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

Vitor Galvão Lopes; Adriano de Britto Chaves Filho; Marcos Yukio Yoshinaga; Mario Hiroyuki Hirata; Glaucio Monteiro Ferreira

doi:10.1016/j.jmgm.2022.108125

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

J Mol Graph Model. 2022 May:112:108125. doi: 10.1016/j.jmgm.2022.108125. Epub 2022 Jan 15.

Authors

Vitor Galvão Lopes¹, Adriano de Britto Chaves Filho², Marcos Yukio Yoshinaga², Mario Hiroyuki Hirata³, Glaucio Monteiro Ferreira⁴

Affiliations

¹ Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av Prof Lineu Prestes 580, 05508-000, São Paulo, Brazil. Electronic address: galvaolopesv@gmail.com.
² Laboratory of Modified Lipids, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.
³ Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av Prof Lineu Prestes 580, 05508-000, São Paulo, Brazil. Electronic address: mhhirata@usp.br.
⁴ Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av Prof Lineu Prestes 580, 05508-000, São Paulo, Brazil. Electronic address: gmf@usp.br.

PMID: 35101729
DOI: 10.1016/j.jmgm.2022.108125

Abstract

The Carnitine Palmitoyltranferase I (CPT1) catalyzes the rate-limiting step of long-chain fatty acid (LCFA) mitochondrial β-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 Å) 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 ligand-complexed 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 α-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), gamma-linolenic (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.

Keywords: Carnitine palmitoyltransferase; Conformational changes; Long-chain fatty acids; Mitochondrial fatty acid β-oxidation; Molecular dynamics.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Acyl Coenzyme A*
Carnitine
Carnitine O-Palmitoyltransferase* / chemistry
Carnitine O-Palmitoyltransferase* / metabolism
Fatty Acids
Ligands
Oxidation-Reduction

Substances

Acyl Coenzyme A
Fatty Acids
Ligands
Carnitine O-Palmitoyltransferase
Carnitine