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Thangappan J, Wu S, Lee SG. Joint-based description of protein structure: its application to the geometric characterization of membrane proteins. Sci Rep 2017; 7:1056. [PMID: 28432363 PMCID: PMC5430719 DOI: 10.1038/s41598-017-01011-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 03/28/2017] [Indexed: 11/17/2022] Open
Abstract
A macroscopic description of a protein structure allows an understanding of the protein conformations in a more simplistic manner. Here, a new macroscopic approach that utilizes the joints of the protein secondary structures as a basic descriptor for the protein structure is proposed and applied to study the arrangement of secondary structures in helical membrane proteins. Two types of dihedral angle, Ω and λ, were defined based on the joint points of the transmembrane (TM) helices and loops, and employed to analyze 103 non-homologous membrane proteins with 3 to 14 TM helices. The Ω-λ plot, which is a distribution plot of the dihedral angles of the joint points, identified the allowed and disallowed regions of helical arrangement. Analyses of consecutive dihedral angle patterns indicated that there are preferred patterns in the helical alignment and extension of TM proteins, and helical extension pattern in TM proteins is varied as the size of TM proteins increases. Finally, we could identify some symmetric protein pairs in TM proteins under the joint-based coordinate and 3-dimensional coordinates. The joint-based approach is expected to help better understand and model the overall conformational features of complicated large-scale proteins, such as membrane proteins.
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Affiliation(s)
- Jayaraman Thangappan
- Department of Chemical Engineering, Pusan National University, Busan, 609-735, Republic of Korea
| | - Sangwook Wu
- Department of Physics, Pukyong National University, Busan, 608-737, Republic of Korea.
| | - Sun-Gu Lee
- Department of Chemical Engineering, Pusan National University, Busan, 609-735, Republic of Korea.
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2
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Dynamics of the Glycophorin A Dimer in Membranes of Native-Like Composition Uncovered by Coarse-Grained Molecular Dynamics Simulations. PLoS One 2015. [PMID: 26222139 PMCID: PMC4519189 DOI: 10.1371/journal.pone.0133999] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Membranes are central for cells as borders to the environment or intracellular organelle definition. They are composed of and harbor different molecules like various lipid species and sterols, and they are generally crowded with proteins. The membrane system is very dynamic and components show lateral, rotational and translational diffusion. The consequence of the latter is that phase separation can occur in membranes in vivo and in vitro. It was documented that molecular dynamics simulations of an idealized plasma membrane model result in formation of membrane areas where either saturated lipids and cholesterol (liquid-ordered character, Lo) or unsaturated lipids (liquid-disordered character, Ld) were enriched. Furthermore, current discussions favor the idea that proteins are sorted into the liquid-disordered phase of model membranes, but experimental support for the behavior of isolated proteins in native membranes is sparse. To gain insight into the protein behavior we built a model of the red blood cell membrane with integrated glycophorin A dimer. The sorting and the dynamics of the dimer were subsequently explored by coarse-grained molecular dynamics simulations. In addition, we inspected the impact of lipid head groups and the presence of cholesterol within the membrane on the dynamics of the dimer within the membrane. We observed that cholesterol is important for the formation of membrane areas with Lo and Ld character. Moreover, it is an important factor for the reproduction of the dynamic behavior of the protein found in its native environment. The protein dimer was exclusively sorted into the domain of Ld character in the model red blood cell plasma membrane. Therefore, we present structural information on the glycophorin A dimer distribution in the plasma membrane in the absence of other factors like e.g. lipid anchors in a coarse grain resolution.
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Critical glycosylated residues in exon three of erythrocyte glycophorin A engage Plasmodium falciparum EBA-175 and define receptor specificity. mBio 2014; 5:e01606-14. [PMID: 25205096 PMCID: PMC4173783 DOI: 10.1128/mbio.01606-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Erythrocyte invasion is an essential step in the pathogenesis of malaria. The erythrocyte binding-like (EBL) family of Plasmodium falciparum proteins recognizes glycophorins (Gp) on erythrocytes and plays a critical role in attachment during invasion. However, the molecular basis for specific receptor recognition by each parasite ligand has remained elusive, as is the case with the ligand/receptor pair P. falciparum EBA-175 (PfEBA-175)/GpA. This is due largely to difficulties in producing properly glycosylated and functional receptors. Here, we developed an expression system to produce recombinant glycosylated and functional GpA, as well as mutations and truncations. We identified the essential binding region and determinants for PfEBA-175 engagement, demonstrated that these determinants are required for the inhibition of parasite growth, and identified the glycans important in mediating the PfEBA-175–GpA interaction. The results suggest that PfEBA-175 engages multiple glycans of GpA encoded by exon 3 and that the presentation of glycans is likely required for high-avidity binding. The absence of exon 3 in GpB and GpE due to a splice site mutation confers specific recognition of GpA by PfEBA-175. We speculate that GpB and GpE may have arisen due to selective pressure to lose the PfEBA-175 binding site in GpA. The expression system described here has wider application for examining other EBL members important in parasite invasion, as well as additional pathogens that recognize glycophorins. The ability to define critical binding determinants in receptor-ligand interactions, as well as a system to genetically manipulate glycosylated receptors, opens new avenues for the design of interventions that disrupt parasite invasion. Plasmodium falciparum uses distinct ligands that bind host cell receptors for invasion of red blood cells (RBCs) during malaria infection. A key entry pathway involves P. falciparum EBA-175 (PfEBA-175) recognizing glycophorin A (GpA) on RBCs. Despite knowledge of this protein-protein interaction, the complete mechanism for specific receptor engagement is not known. PfEBA-175 recognizes GpA but is unable to engage the related RBC receptor GpB or GpE. Understanding the necessary elements that enable PfEBA-175 to specifically recognize GpA is critical in developing specific and potent inhibitors of PfEBA-175 that disrupt host cell invasion and aid in malaria control. Here, we describe a novel system to produce and manipulate the host receptor GpA. Using this system, we probed the elements in GpA necessary for engagement and thus for host cell invasion. These studies have important implications for understanding how ligands and receptors interact and for the future development of malaria interventions.
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Kar P, Gopal SM, Cheng YM, Panahi A, Feig M. Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix-Helix Association. J Chem Theory Comput 2014; 10:3459-3472. [PMID: 25136271 PMCID: PMC4132866 DOI: 10.1021/ct500443v] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Indexed: 12/03/2022]
Abstract
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An
extension of the recently developed PRIMO coarse-grained force
field to membrane environments, PRIMO-M, is described. The membrane
environment is modeled with the heterogeneous dielectric generalized
Born (HDGB) methodology that simply replaces the standard generalized
Born model in PRIMO without further parametrization. The resulting
model was validated by comparing amino acid insertion free energy
profiles and application in molecular dynamics simulations of membrane
proteins and membrane-interacting peptides. Membrane proteins with
148–661 amino acids show stable root-mean-squared-deviations
(RMSD) between 2 and 4 Å for most systems. Transmembrane helical
peptides maintain helical shape and exhibit tilt angles in good agreement
with experimental or other simulation data. The association of two
glycophorin A (GpA) helices was simulated using replica exchange molecular
dynamics simulations yielding the correct dimer structure with a crossing
angle in agreement with previous studies. Finally, conformational
sampling of the influenza fusion peptide also generates structures
in agreement with previous studies. Overall, these findings suggest
that PRIMO-M can be used to study membrane bound peptides and proteins
and validates the transferable nature of the PRIMO coarse-grained
force field.
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Affiliation(s)
- Parimal Kar
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Srinivasa Murthy Gopal
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Yi-Ming Cheng
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Afra Panahi
- Departments of Chemistry and Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Michael Feig
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States ; Department of Biochemistry and Molecular Biology and Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
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5
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Li LH, Hsu HJ, Fischer WB. Assembling viral channel forming proteins: Vpu from HIV-1. Biopolymers 2013; 99:517-29. [DOI: 10.1002/bip.22210] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Revised: 10/17/2012] [Accepted: 12/22/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Li-Hua Li
- Institute of Biophotonics, School of Biomedical Science and Engineering and Biophotonics and Molecular Imaging Research Center (BMIRC); National Yang-Ming University; Taipei 112; Taiwan
| | - Hao-Jen Hsu
- Institute of Biophotonics, School of Biomedical Science and Engineering and Biophotonics and Molecular Imaging Research Center (BMIRC); National Yang-Ming University; Taipei 112; Taiwan
| | - Wolfgang B. Fischer
- Institute of Biophotonics, School of Biomedical Science and Engineering and Biophotonics and Molecular Imaging Research Center (BMIRC); National Yang-Ming University; Taipei 112; Taiwan
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6
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Bocharov EV, Mineev KS, Goncharuk MV, Arseniev AS. Structural and thermodynamic insight into the process of “weak” dimerization of the ErbB4 transmembrane domain by solution NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2158-70. [DOI: 10.1016/j.bbamem.2012.05.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 04/20/2012] [Accepted: 05/01/2012] [Indexed: 10/28/2022]
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Polyansky AA, Volynsky PE, Efremov RG. Structural, dynamic, and functional aspects of helix association in membranes: a computational view. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 83:129-61. [PMID: 21570667 DOI: 10.1016/b978-0-12-381262-9.00004-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
This review surveys recent achievements of molecular computer modeling in understanding spatial structure, dynamics, and mechanisms of functioning of transmembrane α-helical dimers in membranes. The factors driving self-association of hydrophobic helices in the membrane milieu are considered with examples of their applications to biologically relevant problems. The emphasis is made on the recent results, which help to understand important aspects of structure-function relations for these systems and their biological activity. Limitations and shortcomings of the methods, along with their perspectives in design of new membrane active agents, are discussed.
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Affiliation(s)
- Anton A Polyansky
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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8
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Wan CK, Han W, Wu YD. Parameterization of PACE Force Field for Membrane Environment and Simulation of Helical Peptides and Helix–Helix Association. J Chem Theory Comput 2011; 8:300-13. [DOI: 10.1021/ct2004275] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Cheuk-Kin Wan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Wei Han
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yun-Dong Wu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- School of Chemical Biology and Biotechnology, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- College of Chemistry, Peking University, Beijing, 100871, China
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9
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Mineev KS, Khabibullina NF, Lyukmanova EN, Dolgikh DA, Kirpichnikov MP, Arseniev AS. Spatial structure and dimer--monomer equilibrium of the ErbB3 transmembrane domain in DPC micelles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2081-8. [PMID: 21575594 DOI: 10.1016/j.bbamem.2011.04.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 04/18/2011] [Accepted: 04/29/2011] [Indexed: 11/26/2022]
Abstract
In present work the interaction of two TM α-helices of the ErbB3 receptor tyrosine kinase from the ErbB or HER family (residues 639-670) was studied by means of NMR spectroscopy in a membrane-mimicking environment provided by the DPC micelles. The ErbB3 TM segment appeared to form a parallel symmetric dimer in a left-handed orientation. The interaction between TM spans is accomplished via the non-standard motif and is supported by apolar contacts of bulky side chains and by stacking of aromatic rings together with π-cation interactions of Phe and Arg side chains. The investigation of the dimer--monomer equilibrium revealed thermodynamic properties of the assembly and the presence of two distinct regimes of the dimerization at low and at high peptide/detergent ratio. It was found that the detergent in case of ErbB3 behaves not as an ideal solvent, thus affecting the dimer--monomer equilibrium. Such behavior may account for the problems occurring with the refolding and stability of multispan helical membrane proteins in detergent solutions. The example of ErbB3 allows us to conclude that the thermodynamic parameters of dimerization, measured in micelles for two different helical pairs, cannot be compared without the investigation of their dependence on detergent concentration.
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Affiliation(s)
- K S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation.
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10
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Bocharov EV, Volynsky PE, Pavlov KV, Efremov RG, Arseniev AS. Structure elucidation of dimeric transmembrane domains of bitopic proteins. Cell Adh Migr 2010; 4:284-98. [PMID: 20421711 DOI: 10.4161/cam.4.2.11930] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The interaction between transmembrane helices is of great interest because it directly determines biological activity of a membrane protein. Either destroying or enhancing such interactions can result in many diseases related to dysfunction of different tissues in human body. One much studied form of membrane proteins known as bitopic protein is a dimer containing two membrane-spanning helices associating laterally. Establishing structure-function relationship as well as rational design of new types of drugs targeting membrane proteins requires precise structural information about this class of objects. At present time, to investigate spatial structure and internal dynamics of such transmembrane helical dimers, several strategies were developed based mainly on a combination of NMR spectroscopy, optical spectroscopy, protein engineering and molecular modeling. These approaches were successfully applied to homo- and heterodimeric transmembrane fragments of several bitopic proteins, which play important roles in normal and in pathological conditions of human organism.
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Affiliation(s)
- Eduard V Bocharov
- Division of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.
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11
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Volynsky PE, Mineeva EA, Goncharuk MV, Ermolyuk YS, Arseniev AS, Efremov RG. Computer simulations and modeling-assisted ToxR screening in deciphering 3D structures of transmembrane alpha-helical dimers: ephrin receptor A1. Phys Biol 2010; 7:16014. [PMID: 20228445 DOI: 10.1088/1478-3975/7/1/016014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Membrane-spanning segments of numerous proteins (e.g. receptor tyrosine kinases) represent a novel class of pharmacologically important targets, whose activity can be modulated by specially designed artificial peptides, the so-called interceptors. Rational construction of such peptides requires understanding of the main factors driving peptide-peptide association in lipid membranes. Here we present a new method for rapid prediction of the spatial structure of transmembrane (TM) helix-helix complexes. It is based on computer simulations in membrane-like media and subsequent refinement/validation of the results using experimental studies of TM helix dimerization in a bacterial membrane by means of the ToxR system. The approach was applied to TM fragments of the ephrin receptor A1 (EphA1). A set of spatial structures of the dimer was proposed based on Monte Carlo simulations in an implicit membrane followed by molecular dynamics relaxation in an explicit lipid bilayer. The resulting models were employed for rational design of wild-type and mutant genetic constructions for ToxR assays. The computational and the experimental data are self-consistent and provide an unambiguous spatial model of the TM dimer of EphA1. The results of this work can be further used to develop new biologically active 'peptide interceptors' specifically targeting membrane domains of proteins.
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Affiliation(s)
- P E Volynsky
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences Ul, Miklukho-Maklaya, 16/10, 117997 GSP, Moscow V-437, Russia.
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12
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Chugunov AO, Efremov RG. [Prediction of the spatial structure of proteins: emphasis on membrane targets]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 35:744-60. [PMID: 20208575 DOI: 10.1134/s106816200906003x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Knowledge of the spatial structure of proteins is a prerequisite for both awareness of their functional mechanisms and the framework for rational drug discovery and design. Meanwhile, direct structural determination is often hampered or impractical due to the complexity, expensiveness, and limited capabilities of experimental techniques. These issues are especially pronounced for integral membrane proteins. On numerous occasions, the theoretical prediction of protein structures may facilitate the process by exploiting physical or empirical principles. This paper surveys modern techniques for the prediction of the spatial structure of proteins using computer algorithms, and the main emphasis is placed on the most "complex" targets - membrane proteins (MPs). The first part of the review describes de novo methods based on empirical physical principles; in the second part, a comparative modeling philosophy, which accounts for the structure of related proteins, is described. Special focus is made regarding pharmacologically relevant classes of G-coupled receptors, receptor tyrosine ki-nases, and other MPs. Algorithms for the assessment of the models quality and potential fields of application of computer models are discussed.
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Li H, Luo Y, Derreumaux P, Wei G. Effects of the RGTFEGKF Inhibitor on the Structures of the Transmembrane Fragment 70−86 of Glycophorin A: An All-Atom Molecular Dynamics Study. J Phys Chem B 2009; 114:1004-9. [DOI: 10.1021/jp908889q] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Huiyu Li
- Surface Physics Laboratory (National Key Laboratory) and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, People’s Republic of China and Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico−Chimique et Université Paris Diderot, Paris 7,13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Yin Luo
- Surface Physics Laboratory (National Key Laboratory) and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, People’s Republic of China and Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico−Chimique et Université Paris Diderot, Paris 7,13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Surface Physics Laboratory (National Key Laboratory) and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, People’s Republic of China and Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico−Chimique et Université Paris Diderot, Paris 7,13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Guanghong Wei
- Surface Physics Laboratory (National Key Laboratory) and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, People’s Republic of China and Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico−Chimique et Université Paris Diderot, Paris 7,13 rue Pierre et Marie Curie, 75005 Paris, France
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14
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Vereshaga YA, Volynsky PE, Pustovalova JE, Nolde DE, Arseniev AS, Efremov RG. Specificity of helix packing in transmembrane dimer of the cell death factor BNIP3: a molecular modeling study. Proteins 2009; 69:309-25. [PMID: 17600828 DOI: 10.1002/prot.21555] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BNIP3 is a mitochondrial 19-kDa proapoptotic protein, a member of the Bcl-2 family. It has a single COOH-terminal transmembrane (TM) alpha-helical domain, which is required for membrane targeting, proapoptotic activity, hetero- and homo-dimerization in membrane. The role and the molecular details of association of TM helices of BNIP3 are yet to be established. Here, we present a molecular modeling study of helix interactions in its membrane domain. The approach combines Monte Carlo conformational search in an implicit hydrophobic slab followed by molecular dynamics simulations in a hydrated full-atom lipid bilayer. The former technique was used for exhaustive sampling of the peptides' conformational space and for generation of putative "native-like" structures of the dimer. The latter ones were taken as realistic starting points to assess stability and dynamic behavior of the complex in explicit lipid-water surrounding. As a result, several groups of tightly packed right-handed structures of the dimer were proposed. They have almost similar helix-helix interface, which includes the motif A(176)xxxG(180)xxxG(184) and agrees well with previous mutagenesis data and preliminary NMR analysis. Molecular dynamics simulations of these structures reveal perfect adaptation of most of them to heterogeneous membrane environment. A remarkable feature of the predicted dimeric structures is the occurrence of a cluster of H-bonded histidine 173 and serines 168 and 172 on the helix interface, near the N-terminus. Because of specific polar interactions between the monomers, this part of the dimer has no such dense packing as the C-terminal one, thus allowing penetration of water from the extramembrane side into the membrane interior. We propose that the ionization state of His(173) can mediate structural and dynamic properties of the dimer. This, in turn, may be related to pH-dependent proapoptotic activity of BNIP3, which is triggering on by acidosis appearing under hypoxic conditions.
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Affiliation(s)
- Yana A Vereshaga
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow V-437, 117997 GSP, Russia
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15
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Volynsky PE, Bocharov EV, Nolde DE, Vereschaga YA, Mayzel ML, Mineev KS, Mineeva EA, Pustovalova YE, Gagnidze IA, Efremov RG, Arseniev AS. Solution of the spatial structure of dimeric transmembrane domains of proteins by heteronuclear NMR spectroscopy and molecular modeling. Biophysics (Nagoya-shi) 2008. [DOI: 10.1134/s0006350906070050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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16
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Dell'Orco D, De Benedetti PG, Fanelli F. In Silico Screening of Mutational Effects on Transmembrane Helix Dimerization: Insights from Rigid-Body Docking and Molecular Dynamics Simulations. J Phys Chem B 2007; 111:9114-24. [PMID: 17602582 DOI: 10.1021/jp071383r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, a docking-based protocol has been probed for its ability to predict the effects of 32 single and double mutations on glycophorin A (GpA) homodimerization. Rigid-body docking simulations have been paralleled by molecular dynamics (MD) simulations in implicit membrane. The rigid-body docking-based approach proved effective in reconstituting the native architecture of the GpA dimer for the wild type and the wild-type-like mutants. The good correlative models between the intermolecular interaction descriptors derived both by rigid-body docking simulations and by MD simulations and experimental relative free energies support the assumption that the mutation-induced changes in the association free energy of GpA helices are essentially ascribed to differences in the packing interactions, whereas almost all the variations in the entropic contributions to the association free energy are constant and/or negligible. The MD-based models achieved provide insights into the structural determinants for disruptive and restoring mutational effects. The computational approaches presented in this study are fast and effective, and constitute simple and promising tools for in silico screening of mutational effects on the association properties of integral membrane proteins.
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Affiliation(s)
- Daniele Dell'Orco
- Department of Chemistry and Dulbecco Telethon Institute, University of Modena and Reggio Emilia, via Campi 183, 41100 Modena, Italy
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Cuthbertson JM, Bond PJ, Sansom MSP. Transmembrane Helix−Helix Interactions: Comparative Simulations of the Glycophorin A Dimer. Biochemistry 2006; 45:14298-310. [PMID: 17128969 DOI: 10.1021/bi0610911] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The glycophorin helix dimer is a paradigm for the exploration of helix-helix interactions in integral membrane proteins. Two NMR structures of the dimer are known, one in a detergent micelle and one in a lipid bilayer. Multiple (4 x 50 ns) molecular dynamics simulations starting from each of the two NMR structures, with each structure in either a dodecyl phosphocholine (DPC) micelle or a dimyristoyl phosphatidylcholine (DMPC) bilayer, have been used to explore the conformational dynamics of the helix dimer. Analysis of the helix-helix interaction, mediated by the GxxxG sequence motif, suggests convergence of the simulations to a common model. This is closer to the NMR structure determined in a bilayer than to micelle structure. The stable dimer interface in the final simulation model is characterized by (i) Gly/Gly packing and (ii) Thr/Thr interhelix H-bonds. These results demonstrate the ability of extended molecular dynamics simulations in a lipid bilayer environment to refine membrane protein structures or models derived from experimental data obtained in protein/detergent micelles.
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