1
|
Kasparyan G, Hub JS. Equivalence of Charge Imbalance and External Electric Fields during Free Energy Calculations of Membrane Electroporation. J Chem Theory Comput 2023; 19:2676-2683. [PMID: 37052575 DOI: 10.1021/acs.jctc.3c00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Electric fields across lipid membranes play important roles in physiology, medicine, and biotechnology, rationalizing the wide interest in modeling transmembrane potentials in molecular dynamics simulations. Transmembrane potentials have been implemented with external electric fields or by imposing charge imbalance between the two water compartments of a stacked double-membrane system. We compare the two methods in the context of membrane electroporation, which involves a large change of membrane structure and capacitance. We show that, given that Ewald electrostatics are defined with tinfoil boundary conditions, the two methods lead to (i) identical potentials of mean force (PMFs) of pore formation and expansion at various potentials, demonstrating that the two methods impose equivalent driving forces for large-scale transitions at membranes, and (ii) to identical polarization of water within thin water wires or open pores, suggesting that the two methods furthermore impose equivalent local electric fields. Without tinfoil boundary conditions, effects from external fields on pore formation are spuriously suppressed or even removed. Together, our study shows that both methods, external fields and charge imbalance, are well suitable for studying large-scale transitions of lipid membranes that involve changes of membrane capacitance. However, using charge imbalance is technically more challenging for maintaining a constant transmembrane potential since it requires updating of the charge imbalance as the membrane capacitance changes.
Collapse
Affiliation(s)
- Gari Kasparyan
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| |
Collapse
|
2
|
Wilson MA, Pohorille A. Structure and Computational Electrophysiology of Ac-LS3, a Synthetic Ion Channel. J Phys Chem B 2022; 126:8985-8999. [PMID: 36306164 DOI: 10.1021/acs.jpcb.2c05965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Computer simulations are reported on Ac-LS3, a synthetic ion channel, containing 21 residues with a Leu-Ser-Ser-Leu-Leu-Ser-Leu heptad repeat, which forms ions channels upon application of voltage. A hexameric, coiled-coil bundle initially positioned perpendicular to the membrane settled into a stable, tilted structure after 1.5 μs, most likely to improve contacts between the non-polar exterior of the channel and the hydrophobic core of the membrane. Once tilted, the bundle remained in this state during subsequent simulations of nearly 10 μs at voltages ranging from 200 to -100 mV. In contrast, attempts to identify a stable pentameric structure failed, thus supporting the hypothesis that the channel is a hexamer. Results at 100 mV were used to reconstruct the free energy profiles for K+ and Cl- in the channel. This was done by way of several methods in which results of molecular dynamics (MD) simulations were combined with the electrodiffusion model. Two of them developed recently do not require knowledge of the diffusivity. Instead, they utilize one-sided density profiles and committor probabilities. The consistency between different methods is very good, supporting the utility of the newly developed methods for reconstructing free energies of ions in channels. The flux of K+, which accounts for most of the current through the channel, calculated directly from MD matches well the total measured current. However, the current of Cl- is somewhat overestimated, possibly due to a slightly unbalanced force field involving chloride. The current-voltage dependence was also reconstructed by way of a recently developed, efficient method that requires simulations only at a single voltage, yielding good agreement with the experiment. Taken together, the results demonstrate that computational electrophysiology has become a reliable tool for studying how channels mediate ion transport through membranes.
Collapse
Affiliation(s)
- Michael A Wilson
- Exobiology Branch, MS239-4, NASA Ames Research Center, Moffett Field, California94035, United States.,SETI Institute, 189 Bernardo Avenue, Suite 200, Mountain View, California94043, United States
| | - Andrew Pohorille
- Exobiology Branch, MS239-4, NASA Ames Research Center, Moffett Field, California94033, United States.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California94132, United States
| |
Collapse
|
3
|
Kratochvil HT, Newberry RW, Mensa B, Mravic M, DeGrado WF. Spiers Memorial Lecture: Analysis and de novo design of membrane-interactive peptides. Faraday Discuss 2021; 232:9-48. [PMID: 34693965 PMCID: PMC8979563 DOI: 10.1039/d1fd00061f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Membrane-peptide interactions play critical roles in many cellular and organismic functions, including protection from infection, remodeling of membranes, signaling, and ion transport. Peptides interact with membranes in a variety of ways: some associate with membrane surfaces in either intrinsically disordered conformations or well-defined secondary structures. Peptides with sufficient hydrophobicity can also insert vertically as transmembrane monomers, and many associate further into membrane-spanning helical bundles. Indeed, some peptides progress through each of these stages in the process of forming oligomeric bundles. In each case, the structure of the peptide and the membrane represent a delicate balance between peptide-membrane and peptide-peptide interactions. We will review this literature from the perspective of several biologically important systems, including antimicrobial peptides and their mimics, α-synuclein, receptor tyrosine kinases, and ion channels. We also discuss the use of de novo design to construct models to test our understanding of the underlying principles and to provide useful leads for pharmaceutical intervention of diseases.
Collapse
Affiliation(s)
- Huong T Kratochvil
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Robert W Newberry
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Bruk Mensa
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Marco Mravic
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
4
|
Kutzner C, Köpfer DA, Machtens JP, de Groot BL, Song C, Zachariae U. Insights into the function of ion channels by computational electrophysiology simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1741-52. [PMID: 26874204 DOI: 10.1016/j.bbamem.2016.02.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 12/11/2022]
Abstract
Ion channels are of universal importance for all cell types and play key roles in cellular physiology and pathology. Increased insight into their functional mechanisms is crucial to enable drug design on this important class of membrane proteins, and to enhance our understanding of some of the fundamental features of cells. This review presents the concepts behind the recently developed simulation protocol Computational Electrophysiology (CompEL), which facilitates the atomistic simulation of ion channels in action. In addition, the review provides guidelines for its application in conjunction with the molecular dynamics software package GROMACS. We first lay out the rationale for designing CompEL as a method that models the driving force for ion permeation through channels the way it is established in cells, i.e., by electrochemical ion gradients across the membrane. This is followed by an outline of its implementation and a description of key settings and parameters helpful to users wishing to set up and conduct such simulations. In recent years, key mechanistic and biophysical insights have been obtained by employing the CompEL protocol to address a wide range of questions on ion channels and permeation. We summarize these recent findings on membrane proteins, which span a spectrum from highly ion-selective, narrow channels to wide diffusion pores. Finally we discuss the future potential of CompEL in light of its limitations and strengths. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
Collapse
Affiliation(s)
- Carsten Kutzner
- Department of Theoretical and Computational Biophysics, Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - David A Köpfer
- Department of Theoretical and Computational Biophysics, Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jan-Philipp Machtens
- Institute of Complex Systems, Zelluläre Biophysik (ICS-4), Forschungszentrum Jülich, Jülich, Germany
| | - Bert L de Groot
- Department of Theoretical and Computational Biophysics, Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Chen Song
- Department of Biochemistry, University of Oxford, United Kingdom
| | - Ulrich Zachariae
- Physics, School of Science and Engineering, University of Dundee, United Kingdom; Computational Biology, School of Life Sciences, University of Dundee, United Kingdom.
| |
Collapse
|
5
|
Pothula KR, Solano CJF, Kleinekathöfer U. Simulations of outer membrane channels and their permeability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:1760-71. [PMID: 26721326 DOI: 10.1016/j.bbamem.2015.12.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 12/25/2022]
Abstract
Channels in the outer membrane of Gram-negative bacteria provide essential pathways for the controlled and unidirectional transport of ions, nutrients and metabolites into the cell. At the same time the outer membrane serves as a physical barrier for the penetration of noxious substances such as antibiotics into the bacteria. Most antibiotics have to pass through these membrane channels to either reach cytoplasmic bound targets or to further cross the hydrophobic inner membrane. Considering the pharmaceutical significance of antibiotics, understanding the functional role and mechanism of these channels is of fundamental importance in developing strategies to design new drugs with enhanced permeation abilities. Due to the biological complexity of membrane channels and experimental limitations, computer simulations have proven to be a powerful tool to investigate the structure, dynamics and interactions of membrane channels. Considerable progress has been made in computer simulations of membrane channels during the last decade. The goal of this review is to provide an overview of the computational techniques and their roles in modeling the transport across outer membrane channels. A special emphasis is put on all-atom molecular dynamics simulations employed to better understand the transport of molecules. Moreover, recent molecular simulations of ion, substrate and antibiotics translocation through membrane pores are briefly summarized. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
Collapse
Affiliation(s)
- Karunakar R Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Carlos J F Solano
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| |
Collapse
|
6
|
Casciola M, Bonhenry D, Liberti M, Apollonio F, Tarek M. A molecular dynamic study of cholesterol rich lipid membranes: comparison of electroporation protocols. Bioelectrochemistry 2014; 100:11-7. [DOI: 10.1016/j.bioelechem.2014.03.009] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 03/20/2014] [Accepted: 03/20/2014] [Indexed: 01/25/2023]
|
7
|
Breton M, Delemotte L, Silve A, Mir LM, Tarek M. Transport of siRNA through Lipid Membranes Driven by Nanosecond Electric Pulses: An Experimental and Computational Study. J Am Chem Soc 2012; 134:13938-41. [DOI: 10.1021/ja3052365] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marie Breton
- Université Paris-Sud, Laboratoire de Vectorologie et Thérapeutiques
Anticancéreuses, UMR 8203, Orsay F-91405, France
- CNRS,
Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses,
UMR 8203, Orsay F-91405, France
- Institut Gustave Roussy, Laboratoire de Vectorologie et Thérapeutiques
Anticancéreuses, UMR 8203, Villejuif F-94805, France
| | - Lucie Delemotte
- Université de Lorraine, UMR Structure et Réactivité
des Systèmes Moléculaires Complexes, CNRS, Nancy 54003,
France
| | - Aude Silve
- Université Paris-Sud, Laboratoire de Vectorologie et Thérapeutiques
Anticancéreuses, UMR 8203, Orsay F-91405, France
- CNRS,
Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses,
UMR 8203, Orsay F-91405, France
- Institut Gustave Roussy, Laboratoire de Vectorologie et Thérapeutiques
Anticancéreuses, UMR 8203, Villejuif F-94805, France
| | - Lluis M. Mir
- Université Paris-Sud, Laboratoire de Vectorologie et Thérapeutiques
Anticancéreuses, UMR 8203, Orsay F-91405, France
- CNRS,
Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses,
UMR 8203, Orsay F-91405, France
- Institut Gustave Roussy, Laboratoire de Vectorologie et Thérapeutiques
Anticancéreuses, UMR 8203, Villejuif F-94805, France
| | - Mounir Tarek
- Université de Lorraine, UMR Structure et Réactivité
des Systèmes Moléculaires Complexes, CNRS, Nancy 54003,
France
| |
Collapse
|
8
|
Molecular Dynamics Simulations of Lipid Membrane Electroporation. J Membr Biol 2012; 245:531-43. [DOI: 10.1007/s00232-012-9434-6] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 04/30/2012] [Indexed: 10/28/2022]
|
9
|
Nguyen THT, Rao NZ, Schroeder WM, Moore PB. Coarse-grained molecular dynamics of tetrameric transmembrane peptide bundles within a lipid bilayer. Chem Phys Lipids 2010; 163:530-7. [PMID: 20433819 DOI: 10.1016/j.chemphyslip.2010.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 03/05/2010] [Accepted: 04/19/2010] [Indexed: 01/17/2023]
Abstract
The conformations of model transmembrane peptides are studied to understand the structural and dynamical aspects of tetrameric bundles using a series of coarse grain (CG) molecular dynamics (MD) simulations since membrane proteins play a crucial role in cell function. In this work, two different amphipathic models have been constructed using similar hydrophobic/hydrophilic characteristics with two structurally distinct morphologies to evaluate the effect of roughness and hydrophilic topology on the structure of tetrameric bundles, one class that forms an ion-channel and one class that does not. Free energy calculations of typical amphipathic peptide topologies show that using a relatively smooth surface morphology allows for a stable conformation of the tetramer bundle in a diamond formation. However, the model with side chains attached to the core in order to roughen the surface has a stable square tetramer bundle which is consistent with experimental data and all-atom (AA) MD simulations. Comparisons of the CG simulations with AA MD simulations are in reasonable agreement with the formation of tetrameric homo-oligomers, partitioning within the lipid bilayer and tilt angle with respect to the bilayer normal. We concluded that a square or diamond shape tetrameric homo-oligomers could be stabilized by rational design of the peptide morphology and topology of the surface, thus allowing us to tune the permeability of the bundle or channel.
Collapse
Affiliation(s)
- Thuy Hien T Nguyen
- Department of Chemistry & Biochemistry and the West Center for Computational Chemistry and Drug Design, University of the Sciences in Philadelphia, 600 South 43rd Street, Philadelphia, PA 19104-4495, United States
| | | | | | | |
Collapse
|
10
|
Pendley SS, Yu YB, Cheatham TE. Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils. Proteins 2009; 74:612-29. [PMID: 18704948 PMCID: PMC2692595 DOI: 10.1002/prot.22177] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The alpha-helical coiled-coil is one of the most common oligomerization motifs found in both native and engineered proteins. To better understand the stability and dynamics of the coiled-coil motifs, including those modified by fluorination, several fluorinated and nonfluorinated parallel dimeric coiled-coil protein structures were designed and modeled. We also attempt to investigate how changing the length and geometry of the important stabilizing salt bridges influences the coiled-coil protein structure. Molecular dynamics (MD) and free energy simulations with AMBER used a particle mesh Ewald treatment of the electrostatics in explicit TIP3P solvent with balanced force field treatments. Preliminary studies with legacy force fields (ff94, ff96, and ff99) show a profound instability of the coiled-coil structures in short MD simulation. Significantly, better behavior is evident with the more balanced ff99SB and ff03 protein force fields. Overall, the results suggest that the coiled-coil structures can readily accommodate the larger acidic arginine or S-2,7-diaminoheptanedoic acid mutants in the salt bridge, whereas substitution of the smaller L-ornithine residue leads to rapid disruption of the coiled-coil structure on the MD simulation time scale. This structural distortion of the secondary structure allows both the formation of large hydration pockets proximal to the charged groups and within the hydrophobic core. Moreover, the increased structural fluctuations and movement lead to a decrease in the water occupancy lifetimes in the hydration pockets. In contrast, analysis of the hydration in the stable dimeric coiled-coils shows high occupancy water sites along the backbone residues with no water occupancy in the hydrophobic core, although transitory water interactions with the salt bridge residues are evident. The simulations of the fluorinated coiled-coils suggest that in some cases fluorination electrostatically stabilizes the intermolecular coiled-coil salt bridges. Structural analyses also reveal different side chain rotamer preferences for leucine when compared with 5,5,5,5',5',5'-hexafluoroleucine mutants. These observed differences in the side chain rotamer populations suggest differential changes in the side chain conformational entropy upon coiled-coil formation when the protein is fluorinated. The free energy of hydration of the isolated 5,5,5,5',5',5'-hexafluoroleucine amino acid is calculated to be 1.1 kcal/mol less stable than leucine; this hydrophobic penalty in the monomer may provide a driving force for coiled-coil dimer formation. Estimation of the ellipticity at 222 nm from a series of snapshots from the MD simulations with DicroCalc shows distinct increases in the ellipticity when the coiled-coil is fluorinated, which suggests that the helicity in the folded coiled-coils is greater when fluorinated.
Collapse
Affiliation(s)
- Scott S. Pendley
- Departments of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
| | - Yihua B. Yu
- Departments of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
- Departments of Pharmaceutical Sciences and Bioengineering, University of Maryland, University of Maryland, 20 Penn Street, Rm. 635, Baltimore, MD 21201
| | - Thomas E. Cheatham
- Departments of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
- Department of Medicinal Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
- Department of Bioengineering, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
| |
Collapse
|
11
|
The membrane potential and its representation by a constant electric field in computer simulations. Biophys J 2008; 95:4205-16. [PMID: 18641071 DOI: 10.1529/biophysj.108.136499] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A theoretical framework is elaborated to account for the effect of a transmembrane potential in computer simulations. It is shown that a simulation with a constant external electric field applied in the direction normal to the membrane is equivalent to the influence of surrounding infinite baths maintained to a voltage difference via ion-exchanging electrodes connected to an electromotive force. It is also shown that the linearly-weighted displacement charge within the simulation system tracks the net flow of charge through the external circuit comprising the electromotive force and the electrodes. Using a statistical mechanical reduction of the degrees of freedom of the external system, three distinct theoretical routes are formulated and examined for the purpose of characterizing the free energy of a protein embedded in a membrane that is submitted to a voltage difference. The W-route is constructed from the variations in the voltage-dependent potential of mean force along a reaction path connecting two conformations of the protein. The Q-route is based on the average displacement charge as a function of the conformation of the protein. Finally, the G-route considers the relative charging free energy of specific residues, with and without applied membrane potentials. The theoretical formulation is illustrated with a simple model of an ion crossing a vacuum slab surrounded by two aqueous bulk phases and with a fragment of the voltage-sensor of the KvAP potassium channel.
Collapse
|
12
|
Delemotte L, Dehez F, Treptow W, Tarek M. Modeling Membranes under a Transmembrane Potential. J Phys Chem B 2008; 112:5547-50. [DOI: 10.1021/jp710846y] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
13
|
Belof JL, Stern AC, Eddaoudi M, Space B. On the Mechanism of Hydrogen Storage in a Metal−Organic Framework Material. J Am Chem Soc 2007; 129:15202-10. [DOI: 10.1021/ja0737164] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Jonathan L. Belof
- Contribution from the Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, CHE205, Tampa, Florida 33620-5250
| | - Abraham C. Stern
- Contribution from the Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, CHE205, Tampa, Florida 33620-5250
| | - Mohamed Eddaoudi
- Contribution from the Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, CHE205, Tampa, Florida 33620-5250
| | - Brian Space
- Contribution from the Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, CHE205, Tampa, Florida 33620-5250
| |
Collapse
|
14
|
Lopez CF, Nielsen SO, Ensing B, Moore PB, Klein ML. Structure and dynamics of model pore insertion into a membrane. Biophys J 2005; 88:3083-94. [PMID: 15722425 PMCID: PMC1305460 DOI: 10.1529/biophysj.104.053769] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A cylindrical transmembrane molecule is constructed by linking hydrophobic sites selected from a coarse grain model. The resulting hollow tube assembly serves as a representation of a transmembrane channel, pore, or a carbon nanotube. The interactions of a coarse grain di-myristoyl-phosphatidyl-choline hydrated bilayer with both a purely hydrophobic tube and a tube with hydrophilic caps are studied. The hydrophobic tube rotates in the membrane and becomes blocked by lipid tails after a few tens of nanoseconds. The hydrophilic sites of the capped tube stabilize it by anchoring the tube in the lipid headgroup/water interfacial region of each membrane leaflet. The capped tube remains free of lipid tails. The capped tube spontaneously conducts coarse grain water sites; the free-energy profile of this process is calculated using three different methods and is compared to the barrier for water permeation through the lipid bilayer. Spontaneous tube insertion into an undisturbed lipid bilayer is also studied, which we reported briefly in a previous publication. The hydrophobic tube submerges into the membrane core in a carpetlike manner. The capped tube laterally fuses with the closest leaflet, and then, after plunging into the membrane interior, rotates to assume a transbilayer orientation. Two lipids become trapped at the end of the tube as it penetrates the membrane. The hydrophilic headgroups of these lipids associate with the lower tube cap and assist the tube in crossing the interior of the membrane. When the rotation is complete these lipids detach from the tube caps and fuse with the lower leaflet lipids.
Collapse
Affiliation(s)
- Carlos F Lopez
- Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | | |
Collapse
|
15
|
DeVane R, Ridley C, Larsen RW, Space B, Moore PB, Chan SI. A molecular dynamics method for calculating molecular volume changes appropriate for biomolecular simulation. Biophys J 2003; 85:2801-7. [PMID: 14581185 PMCID: PMC1303561 DOI: 10.1016/s0006-3495(03)74703-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2002] [Accepted: 05/06/2003] [Indexed: 11/28/2022] Open
Abstract
Photothermal methods permit measurement of molecular volume changes of solvated molecules over nanosecond timescales. Such experiments are an important tool in investigating complex biophysical phenomena including identifying transient species in solution. Developing a microscopic understanding of the origin of volume changes in the condensed phase is needed to complement the experimental measurements. A molecular dynamics (MD) method exploiting available simulation methodology is demonstrated here that both mimics experimental measurements and provides microscopic resolution to the thermodynamic measurements. To calculate thermodynamic volume changes over time, isothermal-isobaric (NPT) MD is performed on a solution for a chosen length of time and the volume of the system is thus established. A further simulation is then performed by "plucking" out a solute molecule of interest to determine the volume of the system in its absence. The difference between these volumes is the thermodynamic volume of the solute molecule. NPT MD allows the volume of the system to fluctuate over time and this results in a statistical uncertainty in volumes that are calculated. It is found in the systems investigated here that simulations lasting a few nanoseconds can discern volume changes of approximately 1.0 ml/mole. This precision is comparable to that achieved empirically, making the experimental and theoretical techniques synergistic. The technique is demonstrated here on model systems including neat water, both charged and neutral aqueous methane, and an aqueous beta-sheet peptide.
Collapse
Affiliation(s)
- Russell DeVane
- Department of Chemistry, University of South Florida, Tampa, Florida 33620-5250, USA
| | | | | | | | | | | |
Collapse
|
16
|
Law RJ, Tieleman DP, Sansom MSP. Pores formed by the nicotinic receptor m2delta Peptide: a molecular dynamics simulation study. Biophys J 2003; 84:14-27. [PMID: 12524262 PMCID: PMC1302590 DOI: 10.1016/s0006-3495(03)74829-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The M2delta peptide self-assembles to form a pentameric bundle of transmembrane alpha-helices that is a model of the pore-lining region of the nicotinic acetylcholine receptor. Long (>15 ns) molecular dynamics simulations of a model of the M2delta(5) bundle in a POPC bilayer have been used to explore the conformational dynamics of the channel assembly. On the timescale of the simulation, the bundle remains relatively stable, with the polar pore-lining side chains remaining exposed to the lumen of the channel. Fluctuations at the helix termini, and in the helix curvature, result in closing/opening transitions at both mouths of the channel, on a timescale of approximately 10 ns. On average, water within the pore lumen diffuses approximately 4x more slowly than water outside the channel. Examination of pore water trajectories reveals both single-file and path-crossing regimes to occur at different times within the simulation.
Collapse
Affiliation(s)
- R J Law
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, United Kingdom
| | | | | |
Collapse
|
17
|
Guidoni L, Carloni P. Tetraethylammonium binding to the outer mouth of the KcsA potassium channel: implications for ion permeation. J Recept Signal Transduct Res 2002; 22:315-31. [PMID: 12503624 DOI: 10.1081/rrs-120014604] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Extracellular tetraethylammonium (TEA+) inhibits the current carried out by K+ ions in potassium channels. Structural models of wild-type (WT) and Y82C KcsA K+ channel/TEA+ complexes are here built using docking procedures, electrostatics calculations and molecular dynamics simulations. The calculations are based on the structure determined by Doyle et al. (11) Our calculations suggest that in WT, the TEA+ cation turns binds at the outer mouth of the selectivity filter, stabilized by electrostatic and hydrophobic interactions with the four Tyr82 side chains. Replacement of Tyr82 with Cys causes a decrease of the affinity of the cation for the channel, consistently with the available site-directed mutagenesis data (16). An MD simulation in which K+ replaces TEA+ provides evidence that TEA+ binding site can accommodate a potassium ion, in agreement with the high-resolution structure recently reported by Zhou et al. (20)
Collapse
Affiliation(s)
- Leonardo Guidoni
- INFM-Democritos Center for Molecular Simulations and International School for Advanced Studies (SISSA), Via Beirut 4, 1-34014 Trieste, Italy
| | | |
Collapse
|
18
|
Tobias DJ. Electrostatics calculations: recent methodological advances and applications to membranes. Curr Opin Struct Biol 2001; 11:253-61. [PMID: 11297936 DOI: 10.1016/s0959-440x(00)00198-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Calculations of electrostatic energies and forces are at the heart of the theoretical modeling of biological molecules. During the past year, new methods for accurately treating electrostatic interactions have been developed for all-atom simulations and for modeling systems in which the uninteresting part of the system, for example, the solvent, is represented implicitly. Recent applications of electrostatic energy calculations have revealed new principles concerning the role of electrostatics in peptide binding to membranes and ion transport across membranes through protein channels.
Collapse
Affiliation(s)
- D J Tobias
- Department of Chemistry and Institute for Surface and Interface Science, University of California, Irvine, CA 92697-2025, USA.
| |
Collapse
|
19
|
Roux B, Bernèche S, Im W. Ion channels, permeation, and electrostatics: insight into the function of KcsA. Biochemistry 2000; 39:13295-306. [PMID: 11063565 DOI: 10.1021/bi001567v] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- B Roux
- Department of Biochemistry, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10021, USA.
| | | | | |
Collapse
|
20
|
Im W, Seefeld S, Roux B. A Grand Canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels. Biophys J 2000; 79:788-801. [PMID: 10920012 PMCID: PMC1300978 DOI: 10.1016/s0006-3495(00)76336-3] [Citation(s) in RCA: 187] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
A computational algorithm based on Grand Canonical Monte Carlo (GCMC) and Brownian Dynamics (BD) is described to simulate the movement of ions in membrane channels. The proposed algorithm, GCMC/BD, allows the simulation of ion channels with a realistic implementation of boundary conditions of concentration and transmembrane potential. The method is consistent with a statistical mechanical formulation of the equilibrium properties of ion channels (; Biophys. J. 77:139-153). The GCMC/BD algorithm is illustrated with simulations of simple test systems and of the OmpF porin of Escherichia coli. The approach provides a framework for simulating ion permeation in the context of detailed microscopic models.
Collapse
Affiliation(s)
- W Im
- Groupe de Recherche en Transport Membranaire (GRTM), Départements de Physique et de Chimie, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | | | | |
Collapse
|
21
|
Abstract
Molecular dynamics simulations and electrostatic modeling are used to investigate structural and dynamical properties of the potassium ions and of water molecules inside the KcsA channel immersed in a membrane-mimetic environment. Two potassium ions, initially located in the selectivity filter binding sites, maintain their position during 2 ns of dynamics. A third potassium ion is very mobile in the water-filled cavity. The protein appears engineered so as to polarize water molecules inside the channel cavity. The resulting water induced dipole and the positively charged potassium ion within the cavity are the key ingredients for stabilizing the two K(+) ions in the binding sites. These two ions experience single file movements upon removal of the potassium in the cavity, confirming the role of the latter in ion transport through the channel.
Collapse
Affiliation(s)
- L Guidoni
- Istituto Nazionale per la Fisica della Materia, Italy and International School for Advanced Studies, Via Beirut 4, 34014 Trieste, Italy
| | | | | |
Collapse
|
22
|
Zhong Q, Newns DM, Pattnaik P, Lear JD, Klein ML. Two possible conducting states of the influenza A virus M2 ion channel. FEBS Lett 2000; 473:195-8. [PMID: 10812073 DOI: 10.1016/s0014-5793(00)01522-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Molecular dynamics simulations have been performed on protonated four-helix bundles based on the 25-residue Duff-Ashley transmembrane sequence of the M2 channel of the influenza A virus. Well-equilibrated tetrameric channels, with one, two and four of the H37 residues protonated, were investigated. The protonated peptide bundles were immersed in the octane portion of a phase-separated water/octane system, which provided a membrane-mimetic environment. The simulations suggest that there could be two conducting states of the M2 channel corresponding to tetramers containing one or two protonated histidines. The more open structure of the doubly protonated state suggests it would have the higher conductance.
Collapse
Affiliation(s)
- Q Zhong
- Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | | |
Collapse
|
23
|
Shrivastava IH, Sansom MS. Simulations of ion permeation through a potassium channel: molecular dynamics of KcsA in a phospholipid bilayer. Biophys J 2000; 78:557-70. [PMID: 10653771 PMCID: PMC1300661 DOI: 10.1016/s0006-3495(00)76616-1] [Citation(s) in RCA: 228] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Potassium channels enable K(+) ions to move passively across biological membranes. Multiple nanosecond-duration molecular dynamics simulations (total simulation time 5 ns) of a bacterial potassium channel (KcsA) embedded in a phospholipid bilayer reveal motions of ions, water, and protein. Comparison of simulations with and without K(+) ions indicate that the absence of ions destabilizes the structure of the selectivity filter. Within the selectivity filter, K(+) ions interact with the backbone (carbonyl) oxygens, and with the side-chain oxygen of T75. Concerted single-file motions of water molecules and K(+) ions within the selectivity filter of the channel occur on a 100-ps time scale. In a simulation with three K(+) ions (initially two in the filter and one in the cavity), the ion within the central cavity leaves the channel via its intracellular mouth after approximately 900 ps; within the cavity this ion interacts with the Ogamma atoms of two T107 side chains, revealing a favorable site within the otherwise hydrophobically lined cavity. Exit of this ion from the channel is enabled by a transient increase in the diameter of the intracellular mouth. Such "breathing" motions may form the molecular basis of channel gating.
Collapse
Affiliation(s)
- I H Shrivastava
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | | |
Collapse
|
24
|
Tuckerman ME, Martyna GJ. Understanding Modern Molecular Dynamics: Techniques and Applications. J Phys Chem B 1999. [DOI: 10.1021/jp992433y] [Citation(s) in RCA: 248] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mark E. Tuckerman
- Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, New York 10003
| | - Glenn J. Martyna
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| |
Collapse
|
25
|
Randa HS, Forrest LR, Voth GA, Sansom MS. Molecular dynamics of synthetic leucine-serine ion channels in a phospholipid membrane. Biophys J 1999; 77:2400-10. [PMID: 10545343 PMCID: PMC1300517 DOI: 10.1016/s0006-3495(99)77077-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Molecular dynamics calculations were carried out on models of two synthetic leucine-serine ion channels: a tetrameric bundle with sequence (LSLLLSL)(3)NH(2) and a hexameric bundle with sequence (LSSLLSL)(3)NH(2). Each protein bundle is inserted in a palmitoyloleoylphosphatidylcholine bilayer membrane and solvated by simple point charge water molecules inside the pore and at both mouths. Both systems appear to be stable in the absence of an electric field during the 4 ns of molecular dynamics simulation. The water motion in the narrow pore of the four-helix bundle is highly restricted and may provide suitable conditions for proton transfer via a water wire mechanism. In the wider hexameric pore, the water diffuses much more slowly than in bulk but is still mobile. This, along with the dimensions of the pore, supports the observation that this peptide is selective for monovalent cations. Reasonable agreement of predicted conductances with experimentally determined values lends support to the validity of the simulations.
Collapse
Affiliation(s)
- H S Randa
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
| | | | | | | |
Collapse
|
26
|
|
27
|
Abstract
A rigorous statistical mechanical formulation of the equilibrium properties of selective ion channels is developed, incorporating the influence of the membrane potential, multiple occupancy, and saturation effects. The theory provides a framework for discussing familiar quantities and concepts in the context of detailed microscopic models. Statistical mechanical expressions for the free energy profile along the channel axis, the cross-sectional area of the pore, and probability of occupancy are given and discussed. In particular, the influence of the membrane voltage, the significance of the electric distance, and traditional assumptions concerning the linearity of the membrane electric field along the channel axis are examined. Important findings are: 1) the equilibrium probabilities of occupancy of multiply occupied channels have the familiar algebraic form of saturation properties which is obtained from kinetic models with discrete states of denumerable ion occupancy (although this does not prove the existence of specific binding sites; 2) the total free energy profile of an ion along the channel axis can be separated into an intrinsic ion-pore free energy potential of mean force, independent of the transmembrane potential, and other contributions that arise from the interfacial polarization; 3) the transmembrane potential calculated numerically for a detailed atomic configuration of the gramicidin A channel embedded in a bilayer membrane with explicit lipid molecules is shown to be closely linear over a distance of 25 A along the channel axis. Therefore, the present analysis provides some support for the constant membrane potential field approximation, a concept that has played a central role in the interpretation of flux data based on traditional models of ion permeation. It is hoped that this formulation will provide a sound physical basis for developing nonequilibrium theories of ion transport in selective biological channels.
Collapse
Affiliation(s)
- B Roux
- Groupe de Recherche en Transport Membranaire, Départements de physique et de chimie, Université de Montréal, C.P. 6128, Montréal H3C 3J7, Canada.
| |
Collapse
|
28
|
Tieleman DP, Berendsen HJ, Sansom MS. An alamethicin channel in a lipid bilayer: molecular dynamics simulations. Biophys J 1999; 76:1757-69. [PMID: 10096876 PMCID: PMC1300154 DOI: 10.1016/s0006-3495(99)77337-6] [Citation(s) in RCA: 145] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present the results of 2-ns molecular dynamics (MD) simulations of a hexameric bundle of Alm helices in a 1-palmitoyl-2-oleoylphosphatidylcholine bilayer. These simulations explore the dynamic properties of a model of a helix bundle channel in a complete phospholipid bilayer in an aqueous environment. We explore the stability and conformational dynamics of the bundle in a phospholipid bilayer. We also investigate the effect on bundle stability of the ionization state of the ring of Glu18 side chains. If all of the Glu18 side chains are ionised, the bundle is unstable; if none of the Glu18 side chains are ionized, the bundle is stable. pKA calculations suggest that either zero or one ionized Glu18 is present at neutral pH, correlating with the stable form of the helix bundle. The structural and dynamic properties of water in this model channel were examined. As in earlier in vacuo simulations (Breed et al., 1996 .Biophys. J. 70:1643-1661), the dipole moments of water molecules within the pore were aligned antiparallel to the helix dipoles. This contributes to the stability of the helix bundle.
Collapse
Affiliation(s)
- D P Tieleman
- BIOSON Research Institute and Department of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | | | | |
Collapse
|
29
|
Abstract
Membrane proteins, of which the majority seem to contain one or more alpha-helix, constitute approx. 30% of most genomes. A complete understanding of the nature of helix/bilayer interactions is necessary for an understanding of the structural principles underlying membrane proteins. This review describes computer simulation studies of helix/bilayer interactions. Key experimental studies of the interactions of alpha-helices and lipid bilayers are briefly reviewed. Surface associated helices are found in some membrane-bound enzymes (e.g. prostaglandin synthase), and as stages in the mechanisms of antimicrobial peptides and of pore-forming bacterial toxins. Transmembrane alpha-helices are found in most integral membrane proteins, and also in channels formed by amphipathic peptides or by bacterial toxins. Mean field simulations, in which the lipid bilayer is approximated as a hydrophobic continuum, have been used in studies of membrane-active peptides (e.g. alamethicin, melittin, magainin and dermaseptin) and of simple membrane proteins (e.g. phage Pf1 coat protein). All atom molecular dynamics simulations of fully solvated bilayers with transmembrane helices have been applied to: the constituent helices of bacteriorhodopsin; peptide-16 (a simple model TM helix); and a number of pore-lining helices from ion channels. Surface associated helices (e.g. melittin and dermaseptin) have been simulated, as have alpha-helical bundles such as bacteriorhodopsin and alamethicin. From comparison of the results from the two classes of simulation, it emerges that a major theoretical challenge is to exploit the results of all atom simulations in order to improve the mean field approach.
Collapse
Affiliation(s)
- P C Biggin
- Salk Institute for Biological Studies, La Jolla, CA 92109, USA
| | | |
Collapse
|
30
|
Dieckmann GR, Lear JD, Zhong Q, Klein ML, DeGrado WF, Sharp KA. Exploration of the structural features defining the conduction properties of a synthetic ion channel. Biophys J 1999; 76:618-30. [PMID: 9929468 PMCID: PMC1300068 DOI: 10.1016/s0006-3495(99)77230-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The finite-difference Poisson-Boltzmann methodology was applied to a series of parallel, alpha-helical bundle models of the designed ion channel peptide Ac-(LSSLLSL)3-CONH2. This method is able to fully describe the current-voltage curves for this channel and quantitatively explains their cation selectivity and rectification. We examined a series of energy-minimized models representing different aggregation states, side-chain rotamers, and helical rotations, as well as an ensemble of structures from a molecular dynamics trajectory. Potential energies were computed for single, permeating K+ and Cl- ions at a series of positions along a central pathway through the models. A variable-electric-field Nernst-Planck electrodiffusion model was used, with two adjustable parameters representing the diffusion coefficients of K+ and Cl- to scale the individual ion current magnitudes. The ability of a given DelPhi potential profile to fit the experimental data depended strongly on the magnitude of the desolvation of the permeating ion. Below a pore radius of 3.8 A, the predicted profiles showed large energy barriers, and the experimental data could be fit only with unrealistically high values for the K+ and Cl- diffusion coefficients. For pore radii above 3.8 A, the desolvation energies were 2kT or less. The electrostatic calculations were sensitive to positioning of the Ser side chains, with the best fits associated with maximum exposure of the Ser side-chain hydroxyls to the pore. The backbone component was shown to be the major source of asymmetry in the DelPhi potential profiles. Only two of the energy-minimized structures were able to explain the experimental data, whereas an average of the dynamics structures gave excellent agreement with experimental results. Thus this method provides a promising approach to prediction of current-voltage curves from three-dimensional structures of ion channel proteins.
Collapse
Affiliation(s)
- G R Dieckmann
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
| | | | | | | | | | | |
Collapse
|
31
|
Interactions of Small Molecules and Peptides with Membranes. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s1380-7323(99)80088-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
32
|
Zhong Q, Husslein T, Moore PB, Newns DM, Pattnaik P, Klein ML. The M2 channel of influenza A virus: a molecular dynamics study. FEBS Lett 1998; 434:265-71. [PMID: 9742936 DOI: 10.1016/s0014-5793(98)00988-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Molecular dynamics simulations have been performed on a tetramer of the 25-residue (SSDPLVVAASIIGILHLILWILDRL) synthetic peptide [1] which contains the transmembrane domain of the influenza A virus M2 coat protein. The peptide bundle was initially assembled as a parallel alpha-helix bundle in the octane portion of a phase separated water/octane system, which provided a membrane-mimetic environment. A 4-ns dynamics trajectory identified a left-handed coiled coil state of the neutral bundle, with a water filled funnel-like structural motif at the N-terminus involving the long hydrophobic sequence. The neck of the funnel begins at V27 and terminates at H37, which blocks the channel. The C-terminus is held together by inter-helix hydrogen bonds and contains water below H37. Solvation of the S23 and D24 residues, located at the rim of the funnel, appears to be important for stability of the structure. The calculated average tilt of the helices in the neutral bundle is 27 +/- 5 degrees, which agrees well with recent NMR data.
Collapse
Affiliation(s)
- Q Zhong
- Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, Philadelphia 19104-6323, USA
| | | | | | | | | | | |
Collapse
|
33
|
Moore PB, Zhong Q, Husslein T, Klein ML. Simulation of the HIV-1 Vpu transmembrane domain as a pentameric bundle. FEBS Lett 1998; 431:143-8. [PMID: 9708891 DOI: 10.1016/s0014-5793(98)00714-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The transmembrane domain of oligomeric protein Vpu encoded by HIV-1 has been studied by means of a molecular dynamics simulation. A pentameric bundle of unconstrained helices (residues 6-28 of Vpu) with a water filled pore was initially assembled in a membrane mimetic octane/water system. This system was simulated, using the CHARMm19 and OPLS united atom force fields with no constraints at a temperature of 300 K and a pressure of 1 atm. For these forcefields and the initial conditions tested, the oligomeric bundle expelled most of the pore water molecules. The resulting bundle and residual waters adopt a conical structural motif with some resemblance to a potassium channel.
Collapse
Affiliation(s)
- P B Moore
- Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, Philadephia 19104-6323, USA.
| | | | | | | |
Collapse
|