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Alvarez HA, Cousido-Siah A, Espinosa YR, Podjarny A, Carlevaro CM, Howard E. Lipid exchange in crystal-confined fatty acid binding proteins: X-ray evidence and molecular dynamics explanation. Proteins 2023; 91:1525-1534. [PMID: 37462340 DOI: 10.1002/prot.26546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/07/2023] [Accepted: 06/14/2023] [Indexed: 10/07/2023]
Abstract
Fatty acid binding proteins (FABPs) are responsible for the long-chain fatty acids (FAs) transport inside the cell. However, despite the years, since their structure is known and the many studies published, there is no definitive answer about the stages of the lipid entry-exit mechanism. Their structure forms a β -barrel of 10 anti-parallel strands with a cap in a helix-turn-helix motif, and there is some consensus on the role of the so-called portal region, involving the second α -helix from the cap ( α 2), β C- β D, and β E- β F turns in FAs exchange. To test the idea of a lid that opens, we performed a soaking experiment on an h-FABP crystal in which the cap is part of the packing contacts, and its movement is strongly restricted. Even in these conditions, we observed the replacement of palmitic acid by 2-Bromohexadecanoic acid (Br-palmitic acid). Our MD simulations reveal a two-step lipid entry process: (i) The travel of the lipid head through the cavity in the order of tens of nanoseconds, and (ii) The accommodation of its hydrophobic tail in hundreds to thousands of nanoseconds. We observed this even in the cases in which the FAs enter the cavity by their tail. During this process, the FAs do not follow a single trajectory, but multiple ones through which they get into the protein cavity. Thanks to the complementary views between experiment and simulation, we can give an approach to a mechanistic view of the exchange process.
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Affiliation(s)
- H Ariel Alvarez
- Instituto de Fisica de Liquidos y Sistemas Biologicos (UNLP-CONICET), Buenos Aires, Argentina
- Departamento de Ciencias Biologicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Buenos Aires, Argentina
- Instituto de Ciencias de la Salud, Universidad Nacional Arturo Jauretche, Buenos Aires, Argentina
| | - Alexandra Cousido-Siah
- Institut de Genetique et de Biologie Moleculaire et Cellulaire, Illkirch-Graffenstaden, France
| | - Yanis R Espinosa
- Instituto de Fisica de Liquidos y Sistemas Biologicos (UNLP-CONICET), Buenos Aires, Argentina
- Departamento de Ciencias del Medio Ambiente, Universidad Francisco de Paula Santander, Facultad de Ciencias Agrarias y del Ambiente, Cúcuta, Colombia
| | - Alberto Podjarny
- Institut de Genetique et de Biologie Moleculaire et Cellulaire, Illkirch-Graffenstaden, France
| | - C Manuel Carlevaro
- Instituto de Fisica de Liquidos y Sistemas Biologicos (UNLP-CONICET), Buenos Aires, Argentina
- Facultad Regional La Plata, Universidad Tecnologica Nacional, Buenos Aires, Argentina
| | - Eduardo Howard
- Instituto de Fisica de Liquidos y Sistemas Biologicos (UNLP-CONICET), Buenos Aires, Argentina
- Facultad Regional Tierra del Fuego, Universidad Tecnologica Nacional, Ushuaia, Tierra del Fuego, Argentina
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2
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Espinosa YR, Alvarez HA, Howard EI, Carlevaro CM. Molecular dynamics simulation of the heart type fatty acid binding protein in a crystal environment. J Biomol Struct Dyn 2020; 39:3459-3468. [PMID: 32448092 DOI: 10.1080/07391102.2020.1773315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Crystallographic data comes from a space-time average over all the unit cells within the crystal, so dynamic phenomena do not contribute significantly to the diffraction data. Many efforts have been made to reconstitute the movement of the macromolecules and explore the microstates that the confined proteins can adopt in the crystalline network. We explored different strategies to simulate a heart fatty acid binding protein (H-FABP) crystal by means of Molecular Dynamics (MD) simulations. We evaluate the effect of introducing restraints according to experimental isotropic B-factors and we analyzed the H-FABP motions in the crystal using Principal Component Analysis (PCA), isotropic and anisotropic B-factors. We compared the behavior of the protein simulated in the crystal confinement versus in solution, and we observed the effect of that confinement in the mobility of the protein residues. Restraining one-third of Cα atoms based on experimental B-factors produce lower B-factors than simulations without restraints, showing that the position restraint of the atoms with the lowest experimental B-factor is a good strategy to maintain the geometry of the crystal with an obvious decrease in the degrees of motion of the protein. PCA shows that, as position restraint reduces the conformational space explored by the system, the motion of the crystal is better recovered, for an essential subspace of the same size, in the simulations without restraints. Restraining only one Cα seems to be a good balance between giving flexibility to the system and preserving its structure. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yanis R Espinosa
- Instituto de Física de Líquidos y Sistemas Biológicos (CONICET-UNLP), La Plata, Argentina.,Grupo de Bioquímica Teórica, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - H Ariel Alvarez
- Instituto de Física de Líquidos y Sistemas Biológicos (CONICET-UNLP), La Plata, Argentina.,Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, UNLP, La Plata, Argentina.,Instituto de Ciencias de la Salud, Universidad Nacional Arturo Jauretche, Buenos Aires, Argentina
| | - Eduardo I Howard
- Instituto de Física de Líquidos y Sistemas Biológicos (CONICET-UNLP), La Plata, Argentina.,Universidad Tecnológica Nacional- Facultad Regional Tierra del Fuego, Ushuaia, Tierra del Fuego, Argentina
| | - C Manuel Carlevaro
- Instituto de Física de Líquidos y Sistemas Biológicos (CONICET-UNLP), La Plata, Argentina.,Departamento de Ingeniería Mecánica, Universidad Tecnológica Nacional, Facultad Regional La Plata, La Plata, Argentina
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3
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Laulumaa S, Nieminen T, Raasakka A, Krokengen OC, Safaryan A, Hallin EI, Brysbaert G, Lensink MF, Ruskamo S, Vattulainen I, Kursula P. Structure and dynamics of a human myelin protein P2 portal region mutant indicate opening of the β barrel in fatty acid binding proteins. BMC STRUCTURAL BIOLOGY 2018; 18:8. [PMID: 29940944 PMCID: PMC6020228 DOI: 10.1186/s12900-018-0087-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/13/2018] [Indexed: 02/04/2023]
Abstract
Background Myelin is a multilayered proteolipid sheath wrapped around selected axons in the nervous system. Its constituent proteins play major roles in forming of the highly regular membrane structure. P2 is a myelin-specific protein of the fatty acid binding protein (FABP) superfamily, which is able to stack lipid bilayers together, and it is a target for mutations in the human inherited neuropathy Charcot-Marie-Tooth disease. A conserved residue that has been proposed to participate in membrane and fatty acid binding and conformational changes in FABPs is Phe57. This residue is thought to be a gatekeeper for the opening of the portal region upon ligand entry and egress. Results We performed a structural characterization of the F57A mutant of human P2. The mutant protein was crystallized in three crystal forms, all of which showed changes in the portal region and helix α2. In addition, the behaviour of the mutant protein upon lipid bilayer binding suggested more unfolding than previously observed for wild-type P2. On the other hand, membrane binding rendered F57A heat-stable, similarly to wild-type P2. Atomistic molecular dynamics simulations showed opening of the side of the discontinuous β barrel, giving important indications on the mechanism of portal region opening and ligand entry into FABPs. The results suggest a central role for Phe57 in regulating the opening of the portal region in human P2 and other FABPs, and the F57A mutation disturbs dynamic cross-correlation networks in the portal region of P2. Conclusions Overall, the F57A variant presents similar properties to the P2 patient mutations recently linked to Charcot-Marie-Tooth disease. Our results identify Phe57 as a residue regulating conformational changes that may accompany membrane surface binding and ligand exchange in P2 and other FABPs. Electronic supplementary material The online version of this article (10.1186/s12900-018-0087-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Saara Laulumaa
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,European Spallation Source (ESS), Lund, Sweden
| | - Tuomo Nieminen
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Oda C Krokengen
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Erik I Hallin
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Guillaume Brysbaert
- Unité de Glycobiologie Structurale et Fonctionnelle, University of Lille, CNRS UMR8576 UGSF, F-59000, Lille, France
| | - Marc F Lensink
- Unité de Glycobiologie Structurale et Fonctionnelle, University of Lille, CNRS UMR8576 UGSF, F-59000, Lille, France
| | - Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, Tampere, Finland.,Department of Physics, University of Helsinki, Helsinki, Finland
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland. .,Department of Biomedicine, University of Bergen, Bergen, Norway.
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5
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Hunter NH, Bakula BC, Bruce CD. Molecular dynamics simulations of apo and holo forms of fatty acid binding protein 5 and cellular retinoic acid binding protein II reveal highly mobile protein, retinoic acid ligand, and water molecules. J Biomol Struct Dyn 2017; 36:1893-1907. [PMID: 28566049 DOI: 10.1080/07391102.2017.1337591] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Structural and dynamic properties from a series of 300 ns molecular dynamics, MD, simulations of two intracellular lipid binding proteins, iLBPs, (Fatty Acid Binding Protein 5, FABP5, and Cellular Retinoic Acid Binding Protein II, CRABP-II) in both the apo form and when bound with retinoic acid reveal a high degree of protein and ligand flexibility. The ratio of FABP5 to CRABP-II in a cell may determine whether it undergoes natural apoptosis or unrestricted cell growth in the presence of retinoic acid. As a result, FABP5 is a promising target for cancer therapy. The MD simulations presented here reveal distinct differences in the two proteins and provide insight into the binding mechanism. CRABP-II is a much larger, more flexible protein that closes upon ligand binding, where FABP5 transitions to an open state in the holo form. The traditional understanding obtained from crystal structures of the gap between two β-sheets of the β-barrel common to iLBPs and the α-helix cap that forms the portal to the binding pocket is insufficient for describing protein conformation (open vs. closed) or ligand entry and exit. When the high degree of mobility between multiple conformations of both the ligand and protein are examined via MD simulation, a new mode of ligand motion that improves understanding of binding dynamics is revealed.
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Affiliation(s)
- Nathanael H Hunter
- a Department of Chemistry , John Carroll University , University Heights , OH , USA
| | - Blair C Bakula
- a Department of Chemistry , John Carroll University , University Heights , OH , USA
| | - Chrystal D Bruce
- a Department of Chemistry , John Carroll University , University Heights , OH , USA
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6
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Rizzuti B, Bartucci R, Sportelli L, Guzzi R. Fatty acid binding into the highest affinity site of human serum albumin observed in molecular dynamics simulation. Arch Biochem Biophys 2015; 579:18-25. [PMID: 26048999 DOI: 10.1016/j.abb.2015.05.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 11/24/2022]
Abstract
Multiple molecular dynamics simulations were performed to investigate the association of stearic acid into the highest affinity binding site of human serum albumin. All binding events ended with a rapid (<10 ps) lock-in of the fatty acid due to formation of a hydrogen bond with Tyr401. The kinetics and energetics of the penetration process both depended linearly on the positional shift of the fatty acid, with an average insertion time and free energy reduction of, respectively, 32 ± 20 ps and 0.70 ± 0.15 kcal/mol per methylene group absorbed. Binding events of longer duration (tbind>1 ns) were characterized by a slow exploration of the pocket entry and, frequently, of a nearby protein crevice corresponding to a metastable state along the route to the binding site. Taken all together, these findings reconstruct the following pathway for the binding process of stearic acid: (i) contact with the protein surface, possibly facilitated by the presence of an intermediate location, (ii) probing of the site entry, (iii) insertion into the protein, and (iv) lock-in at the final position. This general description may also apply to other long-chain fatty acids binding into any of the high-affinity sites of albumin, or to specific sites of other lipid-binding proteins.
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Affiliation(s)
- Bruno Rizzuti
- Licryl Laboratory, CNR-NANOTEC and CEMIF.Cal, University of Calabria, 87036 Rende, Italy.
| | - Rosa Bartucci
- Molecular Biophysics Laboratory and CNISM Unit, Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Luigi Sportelli
- Molecular Biophysics Laboratory and CNISM Unit, Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Rita Guzzi
- Molecular Biophysics Laboratory and CNISM Unit, Department of Physics, University of Calabria, 87036 Rende, Italy
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7
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Chun BJ, Lee SG, Choi JI, Jang SS. Adsorption of carboxylate on calcium carbonate (10 1¯ 4) surface: Molecular simulation approach. Colloids Surf A Physicochem Eng Asp 2015. [DOI: 10.1016/j.colsurfa.2015.03.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Esteves A, Paulino Zunini M. In silicostudies ofEchinococcus granulosusFABPs. J Biomol Struct Dyn 2013; 31:224-39. [DOI: 10.1080/07391102.2012.698246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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9
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Paramo T, Garzón D, Holdbrook DA, Khalid S, Bond PJ. The simulation approach to lipid-protein interactions. Methods Mol Biol 2013; 974:435-455. [PMID: 23404287 DOI: 10.1007/978-1-62703-275-9_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The interactions between lipids and proteins are crucial for a range of biological processes, from the folding and stability of membrane proteins to signaling and metabolism facilitated by lipid-binding proteins. However, high-resolution structural details concerning functional lipid/protein interactions are scarce due to barriers in both experimental isolation of native lipid-bound complexes and subsequent biophysical characterization. The molecular dynamics (MD) simulation approach provides a means to complement available structural data, yielding dynamic, structural, and thermodynamic data for a protein embedded within a physiologically realistic, modelled lipid environment. In this chapter, we provide a guide to current methods for setting up and running simulations of membrane proteins and soluble, lipid-binding proteins, using standard atomistically detailed representations, as well as simplified, coarse-grained models. In addition, we outline recent studies that illustrate the power of the simulation approach in the context of biologically relevant lipid/protein interactions.
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Affiliation(s)
- Teresa Paramo
- Department of Chemistry, Unilever Centre for Molecular Informatics, University of Cambridge, Cambridge, UK
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10
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Comparative study of the fatty acid binding process of a new FABP from Cherax quadricarinatus by fluorescence intensity, lifetime and anisotropy. PLoS One 2012; 7:e51079. [PMID: 23284658 PMCID: PMC3528769 DOI: 10.1371/journal.pone.0051079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 10/29/2012] [Indexed: 12/31/2022] Open
Abstract
Fatty acid-binding proteins (FABPs) are small cytosolic proteins, largely distributed in invertebrates and vertebrates, which accomplish uptake and intracellular transport of hydrophobic ligands such as fatty acids. Although long chain fatty acids play multiple crucial roles in cellular functions (structural, energy metabolism, regulation of gene expression), the precise functions of FABPs, especially those of invertebrate species, remain elusive. Here, we have identified and characterized a novel FABP family member, Cq-FABP, from the hepatopancreas of red claw crayfish Cherax quadricarinatus. We report the characterization of fatty acid-binding affinity of Cq-FABP by four different competitive fluorescence-based assays. In the two first approaches, the fluorescent probe 8-Anilino-1-naphthalenesulfonate (ANS), a binder of internal cavities of protein, was used either by directly monitoring its fluorescence emission or by monitoring the fluorescence resonance energy transfer occurring between the single tryptophan residue of Cq-FABP and ANS. The third and the fourth approaches were based on the measurement of the fluorescence emission intensity of the naturally fluorescent cis-parinaric acid probe or the steady-state fluorescence anisotropy measurements of a fluorescently labeled fatty acid (BODIPY-C16), respectively. The four methodologies displayed consistent equilibrium constants for a given fatty acid but were not equivalent in terms of analysis. Indeed, the two first methods were complicated by the existence of non specific binding modes of ANS while BODIPY-C16 and cis-parinaric acid specifically targeted the fatty acid binding site. We found a relationship between the affinity and the length of the carbon chain, with the highest affinity obtained for the shortest fatty acid, suggesting that steric effects primarily influence the interaction of fatty acids in the binding cavity of Cq-FABP. Moreover, our results show that the binding affinities of several fatty acids closely parallel their prevalences in the hepatopancreas of C. quadricarinatus as measured under specific diet conditions.
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Lemkul JA, Allen WJ, Bevan DR. Practical considerations for building GROMOS-compatible small-molecule topologies. J Chem Inf Model 2010; 50:2221-35. [PMID: 21117688 DOI: 10.1021/ci100335w] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Molecular dynamics simulations are being applied to increasingly complex systems, including those involving small endogenous compounds and drug molecules. In order to obtain meaningful and accurate data from these simulations, high-quality topologies for small molecules must be generated in a manner that is consistent with the derivation of the force field applied to the system. Often, force fields are designed for use with macromolecules such as proteins, making their transferability to other species challenging. Investigators are increasingly attracted to automated topology generation programs, although the quality of the resulting topologies remains unknown. Here we assess the applicability of the popular PRODRG server that generates small-molecule topologies for use with the GROMOS family of force fields. We find that PRODRG does not reproduce topologies for even the most well-characterized species in the force field due to inconsistent charges and charge groups. We assessed the effects of PRODRG-derived charges on several systems: pure liquids, amino acids at a hydrophobic-hydrophilic interface, and an enzyme-cofactor complex. We found that partial atomic charges generated by PRODRG are largely incompatible with GROMOS force fields, and the behavior of these systems deviates substantially from that of simulations using GROMOS parameters. We conclude by proposing several points as "best practices" for parametrization of small molecules under the GROMOS force fields.
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Affiliation(s)
- Justin A Lemkul
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
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