Abstract
BackgroundCellular respiration is a catabolic pathway for producing adenosine triphosphate (ATP) and is the most efficient process through which cells harvest energy from consumed food. When cells undergo cellular respiration, they require a pathway to keep and transfer electrons (i.e., the electron transport chain). Due to oxidation-reduction reactions, the electron transport chain produces a transmembrane proton electrochemical gradient. In case protons flow back through this membrane, this mechanical energy is converted into chemical energy by ATP synthase. The convert process is involved in producing ATP which provides energy in a lot of cellular processes. In the electron transport chain process, flavin adenine dinucleotide (FAD) is one of the most vital molecules for carrying and transferring electrons. Therefore, predicting FAD binding sites in the electron transport chain is vital for helping biologists understand the electron transport chain process and energy production in cells.ResultsWe used an independent data set to evaluate the performance of the proposed method, which had an accuracy of 69.84 %. We compared the performance of the proposed method in analyzing two newly discovered electron transport protein sequences with that of the general FAD binding predictor presented by Mishra and Raghava and determined that the accuracy of the proposed method improved by 9–45 % and its Matthew’s correlation coefficient was 0.14–0.5. Furthermore, the proposed method enabled reducing the number of false positives significantly and can provide useful information for biologists.ConclusionsWe developed a method that is based on PSSM profiles and SAAPs for identifying FAD binding sites in newly discovered electron transport protein sequences. This approach achieved a significant improvement after we added SAAPs to PSSM features to analyze FAD binding proteins in the electron transport chain. The proposed method can serve as an effective tool for predicting FAD binding sites in electron transport proteins and can help biologists understand the functions of the electron transport chain, particularly those of FAD binding sites. We also developed a web server which identifies FAD binding sites in electron transporters available for academics.
Highlights
Cellular respiration is a catabolic pathway for producing adenosine triphosphate (ATP) and is the most efficient process through which cells harvest energy from consumed food
We developed a method that is based on position specific scoring matrix (PSSM) profiles and significant amino acid pairs (SAAPs) for identifying flavin adenine dinucleotide (FAD) binding residues in electron transport proteins
The proposed method can serve as an effective tool for predicting FAD binding sites in electron transport proteins and can help biologists understand electron transport chain functions, those of FAD binding sites
Summary
Cellular respiration is a catabolic pathway for producing adenosine triphosphate (ATP) and is the most efficient process through which cells harvest energy from consumed food. When cells undergo cellular respiration, they require a pathway to keep and transfer electrons (i.e., the electron transport chain). In the electron transport chain process, flavin adenine dinucleotide (FAD) is one of the most vital molecules for carrying and transferring electrons. Cellular respiration is the process for producing adenosine triphosphate (ATP) and enables cells to obtain energy from foods. The electron transport chain components are organized into four complexes (Complex I, Complex II, Complex III, and Complex IV) and ATP synthase (which can be called Complex V). The process of electron transport chain starts from the mitochondrial inner membrane, which electrons transfer from Complex I with nicotinamide adenine dinucleotide (NADH) and succinate (Complex II) to oxygen. ATP synthase is active by the proton electrochemical to utilize the flow of H+ to generate ATP, which provides energy in numerous cellular processes
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