101
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Pogorelov TV, Vermaas JV, Arcario MJ, Tajkhorshid E. Partitioning of amino acids into a model membrane: capturing the interface. J Phys Chem B 2014; 118:1481-92. [PMID: 24451004 PMCID: PMC3983343 DOI: 10.1021/jp4089113] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Energetics
of protein side chain partitioning between aqueous solution
and cellular membranes is of fundamental importance for correctly
capturing the membrane binding and specific protein–lipid interactions
of peripheral membrane proteins. We recently reported a highly mobile
membrane mimetic (HMMM) model that accelerates lipid dynamics by modeling
the membrane interior partially as a fluid organic solvent while retaining
a literal description of the lipid head groups and the beginning of
the tails. While the HMMM has been successfully applied to study spontaneous
insertion of a number of peripheral proteins into membranes, a quantitative
characterization of the energetics of membrane–protein interactions
in HMMM membranes has not been performed. We report here the free
energy profiles for partitioning of 10 protein side chain analogues
into a HMMM membrane. In the interfacial and headgroup regions of
the membrane, the side chain free energy profiles show excellent agreement
with profiles previously reported for conventional membranes with
full-tail lipids. In regions where the organic solvent is prevalent,
the increased dipole and fluidity of the solvent generally result
in a less accurate description, most notably overstabilization of
aromatic and polar amino acids. As an additional measure of the ability
of the HMMM model to describe membrane–protein interactions,
the water-to-membrane interface transfer energies were analyzed and
found to be in agreement with the previously reported experimental
and computational hydrophobicity scales. We discuss strengths and
weaknesses of HMMM in describing protein–membrane interactions
as well as further development of model membranes.
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Affiliation(s)
- Taras V Pogorelov
- Center for Biophysics and Computational Biology, School of Chemical Sciences, Departments of Chemistry and Biochemistry, College of Medicine, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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102
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Van Lehn RC, Alexander-Katz A. Free energy change for insertion of charged, monolayer-protected nanoparticles into lipid bilayers. SOFT MATTER 2014; 10:648-58. [PMID: 24795979 DOI: 10.1039/c3sm52329b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Charged, monolayer-protected gold nanoparticles (AuNPs) with core diameters smaller than 10 nm have recently emerged as a prominent class of nanomaterial for use in targeted drug delivery and biosensing. In particular, recent experimental studies showed that AuNPs protected by a binary mixture of purely hydrophobic and anionic, end-functionalized alkanethiol ligands were able to spontaneously penetrate through cell membranes via a non-endocytic, non-disruptive mechanism. The critical step in the penetration process is a fusion step during which the AuNPs insert into the hydrophobic core of the bilayer. This fusion step is driven by hydrophobic forces as inserted AuNPs minimize their exposed hydrophobic surface area and thereby lower their free energy compared to particles in the bulk. Here, we explore the effect of the large parameter space of composition, size, ligand length, morphology, and hydrophobicity strength on the change in the free energy upon insertion. Using a newly developed implicit bilayer, implicit solvent simulation model, our work shows that there is a size cutoff for insertion that has a strong dependence on surface composition and ligand chemistry. Our results agree well with previous experimental findings for a particular value of the hydrophobicity strength. This work provides physical insight that may be used to both understand the insertion of AuNPs into bilayers and guide the design of monolayers to either encourage or inhibit insertion.
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103
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Martin LJ, Chao R, Corry B. Molecular dynamics simulation of the partitioning of benzocaine and phenytoin into a lipid bilayer. Biophys Chem 2013; 185:98-107. [PMID: 24406394 DOI: 10.1016/j.bpc.2013.12.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 12/04/2013] [Accepted: 12/04/2013] [Indexed: 10/25/2022]
Abstract
Molecular dynamics simulations were used to examine the partitioning behaviour of the local anaesthetic benzocaine and the anti-epileptic phenytoin into lipid bilayers, a factor that is critical to their mode of action. Free energy methods are used to quantify the thermodynamics of drug movement between water and octanol as well as for permeation across a POPC membrane. Both drugs are shown to favourably partition into the lipid bilayer from water and are likely to accumulate just inside the lipid headgroups where they may alter bilayer properties or interact with target proteins. Phenytoin experiences a large barrier to cross the centre of the bilayer due to less favourable energetic interactions in this less dense region of the bilayer. Remarkably, in our simulations both drugs are able to pull water into the bilayer, creating water chains that extend back to bulk, and which may modify the local bilayer properties. We find that the choice of atomic partial charges can have a significant impact on the quantitative results, meaning that careful validation of parameters for new drugs, such as performed here, should be performed prior to their use in biomolecular simulations.
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Affiliation(s)
- Lewis J Martin
- Research School of Biology, Australian National University, Canberra 0200, Australia
| | - Rebecca Chao
- Research School of Biology, Australian National University, Canberra 0200, Australia
| | - Ben Corry
- Research School of Biology, Australian National University, Canberra 0200, Australia.
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104
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Bonhenry D, Tarek M, Dehez F. Effects of Phospholipid Composition on the Transfer of a Small Cationic Peptide Across a Model Biological Membrane. J Chem Theory Comput 2013; 9:5675-84. [PMID: 26592298 DOI: 10.1021/ct400576e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The transfer of a lysine amino acid analogue across phospholipid membrane models was investigated using molecular-dynamics simulations. The evolution of the protonation state of this small peptide as a function of its position inside the membrane was studied by determining the local pKa by means of free-energy calculations. Permeability and mean-first-passage time were evaluated and showed that the transfer occurs on the submillisecond time scale. Comparative studies were conducted to evaluate changes in the pKa arising from differences in the phospholipid chemical structure. We compared, hence, the effect of an ether vs an ester linkage of the lipid headgroup as well as linear vs branched lipid tails. The study reveals that protonated lysine residues can be buried further inside an ether lipid membrane than an ester lipid membrane, while branched lipids are found to stabilize less the charged form compared to their unbranched lipid chain counterparts.
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Affiliation(s)
- Daniel Bonhenry
- Université de Lorraine, SRSMC, UMR 7565 , Vandoeuvre-lès-Nancy, F-54500, France.,CNRS, SRSMC, UMR 7565 , Vandoeuvre-lès-Nancy, F-54500, France
| | - Mounir Tarek
- Université de Lorraine, SRSMC, UMR 7565 , Vandoeuvre-lès-Nancy, F-54500, France.,CNRS, SRSMC, UMR 7565 , Vandoeuvre-lès-Nancy, F-54500, France
| | - François Dehez
- Université de Lorraine, SRSMC, UMR 7565 , Vandoeuvre-lès-Nancy, F-54500, France.,CNRS, SRSMC, UMR 7565 , Vandoeuvre-lès-Nancy, F-54500, France
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105
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Rychkova A, Warshel A. On the nature of the apparent free energy of inserting amino acids into membrane through the translocon. J Phys Chem B 2013; 117:13748-54. [PMID: 24087983 DOI: 10.1021/jp406925y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The nature of the biological free energy scale (ΔGapp), obtained from translocon mediated insertion studies, has been a major puzzle and the subject of major controversies. Part of the problem has been the complexity of the insertion process that discouraged workers from considering the feasible kinetics schemes and left the possible impression that ΔGapp presents some simple partition. Here we extend and clarify our recent analysis of the insertion problem using well-defined kinetics schemes and a free energy profile. We point out that although the rate constants of some steps are far from being obvious, it is essential to consider explicitly such schemes in order to advance in analyzing the meaning of ΔGapp. It is then shown that under some equilibrium conditions the kinetics scheme leads to a simple formula that allows one to relate ΔGapp to the actual free energy of partitioning between the water, the membrane, and the translocon. Other options are also considered (including limits with irreversible transitions that can be described by linear free energy relationships (LFERs)). It is concluded that it is unlikely that a kinetics plus thermodynamic based analysis can lead to a result that identifies ΔGapp with the partition between the membrane and the translocon. Thus, we argue that unless such analysis is presented, it is unjustified to assume that ΔGapp corresponds to the membrane translocon equilibrium or to some other arbitrary definition. Furthermore, we point out that the presumption that it is sufficient to just calculate the PMF for going from the translocon (TR) to the membrane and then to assume irreversible diffusive motion to water and for further entrance to the membrane is not a valid analysis. Overall, we point out that it is important to try to relate ΔGapp to a well-defined kinetics scheme (regardless of the complication of the system) in order to determine whether the energies of inserting positively charged residues to the membrane are related to the corresponding ΔGapp. It is also suggested that deviations from our simple formula for equilibrium conditions can help in identifying and analyzing kinetics barriers.
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Affiliation(s)
- Anna Rychkova
- Department of Genetics, Stanford University , 365 Lasuen Street, Littlefield Center, MC2069, Stanford, California 94305, United States
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106
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Loo TW, Clarke DM. Drug rescue distinguishes between different structural models of human P-glycoprotein. Biochemistry 2013; 52:7167-9. [PMID: 24083983 PMCID: PMC3798097 DOI: 10.1021/bi401269m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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There
is no high-resolution crystal structure of the human P-glycoprotein
(P-gp) drug pump. Homology models of human P-gp based on the crystal
structures of mouse or Caenorhabditis elegans P-gps
show large differences in the orientation of transmembrane segment
5 (TM5). TM5 is one of the most important transmembrane segments involved
in drug–substrate interactions. Drug rescue of P-gp processing
mutants containing an arginine at each position in TM5 was used to
identify positions facing the lipid or internal aqueous chamber. Only
the model based on the C. elegans P-gp structure
was compatible with the drug rescue results.
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Affiliation(s)
- Tip W Loo
- Departments of Medicine and Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
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107
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Li L, Vorobyov I, Allen TW. The different interactions of lysine and arginine side chains with lipid membranes. J Phys Chem B 2013; 117:11906-20. [PMID: 24007457 DOI: 10.1021/jp405418y] [Citation(s) in RCA: 224] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The basic amino acids lysine (Lys) and arginine (Arg) play important roles in membrane protein activity, the sensing of membrane voltages, and the actions of antimicrobial, toxin, and cell-penetrating peptides. These roles are thought to stem from the strong interactions and disruptive influences of these amino acids on lipid membranes. In this study, we employ fully atomistic molecular dynamics simulations to observe, quantify, and compare the interactions of Lys and Arg with saturated phosphatidylcholine membranes of different thickness. We make use of both charged (methylammonium and methylguanidinium) and neutral (methylamine and methylguanidine) analogue molecules, as well as Lys and Arg side chains on transmembrane helix models. We find that the free energy barrier experienced by a charged Lys crossing the membrane is strikingly similar to that of a charged Arg (to within 2 kcal/mol), despite the two having different chemistries, H-bonding capability, and hydration free energies that differ by ∼10 kcal/mol. In comparison, the barrier for neutral Arg is higher than that for neutral Lys by around 5 kcal/mol, being more selective than that for the charged species. This can be explained by the different transport mechanisms for charged or neutral amino acid side chains in the membrane, involving membrane deformations or simple dehydration, respectively. As a consequence, we demonstrate that Lys would be deprotonated in the membrane, whereas Arg would maintain its charge. Our simulations also reveal that Arg attracts more phosphate and water in the membrane, and can form extensive H-bonding with its five H-bond donors to stabilize Arg-phosphate clusters. This leads to enhanced interfacial binding and membrane perturbations, including the appearance of a trans-membrane pore in a thinner membrane. These results highlight the special role played by Arg as an amino acid to bind to, disrupt, and permeabilize lipid membranes, as well as to sense voltages for a range of peptide and protein activities in nature and in engineered bionanodevices.
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Affiliation(s)
- Libo Li
- Department of Chemistry, University of California, Davis , Davis, California 95616, United States
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108
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Hu Y, Ou S, Patel S. Free energetics of arginine permeation into model DMPC lipid bilayers: coupling of effective counterion concentration and lateral bilayer dimensions. J Phys Chem B 2013; 117:11641-53. [PMID: 23888915 DOI: 10.1021/jp404829y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Mechanisms and underlying thermodynamic determinants of translocation of charged cationic peptides such as cell-penetrating peptides across the cellular membrane continue to receive much attention. Two widely held views include endocytotic and non-endocytotic (diffusive) processes of permeant transfer across the bilayer. Considering a purely diffusive process, we consider the free energetics of translocation of a monoarginine peptide mimic across a model DMPC bilayer. We compute potentials of mean force for the transfer of a charged monoarginine peptide unit from water to the center of a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) model lipid bilayer. We use fully atomistic molecular dynamics simulations coupled with the adaptive biasing force (ABF) method for free energy estimation. The estimated potential of mean force difference from bulk to bilayer center is 6.94 ± 0.28 kcal/mol. The order of magnitude of this prediction is consistent with past experimental estimates of arginine partitioning into physiological bilayers in the context of translocon-based experiments, though the correlation between the bench and computer experiments is not unambiguous. Moreover, the present value is roughly one-half of previous estimates based on all-atom molecular dynamics free energy calculations. We trace the differences between the present and earlier calculations to system sizes used in the simulations and the dependence of the contributions to the free energy from various system components (water, lipids, ions, peptide) on overall system size. By varying the bilayer lateral dimensions in simulations using only sufficient numbers of counterions to maintain overall system charge neutrality, we find the possibility of an inherent convergent transfer free energy value.
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Affiliation(s)
- Yuan Hu
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
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109
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Van Lehn RC, Atukorale PU, Carney RP, Yang YS, Stellacci F, Irvine DJ, Alexander-Katz A. Effect of particle diameter and surface composition on the spontaneous fusion of monolayer-protected gold nanoparticles with lipid bilayers. NANO LETTERS 2013; 13:4060-7. [PMID: 23915118 PMCID: PMC4177149 DOI: 10.1021/nl401365n] [Citation(s) in RCA: 195] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Anionic, monolayer-protected gold nanoparticles (AuNPs) have been shown to nondisruptively penetrate cellular membranes. Here, we show that a critical first step in the penetration process is potentially the fusion of such AuNPs with lipid bilayers. Free energy calculations, experiments on unilamellar and multilamellar vesicles, and cell studies all support this hypothesis. Furthermore, we show that fusion is only favorable for AuNPs with core diameters below a critical size that depends on the monolayer composition.
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Affiliation(s)
- Reid C. Van Lehn
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Prabhani U. Atukorale
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Randy P. Carney
- Institute of Materials, École Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| | - Yu-Sang Yang
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Francesco Stellacci
- Institute of Materials, École Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| | - Darrell J. Irvine
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
| | - Alfredo Alexander-Katz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Corresponding Author
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110
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Wang YT, Hsu HJ, Fischer WB. Computational modeling of the p7 monomer from HCV and its interaction with small molecule drugs. SPRINGERPLUS 2013; 2:324. [PMID: 23961398 PMCID: PMC3724979 DOI: 10.1186/2193-1801-2-324] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 07/11/2013] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus p7 protein is a 63 amino acid polytopic protein with two transmembrane domains (TMDs) and one of the prime targets for anti HCV drug development. A bio-inspired modeling pathway is used to generate plausible computational models of the two TMDs forming the monomeric protein model. A flexible region between Leu-13 and Gly-15 is identified for TMD11-32 and a region around Gly-46 to Trp-48 for TMD236-58. Mutations of the tyrosine residues in TMD236-58 into phenylalanine and serine are simulated to identify their role in shaping TMD2. Lowest energy structures of the two TMDs connected with the loop residues are used for a posing study in which small molecule drugs BIT225, amantadine, rimantadine and NN-DNJ, are identified to bind to the loop region. BIT225 is identified to interact with the backbone of the functionally important residues Arg-35 and Trp-36.
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Affiliation(s)
- Yi-Ting Wang
- Department of Life Science, Tzu Chi University, Hualien, 970 Taiwan
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111
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Neale C, Madill C, Rauscher S, Pomès R. Accelerating Convergence in Molecular Dynamics Simulations of Solutes in Lipid Membranes by Conducting a Random Walk along the Bilayer Normal. J Chem Theory Comput 2013; 9:3686-703. [DOI: 10.1021/ct301005b] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chris Neale
- Molecular Structure
and Function,
The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario,
M5G 1X8, Canada
- Department
of Biochemistry,
University of Toronto, 101 College Street, Toronto, Ontario, M5G 1L7,
Canada
| | - Chris Madill
- Molecular Structure
and Function,
The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario,
M5G 1X8, Canada
- Department
of Biochemistry,
University of Toronto, 101 College Street, Toronto, Ontario, M5G 1L7,
Canada
| | - Sarah Rauscher
- Molecular Structure
and Function,
The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario,
M5G 1X8, Canada
- Department
of Biochemistry,
University of Toronto, 101 College Street, Toronto, Ontario, M5G 1L7,
Canada
| | - Régis Pomès
- Molecular Structure
and Function,
The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario,
M5G 1X8, Canada
- Department
of Biochemistry,
University of Toronto, 101 College Street, Toronto, Ontario, M5G 1L7,
Canada
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112
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Abstract
MOTIVATION Outer membrane beta-barrels (OMBBs) are the proteins found in the outer membrane of bacteria, mitochondria and chloroplasts. There are thousands of beta-barrels reported in genomic databases with ∼2-3% of the genes in gram-negative bacteria encoding these proteins. These proteins have a wide variety of biological functions including active and passive transport, cell adhesion, catalysis and structural anchoring. Of the non-redundant OMBB structures in the Protein Data Bank, half have been solved during the past 5 years. This influx of information provides new opportunities for understanding the chemistry of these proteins. The distribution of charges in proteins in the outer membrane has implications for how the mechanism of outer membrane protein insertion is understood. Understanding the distribution of charges might also assist in organism selection for the heterologous expression of mitochondrial OMBBs. RESULTS We find a strong asymmetry in the charge distribution of these proteins. For the outward-facing residues of the beta-barrel within regions of similar amino acid density for both membrane leaflets, the external side of the outer membrane contains almost three times the number of charged residues as the internal side of the outer membrane. Moreover, the lipid bilayer of the outer membrane is asymmetric, and the overall preference for amino acid types to be in the external leaflet of the membrane correlates roughly with the hydrophobicity of the membrane lipids. This preference is demonstrably related to the difference in lipid composition of the external and internal leaflets of the membrane.
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Affiliation(s)
- Joanna S G Slusky
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA 19111, USA.
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113
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Chipot C. Frontiers in free-energy calculations of biological systems. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1157] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Christophe Chipot
- Laboratoire International Associé CNRS-UIUC; Unité mixte de recherche 7565; Université de Lorraine; Cedex France
- Beckman Institute for Advanced Science and Technology; University of Illinois; Urbana-Champaign IL USA
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114
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Mondal S, Khelashvili G, Shi L, Weinstein H. The cost of living in the membrane: a case study of hydrophobic mismatch for the multi-segment protein LeuT. Chem Phys Lipids 2013; 169:27-38. [PMID: 23376428 PMCID: PMC3631462 DOI: 10.1016/j.chemphyslip.2013.01.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 01/15/2013] [Accepted: 01/15/2013] [Indexed: 12/27/2022]
Abstract
Many observations of the role of the membrane in the function and organization of transmembrane (TM) proteins have been explained in terms of hydrophobic mismatch between the membrane and the inserted protein. For a quantitative investigation of this mechanism in the lipid-protein interactions of functionally relevant conformations adopted by a multi-TM segment protein, the bacterial leucine transporter (LeuT), we employed a novel method, Continuum-Molecular Dynamics (CTMD), that quantifies the energetics of hydrophobic mismatch by combining the elastic continuum theory of membrane deformations with an atomistic level description of the radially asymmetric membrane-protein interface from MD simulations. LeuT has been serving as a model for structure-function studies of the mammalian neurotransmitter:sodium symporters (NSSs), such as the dopamine and serotonin transporters, which are the subject of intense research in the field of neurotransmission. The membrane models in which LeuT was embedded for these studies were composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid, or 3:1 mixture of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) lipids. The results show that deformation of the host membrane alone is not sufficient to alleviate the hydrophobic mismatch at specific residues of LeuT. The calculations reveal significant membrane thinning and water penetration due to the specific local polar environment produced by the charged K288 of TM7 in LeuT, that is membrane-facing deep inside the hydrophobic milieu of the membrane. This significant perturbation is shown to result in unfavorable polar-hydrophobic interactions at neighboring hydrophobic residues in TM1a and TM7. We show that all the effects attributed to the K288 residue (membrane thinning, water penetration, and the unfavorable polar-hydrophobic interactions at TM1a and TM7), are abolished in calculations with the K288A mutant. The involvement of hydrophobic mismatch is somewhat different in the functionally distinct conformations (outward-open, occluded, inward-open) of LeuT, and the differences are shown to connect to structural elements (e.g., TM1a) known to play key roles in transport. This finding suggests a mechanistic hypothesis for the enhanced transport activity observed for the K288A mutant, suggesting that the unfavorable hydrophobic-hydrophilic interactions hinder the motion of TM1a in the functionally relevant conformational transition to the inward-open state. Various extents of such unfavorable interactions, involving exposure to the lipid environment of adjacent hydrophobic and polar residues, are common in multi-segment transmembrane proteins, and must be considered to affect functionally relevant conformational transitions.
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Affiliation(s)
- Sayan Mondal
- Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, NY 10065
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, NY 10065
| | - Lei Shi
- Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, NY 10065
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, Cornell University, New York, NY 10065
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, NY 10065
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, Cornell University, New York, NY 10065
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115
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Ou S, Lucas TR, Zhong Y, Bauer BA, Hu Y, Patel S. Free energetics and the role of water in the permeation of methyl guanidinium across the bilayer-water interface: insights from molecular dynamics simulations using charge equilibration potentials. J Phys Chem B 2013; 117:3578-92. [PMID: 23409975 DOI: 10.1021/jp400389z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Combining umbrella sampling molecular dynamics (MD) simulations, the weighted histogram analysis method (WHAM) for unbiasing probabilities, and polarizable charge equilibration force fields, we compute the potential of mean force for the reversible transfer of methyl guanidinium from bulk solution to the center of a model DPPC bilayer. A 5 kcal/mol minimum in the potential of mean force profile for membrane permeation suggests that the analogue will preferentially reside in the headgroup region of the lipid, qualitatively in agreement with previously published results. We find the potential of mean force for permeation to be approximately 28 kcal/mol (relative to the minimum in the headgroups), within the range of values reported for similar types of simulations using fixed-charge force fields. From analysis of the lipid structure, we find that the lipid deformation leads to a substantial destabilizing contribution to the free energy of the methyl guanidinium as it resides in the bilayer center, though this deformation allows more efficient stabilization by water defects and transient pores. Water in the bilayer core stabilizes the charged residue. The role of water in stabilizing or destabilizing the solute as it crosses the bilayer depends on bulk electrolyte concentration. In 1 M KCl solution, the water contribution to the potential of mean force is stabilizing over the entire range of the permeation coordinate, with the sole destabilizing force originating from the anionic species in solution. Conversely, methyl guanidinium experiences net destabilization from water in the absence of electrolyte. The difference in solvent contributions to permeation free energy is traced to a local effect arising from differences in water density in the bilayer-water solution interface, thus leading to starkly opposite net forces on the permeant. The origin of the local water density differential rests with the penetration of hydrated chloride anions into the solution-bilayer interface. Finally, water permeation into the bilayer is required for the deformation of individual lipid molecules and permeation of ions into the membrane. From simulations where water is first excluded from the bilayer center where methyl guanidinium is restrained and then, after equilibration, allowed to enter the bilayer, we find that in the absence of any water defects/permeation into the bilayer, the lipid headgroups do not follow the methyl guanidinium. Only when water enters the bilayer do we see deformation of individual lipid molecules to associate with the amino acid analogue at bilayer center.
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Affiliation(s)
- Shuching Ou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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116
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Panahi A, Feig M. Dynamic Heterogeneous Dielectric Generalized Born (DHDGB): An implicit membrane model with a dynamically varying bilayer thickness. J Chem Theory Comput 2013; 9:1709-1719. [PMID: 23585740 PMCID: PMC3622271 DOI: 10.1021/ct300975k] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
An extension to the heterogeneous dielectric generalized Born (HDGB) implicit membrane formalism is presented to allow dynamic membrane deformations in response to membrane-inserted biomolecules during molecular dynamic simulations. The flexible membrane is implemented through additional degrees of freedom that represent the membrane deformation at the contact points of a membrane-inserted solute with the membrane. The extra degrees of freedom determine the dielectric and non-polar solvation free energy profiles that are used to obtain the solvation free energy in the presence of the membrane and are used to calculate membrane deformation free energies according to an elastic membrane model. With the dynamic HDGB (DHDGB) model the membrane is able to deform in response to the insertion of charged molecules thereby avoiding the overestimation of insertion free energies with static membrane models. The DHDGB model also allows the membrane to respond to the insertion of membrane-spanning solutes with hydrophobic mismatch. The model is tested with the membrane insertion of amino acid side chain analogs, arginine-containing helices, the WALP23 peptide, and the gramicidin A channel.
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Affiliation(s)
- Afra Panahi
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824
| | - Michael Feig
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824
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117
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Su Y, Li S, Hong M. Cationic membrane peptides: atomic-level insight of structure-activity relationships from solid-state NMR. Amino Acids 2013; 44:821-33. [PMID: 23108593 PMCID: PMC3570695 DOI: 10.1007/s00726-012-1421-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 10/11/2012] [Indexed: 12/24/2022]
Abstract
Many membrane-active peptides, such as cationic cell-penetrating peptides (CPPs) and antimicrobial peptides (AMPs), conduct their biological functions by interacting with the cell membrane. The interactions of charged residues with lipids and water facilitate membrane insertion, translocation or disruption of these highly hydrophobic species. In this review, we will summarize high-resolution structural and dynamic findings towards the understanding of the structure-activity relationship of lipid membrane-bound CPPs and AMPs, as examples of the current development of solid-state NMR (SSNMR) techniques for studying membrane peptides. We will present the most recent atomic-resolution structure of the guanidinium-phosphate complex, as constrained from experimentally measured site-specific distances. These SSNMR results will be valuable specifically for understanding the intracellular translocation pathway of CPPs and antimicrobial mechanism of AMPs, and more generally broaden our insight into how cationic macromolecules interact with and cross the lipid membrane.
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Affiliation(s)
- Yongchao Su
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA.
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118
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Karlsson BCG, Olsson GD, Friedman R, Rosengren AM, Henschel H, Nicholls IA. How Warfarin’s Structural Diversity Influences Its Phospholipid Bilayer Membrane Permeation. J Phys Chem B 2013; 117:2384-95. [DOI: 10.1021/jp400264x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Björn C. G. Karlsson
- Bioorganic and Biophysical Chemistry
Laboratory, Linnæus University Centre for Biomaterials Chemistry,
Department of Chemistry and Biomedical Sciences, Linnæus University, SE-391 82 Kalmar, Sweden
| | - Gustaf D. Olsson
- Bioorganic and Biophysical Chemistry
Laboratory, Linnæus University Centre for Biomaterials Chemistry,
Department of Chemistry and Biomedical Sciences, Linnæus University, SE-391 82 Kalmar, Sweden
| | - Ran Friedman
- Computational Chemistry and
Biochemistry Group, Linnæus University Centre for Biomaterials
Chemistry, Department of Chemistry and Biomedical Sciences, Linnæus University, SE-391 82 Kalmar, Sweden
| | - Annika M. Rosengren
- Bioorganic and Biophysical Chemistry
Laboratory, Linnæus University Centre for Biomaterials Chemistry,
Department of Chemistry and Biomedical Sciences, Linnæus University, SE-391 82 Kalmar, Sweden
| | - Henning Henschel
- Bioorganic and Biophysical Chemistry
Laboratory, Linnæus University Centre for Biomaterials Chemistry,
Department of Chemistry and Biomedical Sciences, Linnæus University, SE-391 82 Kalmar, Sweden
- Division of Atmospheric Sciences,
Department of Physics, University of Helsinki, P.O. Box 64, Helsinki, Finland
| | - Ian A. Nicholls
- Bioorganic and Biophysical Chemistry
Laboratory, Linnæus University Centre for Biomaterials Chemistry,
Department of Chemistry and Biomedical Sciences, Linnæus University, SE-391 82 Kalmar, Sweden
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
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119
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Huang K, García A. Free energy of translocating an arginine-rich cell-penetrating peptide across a lipid bilayer suggests pore formation. Biophys J 2013; 104:412-20. [PMID: 23442863 PMCID: PMC3552254 DOI: 10.1016/j.bpj.2012.10.027] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 10/16/2012] [Accepted: 10/23/2012] [Indexed: 10/27/2022] Open
Abstract
The molecular mechanism and energetics of the translocation of arginine-rich, cell-penetrating peptides through membranes are still under debate. One possible mechanism involves the formation of a water pore in the membrane such that the hydrophilic residues of the peptide are solvated throughout the translocating process. In this work, employing two different order parameters, we calculate the free energies of translocating a cyclic Arg(9) peptide into a lipid bilayer along one path that involves a water-pore formation and another path that does not form a separate pore. The free-energy barrier of translocating the peptide along a pore path is 80 kJ/mol lower than along a pore-free path. This suggests that the peptide translocation is more likely associated with a water-pore formation.
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Affiliation(s)
- Kun Huang
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, Troy, New York
| | - Angel E. García
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, Troy, New York
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
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120
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Buried lysine, but not arginine, titrates and alters transmembrane helix tilt. Proc Natl Acad Sci U S A 2013; 110:1692-5. [PMID: 23319623 DOI: 10.1073/pnas.1215400110] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The ionization states of individual amino acid residues of membrane proteins are difficult to decipher or assign directly in the lipid-bilayer membrane environment. We address this issue for lysines and arginines in designed transmembrane helices. For lysines (but not arginines) at two locations within dioleoyl-phosphatidylcholine bilayer membranes, we measure pK(a) values below 7.0. We find that buried charged lysine, in fashion similar to arginine, will modulate helix orientation to maximize its own access to the aqueous interface or, if occluded by aromatic rings, may cause a transmembrane helix to exit the lipid bilayer. Interestingly, the influence of neutral lysine (vis-à-vis leucine) upon helix orientation also depends upon its aqueous access. Our results suggest that changes in the ionization states of particular residues will regulate membrane protein function and furthermore illustrate the subtle complexity of ionization behavior with respect to the detailed lipid and protein environment.
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121
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Jämbeck JPM, Lyubartsev AP. Implicit inclusion of atomic polarization in modeling of partitioning between water and lipid bilayers. Phys Chem Chem Phys 2013; 15:4677-86. [DOI: 10.1039/c3cp44472d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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122
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Vostrikov VV, Hall BA, Sansom MSP, Koeppe RE. Accommodation of a central arginine in a transmembrane peptide by changing the placement of anchor residues. J Phys Chem B 2012; 116:12980-90. [PMID: 23030363 DOI: 10.1021/jp308182b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Both Trp and Arg in transmembrane protein domains make important interactions with lipids at the membrane/water interface, but at different depths. Derivatives of the designed peptide GWALP23, acetyl-GGALW(5)LALALALALALALW(19)LAGA-amide, with single Trp anchors, have proven useful for characterizing such interactions. Indeed, previous work revealed quite different effects emanating from Arg substitutions at positions 12 and 14 within GWALP23, with the R12 peptide exhibiting multiple positions and orientations with respect to DOPC bilayer membranes (Vostrikov et al. J. Am. Chem. Soc. 2010, 132, 5803-5811). To gain further understanding of the multistate behavior, we moved the Trp "anchor" residues to more outer positions 3 and 21 in GWALP23 itself, and in the R12 and R14 derivatives. The locations and orientations of the peptides with respect to lipid bilayer membranes of differing thickness were investigated by means of solid-state (2)H NMR spectroscopy, using labeled alanines, and coarse-grained molecular dynamics simulations. Interestingly, relatively intense and narrow (2)H resonances from selected backbone C(α) deuterons were observed over quite narrow ranges of frequency and sample orientation. The backbone resonances reflect dynamic complexities and at the same time provide important contributions for the analysis of peptide transmembrane orientation. With the Trp(3,21) anchors relatively far from the peptide and bilayer center, the results indicate significantly large apparent tilt angles, for example, close to 30° for the new R12 and R14 peptides with respect to the bilayer normal of DLPC membranes. The R12 side chain indeed is "rescued" to a stable position, where it is accommodated within the transmembrane helix, when the Trp anchors are moved outward and to another face of the helix. At the same time, the R14 side chain of transmembrane GW(3,21)ALP23 also retains a stable favored position.
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Affiliation(s)
- Vitaly V Vostrikov
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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123
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Callenberg KM, Latorraca NR, Grabe M. Membrane bending is critical for the stability of voltage sensor segments in the membrane. ACTA ACUST UNITED AC 2012; 140:55-68. [PMID: 22732310 PMCID: PMC3382720 DOI: 10.1085/jgp.201110766] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The interaction between membrane proteins and the surrounding membrane is becoming increasingly appreciated for its role in regulating protein function, protein localization, and membrane morphology. In particular, recent studies have suggested that membrane deformation is needed to stably accommodate proteins harboring charged amino acids in their transmembrane (TM) region, as it is energetically prohibitive to bury charge in the hydrophobic core of the bilayer. Unfortunately, current computational methods are poorly equipped for describing such deformations, as atomistic simulations are often too short to observe large-scale membrane reorganization and most continuum approaches assume a flat membrane. Previously, we developed a method that overcomes these shortcomings by using elasticity theory to characterize equilibrium membrane distortions in the presence of a TM protein, while using traditional continuum electrostatic and nonpolar energy models to determine the energy of the protein in the membrane. Here, we linked the elastostatics, electrostatics, and nonpolar numeric solvers to permit the calculation of energies for nontrivial membrane deformations. We then coupled this procedure to a robust search algorithm that identifies optimal membrane shapes for a TM protein of arbitrary chemical composition. This advance now permits us to explore a host of biological phenomena that were beyond the scope of our original method. We show that the energy required to embed charged residues in the membrane can be highly nonadditive, and our model provides a simple mechanical explanation for this nonadditivity. Our results also predict that isolated voltage sensor segments do not insert into rigid membranes, but membrane bending dramatically stabilizes these proteins in the bilayer despite their high charge content. Additionally, we use the model to explore hydrophobic mismatch with regard to nonpolar peptides and mechanosensitive channels. Our method is in quantitative agreement with molecular dynamics simulations at a tiny fraction of the computational cost.
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Affiliation(s)
- Keith M Callenberg
- Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA 15213, USA
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124
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de Jesus AJ, Allen TW. The determinants of hydrophobic mismatch response for transmembrane helices. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:851-63. [PMID: 22995244 DOI: 10.1016/j.bbamem.2012.09.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 10/27/2022]
Abstract
Hydrophobic mismatch arises from a difference in the hydrophobic thickness of a lipid membrane and a transmembrane protein segment, and is thought to play an important role in the folding, stability and function of membrane proteins. We have investigated the possible adaptations that lipid bilayers and transmembrane α-helices undergo in response to mismatch, using fully-atomistic molecular dynamics simulations totaling 1.4 μs. We have created 25 different tryptophan-alanine-leucine transmembrane α-helical peptide systems, each composed of a hydrophobic alanine-leucine stretch, flanked by 1-4 tryptophan side chains, as well as the β-helical peptide dimer, gramicidin A. Membrane responses to mismatch include changes in local bilayer thickness and lipid order, varying systematically with peptide length. Adding more flanking tryptophan side chains led to an increase in bilayer thinning for negatively mismatched peptides, though it was also associated with a spreading of the bilayer interface. Peptide tilting, bending and stretching were systematic, with tilting dominating the responses, with values of up to ~45° for the most positively mismatched peptides. Peptide responses were modulated by the number of tryptophan side chains due to their anchoring roles and distributions around the helices. Potential of mean force calculations for local membrane thickness changes, helix tilting, bending and stretching revealed that membrane deformation is the least energetically costly of all mismatch responses, except for positively mismatched peptides where helix tilting also contributes substantially. This comparison of energetic driving forces of mismatch responses allows for deeper insight into protein stability and conformational changes in lipid membranes.
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125
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de Jesus AJ, Allen TW. The role of tryptophan side chains in membrane protein anchoring and hydrophobic mismatch. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:864-76. [PMID: 22989724 DOI: 10.1016/j.bbamem.2012.09.009] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 12/27/2022]
Abstract
Tryptophan (Trp) is abundant in membrane proteins, preferentially residing near the lipid-water interface where it is thought to play a significant anchoring role. Using a total of 3 μs of molecular dynamics simulations for a library of hydrophobic WALP-like peptides, a long poly-Leu α-helix, and the methyl-indole analog, we explore the thermodynamics of the Trp movement in membranes that governs the stability and orientation of transmembrane protein segments. We examine the dominant hydrogen-bonding interactions between the Trp and lipid carbonyl and phosphate moieties, cation-π interactions to lipid choline moieties, and elucidate the contributions to the thermodynamics that serve to localize the Trp, by ~4 kcal/mol, near the membrane glycerol backbone region. We show a striking similarity between the free energy to move an isolated Trp side chain to that found from a wide range of WALP peptides, suggesting that the location of this side chain is nearly independent of the host transmembrane segment. Our calculations provide quantitative measures that explain Trp's role as a modulator of responses to hydrophobic mismatch, providing a deeper understanding of how lipid composition may control a range of membrane active peptides and proteins.
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126
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Nugent T, Jones DT. Membrane protein structural bioinformatics. J Struct Biol 2012; 179:327-37. [DOI: 10.1016/j.jsb.2011.10.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 10/25/2011] [Indexed: 10/15/2022]
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127
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Heyden M, Freites JA, Ulmschneider MB, White SH, Tobias DJ. Assembly and Stability of α-Helical Membrane Proteins. SOFT MATTER 2012; 8:7742-7752. [PMID: 23166562 PMCID: PMC3500387 DOI: 10.1039/c2sm25402f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Grease to grease - this is how one might begin to describe the tendency of hydrophobic stretches in protein amino acid sequences to form transmembrane domains. While this simple rule contains a lot of truth, the mechanisms of membrane protein folding, the insertion of hydrophobic protein domains into the lipid bilayer, and the apparent existence of highly polar residues in some proteins in the hydrophobic membrane core are subjects of lively debate - an indication that many details remain unresolved. Here, we present a historical survey of recent insights from experiments and computational studies into the rules and mechanisms of α-helical membrane protein assembly and stability.
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Affiliation(s)
- Matthias Heyden
- Department of Chemistry, University of California, Irvine, CA 92697, U.S.A
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128
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Zhang B, Miller TF. Direct simulation of early-stage Sec-facilitated protein translocation. J Am Chem Soc 2012; 134:13700-7. [PMID: 22852862 DOI: 10.1021/ja3034526] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Direct simulations reveal key mechanistic features of early-stage protein translocation and membrane integration via the Sec-translocon channel. We present a novel computational protocol that combines non-equilibrium growth of the nascent protein with microsecond timescale molecular dynamics trajectories. Analysis of multiple, long timescale simulations elucidates molecular features of protein insertion into the translocon, including signal-peptide docking at the translocon lateral gate (LG), large lengthscale conformational rearrangement of the translocon LG helices, and partial membrane integration of hydrophobic nascent-protein sequences. Furthermore, the simulations demonstrate the role of specific molecular interactions in the regulation of protein secretion, membrane integration, and integral membrane protein topology. Salt-bridge contacts between the nascent-protein N-terminus, cytosolic translocon residues, and phospholipid head groups are shown to favor conformations of the nascent protein upon early-stage insertion that are consistent with the Type II (N(cyt)/C(exo)) integral membrane protein topology, and extended hydrophobic contacts between the nascent protein and the membrane lipid bilayer are shown to stabilize configurations that are consistent with the Type III (N(exo)/C(cyt)) topology. These results provide a detailed, mechanistic basis for understanding experimentally observed correlations between integral membrane protein topology, translocon mutagenesis, and nascent-protein sequence.
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Affiliation(s)
- Bin Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA
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129
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Li Y, Li X, Li Z, Gao H. Surface-structure-regulated penetration of nanoparticles across a cell membrane. NANOSCALE 2012; 4:3768-75. [PMID: 22609866 DOI: 10.1039/c2nr30379e] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The cell uptake rate of nanoparticles (NPs) coated with mixed hydrophilic/hydrophobic ligands is known to be strongly influenced by the ligand pattern on the nanoparticle surface. To help reveal the physical mechanism behind this intriguing phenomenon, here we perform dissipative particle dynamics simulations to analyze the evolution of free energy as the ligand-coated NPs pierce through a lipid bilayer. Four characteristic ligand patterns are considered: striated NPs with alternating hydrophilic and hydrophobic groups compared to NPs with randomly mixed ligands at the same hydrophilic to hydrophobic ratio, as well as NPs coated with homogeneous hydrophilic or hydrophobic ligands. The free energy analysis indicates that among the four ligand patterns under study, the striated NP encounters the lowest energy barrier during translocation across the membrane. Further analysis reveals that the translocation of the striated NP is facilitated by the constraint of its rotational degree of freedom by the anisotropic ligand pattern, which prevented the free energy of the system from sinking to a deeper valley as the NP passes through the hydrophobic core of the bilayer. Finally, the critical forces required for almost instant penetration of these patterned NPs across the bilayer are calculated and shown to be consistent with the free energy analysis. These findings provide useful guidelines for the molecular design of patterned NPs for controllable cell penetrability.
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Affiliation(s)
- Yinfeng Li
- Department of Engineering Mechanics, Shanghai Jiao Tong University, Shanghai 200240, China
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130
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Abstract
Of great interest to the academic and pharmaceutical research communities, helical transmembrane proteins are characterized by their ability to dissolve and fold in lipid bilayers—properties conferred by polypeptide spans termed transmembrane domains (TMDs). The apolar nature of TMDs necessitates the use of membrane-mimetic solvents for many structure and folding studies. This review examines the relationship between TMD structure and solvent environment, focusing on principles elucidated largely in membrane-mimetic environments with single-TMD protein and peptide models. Following a brief description of TMD sequence and conformational characteristics gleaned from the structural database, we present an overview of the conceptual models used to study folding in vitro. The impact of sequence and solvent context on the incorporation of TMDs into membranes, and its role in measurements of TMD self-assembly strengths, is then described. We conclude with a discussion of the nonspecific effects of membrane components on TMD stability.
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Affiliation(s)
- Arianna Rath
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, M5G 1X8 Canada
| | - Charles M. Deber
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, M5G 1X8 Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
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131
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Cahill K. Models of membrane electrostatics. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:051921. [PMID: 23004801 DOI: 10.1103/physreve.85.051921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 04/09/2012] [Indexed: 06/01/2023]
Abstract
Formulas are derived for the electrostatic potential of a charge in or near a membrane modeled as one or more dielectric slabs lying between two semi-infinite dielectrics. One can use these formulas in Monte Carlo codes to compute the distribution of ions near cell membranes more accurately than by using Poisson-Boltzmann theory or its linearized version. Here I use them to discuss the electric field of a uniformly charged membrane, the image charges of an ion, the distribution of salt ions near a charged membrane, the energy of a zwitterion near a lipid slab, and the effect of including the phosphate head groups as thin layers of high electric permittivity.
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Affiliation(s)
- Kevin Cahill
- Biophysics Group, Department of Physics & Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA.
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132
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Membrane fusion and cell entry of XMRV are pH-independent and modulated by the envelope glycoprotein's cytoplasmic tail. PLoS One 2012; 7:e33734. [PMID: 22479434 PMCID: PMC3313918 DOI: 10.1371/journal.pone.0033734] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 02/16/2012] [Indexed: 11/19/2022] Open
Abstract
Xenotropic murine leukemia virus-related virus (XMRV) is a gammaretrovirus that was originally identified from human prostate cancer patients and subsequently linked to chronic fatigue syndrome. Recent studies showed that XMRV is a recombinant mouse retrovirus; hence, its association with human diseases has become questionable. Here, we demonstrated that XMRV envelope (Env)-mediated pseudoviral infection is not blocked by lysosomotropic agents and cellular protease inhibitors, suggesting that XMRV entry is not pH-dependent. The full length XMRV Env was unable to induce syncytia formation and cell-cell fusion, even in cells overexpressing the viral receptor, XPR1. However, truncation of the C-terminal 21 or 33 amino acid residues in the cytoplasmic tail (CT) of XMRV Env induced substantial membrane fusion, not only in the permissive 293 cells but also in the nonpermissive CHO cells that lack a functional XPR1 receptor. The increased fusion activities of these truncations correlated with their enhanced SU shedding into culture media, suggesting conformational changes in the ectodomain of XMRV Env. Noticeably, further truncation of the CT of XMRV Env proximal to the membrane-spanning domain severely impaired the Env fusogenicity, as well as dramatically decreased the Env incorporations into MoMLV oncoretroviral and HIV-1 lentiviral vectors resulting in greatly reduced viral transductions. Collectively, our studies reveal that XMRV entry does not require a low pH or low pH-dependent host proteases, and that the cytoplasmic tail of XMRV Env critically modulates membrane fusion and cell entry. Our data also imply that additional cellular factors besides XPR1 are likely to be involved in XMRV entry.
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133
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Bauer BA, Patel S. Recent applications and developments of charge equilibration force fields for modeling dynamical charges in classical molecular dynamics simulations. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1153-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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134
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Gumbart J, Roux B. Determination of membrane-insertion free energies by molecular dynamics simulations. Biophys J 2012; 102:795-801. [PMID: 22385850 DOI: 10.1016/j.bpj.2012.01.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 01/15/2012] [Accepted: 01/17/2012] [Indexed: 11/19/2022] Open
Abstract
The accurate prediction of membrane-insertion probability for arbitrary protein sequences is a critical challenge to identifying membrane proteins and determining their folded structures. Although algorithms based on sequence statistics have had moderate success, a complete understanding of the energetic factors that drive the insertion of membrane proteins is essential to thoroughly meeting this challenge. In the last few years, numerous attempts to define a free-energy scale for amino-acid insertion have been made, yet disagreement between most experimental and theoretical scales persists. However, for a recently resolved water-to-bilayer scale, it is found that molecular dynamics simulations that carefully mimic the conditions of the experiment can reproduce experimental free energies, even when using the same force field as previous computational studies that were cited as evidence of this disagreement. Therefore, it is suggested that experimental and simulation-based scales can both be accurate and that discrepancies stem from disparities in the microscopic processes being considered rather than methodological errors. Furthermore, these disparities make the development of a single universally applicable membrane-insertion free energy scale difficult.
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Affiliation(s)
- James Gumbart
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.
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135
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Lucas TR, Bauer BA, Patel S. Charge equilibration force fields for molecular dynamics simulations of lipids, bilayers, and integral membrane protein systems. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1818:318-29. [PMID: 21967961 PMCID: PMC4216680 DOI: 10.1016/j.bbamem.2011.09.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2011] [Revised: 09/13/2011] [Accepted: 09/14/2011] [Indexed: 01/06/2023]
Abstract
With the continuing advances in computational hardware and novel force fields constructed using quantum mechanics, the outlook for non-additive force fields is promising. Our work in the past several years has demonstrated the utility of polarizable force fields, those based on the charge equilibration formalism, for a broad range of physical and biophysical systems. We have constructed and applied polarizable force fields for lipids and lipid bilayers. In this review of our recent work, we discuss the formalism we have adopted for implementing the charge equilibration (CHEQ) method for lipid molecules. We discuss the methodology, related issues, and briefly discuss results from recent applications of such force fields. Application areas include DPPC-water monolayers, potassium ion permeation free energetics in the gramicidin A bacterial channel, and free energetics of permeation of charged amino acid analogs across the water-bilayer interface. This article is part of a Special Issue entitled: Membrane protein structure and function.
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Affiliation(s)
- Timothy R. Lucas
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Brad A. Bauer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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136
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Vorobyov I, Bennett WFD, Tieleman DP, Allen TW, Noskov S. The Role of Atomic Polarization in the Thermodynamics of Chloroform Partitioning to Lipid Bilayers. J Chem Theory Comput 2012; 8:618-28. [PMID: 26596610 DOI: 10.1021/ct200417p] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In spite of extensive research and use in medical practice, the precise molecular mechanism of volatile anesthetic action remains unknown. The distribution of anesthetics within lipid bilayers and potential targeting to membrane proteins is thought to be central to therapeutic function. Therefore, obtaining a molecular level understanding of volatile anesthetic partitioning into lipid bilayers is of vital importance to modern pharmacology. In this study we investigate the partitioning of the prototypical anesthetic, chloroform, into lipid bilayers and different organic solvents using molecular dynamics simulations with potential models ranging from simplified coarse-grained MARTINI to additive and polarizable CHARMM all-atom force fields. Many volatile anesthetics display significant inducible dipole moments, which correlate with their potency, yet the exact role of molecular polarizability in their stabilization within lipid bilayers remains unknown. We observe that explicit treatment of atomic polarizability makes it possible to accurately reproduce solvation free energies in solvents with different polarities, allowing for quantitative studies in heterogeneous molecular distributions, such as lipid bilayers. We calculate the free energy profiles for chloroform crossing lipid bilayers to reveal a role of polarizability in modulating chloroform partitioning thermodynamics via the chloroform-induced dipole moment and highlight competitive binding to the membrane core and toward the glycerol backbone that may have significant implications for understanding anesthetic action.
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Affiliation(s)
- Igor Vorobyov
- Department of Chemistry, University of California , Davis, One Shields Avenue, Davis, California 95616, United States
| | - W F Drew Bennett
- Department of Biological Sciences, University of Calgary , 2500 University Drive, Calgary, Canada, T2N 2N4
| | - D Peter Tieleman
- Department of Biological Sciences, University of Calgary , 2500 University Drive, Calgary, Canada, T2N 2N4
| | - Toby W Allen
- Department of Chemistry, University of California , Davis, One Shields Avenue, Davis, California 95616, United States
| | - Sergei Noskov
- Department of Biological Sciences, University of Calgary , 2500 University Drive, Calgary, Canada, T2N 2N4
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137
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Lucas TR, Bauer BA, Davis JE, Patel S. Molecular dynamics simulation of hydrated DPPC monolayers using charge equilibration force fields. J Comput Chem 2012; 33:141-52. [PMID: 21997857 PMCID: PMC3488352 DOI: 10.1002/jcc.21927] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 06/24/2011] [Accepted: 07/30/2011] [Indexed: 12/21/2022]
Abstract
We present results of molecular dynamics simulations of a model DPPC-water monolayer using charge equilibration (CHEQ) force fields, which explicitly account for electronic polarization in a classical treatment of intermolecular interactions. The surface pressure, determined as the difference between the monolayer and pure water surface tensions at 323 K, is predicted to be 22.92 ±1.29 dyne/cm, just slightly below the broad range of experimental values reported for this system. The surface tension for the DPPC-water monolayer is predicted to be 42.35 ±1.16 dyne/cm, in close agreement with the experimentally determined value of 40.9 dyne/cm. This surface tension is also consistent with the value obtained from DPPC monolayer simulations using state-of-the-art nonpolarizable force fields. The current results of simulations predict a monolayer-water potential difference relative to the pure water-air interface of 0.64 ±0.02 Volts, an improved prediction compared to the fixed-charge CHARMM27 force field, yet still overestimating the experimental range of 0.3 to 0.45 Volts. As the charge equilibration model is a purely charge-based model for polarization, the current results suggest that explicitly modeled polarization effects can offer improvements in describing interfacial electrostatics in such systems.
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Affiliation(s)
- Timothy R. Lucas
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Brad A. Bauer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Joseph E. Davis
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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138
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Yacoub TJ, Reddy AS, Szleifer I. Structural effects and translocation of doxorubicin in a DPPC/Chol bilayer: the role of cholesterol. Biophys J 2011; 101:378-85. [PMID: 21767490 DOI: 10.1016/j.bpj.2011.06.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 05/31/2011] [Accepted: 06/08/2011] [Indexed: 11/28/2022] Open
Abstract
We use molecular dynamics simulations to characterize the influence of cholesterol (Chol) on the interaction between the anticancer drug doxorubicin (DOX) and a dipalmitoyl phosphatidylcholine/Chol lipid bilayer. We calculate the potential of mean force, which gives us an estimate of the free energy barrier for DOX translocation across the membrane. We find free energy barriers of 23.1 ± 3.1 k(B)T, 36.8 ± 5.1 k(B)T, and 54.5 ± 4.7 k(B)T for systems composed of 0%, 15%, and 30% Chol, respectively. Our predictions agree with Arrhenius activation energies from experiments using phospholipid membranes, including 20 k(B)T for 0% Chol and 37.2 k(B)T for 20% Chol. The location of the free energy barrier for translocation across the bilayer is dependent on composition. As Chol concentration increases, this barrier changes from the release of DOX into the water to flip-flop over the membrane center. The drug greatly affects local membrane structure by attracting dipalmitoyl phosphatidylcholine headgroups, curving the membrane, and allowing water penetration. Despite its hydrophobicity, DOX facilitates water transport via its polar groups.
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Affiliation(s)
- Tyrone J Yacoub
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
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139
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Yuzlenko O, Lazaridis T. Interactions between ionizable amino acid side chains at a lipid bilayer-water interface. J Phys Chem B 2011; 115:13674-84. [PMID: 21985663 DOI: 10.1021/jp2052213] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Potentials of mean force (PMF) between ionizable amino acid side chains (Arg, Lys, His, Glu) in the headgroup area of a palmitoyl oleoyl phosphatidylcholine lipid bilayer were obtained from all-atom molecular dynamics simulations and the adaptive biasing force method. Simulations in bulk water were also performed for comparison. Side chains were constrained in collinear, stacking, and orthogonal (T-shaped) orientations. The most structured and attractive PMFs were observed for hydrogen-bonded side chains. Contact minima occurred at a distance of 2.6-3.1 Å between selected atoms or centers of mass with the most attractive interaction (-9.6 kcal/mol) observed between Arg(+) and Glu(-). Hydrogen bonds play a significant role in stabilizing these interactions. Interactions between like charged side chains can also be very attractive if the charges are screened by surrounding molecules or groups (e.g., the PMF value at the contact minimum for Arg(+)···Arg(+) is -7.6 kcal/mol). Like charged side chains can have contact minima as close as 3.6 Å. The PMFs depend strongly on the relative orientation of the side chains. In agreement with experimental studies and other simulations, we found the stacking arrangement of like charged side chains to be the most favorable orientation. Interaction energies and Lennard-Jones energies between side chains, headgroups, and water molecules were analyzed in order to rationalize the observed PMFs and their dependence on orientation. In general, the results cannot be explained by simple dielectric arguments.
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Affiliation(s)
- Olga Yuzlenko
- Department of Chemistry, City College of the City University of New York, 160 Convent Avenue, New York, New York 10031, USA
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140
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Li LB, Vorobyov I, Allen TW. The role of membrane thickness in charged protein-lipid interactions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:135-45. [PMID: 22063722 DOI: 10.1016/j.bbamem.2011.10.026] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 10/23/2011] [Accepted: 10/24/2011] [Indexed: 02/01/2023]
Abstract
Charged amino acids are known to be important in controlling the actions of integral and peripheral membrane proteins and cell disrupting peptides. Atomistic molecular dynamics studies have shed much light on the mechanisms of membrane binding and translocation of charged protein groups, yet the impact of the full diversity of membrane physico-chemical properties and topologies has yet to be explored. Here we have performed a systematic study of an arginine (Arg) side chain analog moving across saturated phosphatidylcholine (PC) bilayers of variable hydrocarbon tail length from 10 to 18 carbons. For all bilayers we observe similar ion-induced defects, where Arg draws water molecules and lipid head groups into the bilayers to avoid large dehydration energy costs. The free energy profiles all exhibit sharp climbs with increasing penetration into the hydrocarbon core, with predictable shifts between bilayers of different thickness, leading to barrier reduction from 26 kcal/mol for 18 carbons to 6 kcal/mol for 10 carbons. For lipids of 10 and 12 carbons we observe narrow transmembrane pores and corresponding plateaus in the free energy profiles. Allowing for movements of the protein and side chain snorkeling, we argue that the energetic cost for burying Arg inside a thin bilayer will be small, consistent with recent experiments, also leading to a dramatic reduction in pK(a) shifts for Arg. We provide evidence that Arg translocation occurs via an ion-induced defect mechanism, except in thick bilayers (of at least 18 carbons) where solubility-diffusion becomes energetically favored. Our findings shed light on the mechanisms of ion movement through membranes of varying composition, with implications for a range of charged protein-lipid interactions and the actions of cell-perturbing peptides. This article is part of a Special Issue entitled: Membrane protein structure and function.
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Affiliation(s)
- Libo B Li
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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141
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MacCallum JL, Bennett WFD, Tieleman DP. Transfer of arginine into lipid bilayers is nonadditive. Biophys J 2011; 101:110-7. [PMID: 21723820 DOI: 10.1016/j.bpj.2011.05.038] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 04/29/2011] [Accepted: 05/17/2011] [Indexed: 01/21/2023] Open
Abstract
Computer simulations suggest that the translocation of arginine through the hydrocarbon core of a lipid membrane proceeds by the formation of a water-filled defect that keeps the arginine molecule hydrated even at the center of the bilayer. We show here that adding additional arginine molecules into one of these water defects causes only a small change in free energy. The barrier for transferring multiple arginines through the membrane is approximately the same as for a single arginine and may even be lower depending on the exact geometry of the system. We discuss these results in the context of arginine-rich peptides such as antimicrobial and cell-penetrating peptides.
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Affiliation(s)
- Justin L MacCallum
- Department of Biological Sciences, Institute for Biocomplexity and Informatics, University of Calgary, Calgary, Alberta, Canada
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142
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Computational studies of membrane proteins: models and predictions for biological understanding. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:927-41. [PMID: 22051023 DOI: 10.1016/j.bbamem.2011.09.026] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 09/22/2011] [Accepted: 09/26/2011] [Indexed: 01/26/2023]
Abstract
We discuss recent progresses in computational studies of membrane proteins based on physical models with parameters derived from bioinformatics analysis. We describe computational identification of membrane proteins and prediction of their topology from sequence, discovery of sequence and spatial motifs, and implications of these discoveries. The detection of evolutionary signal for understanding the substitution pattern of residues in the TM segments and for sequence alignment is also discussed. We further discuss empirical potential functions for energetics of inserting residues in the TM domain, for interactions between TM helices or strands, and their applications in predicting lipid-facing surfaces of the TM domain. Recent progresses in structure predictions of membrane proteins are also reviewed, with further discussions on calculation of ensemble properties such as melting temperature based on simplified state space model. Additional topics include prediction of oligomerization state of membrane proteins, identification of the interfaces for protein-protein interactions, and design of membrane proteins. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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143
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MacCallum JL, Tieleman DP. Hydrophobicity scales: a thermodynamic looking glass into lipid-protein interactions. Trends Biochem Sci 2011; 36:653-62. [PMID: 21930386 DOI: 10.1016/j.tibs.2011.08.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 08/09/2011] [Accepted: 08/11/2011] [Indexed: 11/30/2022]
Abstract
The partitioning of amino acid sidechains into the membrane is a key aspect of membrane protein folding. However, lipid bilayers exhibit rapidly changing physicochemical properties over their nanometer-scale thickness, which complicates understanding the thermodynamics and microscopic details of membrane partitioning. Recent data from diverse approaches, including protein insertion by the Sec translocon, folding of a small beta-barrel membrane protein and computer simulations of the exact distribution of a variety of small molecules and peptides, have joined older hydrophobicity scales for membrane protein prediction. We examine the correlations among the scales and find that they are remarkably correlated even though there are large differences in magnitude. We discuss the implications of these scales for understanding membrane protein structure and function.
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Affiliation(s)
- Justin L MacCallum
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA.
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144
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Bennett WFD, Tieleman DP. Water Defect and Pore Formation in Atomistic and Coarse-Grained Lipid Membranes: Pushing the Limits of Coarse Graining. J Chem Theory Comput 2011; 7:2981-8. [PMID: 26605486 DOI: 10.1021/ct200291v] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Defects in lipid bilayers are important in a range of biological processes, including interactions between antimicrobial peptides and membranes, transport of polar molecules (including drugs) across membranes, and lipid flip-flop from one monolayer to the other. Passive lipid flip-flop and the translocation of polar molecules across lipid membranes occur on a slow time scale because of high-energy intermediates involving water defects and pores in the membrane. Such defects are an interesting test case for coarse-grained models because of their relatively small characteristic size at the level of water molecules and the complex environment of water and polar head groups in a low-dielectric membrane interior. Here we compare coarse-grained simulations with the MARTINI model with the standard MARTINI water and two recently developed coarse-grained polarizable water models to atomistic simulations. Although in several cases the MARTINI model reproduces the correct free energies, there are structural differences between the atomistic and coarse-grained models. The polarizable water model improves the free energies but only moderately improves the structures. Atomistic test simulations in which water molecules are artificially tethered to each other in groups of four, the resolution of MARTINI, suggest that the limiting factor is not the size of the coarse-grained particles but rather the simple interaction potential and/or the entropy lost in coarse graining the system. By increasing the attractive interaction between the lipids' headgroup and water, we did observe pore formation but at the expense of the correct equilibrium properties of the bilayers.
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Affiliation(s)
- W F Drew Bennett
- Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary , 2500 University Drive N.W., Calgary, Alberta T2N 1N4, Canada
| | - D Peter Tieleman
- Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary , 2500 University Drive N.W., Calgary, Alberta T2N 1N4, Canada
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145
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Exploring peptide-membrane interactions with coarse-grained MD simulations. Biophys J 2011; 100:1940-8. [PMID: 21504730 DOI: 10.1016/j.bpj.2011.02.041] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 02/13/2011] [Accepted: 02/18/2011] [Indexed: 12/16/2022] Open
Abstract
The interaction of α-helical peptides with lipid bilayers is central to our understanding of the physicochemical principles of biological membrane organization and stability. Mutations that alter the position or orientation of an α-helix within a membrane, or that change the probability that the α-helix will insert into the membrane, can alter a range of membrane protein functions. We describe a comparative coarse-grained molecular dynamics simulation methodology, based on self-assembly of a lipid bilayer in the presence of an α-helical peptide, which allows us to model membrane transmembrane helix insertion. We validate this methodology against available experimental data for synthetic model peptides (WALP23 and LS3). Simulation-based estimates of apparent free energies of insertion into a bilayer of cystic fibrosis transmembrane regulator-derived helices correlate well with published data for translocon-mediated insertion. Comparison of values of the apparent free energy of insertion from self-assembly simulations with those from coarse-grained molecular dynamics potentials of mean force for model peptides, and with translocon-mediated insertion of cystic fibrosis transmembrane regulator-derived peptides suggests a nonequilibrium model of helix insertion into bilayers.
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146
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Ganesan N, Bauer BA, Lucas TR, Patel S, Taufer M. Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs). J Comput Chem 2011; 32:2958-73. [PMID: 21793003 DOI: 10.1002/jcc.21871] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 04/25/2011] [Accepted: 05/21/2011] [Indexed: 01/19/2023]
Abstract
We present results of molecular dynamics simulations of fully hydrated DMPC bilayers performed on graphics processing units (GPUs) using current state-of-the-art non-polarizable force fields and a local GPU-enabled molecular dynamics code named FEN ZI. We treat the conditionally convergent electrostatic interaction energy exactly using the particle mesh Ewald method (PME) for solution of Poisson's Equation for the electrostatic potential under periodic boundary conditions. We discuss elements of our implementation of the PME algorithm on GPUs as well as pertinent performance issues. We proceed to show results of simulations of extended lipid bilayer systems using our program, FEN ZI. We performed simulations of DMPC bilayer systems consisting of 17,004, 68,484, and 273,936 atoms in explicit solvent. We present bilayer structural properties (atomic number densities, electron density profiles), deuterium order parameters (S(CD)), electrostatic properties (dipole potential, water dipole moments), and orientational properties of water. Predicted properties demonstrate excellent agreement with experiment and previous all-atom molecular dynamics simulations. We observe no statistically significant differences in calculated structural or electrostatic properties for different system sizes, suggesting the small bilayer simulations (less than 100 lipid molecules) provide equivalent representation of structural and electrostatic properties associated with significantly larger systems (over 1000 lipid molecules). We stress that the three system size representations will have differences in other properties such as surface capillary wave dynamics or surface tension related effects that are not probed in the current study. The latter properties are inherently dependent on system size. This contribution suggests the suitability of applying emerging GPU technologies to studies of an important class of biological environments, that of lipid bilayers and their associated integral membrane proteins. We envision that this technology will push the boundaries of fully atomic-resolution modeling of these biological systems, thus enabling unprecedented exploration of meso-scale phenomena (mechanisms, kinetics, energetics) with atomic detail at commodity hardware prices.
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Affiliation(s)
- Narayan Ganesan
- Department of Computer and Information Science, University of Delaware, Newark, Delaware 19716, USA
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147
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Fleming PJ, Freites JA, Moon CP, Tobias DJ, Fleming KG. Outer membrane phospholipase A in phospholipid bilayers: a model system for concerted computational and experimental investigations of amino acid side chain partitioning into lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:126-34. [PMID: 21816133 DOI: 10.1016/j.bbamem.2011.07.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 07/07/2011] [Accepted: 07/09/2011] [Indexed: 12/21/2022]
Abstract
Understanding the forces that stabilize membrane proteins in their native states is one of the contemporary challenges of biophysics. To date, estimates of side chain partitioning free energies from water to the lipid environment show disparate values between experimental and computational measures. Resolving the disparities is particularly important for understanding the energetic contributions of polar and charged side chains to membrane protein function because of the roles these residue types play in many cellular functions. In general, computational free energy estimates of charged side chain partitioning into bilayers are much larger than experimental measurements. However, the lack of a protein-based experimental system that uses bilayers against which to vet these computational predictions has traditionally been a significant drawback. Moon & Fleming recently published a novel hydrophobicity scale that was derived experimentally by using a host-guest strategy to measure the side chain energetic perturbation due to mutation in the context of a native membrane protein inserted into a phospholipid bilayer. These values are still approximately an order of magnitude smaller than computational estimates derived from molecular dynamics calculations from several independent groups. Here we address this discrepancy by showing that the free energy differences between experiment and computation become much smaller if the appropriate comparisons are drawn, which suggests that the two fields may in fact be converging. In addition, we present an initial computational characterization of the Moon & Fleming experimental system used for the hydrophobicity scale: OmpLA in DLPC bilayers. The hydrophobicity scale used OmpLA position 210 as the guest site, and our preliminary results demonstrate that this position is buried in the center of the DLPC membrane, validating its usage in the experimental studies. We further showed that the introduction of charged Arg at position 210 is well tolerated in OmpLA and that the DLPC bilayers accommodate this perturbation by creating a water dimple that allows the Arg side chain to remain hydrated. Lipid head groups visit the dimple and can hydrogen bond with Arg, but these interactions are transient. Overall, our study demonstrates the unique advantages of this molecular system because it can be interrogated by both computational and experimental practitioners, and it sets the stage for free energy calculations in a system for which there is unambiguous experimental data. This article is part of a Special Issue entitled: Membrane protein structure and function.
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Affiliation(s)
- Patrick J Fleming
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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148
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Andersson M, Freites JA, Tobias DJ, White SH. Structural dynamics of the S4 voltage-sensor helix in lipid bilayers lacking phosphate groups. J Phys Chem B 2011; 115:8732-8. [PMID: 21692541 PMCID: PMC3140535 DOI: 10.1021/jp2001964] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Voltage-dependent K(+) (Kv) channels require lipid phosphates for functioning. The S4 helix, which carries the gating charges in the voltage-sensing domain (VSD), inserts into membranes while being stabilized by a protein-lipid interface in which lipid phosphates play an essential role. To examine the physical basis of the protein-lipid interface in the absence of lipid phosphates, we performed molecular dynamics (MD) simulations of a KvAP S4 variant (S4mut) in bilayers with and without lipid phosphates. We find that, in dioleoyltrimethylammoniumpropane (DOTAP) bilayers lacking lipid phosphates, the gating charges are solvated by anionic counterions and, hence, lack the bilayer support provided by phosphate-containing palmitoyloleoylglycerophosphocholine (POPC) bilayers. The result is a water-permeable bilayer with significantly smaller deformations around the peptide. Together, these results provide an explanation for the nonfunctionality of VSDs in terms of a destabilizing protein-lipid interface.
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Affiliation(s)
- Magnus Andersson
- Department of Physiology and Biophysics and the Center for Biomembrane Systems, University of California, Irvine, California, 92697
| | - J. Alfredo Freites
- Department of Chemistry and Institute for Surface and Interface Science, University of California, Irvine, California, 92697
| | - Douglas J. Tobias
- Department of Chemistry and Institute for Surface and Interface Science, University of California, Irvine, California, 92697
| | - Stephen H. White
- Department of Physiology and Biophysics and the Center for Biomembrane Systems, University of California, Irvine, California, 92697
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149
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150
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Steckbeck JD, Craigo JK, Barnes CO, Montelaro RC. Highly conserved structural properties of the C-terminal tail of HIV-1 gp41 protein despite substantial sequence variation among diverse clades: implications for functions in viral replication. J Biol Chem 2011; 286:27156-66. [PMID: 21659530 DOI: 10.1074/jbc.m111.258855] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although the HIV-1 Env gp120 and gp41 ectodomain have been extensively characterized in terms of structure and function, similar characterizations of the C-terminal tail (CTT) of HIV gp41 remain relatively limited and contradictory. The current study was designed to examine in detail CTT sequence conservation relative to gp120 and the gp41 ectodomain and to examine the conservation of predicted physicochemical and structural properties across a number of divergent HIV clades and groups. Results demonstrate that CTT sequences display intermediate levels of sequence evolution and diversity in comparison to the more diverse gp120 and the more conserved gp41 ectodomain. Despite the relatively high level of CTT sequence variation, the physicochemical properties of the lentivirus lytic peptide domains (LLPs) within the CTT are evidently highly conserved across clades/groups. Additionally, predictions using PEP-FOLD indicate a high level of structural similarity in the LLP regions that was confirmed by circular dichroism measurements of secondary structure of LLP peptides from clades B, C, and group O. Results demonstrate that LLP peptides adopt helical structure in the presence of SDS or trifluoroethanol but are predominantly unstructured in aqueous buffer. Thus, these data for the first time demonstrate strong conservations of characteristic CTT physicochemical and structural properties despite substantial sequence diversity, apparently indicating a delicate balance between evolutionary pressures and the conservation of CTT structure and associated functional roles in virus replication.
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Affiliation(s)
- Jonathan D Steckbeck
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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