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Home / Equine Research Bank / PLoS One / Molecular dynamic simulations reveal the structural determin...
PloS one2015; 10(6); e0128496; doi: 10.1371/journal.pone.0128496

Molecular dynamic simulations reveal the structural determinants of Fatty Acid binding to oxy-myoglobin.

Abstract: The mechanism(s) by which fatty acids are sequestered and transported in muscle have not been fully elucidated. A potential key player in this process is the protein myoglobin (Mb). Indeed, there is a catalogue of empirical evidence supporting direct interaction of globins with fatty acid metabolites; however, the binding pocket and regulation of the interaction remains to be established. In this study, we employed a computational strategy to elucidate the structural determinants of fatty acids (palmitic & oleic acid) binding to Mb. Sequence analysis and docking simulations with a horse (Equus caballus) structural Mb reference reveals a fatty acid-binding site in the hydrophobic cleft near the heme region in Mb. Both palmitic acid and oleic acid attain a "U" shaped structure similar to their conformation in pockets of other fatty acid-binding proteins. Specifically, we found that the carboxyl head group of palmitic acid coordinates with the amino group of Lys45, whereas the carboxyl group of oleic acid coordinates with both the amino groups of Lys45 and Lys63. The alkyl tails of both fatty acids are supported by surrounding hydrophobic residues Leu29, Leu32, Phe33, Phe43, Phe46, Val67, Val68 and Ile107. In the saturated palmitic acid, the hydrophobic tail moves freely and occasionally penetrates deeper inside the hydrophobic cleft, making additional contacts with Val28, Leu69, Leu72 and Ile111. Our simulations reveal a dynamic and stable binding pocket in which the oxygen molecule and heme group in Mb are required for additional hydrophobic interactions. Taken together, these findings support a mechanism in which Mb acts as a muscle transporter for fatty acid when it is in the oxygenated state and releases fatty acid when Mb converts to deoxygenated state.
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Publication Date: 2015-06-01 PubMed ID: 26030763PubMed Central: PMC4451517DOI: 10.1371/journal.pone.0128496Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article discusses a study that utilized computational approaches to uncover how fatty acids bind to the muscle protein myoglobin. Specifically, the researchers aimed to identify key structural elements that support the interaction between fatty acids and myoglobin and simulate the behaviour of these interactions under differing conditions.

Objective of the Research

  • The research aimed to better understand how fatty acids are stored and transported in muscles. Researchers focused on the protein myoglobin, hypothesizing it plays a major role in direct interaction with fatty acid metabolites. However, the binding pocket and the specific regulation of this interaction have not been well established. The aim was to identify the structural components responsible for fatty acid binding to myoglobin through exploring the interaction of fatty acids palmitic and oleic acid with myoglobin.

Methods of Research

  • The researchers used sequence analysis and docking simulations, taking a horse’s myoglobin structure as a reference. They identified a fatty acid-binding site in a hydrophobic cleft near the protein’s heme region.
  • Computational simulations were performed to simulate behavior of these fatty acids when they bind to myoglobin. The binding conformations of both palmitic acid and oleic acid were found similar to their conformation in the binding pockets of other fatty acid-binding proteins.

Key Findings

  • It was found that the carboxyl head group of palmitic acid coordinates with the amino group of Lys45 on myoglobin. On the other hand, the carboxyl group of oleic acid coordinates with the amino groups of Lys45 and Lys63 on myoglobin.
  • The alkyl tails of both fatty acids were supported by certain surrounding hydrophobic residues in myoglobin. In the case of palmitic acid, which is saturated, the hydrophobic tail can move freely and make additional contacts with other hydrophobic residues.
  • The simulations further revealed that the oxygen molecule and heme group in myoglobin are important for additional hydrophobic interactions. These findings suggest a mechanism where myoglobin could act as a transporter for fatty acids when in an oxygenated state, and release them upon conversion to a deoxygenated state.

Cite This Article

APA
Chintapalli SV, Bhardwaj G, Patel R, Shah N, Patterson RL, van Rossum DB, Anishkin A, Adams SH. (2015). Molecular dynamic simulations reveal the structural determinants of Fatty Acid binding to oxy-myoglobin. PLoS One, 10(6), e0128496. https://doi.org/10.1371/journal.pone.0128496

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 10
Issue: 6
Pages: e0128496
PII: e0128496

Researcher Affiliations

Chintapalli, Sree V
  • Arkansas Children's Nutrition Center, and Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America.
Bhardwaj, Gaurav
  • Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, California, United States of America.
Patel, Reema
  • Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, California, United States of America; Department of Physiology and Membrane Biology, School of Medicine, University of California Davis, Davis, California, United States of America.
Shah, Natasha
  • Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, California, United States of America; Department of Physiology and Membrane Biology, School of Medicine, University of California Davis, Davis, California, United States of America.
Patterson, Randen L
  • Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, California, United States of America; Department of Physiology and Membrane Biology, School of Medicine, University of California Davis, Davis, California, United States of America.
van Rossum, Damian B
  • Center for Computational Proteomics, The Pennsylvania State University, State College, Pennsylvania, United States of America; Department of Biology, The Pennsylvania State University, State College, Pennsylvania, United States of America.
Anishkin, Andriy
  • Department of Biology, University of Maryland, College Park, Maryland, United States of America.
Adams, Sean H
  • Arkansas Children's Nutrition Center, and Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America.

MeSH Terms

  • Amino Acid Sequence
  • Animals
  • Fatty Acids / chemistry
  • Fatty Acids / metabolism
  • Horses
  • Humans
  • Molecular Dynamics Simulation
  • Molecular Sequence Data
  • Myoglobin / chemistry
  • Myoglobin / metabolism
  • Protein Binding
  • Sequence Homology, Amino Acid

Grant Funding

  • R01 DK078328 / NIDDK NIH HHS
  • R01 GM087410 / NIGMS NIH HHS
  • R01 GM087410-01 / NIGMS NIH HHS
  • R01DK078328-01 / NIDDK NIH HHS

Conflict of Interest Statement

The authors have declared that no competing interests exist.

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This article has been cited 16 times.
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