01.

Abstract

The Carnitine Palmitoyltranferase I (CPT1) catalyzes the rate-limiting step of long-chain fatty acid (LCFA) mitochondrial beta-oxidation. The enzyme promotes the conjugation of LCFA with L-carnitine, which allows LCFA to enter the mitochondria matrix. The structural features involved in CPT1 and LCFA-CoA interactions have not been fully elucidated, mainly due to the absence of CPT1 crystallographic data. Previous studies reported important residues (Lys556, Lys560, and Lys561) crucial to the CPT1 mechanism. Nonetheless, these studies have not explored the LCFA bindings. Using molecular modeling strategies, we aimed to understand the conformational changes in CPT1 structure induced by LCFA-CoA. For this purpose, a tridimensional CPT1A model was built by homology modeling using CRAT protein (PBD:1t7q, resolution 1.8 angstrom) as a template. We simulated the CPT1 structure in the presence and absence of LCFA-CoA by molecular dynamics (MD). By applying a principal component analysis (PCA), two states of apostructure CPT1 based on CoA-Loop (688-711) were observed. In contrast, just one state was evidenced along with smaller conformational subspaces in ligandcomplexed simulations using LCFA-CoA. The CoA moiety of ligands interacts with charged residues, namely Lys560, Lys556, Arg563, and Arg645. The frequency of interactions observed for each of these residues is < 60% of simulation time, suggesting a dynamic profile of interactions in synergy with long-chain carbon interactions over alpha-I (478-492). Collectively, these features may be associated with the catalytic conformation of LCFA-CoA to CPT1a. Further calculations of free-energy for different fatty acids, such as alpha-linolenic (ALA), gammalinolenic (GLA), and arachidonic (ARA) acids, yielded energy values ranging from -76.9 +/- 15.9 to -68.5 +/- 10.0 kcal mol(-1). In conclusion, the present structural model and simulations provide molecular-level insights into LCFA-CoA and CPT1a interactions. These findings may help to further knowledge on the conformational changes of CPT1a induced by LCFA-CoA derivates. (AU)

• FAPESP's process: 20/06490-3 - Search a new PCSK9 inhibitor using techniques of drug planning based on a target structure
• Grantee: Vitor Galvão Lopes
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• FAPESP's process: 21/11205-9 - Development of new drugs based on the structure of essential proteins for cholesterol synthesis and metabolism, integrating genetic studies and molecular modeling of dyslipidemic patients
• Grantee: Glaucio Monteiro Ferreira
• Support Opportunities: Scholarships in Brazil - Post-Doctoral