1
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Smith RS, Weaver DR, King GM, Kosztin I. Chain-Length Dependence of Peptide-Lipid Bilayer Interaction Strength and Binding Kinetics: A Combined Theoretical and Experimental Approach. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024. [PMID: 38963062 DOI: 10.1021/acs.langmuir.4c01218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Physical interactions between polypeptide chains and lipid membranes underlie critical cellular processes. Yet, despite fundamental importance, key mechanistic aspects of these interactions remain elusive. Bulk experiments have revealed a linear relationship between free energy and peptide chain length in a model system, but does this linearity extend to the interaction strength and to the kinetics of lipid binding? To address these questions, we utilized a combination of coarse-grained molecular dynamics (CG MD) simulations, analytical modeling, and atomic force microscopy (AFM)-based single molecule force spectroscopy. Following previous bulk experiments, we focused on interactions between short hydrophobic peptides (WLn, n = 1, ..., 5) with 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) bilayers, a simple system that probes peptide primary structure effects. Potentials of mean force extracted from CG MD recapitulated the linearity of free energy with the chain length. Simulation results were quantitatively connected to bulk biochemical experiments via a single scaling factor of order unity, corroborating the methodology. Additionally, CG MD revealed an increase in the distance to the transition state, a result that weakens the dependence of the dissociation force on the peptide chain length. AFM experiments elucidated rupture force distributions and, through modeling, intrinsic dissociation rates. Taken together, the analysis indicates a rupture force plateau in the WLn-POPC system, suggesting that the final rupture event involves the last 2 or 3 residues. In contrast, the linear dependence on chain length was preserved in the intrinsic dissociation rate. This study advances the understanding of peptide-lipid interactions and provides potentially useful insights for the design of peptides with tailored membrane-interacting properties.
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Affiliation(s)
- Ryan S Smith
- Department of Physics & Astronomy, University of Missouri, Columbia, Missouri 65211, United States
| | - Dylan R Weaver
- Department of Physics & Astronomy, University of Missouri, Columbia, Missouri 65211, United States
| | - Gavin M King
- Department of Physics & Astronomy, University of Missouri, Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Ioan Kosztin
- Department of Physics & Astronomy, University of Missouri, Columbia, Missouri 65211, United States
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2
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Frigini EN, Porasso RD, Beke-Somfai T, López Cascales JJ, Enriz RD, Pantano S. The Mechanism of Antimicrobial Small-Cationic Peptides from Coarse-Grained Simulations. J Chem Inf Model 2023; 63:6877-6889. [PMID: 37905818 DOI: 10.1021/acs.jcim.3c01348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Antimicrobial cationic peptides (AMPs) are excellent candidates for use as therapeutic antimicrobial agents. Among them, short peptides possessing sequences of 9-11 amino acids have some advantages over long-sequence peptides. However, one of the main limitations of short peptides is that their mechanism of action at the molecular level is not well-known. In this article, we report a model based on multiscale molecular dynamics simulations of short peptides interacting with vesicles containing palmitoyl-oleoyl-phosphatidylglycerol (POPG)/palmitoyl-oleoyl-phosphatidylethanolamine (POPE). Simulations using this approach have allowed us to understand the different behaviors of peptides with antimicrobial activity with respect to those that do not produce this effect. We found remarkable agreement with a series of experimental results directly supporting our model. Moreover, these results allow us to understand the mechanism of action at the molecular level of these short peptides. Our simulations suggest that mechanical inhomogeneities appear in the membrane, promoting membrane rupture when a threshold concentration of peptides adsorbed on the membrane is achieved. These results explain the high structural demand for these peptides to maintain a delicate balance between the affinity for the bilayer surface, a low peptide-peptide repulsion (in order to reach the threshold concentration), and an acceptable tendency to penetrate into the bilayer. This mechanism is different from those proposed for peptides with long amino acid sequences. Such information is very useful from the medicinal chemistry point of view for the design of new small antimicrobial peptides.
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Affiliation(s)
- Ezequiel N Frigini
- Facultad de Química, Bioquímica y Farmacia, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Universidad Nacional de San Luis, Ejército de los Andes 950, San Luis 5700, Argentina
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
| | - Rodolfo D Porasso
- Instituto de Matemáticas Aplicada San Luis (IMASL), CONICET, Facultad de Ciencias Físico Matemáticas y Naturales, Universidad Nacional de San Luis, Av. Ejército de los Andes 950, San Luis 5700, Argentina
| | - Tamás Beke-Somfai
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, H-1117 Budapest, Hungary
| | - José Javier López Cascales
- Universidad Politécnica de Cartagena, Grupo de Bioinformática y Macromoleculas (BioMac), Area de Química Física, Aulario II, Campus de Alfonso XIII, 30203 Cartagena, Murcia, Spain
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Universidad Nacional de San Luis, Ejército de los Andes 950, San Luis 5700, Argentina
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
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3
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Lima B, Ricci M, Garro A, Juhász T, Szigyártó IC, Papp ZI, Feresin G, Garcia de la Torre J, Lopez Cascales J, Fülöp L, Beke-Somfai T, Enriz RD. New short cationic antibacterial peptides. Synthesis, biological activity and mechanism of action. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183665. [PMID: 34097861 DOI: 10.1016/j.bbamem.2021.183665] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/07/2021] [Accepted: 06/01/2021] [Indexed: 11/28/2022]
Abstract
We report a theoretical and experimental study on a new series of small-sized antibacterial peptides. Synthesis and bioassays for these peptides are reported here. In addition, we evaluated different physicochemical parameters that modulate antimicrobial activity (charge, secondary structure, amphipathicity, hydrophobicity and polarity). We also performed molecular dynamic simulations to assess the interaction between these peptides and their molecular target (the membrane). Biophysical characterization of the peptides was carried out with different techniques, such as circular dichroism (CD), linear dichroism (LD), infrared spectroscopy (IR), dynamic light scattering (DLS), fluorescence spectroscopy and TEM studies using model systems (liposomes) for mammalian and bacterial membranes. The results of this study allow us to draw important conclusions on three different aspects. Theoretical and experimental results indicate that small-sized peptides have a particular mechanism of action that is different to that of large peptides. These results provide additional support for a previously proposed four-step mechanism of action. The possible pharmacophoric requirement for these small-sized peptides is discussed. Furthermore, our results indicate that a net +4 charge is the adequate for 9 amino acid long peptides to produce antibacterial activity. The information reported here is very important for designing new antibacterial peptides with these structural characteristics.
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Affiliation(s)
- Beatriz Lima
- Instituto de Biotecnología, Universidad Nacional de San Juan, Av. Libertador General San Martín 1109 (O), CP 5400 San Juan, Argentina
| | - Maria Ricci
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, H-1117 Budapest, Hungary
| | - Adriana Garro
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Chacabuco 915, 5700 San Luis, Argentina
| | - Tünde Juhász
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, H-1117 Budapest, Hungary
| | - Imola Csilla Szigyártó
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, H-1117 Budapest, Hungary
| | - Zita I Papp
- Department of Medical Chemistry, University of Szeged, H-6720 Szeged, Dóm tér 8, Hungary
| | - Gabriela Feresin
- Instituto de Biotecnología, Universidad Nacional de San Juan, Av. Libertador General San Martín 1109 (O), CP 5400 San Juan, Argentina
| | - Jose Garcia de la Torre
- Facultad de Química, Departamento de Química Física, Universidad de Murcia, Campus de Espinardo, 30100 Espinardo, Murcia, Spain
| | - Javier Lopez Cascales
- Grupo de Bioinformática y Macromoléculas (BioMac), Área de Química Física, Universidad Politécnica de Cartagena, Aulario II, ́ Campus de Alfonso XIII, 30203 Cartagena, Murcia, Spain
| | - Lívia Fülöp
- Department of Medical Chemistry, University of Szeged, H-6720 Szeged, Dóm tér 8, Hungary.
| | - Tamás Beke-Somfai
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, H-1117 Budapest, Hungary.
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Chacabuco 915, 5700 San Luis, Argentina.
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4
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King GM, Kosztin I. Towards a Quantitative Understanding of Protein-Lipid Bilayer Interactions at the Single Molecule Level: Opportunities and Challenges. J Membr Biol 2020; 254:17-28. [PMID: 33196888 DOI: 10.1007/s00232-020-00151-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/04/2020] [Indexed: 11/28/2022]
Abstract
Protein-lipid interfaces are among the most fundamental in biology. Yet applying conventional techniques to study the biophysical attributes of these systems is challenging and has left many unknowns. For example, what is the kinetic pathway and energy landscape experienced by a polypeptide chain when in close proximity to a fluid lipid bilayer? Here we review the experimental and theoretical progress we have made in addressing this question from a single molecule perspective. Some remaining impediments are also discussed.
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Affiliation(s)
- Gavin M King
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, 65211, USA. .,Department of Biochemistry, University of Missouri-Columbia, Columbia, MO, 65211, USA.
| | - Ioan Kosztin
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, 65211, USA.
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5
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Cao Z, Bian Y, Hu G, Zhao L, Kong Z, Yang Y, Wang J, Zhou Y. Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids. Int J Mol Sci 2018; 19:E885. [PMID: 29547563 PMCID: PMC5877746 DOI: 10.3390/ijms19030885] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/11/2018] [Accepted: 03/12/2018] [Indexed: 11/16/2022] Open
Abstract
Thermodynamics of the permeation of amino acids from water to lipid bilayers is an important first step for understanding the mechanism of cell-permeating peptides and the thermodynamics of membrane protein structure and stability. In this work, we employed bias-exchange metadynamics simulations to simulate the membrane permeation of all 20 amino acids from water to the center of a dipalmitoylphosphatidylcholine (DPPC) membrane (consists of 256 lipids) by using both directional and torsion angles for conformational sampling. The overall accuracy for the free energy profiles obtained is supported by significant correlation coefficients (correlation coefficient at 0.5-0.6) between our results and previous experimental or computational studies. The free energy profiles indicated that (1) polar amino acids have larger free energy barriers than nonpolar amino acids; (2) negatively charged amino acids are the most difficult to enter into the membrane; and (3) conformational transitions for many amino acids during membrane crossing is the key for reduced free energy barriers. These results represent the first set of simulated free energy profiles of membrane crossing for all 20 amino acids.
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Affiliation(s)
- Zanxia Cao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Yunqiang Bian
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Guodong Hu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Liling Zhao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Zhenzhen Kong
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Life Science, Shandong Normal University, Jinan 250014, China.
| | - Yuedong Yang
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr, Southport, QLD 4222, Australia.
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou 510275, China.
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Yaoqi Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr, Southport, QLD 4222, Australia.
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6
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Domański J, Sansom MSP, Stansfeld PJ, Best RB. Balancing Force Field Protein-Lipid Interactions To Capture Transmembrane Helix-Helix Association. J Chem Theory Comput 2018; 14:1706-1715. [PMID: 29424543 PMCID: PMC5852462 DOI: 10.1021/acs.jctc.7b00983] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Indexed: 01/21/2023]
Abstract
Atomistic simulations have recently been shown to be sufficiently accurate to reversibly fold globular proteins and have provided insights into folding mechanisms. Gaining similar understanding from simulations of membrane protein folding and association would be of great medical interest. All-atom simulations of the folding and assembly of transmembrane protein domains are much more challenging, not least due to very slow diffusion within the lipid bilayer membrane. Here, we focus on a simple and well-characterized prototype of membrane protein folding and assembly, namely the dimerization of glycophorin A, a homodimer of single transmembrane helices. We have determined the free energy landscape for association of the dimer using the CHARMM36 force field. We find that the native structure is a metastable state, but not stable as expected from experimental estimates of the dissociation constant and numerous experimental structures obtained under a variety of conditions. We explore two straightforward approaches to address this problem and demonstrate that they result in stable dimers with dissociation constants consistent with experimental data.
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Affiliation(s)
- Jan Domański
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892-0520, United States
| | - Mark S. P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Phillip J. Stansfeld
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Robert B. Best
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892-0520, United States
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7
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Saeedi M, Lyubartsev AP, Jalili S. Anesthetics mechanism on a DMPC lipid membrane model: Insights from molecular dynamics simulations. Biophys Chem 2017; 226:1-13. [DOI: 10.1016/j.bpc.2017.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/23/2017] [Accepted: 03/25/2017] [Indexed: 12/20/2022]
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8
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Lockhart C, Klimov DK. The Alzheimer's disease A β peptide binds to the anionic DMPS lipid bilayer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1118-28. [DOI: 10.1016/j.bbamem.2016.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 02/26/2016] [Accepted: 03/01/2016] [Indexed: 11/24/2022]
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9
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Nguyen MT, Chaffee AL, Boysen RI, Nicolau DV, Hearn MT. A versatile modelling approach to determine the hydrophobicity of peptides at the atomic level. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1038533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Jalili S, Saeedi M. Study of curcumin behavior in two different lipid bilayer models of liposomal curcumin using molecular dynamics simulation. J Biomol Struct Dyn 2015; 34:327-40. [PMID: 25811078 DOI: 10.1080/07391102.2015.1030692] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Liposomal formulation of curcumin is an important therapeutic agent for the treatment of various cancers. Despite extensive studies on the biological effects of this formulation in cancer treatment, much remains unknown about curcumin-liposome interactions. Understanding how different lipid bilayers respond to curcumin molecule may help us to design more effective liposomal curcumin. Here, we used molecular dynamics simulation method to investigate the behavior of curcumin in two lipid bilayers commonly used in preparation of liposomal curcumin, namely dipalmitoylphosphatidylcholine (DPPC) and dimyristoylphosphatidylglycerol (DMPG). First, the free energy barriers for translocation of one curcumin molecule from water to the lipid bilayer were determined by using the potential of mean force (PMF). The computed free energy profile exhibits a global minimum at the solvent-headgroup interface (LH region) for both lipid membranes. We also evaluated the free energy difference between the equilibrium position of curcumin in the lipid bilayer and bulk water as the excess chemical potential. Our results show that curcumin has the higher affinity in DMPG compared to DPPC lipid bilayer (-8.39 vs. -1.69 kBT) and this is related to more hydrogen bond possibility for curcumin in DMPG lipid membrane. Next, using an unconstrained molecular dynamic simulation with curcumin initially positioned at the center of lipid bilayer, we studied various properties of each lipid bilayer system in the presence of curcumin molecule that was in full agreement with PMF and experimental data. The results of these simulation studies suggest that membrane composition could have a large effect on interaction of curcumin-lipid bilayer.
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Affiliation(s)
- Seifollah Jalili
- a Department of Chemistry , K. N. Toosi University of Technology , P.O. Box 15875-4416, Tehran , Iran.,b Computational Physical Sciences Research Laboratory , School of Nano-Science, Institute for Research in Fundamental Sciences (IPM) , P.O. Box 19395-5531, Tehran , Iran
| | - Marzieh Saeedi
- a Department of Chemistry , K. N. Toosi University of Technology , P.O. Box 15875-4416, Tehran , Iran
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11
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Polak A, Velikonja A, Kramar P, Tarek M, Miklavčič D. Electroporation threshold of POPC lipid bilayers with incorporated polyoxyethylene glycol (C12E8). J Phys Chem B 2014; 119:192-200. [PMID: 25495217 DOI: 10.1021/jp509789m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Electroporation relates to a phenomenon in which cell membranes are permeabilized after being exposed to high electric fields. On the molecular level, the mechanism is not yet fully elucidated, although a considerable body of experiments and molecular dynamic (MD) simulations were performed on model membranes. Here we present the results of a combined theoretical and experimental investigation of electroporation of palmitoy-oleoyl-phosphatidylcholine (POPC) bilayers with incorporated polyoxyethylene glycol (C12E8) surfactants. The experimental results show a slight increase of the capacitance and a 22% decrease of the voltage breakdown upon addition of C12E8 to pure POPC bilayers. These results were qualitatively confirmed by the MD simulations. They later revealed that the polyoxyethylene glycol molecules play a major role in the formation of hydrophilic pores in the bilayers above the electroporation threshold. The headgroup moieties of the latter are indeed embedded in the interior of the bilayer, which favors formation of water wires that protrude into its hydrophobic core. When the water wires extend across the whole bilayer, they form channels stabilized by the C12E8 head groups. These hydrophilic channels can transport ions across the membrane without the need of major lipid head-group rearrangements.
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Affiliation(s)
- Andraž Polak
- University of Ljubljana , Faculty of Electrical Engineering, Tržaška cesta 25, SI-1000 Ljubljana, Slovenia
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12
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Cherry MA, Higgins SK, Melroy H, Lee HS, Pokorny A. Peptides with the same composition, hydrophobicity, and hydrophobic moment bind to phospholipid bilayers with different affinities. J Phys Chem B 2014; 118:12462-70. [PMID: 25329983 PMCID: PMC4234449 DOI: 10.1021/jp507289w] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
We investigated the dependence of membrane binding on amino acid
sequence for a series of amphipathic peptides derived from δ-lysin.
δ-Lysin is a 26 amino acid, N-terminally formylated, hemolytic
peptide that forms an amphipathic α-helix bound at membrane–water
interfaces. A shortened peptide, lysette, was derived from δ-lysin
by deletion of the four N-terminal amino acid residues. Five variants
of lysette were synthesized by altering the amino acid sequence such
that the overall hydrophobic moment remained essentially the same
for all peptides. Peptide–lipid equilibrium dissociation constants
and helicities of peptides bound to zwitterionic lipid vesicles were
determined by stopped-flow fluorescence and circular dichroism. We
found that binding to phosphatidylcholine bilayers was a function
of the helicity of the bound peptide alone and independent of the a priori hydrophobic moment or the ability to form intramolecular
salt bridges. Molecular dynamics (MD) simulations on two of the peptides
suggest that sequence determines the insertion depth into the bilayer.
The location of the two aspartate residues at the C-terminus of lysette-2
leads to a loss of helical content in the simulations, which correlates
with faster desorption from the bilayer as compared to lysette. We
also found a systematic deviation of the experimentally determined
dissociation constant and that predicted by the Wimley–White
interfacial hydrophobicity scale. The reason for the discrepancy remains
unresolved but appears to correlate with a predominance of isoleucine
over leucine residues in the lysette family of peptides.
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Affiliation(s)
- Melissa A Cherry
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington , Wilmington, North Carolina 28403, United States
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13
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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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14
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Singh G, Tieleman DP. Atomistic Simulations of Wimley–White Pentapeptides: Sampling of Structure and Dynamics in Solution. J Chem Theory Comput 2013; 9:1657-66. [DOI: 10.1021/ct3008217] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gurpreet Singh
- Department of Biological Sciences and Institute for
Biocomplexity and Informatics, University of Calgary, 2500 University Drive N.W., Calgary, Alberta
T2N1N4, Canada
| | - D. Peter Tieleman
- Department of Biological Sciences and Institute for
Biocomplexity and Informatics, University of Calgary, 2500 University Drive N.W., Calgary, Alberta
T2N1N4, Canada
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15
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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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16
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Wang Y, Schlamadinger DE, Kim JE, McCammon JA. Comparative molecular dynamics simulations of the antimicrobial peptide CM15 in model lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:1402-9. [PMID: 22387432 DOI: 10.1016/j.bbamem.2012.02.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 02/01/2012] [Accepted: 02/15/2012] [Indexed: 10/28/2022]
Abstract
We report altogether 3-μs molecular dynamics (MD) simulations of the antimicrobial peptide CM15 to systematically investigate its interaction with two model lipid bilayers, pure POPC and mixed POPG:POPC (1:2). Starting with either an α-helical or a random-coil conformation, CM15 is found to insert into both bilayers. Peptide-lipid interaction is stronger with the anionic POPG:POPC than the zwitterionic POPC, which is largely attributed to the electrostatic attraction between CM15 and the negatively charged POPG. Simulations initiated with CM15 as a random coil allowed us to study peptide folding at the lipid-water interface. Interestingly, CM15 folding appears to be faster in POPC than POPG:POPC, which may be explained by a lower activation energy barrier of structural rearrangement in the former system. Our data also suggest that compared with the random-coil conformation, CM15 in a pre-folded α-helix has significantly reduced interactions with the lipids, indicating that peptide initial structures may bias the simulation results considerably on the 100-ns timescale. The implications of this result should be considered when preparing and interpreting future AMP simulations.
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Affiliation(s)
- Yi Wang
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA.
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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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18
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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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Pushie MJ, Doonan CJ, Wilson HL, Rajagopalan KV, George GN. Nature of Halide Binding to the Molybdenum Site of Sulfite Oxidase. Inorg Chem 2011; 50:9406-13. [DOI: 10.1021/ic201030u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Jake Pushie
- Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, Saskatchewan S7N 5E2, Canada
| | - Christian J. Doonan
- Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, Saskatchewan S7N 5E2, Canada
- School of Chemistry and Physics, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Heather L. Wilson
- School of Medicine, Duke University, Durham, North Carolina 27710, United States
| | - K. V. Rajagopalan
- School of Medicine, Duke University, Durham, North Carolina 27710, United States
| | - Graham. N. George
- Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, Saskatchewan S7N 5E2, Canada
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20
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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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21
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Singh G, Tieleman DP. Using the Wimley-White Hydrophobicity Scale as a Direct Quantitative Test of Force Fields: The MARTINI Coarse-Grained Model. J Chem Theory Comput 2011; 7:2316-24. [PMID: 26606499 DOI: 10.1021/ct2002623] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The partitioning of proteins and peptides at the membrane/water interface is a key step in many processes, including the action of antimicrobial peptides, cell-penetrating peptides, and toxins, as well as signaling. To develop a computational model that can be used to accurately represent such systems, the underlying model must be able to quantitatively represent the partitioning preferences of amino acids in the lipid membrane. The MARTINI model provides a consistent set of parameters for building coarse-grained models of systems involving lipids and proteins. Even though MARTINI is parametrized to reproduce the partitioning behavior of small molecules, its ability to reproduce partitioning preferences of amino acids at lipid/water interfaces has never been tested. In this study, we measured the partitioning free energies of side chains of amino acids using alchemical simulations and umbrella sampling. The pentapeptides of sequence Ac-WLXLL were simulated at the POPC/water and cyclohexane/water interfaces using MARTINI, and the computed free energies were compared with the Wimley-White hydrophobicity scale. The free energy values obtained using the free energy perturbation, thermodynamic integration, and umbrella sampling methods were compared to gain insight into the most efficient method and the degree of sampling required to obtain statistically accurate free energies for use with atomistic force fields in future work. With the standard MARTINI water model, the amino acids D, E, K, and R were found to be significantly too favorable in hydrophobic environments, whereas with the polarizable water model, the amino acids D, E, K, and R were found to give correct free energies of partitioning. The amino acids P and F showed significant deviations from the experimental values. This model system will be used in future improvements to the MARTINI model.
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Affiliation(s)
- Gurpreet Singh
- Department of Biological Sciences, and ‡Institute for Biocomplexity and Informatics, 2500 University Drive N.W., University of Calgary , Calgary, Alberta, Canada T2N 1N4
| | - D Peter Tieleman
- Department of Biological Sciences, and ‡Institute for Biocomplexity and Informatics, 2500 University Drive N.W., University of Calgary , Calgary, Alberta, Canada T2N 1N4
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22
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Nikolic A, Baud S, Rauscher S, Pomès R. Molecular mechanism of β-sheet self-organization at water-hydrophobic interfaces. Proteins 2010; 79:1-22. [DOI: 10.1002/prot.22854] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2010] [Revised: 07/21/2010] [Accepted: 07/24/2010] [Indexed: 12/20/2022]
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23
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Pushie MJ, George GN. Active-site dynamics and large-scale domain motions of sulfite oxidase: a molecular dynamics study. J Phys Chem B 2010; 114:3266-75. [PMID: 20158265 DOI: 10.1021/jp908731f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The physiologically vital enzyme sulfite oxidase employs rapid intramolecular electron transfer between a molybdenum ion in the C-terminal domain (the site of sulfite oxidation) and a heme moeity in the N-terminal domain to complete its catalytic cycle. Crystal structures of the enzyme show C- and N-terminal domain orientations that are not consistent with rapid intramolecular electron transfer. Domain motion has been postulated to explain this discrepancy. In the present work we employ molecular dynamics simulations to understand the large-scale domain motions of the enzyme. We observe motion of the N-terminal domain into an orientation similar to that postulated for rapid electron transfer. Our simulations also probe the dynamics of the active site and surrounding residues, adding a further level of structural and thermodynamic detail in understanding sulfite oxidase function.
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Affiliation(s)
- M Jake Pushie
- Molecular and Environmental Science Research Group, Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, Saskatchewan, S7N 5E2, Canada
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24
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Davis JE, Patel S. Charge equilibration force fields for lipid environments: applications to fully hydrated DPPC bilayers and DMPC-embedded gramicidin A. J Phys Chem B 2009; 113:9183-96. [PMID: 19526999 PMCID: PMC2746983 DOI: 10.1021/jp901088g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polarizable force fields for lipid and solvent environments are used for molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer and gramicidin A (gA) dimer embedded in a dimyristoylphosphatidylcholine (DMPC) bilayer. The lipid bilayer is modeled using the CHARMM charge equilibration (CHEQ) polarizable force field for lipids and the TIP4P-FQ force field to represent solvent. For the DPPC bilayer system, results are compared to the same system simulated using the nonpolarizable CHARMM27r (C27r) force field and TIP3P water. Calculated atomic and electron density profiles, head group orientations as measured by the phosphorus-nitrogen vector orientation, and deuterium order parameters are found to be consistent with previous simulations and with experiment. The CHEQ model exhibits greater water penetration into the bilayer interior, as demonstrated by the potential of mean force calculated from the water density profile. This is a result of the variation of the water molecular dipole from 2.55 D in the bulk to 1.88 D in the interior. We discuss this finding in the context of previous studies (both simulation and experiment) that have investigated the extent of penetration of water into DPPC bilayers. We also discuss the effects of including explicit polarization on the water dipole moment variation as a function of distance from the bilayer. We show distributions of atomic charges over the course of the simulation since the CHEQ model allows the charges to fluctuate. We have calculated the interfacial dipole potential, which the CHEQ model predicts to be 0.95 V compared to 0.86 V as predicted by the C27r model. We also discuss dielectric permittivity profiles and the differences arising between the two models. We obtain bulk values of 72.77 for the CHEQ model (TIP4P-FQ water) and 91.22 for C27r (TIP3P), and values approaching unity in the membrane interior. Finally, we present results of simulations of gA embedded in a DMPC bilayer using the CHEQ model and discuss structural properties.
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Affiliation(s)
- Joseph E. Davis
- 238 Brown Laboratory, Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Sandeep Patel
- 238 Brown Laboratory, Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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25
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Davis JE, Rahaman O, Patel S. Molecular dynamics simulations of a DMPC bilayer using nonadditive interaction models. Biophys J 2009; 96:385-402. [PMID: 19167291 DOI: 10.1016/j.bpj.2008.09.048] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Accepted: 09/22/2008] [Indexed: 10/21/2022] Open
Abstract
We present a polarizable force field based on the charge-equilibration formalism for molecular dynamics simulations of phospholipid bilayers. We discuss refinement of headgroup dihedral potential parameters to reproduce ab initio conformational energies of dimethylphosphate calculated at the MP2/cc-pVTZ level of theory. We also address the refinement of electrostatic and Lennard-Jones (van der Waals) parameters to reproduce ab initio polarizabilities and water interaction energies of dimethylphosphate and tetramethylammonium. We present results of molecular dynamics simulations of a solvated dimyristoylphosphatidylcholine bilayer using this polarizable force field as well as the nonpolarizable, fixed-charge CHARMM27 and CHARMM27r force fields for comparison. Calculated atomic and electron-density profiles, deuterium order parameters, and headgroup orientations are found to be consistent with previous simulations and with experiment. Polarizable interaction models for solvent and lipid exhibit greater water penetration into the lipid interior; this is due to the variation of water molecular dipole moment from a bulk value of 2.6 Debye to a value of 1.9 Debye in the membrane interior. The reduction in the electrostatic component of the desolvation free-energy penalty allows for greater water density. The surface dipole potential predicted by the polarizable model is 0.95 V compared to the value of 0.8 V based on nonpolarizable force-field calculations. Effects of inclusion of explicit polarization are discussed in relation to water dipole moment and varying charge distributions. Dielectric permittivity profiles for polarizable and nonpolarizable interactions exhibit subtle differences arising from the nature of the individual component parameterizations; for the polarizable force field, we obtain a bulk dielectric permittivity of 79, whereas the nonpolarizable force field plateaus at 97 (the value for pure TIP3P water). In the membrane interior, both models predict unit permittivities, with the polarizable models contributing from one to two more units due to the optical dielectric (high-frequency dipole fluctuations). This contribution is a step toward the continuing development of a CHARMM (Chemistry at Harvard Molecular Mechanics) polarizable force field for simulations of biomacromolecular systems.
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Affiliation(s)
- Joseph E Davis
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
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26
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Partitioning of amino-acid analogues in a five-slab membrane model. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:2234-43. [DOI: 10.1016/j.bbamem.2008.06.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Revised: 05/15/2008] [Accepted: 06/17/2008] [Indexed: 11/20/2022]
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27
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Babakhani A, Gorfe AA, Kim JE, McCammon JA. Thermodynamics of peptide insertion and aggregation in a lipid bilayer. J Phys Chem B 2008; 112:10528-34. [PMID: 18681475 PMCID: PMC2651738 DOI: 10.1021/jp804710v] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A variety of biomolecules mediate physiological processes by inserting and reorganizing in cell membranes, and the thermodynamic forces responsible for their partitioning are of great interest. Recent experiments provided valuable data on the free energy changes associated with the transfer of individual amino acids from water to membrane. However, a complete picture of the pathways and the associated changes in energy of peptide insertion into a membrane remains elusive. To this end, computational techniques supplement the experimental data with atomic-level details and shed light on the energetics of insertion. Here, we employed the technique of umbrella sampling in a total 850 ns of all-atom molecular dynamics simulations to study the free energy profile and the pathway of insertion of a model hexapeptide consisting of a tryptophan and five leucines (WL5). The computed free energy profile of the peptide as it travels from bulk solvent through the membrane core exhibits two minima: a local minimum at the water−membrane interface or the headgroup region and a global minimum at the hydrophobic−hydrophilic interface close to the lipid glycerol region. A rather small barrier of roughly 1 kcal mol−1 exists at the membrane core, which is explained by the enhanced flexibility of the peptide when deeply inserted. Combining our results with those in the literature, we present a thermodynamic model for peptide insertion and aggregation which involves peptide aggregation upon contact with the membrane at the solvent−lipid headgroup interface.
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Affiliation(s)
- Arneh Babakhani
- Department of Chemistry & Biochemistry, and Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Drive, MC 0365 La Jolla, California 92093-0365, USA.
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28
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Langham AA, Ahmad AS, Kaznessis YN. On the nature of antimicrobial activity: a model for protegrin-1 pores. J Am Chem Soc 2008; 130:4338-46. [PMID: 18335931 DOI: 10.1021/ja0780380] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We conducted over 150 ns of simulation of a protegrin-1 octamer pore in a lipid bilayer composed of palmitoyloleoyl-phosphatidylethanolamine (POPE) and palmitoyloleoyl-phosphatidylglycerol (POPG) lipids mimicking the inner membrane of a bacterial cell. The simulations improve on a model of a pore proposed from recent NMR experiments and provide a coherent understanding of the molecular mechanism of antimicrobial activity. Although lipids tilt somewhat toward the peptides, the simulated protegrin-1 pore more closely follows the barrel-stave model than the toroidal-pore model. The movement of ions is investigated through the pore. The pore selectively allows negatively charged chloride ions to pass through at an average rate of one ion every two nanoseconds. Only two events are observed of sodium ions crossing through the pore. The potential of mean force is calculated for the water and both ion types. It is determined that the chloride ions move through the pore with ease, similarly to the water molecules with the exception of a zone of restricted movement midway through the pore. In bacteria, ions moving through the pore will compromise the integrity of the transmembrane potential. Without the transmembrane potential as a countermeasure, water will readily flow inside the higher osmolality cytoplasm. We determine that the diffusivity of water through a single PG-1 pore is sufficient to cause fast cell death by osmotic lysis.
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Affiliation(s)
- Allison A Langham
- Department of Chemical Engineering and Materials Science, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
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29
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Abstract
We have calculated the distribution in a lipid bilayer of small molecules mimicking 17 natural amino acids in atomistic detail by molecular dynamics simulation. We considered both charged and uncharged forms for Lys, Arg, Glu, and Asp. The results give detailed insight in the molecular basis of the preferred location and orientation of each side chain as well the preferred charge state for ionizable residues. Partitioning of charged and polar side chains is accompanied by water defects connecting the side chains to bulk water. These water defects dominate the energetic of partitioning, rather than simple partitioning between water and a hydrophobic phase. Lys, Glu, and Asp become uncharged well before reaching the center of the membrane, but Arg may be either charged or uncharged at the center of the membrane. Phe has a broad distribution in the membrane but Trp and Tyr localize strongly to the interfacial region. The distributions are useful for the development of coarse-grained and implicit membrane potentials for simulation and structure prediction. We discuss the relationship between the distribution in membranes, bulk partitioning to cyclohexane, and several amino acid hydrophobicity scales.
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30
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Sapay N, Tieleman DP. Chapter 4 Molecular Dynamics Simulation of Lipid–Protein Interactions. CURRENT TOPICS IN MEMBRANES 2008. [DOI: 10.1016/s1063-5823(08)00004-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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31
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Babakhani A, Gorfe AA, Gullingsrud J, Kim JE, Andrew McCammon J. Peptide insertion, positioning, and stabilization in a membrane: insight from an all-atom molecular dynamics simulation. Biopolymers 2007; 85:490-7. [PMID: 17274025 DOI: 10.1002/bip.20698] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Peptide insertion, positioning, and stabilization in a model membrane are probed via an all-atom molecular dynamics (MD) simulation. One peptide (WL5) is simulated in each leaflet of a solvated dimyristoylglycero-3-phosphate (DMPC) membrane. Within the first 5 ns, the peptides spontaneously insert into the membrane and then stabilize during the remaining 70 ns of simulation time. In both leaflets, the peptides localize to the membrane interface, and this localization is attributed to the formation of peptide-lipid hydrogen bonds. We show that the single tryptophan residue in each peptide contributes significantly to these hydrogen bonds; specifically, the nitrogen heteroatom of the indole ring plays a critical role. The tilt angles of the indole rings relative to the membrane normal in the upper and lower leaflets are approximately 26 degrees and 54 degrees , respectively. The tilt angles of the entire peptide chain are 62 degrees and 74 degrees . The membrane induces conformations of the peptide that are characteristic of beta-sheets, and the peptide enhances the lipid ordering in the membrane. Finally, the diffusion rate of the peptides in the membrane plane is calculated (based on experimental peptide concentrations) to be approximately 6 A(2)/ns, thus suggesting a 500 ns time scale for intermolecular interactions.
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Affiliation(s)
- Arneh Babakhani
- Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, CA 92093-0365,USA.
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32
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MacCallum JL, Bennett WFD, Tieleman DP. Partitioning of amino acid side chains into lipid bilayers: results from computer simulations and comparison to experiment. ACTA ACUST UNITED AC 2007; 129:371-7. [PMID: 17438118 PMCID: PMC2154372 DOI: 10.1085/jgp.200709745] [Citation(s) in RCA: 226] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Justin L MacCallum
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
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33
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Liu Z, Brady A, Young A, Rasimick B, Chen K, Zhou C, Kallenbach NR. Length effects in antimicrobial peptides of the (RW)n series. Antimicrob Agents Chemother 2006; 51:597-603. [PMID: 17145799 PMCID: PMC1797765 DOI: 10.1128/aac.00828-06] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A class of antimicrobial peptides involved in host defense consists of sequences rich in Arg and Trp-R and -W. Analysis of the pharmacophore in these peptides revealed that chains as short as trimers of sequences such as WRW and RWR have antimicrobial activity (M. B. Strom, B. E. Haug, M. L. Skar, W. Stensen, T. Stiberg, and J. S. Svendsen, J. Med. Chem. 46:1567-1570, 2003). To evaluate the effect of chain length on antimicrobial activity, we synthesized a series of peptides containing simple sequence repeats, (RW)n-NH2 (where n equals 1, 2, 3, 4, or 5), and determined their antimicrobial and hemolytic activity. The antimicrobial activity of the peptides increases with chain length, as does the hemolysis of red blood cells. Within the experimental error, longer peptides (n equals 3, 4, or 5) show similar values for the ratio of hemolytic activity to antibacterial activity, or the hemolytic index. The (RW)3 represents the optimal chain length in terms of the efficacy of synthesis and selectivity as evaluated by the hemolytic index. Circular dichroism spectroscopy indicates that these short peptides appear to be unfolded in aqueous solution but acquire structure in the presence of phospholipids. Interaction of the peptides with model lipid vesicles was examined using tryptophan fluorescence. The (RW)n peptides preferentially interact with bilayers containing the negatively charged headgroup phosphatidylglycerol relative to those containing a zwitterionic headgroup, phosphatidylcholine.
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Affiliation(s)
- Zhigang Liu
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
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34
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Johansson ACV, Lindahl E. Amino-acid solvation structure in transmembrane helices from molecular dynamics simulations. Biophys J 2006; 91:4450-63. [PMID: 17012325 PMCID: PMC1779925 DOI: 10.1529/biophysj.106.092767] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding the solvation of amino acids in biomembranes is an important step to better explain membrane protein folding. Several experimental studies have shown that polar residues are both common and important in transmembrane segments, which means they have to be solvated in the hydrophobic membrane, at least until helices have aggregated to form integral proteins. In this work, we have used computer simulations to unravel these interactions on the atomic level, and classify intramembrane solvation properties of amino acids. Simulations have been performed for systematic mutations in poly-Leu helices, including not only each amino acid type, but also every z-position in a model helix. Interestingly, many polar or charged residues do not desolvate completely, but rather retain hydration by snorkeling or pulling in water/headgroups--even to the extent where many of them exist in a microscopic polar environment, with hydration levels corresponding well to experimental hydrophobicity scales. This suggests that even for polar/charged residues a large part of solvation cost is due to entropy, not enthalpy loss. Both hydration level and hydrogen bonding exhibit clear position-dependence. Basic side chains cause much less membrane distortion than acidic, since they are able to form hydrogen bonds with carbonyl groups instead of water or headgroups. This preference is supported by sequence statistics, where basic residues have increased relative occurrence at carbonyl z-coordinates. Snorkeling effects and N-/C-terminal orientation bias are directly observed, which significantly reduces the effective thickness of the hydrophobic core. Aromatic side chains intercalate efficiently with lipid chains (improving Trp/Tyr anchoring to the interface) and Ser/Thr residues are stabilized by hydroxyl groups sharing hydrogen bonds to backbone oxygens.
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Affiliation(s)
- Anna C V Johansson
- Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden
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Tieleman DP, Maccallum JL, Ash WL, Kandt C, Xu Z, Monticelli L. Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid-protein interactions, side chain transfer free energies and model proteins. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2006; 18:S1221-34. [PMID: 21690838 DOI: 10.1088/0953-8984/18/28/s07] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We have reparameterized the dihedral parameters in a commonly used united-atom lipid force field so that they can be used with the all-atom OPLS force field for proteins implemented in the molecular dynamics simulation software GROMACS. Simulations with this new combination give stable trajectories and sensible behaviour of both lipids and protein. We have calculated the free energy of transfer of amino acid side chains between water and 'lipid-cyclohexane', made of lipid force field methylene groups, as a hydrophobic mimic of the membrane interior, for both the OPLS-AA and a modified OPLS-AA force field which gives better hydration free energies under simulation conditions close to those preferred for the lipid force field. The average error is 4.3 kJ mol(-1) for water-'lipid-cyclohexane' compared to 3.2 kJ mol(-1) for OPLS-AA cyclohexane and 2.4 kJ mol(-1) for the modified OPLS-AA water-'lipid-cyclohexane'. We have also investigated the effect of different methods to combine parameters between the united-atom lipid force field and the united-atom protein force field ffgmx. In a widely used combination, the strength of interactions between hydrocarbon lipid tails and proteins is significantly overestimated, causing a decrease in the area per lipid and an increase in lipid ordering. Using straight combination rules improves the results. Combined, we suggest that using OPLS-AA together with the united-atom lipid force field implemented in GROMACS is a reasonable approach to membrane protein simulations. We also suggest that using partial volume information and free energies of transfer may help to improve the parameterization of lipid-protein interactions and point out the need for accurate experimental data to validate and improve force field descriptions of such interactions.
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