51
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Chen X, Liu S, Deme B, Cristiglio V, Marquardt D, Weller R, Rao P, Wang Y, Bradshaw J. Efficient internalization of TAT peptide in zwitterionic DOPC phospholipid membrane revealed by neutron diffraction. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:910-916. [PMID: 28153495 DOI: 10.1016/j.bbamem.2017.01.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/16/2017] [Accepted: 01/28/2017] [Indexed: 11/19/2022]
Abstract
The aim of this study is to investigate the interactions between TAT peptides and a neutral DOPC bilayer by using neutron lamellar diffraction. The distribution of TAT peptides and the perturbation of water distribution across the DOPC bilayer were revealed. When compared to our previous study on an anionic DOPC/DOPS bilayer (X. Chen et al., Biochim Biophys Acta. 2013. 1828 (8), 1982-1988), a much deeper insertion of TAT peptides was found in the hydrophobic core of DOPC bilayer at a depth of 6.0Å from the center of the bilayer, a position close to the double bond of fatty acyl chain. We conclude that the electrostatic attractions between the positively charged TAT peptides and the negatively charged headgroups of phospholipid are not essential for the direct translocation. Furthermore, the interactions of TAT peptides with the DOPC bilayer were found to vary in a concentration-dependent manner. A limited number of peptides first associate with the phosphate moieties on the lipid headgroups by using the guanidinium ions pairing. Then the energetically favorable water defect structures are adopted to maintain the arginine residues hydrated by drawing water molecules and lipid headgroups into the bilayer core. Such bilayer deformations consequently lead to the deep intercalation of TAT peptides into the bilayer core. Once a threshold concentration of TAT peptide in the bilayer is reached, a significant rearrangement of bilayer will happen and steady-state water pores will form.
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Affiliation(s)
- Xiaochao Chen
- College of Biological Science and Biotechnology, Fuzhou University, 2 Xue Yuan Road, University Town, 350116 Fuzhou, Fujian, PR China.; The University of Edinburgh, Medical Research Council Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh EH16 4TJ, United Kingdom
| | - Shutao Liu
- College of Biological Science and Biotechnology, Fuzhou University, 2 Xue Yuan Road, University Town, 350116 Fuzhou, Fujian, PR China
| | - Bruno Deme
- Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, F-38042 Grenoble Cedex 9, France
| | - Viviana Cristiglio
- Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, F-38042 Grenoble Cedex 9, France
| | - Drew Marquardt
- Canadian Neutron Beam Centre, National Research Council, Chalk River, ON K0J 1P0, Canada
| | - Richard Weller
- The University of Edinburgh, Medical Research Council Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh EH16 4TJ, United Kingdom
| | - Pingfan Rao
- College of Biological Science and Biotechnology, Fuzhou University, 2 Xue Yuan Road, University Town, 350116 Fuzhou, Fujian, PR China
| | - Yunqiang Wang
- College of Biological Science and Biotechnology, Fuzhou University, 2 Xue Yuan Road, University Town, 350116 Fuzhou, Fujian, PR China
| | - Jeremy Bradshaw
- The University of Edinburgh, Royal (Dick) School of Veterinary Studies, Easter Bush, Roslin, Midlothian EH25 9RG, United Kingdom.
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52
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Bethel NP, Grabe M. Atomistic insight into lipid translocation by a TMEM16 scramblase. Proc Natl Acad Sci U S A 2016; 113:14049-14054. [PMID: 27872308 PMCID: PMC5150362 DOI: 10.1073/pnas.1607574113] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The transmembrane protein 16 (TMEM16) family of membrane proteins includes both lipid scramblases and ion channels involved in olfaction, nociception, and blood coagulation. The crystal structure of the fungal Nectria haematococca TMEM16 (nhTMEM16) scramblase suggested a putative mechanism of lipid transport, whereby polar and charged lipid headgroups move through the low-dielectric environment of the membrane by traversing a hydrophilic groove on the membrane-spanning surface of the protein. Here, we use computational methods to explore the membrane-protein interactions involved in lipid scrambling. Fast, continuum membrane-bending calculations reveal a global pattern of charged and hydrophobic surface residues that bends the membrane in a large-amplitude sinusoidal wave, resulting in bilayer thinning across the hydrophilic groove. Atomic simulations uncover two lipid headgroup-interaction sites flanking the groove. The cytoplasmic site nucleates headgroup-dipole stacking interactions that form a chain of lipid molecules that penetrate into the groove. In two instances, a cytoplasmic lipid interdigitates into this chain, crosses the bilayer, and enters the extracellular leaflet, and the reverse process happens twice as well. Continuum membrane-bending analysis carried out on homology models of mammalian homologs shows that these family members also bend the membrane-even those that lack scramblase activity. Sequence alignments show that the lipid-interaction sites are conserved in many family members but less so in those with reduced scrambling ability. Our analysis provides insight into how large-scale membrane bending and protein chemistry facilitate lipid permeation in the TMEM16 family, and we hypothesize that membrane interactions also affect ion permeation.
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Affiliation(s)
- Neville P Bethel
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
- Graduate Group in Biophysics, University of California, San Francisco, CA 94158
| | - Michael Grabe
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158;
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53
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Thibado JK, Martfeld AN, Greathouse DV, Koeppe RE. Influence of High pH and Cholesterol on Single Arginine-Containing Transmembrane Peptide Helices. Biochemistry 2016; 55:6337-6343. [PMID: 27782382 PMCID: PMC5266483 DOI: 10.1021/acs.biochem.6b00896] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
An essential component
of mammalian cells, cholesterol exerts significant
influence on the physical properties of the cell membrane and in turn
its constituents, including membrane proteins. Although sparse, polar
amino acid residues are highly conserved in membrane proteins and
play pivotal roles in determining specific structural and functional
properties. To improve our understanding of particular polar residues
in the membrane environment, we have examined two specific “guest”
Arg residues within a well-defined and deuterium-labeled “host”
framework provided by the transmembrane helical peptide GWALP23 (acetyl-GGALWLALALALALALALWLAGA-amide).
Solid-state 2H nuclear magnetic resonance (NMR) spectra
from aligned bilayer membrane samples effectively report changes in
the host helix properties because of the incorporation of the guest
residues. The focus of this work is two-pronged. First, GWALP23-R14
was examined over a pH range of 2–13 in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) ester- or ether-linked
bilayer membranes. Our findings indicate that the Arg guanidinium
side chain remains charged over this entire range, in agreement with
numerous molecular dynamics simulations. Second, GWALP23-R12 and GWALP23-R14
peptides were characterized in DOPC bilayers with varying cholesterol
content. Our findings suggest that 10 or 20% cholesterol content has
minimal impact on the orientation of the R14 peptide. Although the
NMR signals are broader and weaker in the presence of 20% cholesterol,
the deuterium quadrupolar splittings for [2H]Ala residues
in GWALP23-R14 change very little. Conversely, cholesterol appears
to modulate the multistate behavior of GWALP23-R12 and to favor a
major interfacial state for the helix, bound at the bilayer surface.
These results indicate a conditional sensitivity of a complex multistate
transmembrane Arg-containing peptide helix to the presence of cholesterol.
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Affiliation(s)
- Jordana K Thibado
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
| | - Ashley N Martfeld
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
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54
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Xiang N, Lyu Y, Zhu X, Bhunia AK, Narsimhan G. Methodology for identification of pore forming antimicrobial peptides from soy protein subunits β-conglycinin and glycinin. Peptides 2016; 85:27-40. [PMID: 27612614 DOI: 10.1016/j.peptides.2016.09.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/31/2016] [Accepted: 09/05/2016] [Indexed: 01/07/2023]
Abstract
Antimicrobial peptides (AMPs) inactivate microbial cells through pore formation in cell membrane. Because of their different mode of action compared to antibiotics, AMPs can be effectively used to combat drug resistant bacteria in human health. AMPs can also be used to replace antibiotics in animal feed and immobilized on food packaging films. In this research, we developed a methodology based on mechanistic evaluation of peptide-lipid bilayer interaction to identify AMPs from soy protein. Production of AMPs from soy protein is an attractive, cost-saving alternative for commercial consideration, because soy protein is an abundant and common protein resource. This methodology is also applicable for identification of AMPs from any protein. Initial screening of peptide segments from soy glycinin (11S) and soy β-conglycinin (7S) subunits was based on their hydrophobicity, hydrophobic moment and net charge. Delicate balance between hydrophilic and hydrophobic interactions is necessary for pore formation. High hydrophobicity decreases the peptide solubility in aqueous phase whereas high hydrophilicity limits binding of the peptide to the bilayer. Out of several candidates chosen from the initial screening, two peptides satisfied the criteria for antimicrobial activity, viz. (i) lipid-peptide binding in surface state and (ii) pore formation in transmembrane state of the aggregate. This method of identification of antimicrobial activity via molecular dynamics simulation was shown to be robust in that it is insensitive to the number of peptides employed in the simulation, initial peptide structure and force field. Their antimicrobial activity against Listeria monocytogenes and Escherichia coli was further confirmed by spot-on-lawn test.
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Affiliation(s)
- Ning Xiang
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, United States
| | - Yuan Lyu
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, United States
| | - Xiao Zhu
- Research Computing, Rosen Center for Advanced Computing, Purdue University, West Lafayette, IN 47907, United States
| | - Arun K Bhunia
- Department of Food Science, Purdue University, West Lafayette, IN 47907, United States; Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, United States
| | - Ganesan Narsimhan
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, United States.
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55
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Hoiles W, Gupta R, Cornell B, Cranfield C, Krishnamurthy V. The Effect of Tethers on Artificial Cell Membranes: A Coarse-Grained Molecular Dynamics Study. PLoS One 2016; 11:e0162790. [PMID: 27736860 PMCID: PMC5063460 DOI: 10.1371/journal.pone.0162790] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 08/29/2016] [Indexed: 11/18/2022] Open
Abstract
Tethered bilayer lipid membranes (tBLMs) provide a stable platform for modeling the dynamics and order of biological membranes where the tethers mimic the cytoskeletal supports present in biological cell membranes. In this paper coarse-grained molecular dynamics (CGMD) is applied to study the effects of tethers on lipid membrane properties. Using results from the CGMD model and the overdamped Fokker-Planck equation, we show that the diffusion tensor and particle density of water in the tBLM is spatially dependent. Further, it is shown that the membrane thickness, lipid diffusion, defect density, free energy of lipid flip-flop, and membrane dielectric permittivity are all dependent on the tether density. The numerically computed results from the CGMD model are in agreement with the experimentally measured results from tBLMs containing different tether densities and lipids derived from Archaebacteria. Additionally, using experimental measurements from Escherichia coli bacteria and Saccharomyces Cerevisiae yeast tethered membranes, we illustrate how previous molecular dynamics results can be combined with the proposed model to estimate the dielectric permittivity and defect density of these membranes as a function of tether density.
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Affiliation(s)
- William Hoiles
- Department of Electrical and Computer Engineering, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Rini Gupta
- Department of Electrical and Computer Engineering, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Bruce Cornell
- Director of Science and Technology, Surgical Diagnostics Pty Ltd., Unit 6 30-32 Barcoo Street, Roseville, New South Wales, 2069, Australia
| | - Charles Cranfield
- School of Life Sciences, University of Technology Sydney, Broadway, New South Wales, Australia
| | - Vikram Krishnamurthy
- Electrical and Computer Engineering, Cornell University, New York, New York, United States of America
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56
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Liu Y, Peng B, Sohrabi S, Liu Y. The Configuration of Copolymer Ligands on Nanoparticles Affects Adhesion and Uptake. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:10136-10143. [PMID: 27609544 DOI: 10.1021/acs.langmuir.6b02371] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nanoparticles (NPs) are promising carriers for targeted drug delivery, photodynamic therapy, and imaging probes. A fundamental understanding of the dynamics of polymeric NP targeting to bilayer membranes is important to enhance the design of NPs for higher adhesion, binding percentage, and efficiency. In this study, dissipative particle dynamics simulations are applied to investigate the adhesion and uptake processes of the rod, spherical, and striped NPs to cell membranes. It is observed that the striped ligands can prevent NPs from rotating even in active rotation. We further optimize striped NP to a more stabilized structure. Uptake processes of NPs with different configurations are thoroughly investigated in our simulations and among which Janus NP are indicated to improve the penetration rate to 100%. These findings provide better insight into patterned NP design and may help fabricate new NPs for biomedical applications.
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Affiliation(s)
- Yang Liu
- School of Mechatronics Engineering, University of Electronic Science and Technology of China , Chengdu 611731, China
- Center for Robotics, University of Electronic Science and Technology of China , Chengdu 611731, China
| | - Bei Peng
- School of Mechatronics Engineering, University of Electronic Science and Technology of China , Chengdu 611731, China
- Center for Robotics, University of Electronic Science and Technology of China , Chengdu 611731, China
| | - Salman Sohrabi
- Department of Mechanical Engineering and Mechanics, Lehigh University , Bethlehem, Pennsylvania 18015, United States
| | - Yaling Liu
- Department of Mechanical Engineering and Mechanics, Lehigh University , Bethlehem, Pennsylvania 18015, United States
- Bioengineering, Lehigh University , Bethlehem, Pennsylvania 18015, United States
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57
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Zhang HY, Xu Q, Wang YK, Zhao TZ, Hu D, Wei DQ. Passive Transmembrane Permeation Mechanisms of Monovalent Ions Explored by Molecular Dynamics Simulations. J Chem Theory Comput 2016; 12:4959-4969. [PMID: 27599103 DOI: 10.1021/acs.jctc.6b00695] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Passive or unassisted ion permeation through lipid bilayers involves a type of rare events by which cells regulate their salt concentrations and pH. It is important to understand its mechanism in order to develop technologies of, for example, delivering or maintaining small drug-like molecules inside cells. In earlier simulations of passive ion permeations, the commonly used sampling methods usually define the positions of ions relative to the membrane as a measure of permeation, i.e., the collective variable, ignoring the active participations of other particles. Newly defined collective variables involving the movements of ions, lipids, and water molecules allow us to identify the transition paths on the free energy landscape using the 2D umbrella sampling techniques. In this work, this technique was used to study the permeation processes of some well-known ions, sodium, potassium, and chloride. It is found permeations of sodium and potassium are assisted by important lipid bilayer deformations and massive water solvation, while chloride may not. Chloride may have two different possible pathways, in which the energetic favorable one is similar to the solubility-diffusion model. The free energy barriers for the permeation of these ions are in semiquantitative agreement with experiments. Further analyses on the distributions of oxygens and interaction energies suggest the electrostatic interactions between ions and polar headgroups of lipids may greatly influence membrane deformation as well as the water wire and furthermore the free energy barriers of waterwire mediated pathways. For chloride, the nonwaterwire pathway may be energetically favorable.
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Affiliation(s)
- Hui-Yuan Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology and ‡Department of Mathematics, Institute of Natural Science, and MOE-LEC, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Qin Xu
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology and ‡Department of Mathematics, Institute of Natural Science, and MOE-LEC, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Yu-Kun Wang
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology and ‡Department of Mathematics, Institute of Natural Science, and MOE-LEC, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Tang-Zhen Zhao
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology and ‡Department of Mathematics, Institute of Natural Science, and MOE-LEC, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Dan Hu
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology and ‡Department of Mathematics, Institute of Natural Science, and MOE-LEC, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology and ‡Department of Mathematics, Institute of Natural Science, and MOE-LEC, Shanghai Jiao Tong University , Shanghai 200240, China
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58
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Martfeld AN, Greathouse DV, Koeppe RE. Ionization Properties of Histidine Residues in the Lipid Bilayer Membrane Environment. J Biol Chem 2016; 291:19146-56. [PMID: 27440045 PMCID: PMC5009283 DOI: 10.1074/jbc.m116.738583] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/12/2016] [Indexed: 01/22/2023] Open
Abstract
We address the critically important ionization properties of histidine side chains of membrane proteins, when exposed directly to lipid acyl chains within lipid bilayer membranes. The problem is important for addressing general principles that may underlie membrane protein function. To this end, we have employed a favorable host peptide framework provided by GWALP23 (acetyl-GGALW(5)LALALALALALALW(19)LAGA-amide). We inserted His residues into position 12 or 14 of GWALP23 (replacing either Leu(12) or Leu(14)) and incorporated specific [(2)H]Ala labels within the helical core sequence. Solid-state (2)H NMR spectra report the folding and orientation of the core sequence, revealing marked differences in the histidine-containing transmembrane helix behavior between acidic and neutral pH conditions. At neutral pH, the GWALP23-H12 and GWALP23-H14 helices exhibit well defined tilted transmembrane orientations in dioleoylphosphatidylcholine (DOPC)and dilauroylphosphatidylcholine (DLPC) bilayer membranes. Under acidic conditions, when His(12) is protonated and charged, the GWALP23-H12 helix exhibits a major population that moves to the DOPC bilayer surface and a minor population that occupies multiple transmembrane states. The response to protonation of His(14) is an increase in helix tilt, but GWALP23-H14 remains in a transmembrane orientation. The results suggest pKa values of less than 3 for His(12) and about 3-5 for His(14) in DOPC membranes. In the thinner DLPC bilayers, with increased water access, the helices are less responsive to changes in pH. The combined results enable us to compare the ionization properties of lipid-exposed His, Lys, and Arg side chains in lipid bilayer membranes.
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Affiliation(s)
- Ashley N Martfeld
- From the Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
| | - Denise V Greathouse
- From the Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
| | - Roger E Koeppe
- From the Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
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59
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Molecular Basis of the Membrane Interaction of the β2e Subunit of Voltage-Gated Ca(2+) Channels. Biophys J 2016; 109:922-35. [PMID: 26331250 DOI: 10.1016/j.bpj.2015.07.040] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 07/27/2015] [Accepted: 07/28/2015] [Indexed: 12/30/2022] Open
Abstract
The auxiliary β subunit plays an important role in the regulation of voltage-gated calcium (CaV) channels. Recently, it was revealed that β2e associates with the plasma membrane through an electrostatic interaction between N-terminal basic residues and anionic phospholipids. However, a molecular-level understanding of β-subunit membrane recruitment in structural detail has remained elusive. In this study, using a combination of site-directed mutagenesis, liposome-binding assays, and multiscale molecular-dynamics (MD) simulation, we developed a physical model of how the β2e subunit is recruited electrostatically to the plasma membrane. In a fluorescence resonance energy transfer assay with liposomes, binding of the N-terminal peptide (23 residues) to liposome was significantly increased in the presence of phosphatidylserine (PS) and phosphatidylinositol 4,5-bisphosphate (PIP2). A mutagenesis analysis suggested that two basic residues proximal to Met-1, Lys-2 (K2) and Trp-5 (W5), are more important for membrane binding of the β2e subunit than distal residues from the N-terminus. Our MD simulations revealed that a stretched binding mode of the N-terminus to PS is required for stable membrane attachment through polar and nonpolar interactions. This mode obtained from MD simulations is consistent with experimental results showing that K2A, W5A, and K2A/W5A mutants failed to be targeted to the plasma membrane. We also investigated the effects of a mutated β2e subunit on inactivation kinetics and regulation of CaV channels by PIP2. In experiments with voltage-sensing phosphatase (VSP), a double mutation in the N-terminus of β2e (K2A/W5A) increased the PIP2 sensitivity of CaV2.2 and CaV1.3 channels by ∼3-fold compared with wild-type β2e subunit. Together, our results suggest that membrane targeting of the β2e subunit is initiated from the nonspecific electrostatic insertion of N-terminal K2 and W5 residues into the membrane. The PS-β2e interaction observed here provides a molecular insight into general principles for protein binding to the plasma membrane, as well as the regulatory roles of phospholipids in transporters and ion channels.
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60
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Lee CT, Comer J, Herndon C, Leung N, Pavlova A, Swift RV, Tung C, Rowley CN, Amaro RE, Chipot C, Wang Y, Gumbart JC. Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds. J Chem Inf Model 2016; 56:721-33. [PMID: 27043429 DOI: 10.1021/acs.jcim.6b00022] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Predicting the rate of nonfacilitated permeation of solutes across lipid bilayers is important to drug design, toxicology, and signaling. These rates can be estimated using molecular dynamics simulations combined with the inhomogeneous solubility-diffusion model, which requires calculation of the potential of mean force and position-dependent diffusivity of the solute along the transmembrane axis. In this paper, we assess the efficiency and accuracy of several methods for the calculation of the permeability of a model DMPC bilayer to urea, benzoic acid, and codeine. We compare umbrella sampling, replica exchange umbrella sampling, adaptive biasing force, and multiple-walker adaptive biasing force for the calculation of the transmembrane PMF. No definitive advantage for any of these methods in their ability to predict the membrane permeability coefficient Pm was found, provided that a sufficiently long equilibration is performed. For diffusivities, a Bayesian inference method was compared to a generalized Langevin method, both being sensitive to chosen parameters and the slow relaxation of membrane defects. Agreement within 1.5 log units of the computed Pm with experiment is found for all permeants and methods. Remaining discrepancies can likely be attributed to limitations of the force field as well as slowly relaxing collective movements within the lipid environment. Numerical calculations based on model profiles show that Pm can be reliably estimated from only a few data points, leading to recommendations for calculating Pm from simulations.
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Affiliation(s)
- Christopher T Lee
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Jeffrey Comer
- Nanotechnology Innovation Center of Kansas State, Institute of Computational Comparative Medicine, Department of Anatomy and Physiology, Kansas State University , P-213 Mosier Hall, Manhattan, Kansas 66506, United States
| | - Conner Herndon
- School of Physics, Georgia Institute of Technology , 837 State Street, Atlanta, Georgia 30332, United States
| | - Nelson Leung
- Department of Physics, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology , 837 State Street, Atlanta, Georgia 30332, United States
| | - Robert V Swift
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chris Tung
- Department of Physics, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
| | - Christopher N Rowley
- Department of Chemistry, Memorial University of Newfoundland , St. John's, NL A1B 3X7 Canada
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique and University of Illinois at Urbana-Champaign, UMR n° 7565, Université de Lorraine , B.P. 70239, 54506 Vandœuvre-lès-Nancy, France.,Beckman Institute for Advanced Science and Technology and Department of Physics, University of Illinois at Urbana-Champaign , 405 North Mathews, Urbana, Illinois 61801, United States
| | - Yi Wang
- Department of Physics, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China.,Shenzhen Research Institute, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology , 837 State Street, Atlanta, Georgia 30332, United States.,School of Chemistry and Biochemistry, Georgia Institute of Technology , 901 Atlantic Drive NW, Atlanta, Georgia 30332, United States
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61
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Subramanian N, Schumann-Gillett A, Mark AE, O'Mara ML. Understanding the accumulation of P-glycoprotein substrates within cells: The effect of cholesterol on membrane partitioning. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:776-82. [DOI: 10.1016/j.bbamem.2015.12.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 11/18/2015] [Accepted: 12/21/2015] [Indexed: 11/25/2022]
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62
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Shen Z, Nieh MP, Li Y. Decorating Nanoparticle Surface for Targeted Drug Delivery: Opportunities and Challenges. Polymers (Basel) 2016; 8:E83. [PMID: 30979183 PMCID: PMC6432562 DOI: 10.3390/polym8030083] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 02/25/2016] [Accepted: 03/01/2016] [Indexed: 12/31/2022] Open
Abstract
The size, shape, stiffness (composition) and surface properties of nanoparticles (NPs) have been recognized as key design parameters for NP-mediated drug delivery platforms. Among them, the surface functionalization of NPs is of great significance for targeted drug delivery. For instance, targeting moieties are covalently coated on the surface of NPs to improve their selectively and affinity to cancer cells. However, due to a broad range of possible choices of surface decorating molecules, it is difficult to choose the proper one for targeted functions. In this work, we will review several representative experimental and computational studies in selecting the proper surface functional groups. Experimental studies reveal that: (1) the NPs with surface decorated amphiphilic polymers can enter the cell interior through penetrating pathway; (2) the NPs with tunable stiffness and identical surface chemistry can be selectively accepted by the diseased cells according to their stiffness; and (3) the NPs grafted with pH-responsive polymers can be accepted or rejected by the cells due to the local pH environment. In addition, we show that computer simulations could be useful to understand the detailed physical mechanisms behind these phenomena and guide the design of next-generation NP-based drug carriers with high selectivity, affinity, and low toxicity. For example, the detailed free energy analysis and molecular dynamics simulation reveals that amphiphilic polymer-decorated NPs can penetrate into the cell membrane through the "snorkeling" mechanism, by maximizing the interaction energy between the hydrophobic ligands and lipid tails. We anticipate that this work will inspire future studies in the design of environment-responsive NPs for targeted drug delivery.
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Affiliation(s)
- Zhiqiang Shen
- Department of Mechanical Engineering, University of Connecticut, Storrs, CT 06269, USA.
| | - Mu-Ping Nieh
- Department of Chemical and Biomolecular Engineering, Department of Biomedical Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA.
| | - Ying Li
- Department of Mechanical Engineering, University of Connecticut, Storrs, CT 06269, USA.
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA.
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63
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Characterization of antimicrobial activity against Listeria and cytotoxicity of native melittin and its mutant variants. Colloids Surf B Biointerfaces 2016; 143:194-205. [PMID: 27011349 DOI: 10.1016/j.colsurfb.2016.03.037] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 03/10/2016] [Accepted: 03/13/2016] [Indexed: 01/30/2023]
Abstract
Antimicrobial peptides (AMPs) are relatively short peptides that have the ability to penetrate the cell membrane, form pores leading to cell death. This study compares both antimicrobial activity and cytotoxicity of native melittin and its two mutants, namely, melittin I17K (GIGAVLKVLTTGLPALKSWIKRKRQQ) with a higher charge and lower hydrophobicity and mutant G1I (IIGAVLKVLTTGLPALISWIKRKRQQ) of higher hydrophobicity. The antimicrobial activity against different strains of Listeria was investigated by bioassay, viability studies, fluorescence and transmission electron microscopy. Cytotoxicity was examined by lactate dehydrogenase (LDH) assay on mammalian Caco-2 cells. The minimum inhibitory concentration of native, mutant I17K, mutant G1I against Listeria monocytogenes F4244 was 0.315±0.008, 0.814±0.006 and 0.494±0.037μg/ml respectively, whereas the minimum bactericidal concentration values were 3.263±0.0034, 7.412±0.017 and 5.366±0.019μg/ml respectively. Lag time for inactivation of L. monocytogenes F4244 was observed at concentrations below 0.20 and 0.78μg/ml for native and mutant melittin I17K respectively. The antimicrobial activity against L. monocytogenes F4244 was in the order native>G1I>I17K. Native melittin was cytotoxic to mammalian Caco-2 cells above concentration of 2μg/ml, whereas the two mutants exhibited negligible cytotoxicity up to a concentration of 8μg/ml. Pore formation in cell wall/membrane was observed by transmission electron microscopy. Molecular dynamics (MD) simulation of native and its mutants indicated that (i) surface native melittin and G1I exhibited higher tendency to penetrate a mimic of bacterial cell membrane and (ii) transmembrane native and I17K formed water channel in mimics of bacterial and mammalian cell membranes.
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64
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Neale C, Pomès R. Sampling errors in free energy simulations of small molecules in lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2539-2548. [PMID: 26952019 DOI: 10.1016/j.bbamem.2016.03.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 12/14/2022]
Abstract
Free energy simulations are a powerful tool for evaluating the interactions of molecular solutes with lipid bilayers as mimetics of cellular membranes. However, these simulations are frequently hindered by systematic sampling errors. This review highlights recent progress in computing free energy profiles for inserting molecular solutes into lipid bilayers. Particular emphasis is placed on a systematic analysis of the free energy profiles, identifying the sources of sampling errors that reduce computational efficiency, and highlighting methodological advances that may alleviate sampling deficiencies. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Chris Neale
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, 110 8th St, Troy, New York 12180-3590, USA
| | - Régis Pomès
- Molecular Structure and Function, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada; Department of Biochemistry, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada.
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65
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Li ZL, Ding HM, Ma YQ. Interaction of peptides with cell membranes: insights from molecular modeling. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:083001. [PMID: 26828575 DOI: 10.1088/0953-8984/28/8/083001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The investigation of the interaction of peptides with cell membranes is the focus of active research. It can enhance the understanding of basic membrane functions such as membrane transport, fusion, and signaling processes, and it may shed light on potential applications of peptides in biomedicine. In this review, we will present current advances in computational studies on the interaction of different types of peptides with the cell membrane. Depending on the properties of the peptide, membrane, and external environment, the peptide-membrane interaction shows a variety of different forms. Here, on the basis of recent computational progress, we will discuss how different peptides could initiate membrane pores, translocate across the membrane, induce membrane endocytosis, produce membrane curvature, form fibrils on the membrane surface, as well as interact with functional membrane proteins. Finally, we will present a conclusion summarizing recent progress and providing some specific insights into future developments in this field.
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Affiliation(s)
- Zhen-lu Li
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, People's Republic of China
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66
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Lin M, Gessmann D, Naveed H, Liang J. Outer Membrane Protein Folding and Topology from a Computational Transfer Free Energy Scale. J Am Chem Soc 2016; 138:2592-601. [PMID: 26860422 DOI: 10.1021/jacs.5b10307] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Knowledge of the transfer free energy of amino acids from aqueous solution to a lipid bilayer is essential for understanding membrane protein folding and for predicting membrane protein structure. Here we report a computational approach that can calculate the folding free energy of the transmembrane region of outer membrane β-barrel proteins (OMPs) by combining an empirical energy function with a reduced discrete state space model. We quantitatively analyzed the transfer free energies of 20 amino acid residues at the center of the lipid bilayer of OmpLA. Our results are in excellent agreement with the experimentally derived hydrophobicity scales. We further exhaustively calculated the transfer free energies of 20 amino acids at all positions in the TM region of OmpLA. We found that the asymmetry of the Gram-negative bacterial outer membrane as well as the TM residues of an OMP determine its functional fold in vivo. Our results suggest that the folding process of an OMP is driven by the lipid-facing residues in its hydrophobic core, and its NC-IN topology is determined by the differential stabilities of OMPs in the asymmetrical outer membrane. The folding free energy is further reduced by lipid A and assisted by general depth-dependent cooperativities that exist between polar and ionizable residues. Moreover, context-dependency of transfer free energies at specific positions in OmpLA predict regions important for protein function as well as structural anomalies. Our computational approach is fast, efficient and applicable to any OMP.
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Affiliation(s)
- Meishan Lin
- Department of Bioengineering, University of Illinois at Chicago , Chicago, Illinois 60607, United States
| | - Dennis Gessmann
- Department of Bioengineering, University of Illinois at Chicago , Chicago, Illinois 60607, United States
| | - Hammad Naveed
- Department of Bioengineering, University of Illinois at Chicago , Chicago, Illinois 60607, United States
| | - Jie Liang
- Department of Bioengineering, University of Illinois at Chicago , Chicago, Illinois 60607, United States
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67
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Gumbart JC, Chipot C. Decrypting protein insertion through the translocon with free-energy calculations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1663-71. [PMID: 26896694 DOI: 10.1016/j.bbamem.2016.02.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/11/2016] [Accepted: 02/12/2016] [Indexed: 12/23/2022]
Abstract
Protein insertion into a membrane is a complex process involving numerous players. The most prominent of these players is the Sec translocon complex, a conserved protein-conducting channel present in the cytoplasmic membrane of bacteria and the membrane of the endoplasmic reticulum in eukaryotes. The last decade has seen tremendous leaps forward in our understanding of how insertion is managed by the translocon and its partners, coming from atomic-detailed structures, innovative experiments, and well-designed simulations. In this review, we discuss how experiments and simulations, hand-in-hand, teased out the secrets of the translocon-facilitated membrane insertion process. In particular, we focus on the role of free-energy calculations in elucidating membrane insertion. Amazingly, despite all its apparent complexity, protein insertion into membranes is primarily driven by simple thermodynamic and kinetic principles. This article is part of a Special Issue entitled: Membrane proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique and University of Illinois at Urbana-Champaign, UMR n° 7565, Université de Lorraine, B.P. 70239, 54506 Vandœuvre-lès-Nancy, France; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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68
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Cheng X, Jo S, Qi Y, Marassi FM, Im W. Solid-State NMR-Restrained Ensemble Dynamics of a Membrane Protein in Explicit Membranes. Biophys J 2016; 108:1954-62. [PMID: 25902435 DOI: 10.1016/j.bpj.2015.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/05/2015] [Accepted: 03/10/2015] [Indexed: 10/23/2022] Open
Abstract
Solid-state NMR has been used to determine the structures of membrane proteins in native-like lipid bilayer environments. Most structure calculations based on solid-state NMR observables are performed using simulated annealing with restrained molecular dynamics and an energy function, where all nonbonded interactions are represented by a single, purely repulsive term with no contributions from van der Waals attractive, electrostatic, or solvation energy. To our knowledge, this is the first application of an ensemble dynamics technique performed in explicit membranes that uses experimental solid-state NMR observables to obtain the refined structure of a membrane protein together with information about its dynamics and its interactions with lipids. Using the membrane-bound form of the fd coat protein as a model membrane protein and its experimental solid-state NMR data, we performed restrained ensemble dynamics simulations with different ensemble sizes in explicit membranes. For comparison, a molecular dynamics simulation of fd coat protein was also performed without any restraints. The average orientation of each protein helix is similar to a structure determined by traditional single-conformer approaches. However, their variations are limited in the resulting ensemble of structures with one or two replicas, as they are under the strong influence of solid-state NMR restraints. Although highly consistent with all solid-state NMR observables, the ensembles of more than two replicas show larger orientational variations similar to those observed in the molecular dynamics simulation without restraints. In particular, in these explicit membrane simulations, Lys(40), residing at the C-terminal side of the transmembrane helix, is observed to cause local membrane curvature. Therefore, compared to traditional single-conformer approaches in implicit environments, solid-state NMR restrained ensemble simulations in explicit membranes readily characterize not only protein dynamics but also protein-lipid interactions in detail.
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Affiliation(s)
- Xi Cheng
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Sunhwan Jo
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Yifei Qi
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | | | - Wonpil Im
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas.
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69
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Vorobyov I, Kim I, Chu ZT, Warshel A. Refining the treatment of membrane proteins by coarse-grained models. Proteins 2015; 84:92-117. [PMID: 26531155 DOI: 10.1002/prot.24958] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/19/2015] [Accepted: 10/23/2015] [Indexed: 01/19/2023]
Abstract
Obtaining a quantitative description of the membrane proteins stability is crucial for understanding many biological processes. However the advance in this direction has remained a major challenge for both experimental studies and molecular modeling. One of the possible directions is the use of coarse-grained models but such models must be carefully calibrated and validated. Here we use a recent progress in benchmark studies on the energetics of amino acid residue and peptide membrane insertion and membrane protein stability in refining our previously developed coarse-grained model (Vicatos et al., Proteins 2014;82:1168). Our refined model parameters were fitted and/or tested to reproduce water/membrane partitioning energetics of amino acid side chains and a couple of model peptides. This new model provides a reasonable agreement with experiment for absolute folding free energies of several β-barrel membrane proteins as well as effects of point mutations on a relative stability for one of those proteins, OmpLA. The consideration and ranking of different rotameric states for a mutated residue was found to be essential to achieve satisfactory agreement with the reference data.
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Affiliation(s)
- Igor Vorobyov
- Department of Chemistry, University of Southern California, Los Angeles, California, 90089-1062
| | - Ilsoo Kim
- Department of Chemistry, University of Southern California, Los Angeles, California, 90089-1062
| | - Zhen T Chu
- Department of Chemistry, University of Southern California, Los Angeles, California, 90089-1062
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California, 90089-1062
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70
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Rajapaksha SP, Pal N, Zheng D, Lu HP. Protein-fluctuation-induced water-pore formation in ion channel voltage-sensor translocation across a lipid bilayer membrane. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:052719. [PMID: 26651735 DOI: 10.1103/physreve.92.052719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Indexed: 06/05/2023]
Abstract
We have applied a combined fluorescence microscopy and single-ion-channel electric current recording approach, correlating with molecular dynamics (MD) simulations, to study the mechanism of voltage-sensor domain translocation across a lipid bilayer. We use the colicin Ia ion channel as a model system, and our experimental and simulation results show the following: (1) The open-close activity of an activated colicin Ia is not necessarily sensitive to the amplitude of the applied cross-membrane voltage when the cross-membrane voltage is around the resting potential of excitable membranes; and (2) there is a significant probability that the activation of colicin Ia occurs by forming a transient and fluctuating water pore of ∼15 Å diameter in the lipid bilayer membrane. The location of the water-pore formation is nonrandom and highly specific, right at the insertion site of colicin Ia charged residues in the lipid bilayer membrane, and the formation is intrinsically associated with the polypeptide conformational fluctuations and solvation dynamics. Our results suggest an interesting mechanistic pathway for voltage-sensitive ion channel activation, and specifically for translocation of charged polypeptide chains across the lipid membrane under a transmembrane electric field: the charged polypeptide domain facilitates the formation of hydrophilic water pore in the membrane and diffuses through the hydrophilic pathway across the membrane; i.e., the charged polypeptide chain can cross a lipid membrane without entering into the hydrophobic core of the lipid membrane but entirely through the aqueous and hydrophilic environment to achieve a cross-membrane translocation. This mechanism sheds light on the intensive and fundamental debate on how a hydrophilic and charged peptide domain diffuses across the biologically inaccessible high-energy barrier of the hydrophobic core of a lipid bilayer: The peptide domain does not need to cross the hydrophobic core to move across a lipid bilayer.
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Affiliation(s)
- Suneth P Rajapaksha
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
| | - Nibedita Pal
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
| | - Desheng Zheng
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
| | - H Peter Lu
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
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71
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Loo TW, Clarke DM. Mapping the Binding Site of the Inhibitor Tariquidar That Stabilizes the First Transmembrane Domain of P-glycoprotein. J Biol Chem 2015; 290:29389-401. [PMID: 26507655 PMCID: PMC4705942 DOI: 10.1074/jbc.m115.695171] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Indexed: 11/26/2022] Open
Abstract
ABC (ATP-binding cassette) transporters are clinically important because drug pumps like P-glycoprotein (P-gp, ABCB1) confer multidrug resistance and mutant ABC proteins are responsible for many protein-folding diseases such as cystic fibrosis. Identification of the tariquidar-binding site has been the subject of intensive molecular modeling studies because it is the most potent inhibitor and corrector of P-gp. Tariquidar is a unique P-gp inhibitor because it locks the pump in a conformation that blocks drug efflux but activates ATPase activity. In silico docking studies have identified several potential tariquidar-binding sites. Here, we show through cross-linking studies that tariquidar most likely binds to sites within the transmembrane (TM) segments located in one wing or at the interface between the two wings (12 TM segments form 2 divergent wings). We then introduced arginine residues at all positions in the 12 TM segments (223 mutants) of P-gp. The rationale was that a charged residue in the drug-binding pocket would disrupt hydrophobic interaction with tariquidar and inhibit its ability to rescue processing mutants or stimulate ATPase activity. Arginines introduced at 30 positions significantly inhibited tariquidar rescue of a processing mutant and activation of ATPase activity. The results suggest that tariquidar binds to a site within the drug-binding pocket at the interface between the TM segments of both structural wings. Tariquidar differed from other drug substrates, however, as it stabilized the first TM domain. Stabilization of the first TM domain appears to be a key mechanism for high efficiency rescue of ABC processing mutants that cause disease.
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Affiliation(s)
- Tip W Loo
- From the Departments of Medicine and Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David M Clarke
- From the Departments of Medicine and Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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72
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Neale C, Huang K, García AE, Tristram-Nagle S. Penetration of HIV-1 Tat47-57 into PC/PE Bilayers Assessed by MD Simulation and X-ray Scattering. MEMBRANES 2015; 5:473-94. [PMID: 26402709 PMCID: PMC4584291 DOI: 10.3390/membranes5030473] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 09/09/2015] [Indexed: 01/07/2023]
Abstract
The interactions of the basic, cell-penetrating region (Y47GRKKRRQRRR57) of the HIV-1 Tat protein with dioleoylphosphatidylcholine (DOPC) bilayers were previously assessed by comparing experimental X-ray diffuse scattering with atomistic molecular dynamics simulations. Here, we extend this investigation by evaluating the influence of phosphatidylethanolamine (PE) lipids. Using experimental bilayer form factors derivedfrom X-ray diffuse scattering data as a guide, our simulations indicate that Tat peptides localize close to the carbonyl-glycerol group in the headgroup region of bilayers composed of either DOPC or DOPC:DOPE (1:1) lipid. Our results also suggest that Tat peptides may more frequently insert into the hydrophobic core of bilayers composed of PC:PE (1:1) lipids than into bilayers composed entirely of PC lipids. PE lipids may facilitate peptide translocation across a lipid bilayer by stabilizing intermediate states in which hydrated peptides span the bilayer.
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Affiliation(s)
- Chris Neale
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY 12180-3590, USA.
| | - Kun Huang
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY 12180-3590, USA.
| | - Angel E García
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY 12180-3590, USA.
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY 12180-3590, USA.
| | - Stephanie Tristram-Nagle
- Biological Physics Group, Department of Physics, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.
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73
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Marcoline FV, Bethel N, Guerriero CJ, Brodsky JL, Grabe M. Membrane Protein Properties Revealed through Data-Rich Electrostatics Calculations. Structure 2015; 23:1526-1537. [PMID: 26118532 DOI: 10.1016/j.str.2015.05.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 04/09/2015] [Accepted: 05/02/2015] [Indexed: 01/29/2023]
Abstract
The electrostatic properties of membrane proteins often reveal many of their key biophysical characteristics, such as ion channel selectivity and the stability of charged membrane-spanning segments. The Poisson-Boltzmann (PB) equation is the gold standard for calculating protein electrostatics, and the software APBSmem enables the solution of the PB equation in the presence of a membrane. Here, we describe significant advances to APBSmem, including full automation of system setup, per-residue energy decomposition, incorporation of PDB2PQR, calculation of membrane-induced pKa shifts, calculation of non-polar energies, and command-line scripting for large-scale calculations. We highlight these new features with calculations carried out on a number of membrane proteins, including the recently solved structure of the ion channel TRPV1 and a large survey of 1,614 membrane proteins of known structure. This survey provides a comprehensive list of residues with large electrostatic penalties for being embedded in the membrane, potentially revealing interesting functional information.
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Affiliation(s)
- Frank V Marcoline
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Neville Bethel
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA; Integrative Program in Quantitative Biology, University of California, San Francisco, CA 94158, USA
| | | | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Michael Grabe
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
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74
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Lyu Y, Zhu X, Xiang N, Narsimhan G. Molecular Dynamics Study of Pore Formation by Melittin in a 1,2-Dioleoyl-sn-glycero-3-phosphocholine and 1,2-Di(9Z-octadecenoyl)-sn-glycero-3-phospho-(1′-rac-glycerol) Mixed Lipid Bilayer. Ind Eng Chem Res 2015. [DOI: 10.1021/acs.iecr.5b01217] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuan Lyu
- Department of Agricultural and Biological Engineering and ‡Research Computing,
Rosen Center for Advanced Computing, Purdue University, West Lafayette, Indiana 47907, United States
| | - Xiao Zhu
- Department of Agricultural and Biological Engineering and ‡Research Computing,
Rosen Center for Advanced Computing, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ning Xiang
- Department of Agricultural and Biological Engineering and ‡Research Computing,
Rosen Center for Advanced Computing, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ganesan Narsimhan
- Department of Agricultural and Biological Engineering and ‡Research Computing,
Rosen Center for Advanced Computing, Purdue University, West Lafayette, Indiana 47907, United States
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75
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Supunyabut C, Fuklang S, Sompornpisut P. Continuum electrostatic approach for evaluating positions and interactions of proteins in a bilayer membrane. J Mol Graph Model 2015; 59:81-91. [DOI: 10.1016/j.jmgm.2015.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 04/02/2015] [Accepted: 04/03/2015] [Indexed: 01/08/2023]
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76
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De Marothy MT, Elofsson A. Marginally hydrophobic transmembrane α-helices shaping membrane protein folding. Protein Sci 2015; 24:1057-74. [PMID: 25970811 DOI: 10.1002/pro.2698] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 04/24/2015] [Indexed: 01/12/2023]
Abstract
Cells have developed an incredible machinery to facilitate the insertion of membrane proteins into the membrane. While we have a fairly good understanding of the mechanism and determinants of membrane integration, more data is needed to understand the insertion of membrane proteins with more complex insertion and folding pathways. This review will focus on marginally hydrophobic transmembrane helices and their influence on membrane protein folding. These weakly hydrophobic transmembrane segments are by themselves not recognized by the translocon and therefore rely on local sequence context for membrane integration. How can such segments reside within the membrane? We will discuss this in the light of features found in the protein itself as well as the environment it resides in. Several characteristics in proteins have been described to influence the insertion of marginally hydrophobic helices. Additionally, the influence of biological membranes is significant. To begin with, the actual cost for having polar groups within the membrane may not be as high as expected; the presence of proteins in the membrane as well as characteristics of some amino acids may enable a transmembrane helix to harbor a charged residue. The lipid environment has also been shown to directly influence the topology as well as membrane boundaries of transmembrane helices-implying a dynamic relationship between membrane proteins and their environment.
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Affiliation(s)
- Minttu T De Marothy
- Department of Biochemistry and Biophysics Science for Life Laboratory, Stockholm University, Solna, SE-171 21, Sweden
| | - Arne Elofsson
- Department of Biochemistry and Biophysics Science for Life Laboratory, Stockholm University, Solna, SE-171 21, Sweden
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77
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Cardenas AE, Shrestha R, Webb LJ, Elber R. Membrane permeation of a peptide: it is better to be positive. J Phys Chem B 2015; 119:6412-20. [PMID: 25941740 DOI: 10.1021/acs.jpcb.5b02122] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A joint experimental and computational study investigates the translocation of a tryptophan molecule through a phospholipid membrane. Time dependent spectroscopy of the tryptophan side chain determines the rate of permeation into 150 nm phospholipid vesicles. Atomically detailed simulations are conducted to calculate the free energy profiles and the permeation coefficient. Different charging conditions of the peptide (positive, negative, or zwitterion) are considered. Both experiment and simulation reproduce the qualitative trend and suggest that the fastest permeation is when the tryptophan is positively charged. The permeation mechanism, which is revealed by molecular dynamics simulations, is of a translocation assisted by a local defect. The influence of long-range electrostatic interactions, such as the membrane dipole potential on the permeation process, is not significant.
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Affiliation(s)
- Alfredo E Cardenas
- †Institute for Computational Engineering and Sciences and ‡Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Rebika Shrestha
- †Institute for Computational Engineering and Sciences and ‡Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lauren J Webb
- †Institute for Computational Engineering and Sciences and ‡Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Ron Elber
- †Institute for Computational Engineering and Sciences and ‡Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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78
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Van Lehn RC, Alexander-Katz A. Pathway for insertion of amphiphilic nanoparticles into defect-free lipid bilayers from atomistic molecular dynamics simulations. SOFT MATTER 2015; 11:3165-75. [PMID: 25757187 DOI: 10.1039/c5sm00287g] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Gold nanoparticles (NPs) have been increasingly used in biological applications that involve potential contact with cellular membranes. As a result, it is essential to gain a physical understanding of NP-membrane interactions to guide the design of next-generation bioactive nanoparticles. In previous work, we showed that charged, amphiphilic NPs can fuse with lipid bilayers after contact between protruding solvent-exposed lipid tails and the NP monolayer. Fusion was only observed at the high-curvature edges of large bilayer defects, but not in low-curvature regions where protrusions are rarely observed. Here, we use atomistic molecular dynamics simulations to show that the same NPs can also fuse with low-curvature bilayers in the absence of defects if NP-protrusion contact occurs, generalizing the results of our previous work. Insertion proceeds without applying biasing forces to the NP, driven by the hydrophobic effect, and involves the transient generation of bilayer curvature. We further find that NPs with long hydrophobic ligands can insert a single ligand into the bilayer core in a manner similar to the binding of peripheral proteins. Such anchoring may precede insertion, revealing potential methods for engineering NP monolayers to enhance NP-bilayer fusion in systems with a low likelihood of lipid tail protrusions. These results reveal new pathways for NP-bilayer fusion and provide fundamental insight into behavior at the nano-bio interface.
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Affiliation(s)
- Reid C Van Lehn
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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79
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Yan L, de Jesus AJ, Tamura R, Li V, Cheng K, Yin H. Curvature sensing MARCKS-ED peptides bind to membranes in a stereo-independent manner. J Pept Sci 2015; 21:577-585. [PMID: 25851418 DOI: 10.1002/psc.2772] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/16/2015] [Accepted: 02/18/2015] [Indexed: 12/21/2022]
Abstract
Membrane curvature and lipid composition plays a critical role in interchanging of matter and energy in cells. Peptide curvature sensors are known to activate signaling pathways and promote molecular transport across cell membranes. Recently, the 25-mer MARCKS-ED peptide, which is derived from the effector domain of the myristoylated alanine-rich C kinase substrate protein, has been reported to selectively recognize highly curved membrane surfaces. Our previous studies indicated that the naturally occurring L-MARCKS-ED peptide could simultaneously detect both phosphatidylserine and curvature. Here, we demonstrate that D-MARCKS-ED, composed by unnatural D-amino acids, has the same activities as its enantiomer, L-MARCKS-ED, as a curvature and lipid sensor. An atomistic molecular dynamics simulation suggests that D-MARCKS-ED may change from linear to a boat conformation upon binding to the membrane. Comparable enhancement of fluorescence intensity was observed between D- and L-MARCKS-ED peptides, indicating similar binding affinities. Meanwhile, circular dichroism spectra of D- and L-MARCKS-ED are almost symmetrical both in the presence and absence of liposomes. These results suggest similar behavior of artificial D- and natural L-MARCKS-ED peptides when binding to curved membranes. Our studies may contribute to further understanding of how MARCKS-ED senses membrane curvature as well as provide a new direction to develop novel membrane curvature probes.
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Affiliation(s)
- Lei Yan
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, China, 100082
| | - Armando Jerome de Jesus
- Department of Chemistry and Biochemistry, the BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309-0596, USA
| | - Ryo Tamura
- Department of Chemistry and Biochemistry, the BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309-0596, USA
| | - Victoria Li
- Department of Chemistry and Biochemistry, the BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309-0596, USA
| | - Kui Cheng
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, China, 100082
| | - Hang Yin
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, China, 100082.,Department of Chemistry and Biochemistry, the BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309-0596, USA
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80
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Abstract
![]()
In
this work, we apply the recently developed constant pH molecular
dynamics technique to study protonation equilibria of titratable side
chains in the context of simple transmembrane (TM) helices and explore
the effect of pH on their configurations in membrane bilayers. We
observe that, despite a significant shift toward neutral states, considerable
population of different side chains stay in the charged state that
give rise to pKa values around 9.6 for
Asp and Glu and 4.5 to 6 for His and Lys side chains, respectively.
These charged states are highly stabilized by favorable interactions
between head groups, water molecules, and the charged side chains
that are facilitated by substantial changes in the configuration of
the peptides. The pH dependent configurations and the measured pKa values are in good agreement with relatively
recent solid state NMR measurements. Our results presented here demonstrate
that all-atom constant pH molecular dynamics can be applied to membrane
proteins and peptides to obtain reliable pKa values and pH dependent behavior for these systems.
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Affiliation(s)
- Afra Panahi
- †Department of Chemistry and ‡Biophysics Program, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan, 48109, United States
| | - Charles L Brooks
- †Department of Chemistry and ‡Biophysics Program, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan, 48109, United States
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81
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Sun D, Forsman J, Woodward CE. Evaluating Force Fields for the Computational Prediction of Ionized Arginine and Lysine Side-Chains Partitioning into Lipid Bilayers and Octanol. J Chem Theory Comput 2015; 11:1775-91. [PMID: 26574387 DOI: 10.1021/ct501063a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Abundant peptides and proteins containing arginine (Arg) and lysine (Lys) amino acids can apparently permeate cell membranes with ease. However, the mechanisms by which these peptides and proteins succeed in traversing the free energy barrier imposed by cell membranes remain largely unestablished. Precise thermodynamic studies (both theoretical and experimental) on the interactions of Arg and Lys residues with model lipid bilayers can provide valuable clues to the efficacy of these cationic peptides and proteins. We have carried out molecular dynamics simulations to calculate the interactions of ionized Arg and Lys side-chains with the zwitterionic 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid bilayer for 10 widely used lipid/protein force fields: CHARMM36/CHARMM36, SLIPID/AMBER99SB-ILDN, OPLS-AA/OPLS-AA, Berger/OPLS-AA, Berger/GROMOS87, Berger/GROMOS53A6, GROMOS53A6/GROMOS53A6, nonpolarizable MARTINI, polarizable MARTINI, and BMW MARTINI. We performed umbrella sampling simulations to obtain the potential of mean force for Arg and Lys side-chains partitioning from water to the bilayer interior. We found significant differences between the force fields, both for the interactions between side-chains and bilayer surface, as well as the free energy cost for placing the side-chain at the center of the bilayer. These simulation results were compared with the Wimley-White interfacial scale. We also calculated the free energy cost for transferring ionized Arg and Lys side-chains from water to both dry and wet octanol. Our simulations reveal rapid diffusion of water molecules into octanol whereby the equilibrium mole fraction of water in the wet octanol phase was ∼25%. Surprisingly, our free energy calculations found that the high water content in wet octanol lowered the water-to-octanol partitioning free energies for cationic residues by only 0.6 to 0.7 kcal/mol.
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Affiliation(s)
- Delin Sun
- School of Physical, Environmental and Mathematical Sciences, University of New South Wales , Canberra ACT 2600, Australia
| | - Jan Forsman
- Theoretical Chemistry, Chemical Centre, Lund University , P.O. Box 124, S-221 00 Lund, Sweden
| | - Clifford E Woodward
- School of Physical, Environmental and Mathematical Sciences, University of New South Wales , Canberra ACT 2600, Australia
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82
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Tsoneva Y, Jonker HRA, Wagner M, Tadjer A, Lelle M, Peneva K, Ivanova A. Molecular Structure and Pronounced Conformational Flexibility of Doxorubicin in Free and Conjugated State within a Drug–Peptide Compound. J Phys Chem B 2015; 119:3001-13. [DOI: 10.1021/jp509320q] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yana Tsoneva
- University of Sofia, Faculty of Chemistry and Pharmacy,
Department of Physical Chemistry, 1 James Bourchier Avenue, 1164 Sofia, Bulgaria
| | - Hendrik R. A. Jonker
- Goethe University Frankfurt, Institute for Organic
Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Max von Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Manfred Wagner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Alia Tadjer
- University of Sofia, Faculty of Chemistry and Pharmacy,
Department of Physical Chemistry, 1 James Bourchier Avenue, 1164 Sofia, Bulgaria
| | - Marco Lelle
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kalina Peneva
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Anela Ivanova
- University of Sofia, Faculty of Chemistry and Pharmacy,
Department of Physical Chemistry, 1 James Bourchier Avenue, 1164 Sofia, Bulgaria
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83
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Baker CM. Polarizable force fields for molecular dynamics simulations of biomolecules. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2015. [DOI: 10.1002/wcms.1215] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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84
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Porasso RD, Ale NM, Ciocco Aloia F, Masone D, Del Pópolo MG, Ben Altabef A, Gomez-Zavaglia A, Diaz SB, Vila JA. Interaction of glycine, lysine, proline and histidine with dipalmitoylphosphatidylcholine lipid bilayers: a theoretical and experimental study. RSC Adv 2015. [DOI: 10.1039/c5ra03236a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The interaction of unblocked glycine, lysine, proline and histidine with a DPPC bilayer was assessed using extensive atomistic molecular dynamics simulations.
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Affiliation(s)
- Rodolfo D. Porasso
- Instituto de Matemática Aplicada San Luis (IMASL)
- CONICET
- Universidad Nacional de San Luis
- Argentina
| | - Norma M. Ale
- Instituto de Química Física
- Facultad de Bioquímica, Química y Farmacia
- U. N. T
- San Lorenzo 456
- Argentina
| | - Facundo Ciocco Aloia
- CONICET
- Facultad de Ciencias Exactas y Naturales
- Universidad Nacional de Cuyo
- Mendoza
- Argentina
| | - Diego Masone
- CONICET
- Facultad de Ciencias Exactas y Naturales
- Universidad Nacional de Cuyo
- Mendoza
- Argentina
| | - Mario G. Del Pópolo
- CONICET
- Facultad de Ciencias Exactas y Naturales
- Universidad Nacional de Cuyo
- Mendoza
- Argentina
| | - Aida Ben Altabef
- Instituto de Química Física
- Facultad de Bioquímica, Química y Farmacia
- U. N. T
- San Lorenzo 456
- Argentina
| | - Andrea Gomez-Zavaglia
- Center for Research and Development in Food Cryotechnology (CIDCA, CCT-CONICET, La Plata)
- Argentina
| | - Sonia B. Diaz
- Instituto de Química Física
- Facultad de Bioquímica, Química y Farmacia
- U. N. T
- San Lorenzo 456
- Argentina
| | - Jorge A. Vila
- Instituto de Matemática Aplicada San Luis (IMASL)
- CONICET
- Universidad Nacional de San Luis
- Argentina
- Baker Laboratory of Chemistry and Chemical Biology
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85
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Van Lehn RC, Alexander-Katz A. Membrane-Embedded Nanoparticles Induce Lipid Rearrangements Similar to Those Exhibited by Biological Membrane Proteins. J Phys Chem B 2014; 118:12586-98. [DOI: 10.1021/jp506239p] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Reid C. Van Lehn
- Department of Materials Science
and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alfredo Alexander-Katz
- Department of Materials Science
and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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86
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Spontaneous transmembrane helix insertion thermodynamically mimics translocon-guided insertion. Nat Commun 2014; 5:4863. [PMID: 25204588 PMCID: PMC4161982 DOI: 10.1038/ncomms5863] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 07/30/2014] [Indexed: 01/01/2023] Open
Abstract
The favorable transfer free energy for a transmembrane (TM) α-helix between the aqueous phase and lipid bilayer underlies the stability of membrane proteins. However, the connection between the energetics and process of membrane protein assembly by the Sec61/SecY translocon complex in vivo is not clear. Here, we directly determine the partitioning free energies of a family of designed peptides using three independent approaches: an experimental microsomal Sec61 translocon assay, a biophysical (spectroscopic) characterization of peptide insertion into hydrated planar lipid bilayer arrays, and an unbiased atomic-detail equilibrium folding-partitioning molecular dynamics simulation. Remarkably, the measured free energies of insertion are quantitatively similar for all three approaches. The molecular dynamics simulations show that TM helix insertion involves equilibrium with the membrane interface, suggesting that the interface may play a role in translocon-guided insertion.
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87
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Biophysical investigations with MARCKS-ED: dissecting the molecular mechanism of its curvature sensing behaviors. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:3137-3144. [PMID: 25195712 DOI: 10.1016/j.bbamem.2014.08.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 08/24/2014] [Accepted: 08/27/2014] [Indexed: 11/21/2022]
Abstract
Curved membranes are a common and important attribute in cells. Protein and peptide curvature sensors are known to activate signaling pathways, initiate vesicle budding, trigger membrane fusion, and facilitate molecular transport across cell membranes. Nonetheless, there is little understanding how these proteins and peptides achieve preferential binding of different membrane curvatures. The current study is to elucidate specific factors required for curvature sensing. As a model system, we employed a recently identified peptide curvature sensor, MARCKS-ED, derived from the effector domain of the myristoylated alanine-rich C kinase substrate protein, for these biophysical investigations. An atomistic molecular dynamics (MD) simulation suggested an important role played by the insertion of the Phe residues within MARCKS-ED. To test these observations from our computational simulations, we performed electron paramagnetic resonance (EPR) studies to determine the insertion depth of MARCKS-ED into differently curved membrane bilayers. Next, studies with varied lipid compositions revealed their influence on curvature sensing by MARCKS-ED, suggesting contributions from membrane fluidity, rigidity, as well as various lipid structures. Finally, we demonstrated that the curvature sensing by MARCKS-ED is configuration independent. In summary, our studies have shed further light to the understanding of how MARCKS-ED differentiates between membrane curvatures, which may be generally applicable to protein curvature sensing behavior.
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88
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Bennett WFD, Sapay N, Tieleman DP. Atomistic simulations of pore formation and closure in lipid bilayers. Biophys J 2014; 106:210-9. [PMID: 24411253 DOI: 10.1016/j.bpj.2013.11.4486] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/13/2013] [Accepted: 11/25/2013] [Indexed: 10/25/2022] Open
Abstract
Cellular membranes separate distinct aqueous compartments, but can be breached by transient hydrophilic pores. A large energetic cost prevents pore formation, which is largely dependent on the composition and structure of the lipid bilayer. The softness of bilayers and the disordered structure of pores make their characterization difficult. We use molecular-dynamics simulations with atomistic detail to study the thermodynamics, kinetics, and mechanism of pore formation and closure in DLPC, DMPC, and DPPC bilayers, with pore formation free energies of 17, 45, and 78 kJ/mol, respectively. By using atomistic computer simulations, we are able to determine not only the free energy for pore formation, but also the enthalpy and entropy, which yields what is believed to be significant new insights in the molecular driving forces behind membrane defects. The free energy cost for pore formation is due to a large unfavorable entropic contribution and a favorable change in enthalpy. Changes in hydrogen bonding patterns occur, with increased lipid-water interactions, and fewer water-water hydrogen bonds, but the total number of overall hydrogen bonds is constant. Equilibrium pore formation is directly observed in the thin DLPC lipid bilayer. Multiple long timescale simulations of pore closure are used to predict pore lifetimes. Our results are important for biological applications, including the activity of antimicrobial peptides and a better understanding of membrane protein folding, and improve our understanding of the fundamental physicochemical nature of membranes.
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Affiliation(s)
- W F Drew Bennett
- University of Calgary, Department of Biological Sciences and Centre for Molecular Simulation, Calgary, Alberta, Canada
| | - Nicolas Sapay
- University of Calgary, Department of Biological Sciences and Centre for Molecular Simulation, Calgary, Alberta, Canada
| | - D Peter Tieleman
- University of Calgary, Department of Biological Sciences and Centre for Molecular Simulation, Calgary, Alberta, Canada.
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89
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Protein arcs may form stable pores in lipid membranes. Biophys J 2014; 106:154-61. [PMID: 24411247 DOI: 10.1016/j.bpj.2013.11.4490] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 11/04/2013] [Accepted: 11/22/2013] [Indexed: 01/22/2023] Open
Abstract
Electron microscopy and atomic force microscopy images of cholesterol-dependent cytolysins and related proteins that form large pores in lipid membranes have revealed the presence of incomplete rings, or arcs. Some evidence indicates that these arcs are inserted into the membrane and induce membrane leakage, but other experiments seem to refute that. Could such pores, only partially lined by protein, be kinetically and thermodynamically stable? How would the lipids be structured in such a pore? Using the antimicrobial peptide protegrin-1 as a model, we test the stability of pores only partially lined by peptide using all-atom molecular dynamics simulations in POPC and POPE/POPG membranes. The data show that, whereas pure lipid pores close rapidly, pores partially lined by protegrin arcs are stable for at least 300 ns. Estimates of the thermodynamic stability of these arcs using line tension data and implicit solvent calculations show that these arcs can be marginally stable in both zwitterionic and anionic membranes. Arcs provide an explanation for the observed ion selectivity in protegrin electrophysiology experiments and could possibly be involved in other membrane permeabilization processes where lipids are thought to participate, such as those induced by antimicrobial peptides and colicins, as well as the Bax apoptotic pore.
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90
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Bennett WFD, Tieleman DP. The importance of membrane defects-lessons from simulations. Acc Chem Res 2014; 47:2244-51. [PMID: 24892900 DOI: 10.1021/ar4002729] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The defects and pores within lipid membranes are scientifically interesting and have a number of biological applications. Although lipid bilayers are extremely thin hydrophobic barriers, just ∼3 nm thick, they include diverse chemistry and have complex structures. Bilayers are soft and dynamic, and as a result, they can bend and deform in response to different stimuli by means of structural changes in their component lipids. Though defects occur within these structures, their transience and small size have made it difficult to characterize them. However, with recent advances in computer power and computational modeling techniques, researchers can now use simulations as a powerful tool to probe the mechanism and energies of defect and pore formation in a number of situations. In this Account, we present results from our detailed molecular dynamics computer simulations of hydrophilic pores and related defects in lipid bilayers at an atomistic level. Electroporation can be used to increase the permeability of cellular membranes, with potential therapeutic applications. Atomistic simulations of electroporation have illustrated the molecular details of this process, including the importance of water dipole interactions at the water-membrane interface. Characterization of the lipid-protein interactions provides an important tool for understanding transmembrane protein structure and thermodynamic stability. Atomistic simulations give a detailed picture of the free energies of model peptides and side chains in lipid membranes; the energetic cost of defect formation strongly influences the energies of interactions between lipids and polar and charged residues. Many antimicrobial peptides form hydrophilic pores in lipid membranes, killing bacteria or cancer cells. On the basis of simulation data, at least some of these peptides form defects and pores near the center of the bilayer, with a common disordered structure where hydrated headgroups form an approximately toroidal shape. The localization and trafficking of lipids supports general membrane structure and a number of important signaling cascades, such as those involving ceramide, diacylglycerol, and cholesterol. Atomistic simulations have determined the rates and free energies of lipid flip-flop. During the flip-flop of most phosphatidylcholine lipids, a hydrophilic pore forms when the headgroup moves near the center of the bilayer. Simulations have provided novel insight into many features of defects and pores in lipid membranes. Simulation data from very different systems and models show how water penetration and defect formation can determine the free energies of many membrane processes. Bilayers can deform and allow transient defects and pores when exposed to a diverse range of stimuli. Future work will explore many aspects of membrane defects with increased resolution and scope, including the study of more complex lipid mixtures, membrane domains, and large-scale membrane remodeling. Such studies will examine processes including vesicle budding and fusion, non-bilayer lipid phases, and interactions between lipid bilayers and other biomolecules. Simulations provide information that complements experimental studies, allowing microscopic insight into experimental observations and suggesting novel hypotheses and experiments. These studies should enable a deeper understanding of the role of lipid bilayers in cellular biology and support the development of future lipid-based biotechnology.
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Affiliation(s)
- W. F. Drew Bennett
- Department of Biological
Sciences and Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - D. Peter Tieleman
- Department of Biological
Sciences and Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
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91
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Hausrath AC. Model for coupled insertion and folding of membrane-spanning proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:022707. [PMID: 25215758 DOI: 10.1103/physreve.90.022707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Indexed: 06/03/2023]
Abstract
Current understanding of the forces directing the folding of integral membrane proteins is very limited compared to the detailed picture available for water-soluble proteins. While mechanistic studies of the folding process in vitro have been conducted for only a small number of membrane proteins, the available evidence indicates that their folding process is thermodynamically driven like that of soluble proteins. In vivo, however, the majority of integral membrane proteins are installed in membranes by dedicated machinery, suggesting that the cellular systems may act to facilitate and regulate the spontaneous physical process of folding. Both the in vitro folding process and the in vivo pathway must navigate an energy landscape dominated by the energetically favorable burial of hydrophobic segments in the membrane interior and the opposition to folding due to the need for passage of polar segments across the membrane. This manuscript describes a simple, exactly solvable model which incorporates these essential features of membrane protein folding. The model is used to compare the folding time under conditions which depict both the in vitro and in vivo pathways. It is proposed that the cellular complexes responsible for insertion of membrane proteins act by lowering the energy barrier for passage of polar regions through the membrane, thereby allowing the chain to more rapidly achieve the folded state.
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Affiliation(s)
- Andrew C Hausrath
- Department of Chemistry and Biochemistry and Program in Applied Mathematics, University of Arizona, Tucson, Arizona 85721, USA
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92
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Van Lehn RC, Ricci M, Silva PH, Andreozzi P, Reguera J, Voïtchovsky K, Stellacci F, Alexander-Katz A. Lipid tail protrusions mediate the insertion of nanoparticles into model cell membranes. Nat Commun 2014; 5:4482. [DOI: 10.1038/ncomms5482] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 06/23/2014] [Indexed: 12/30/2022] Open
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93
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Virkki MT, Agrawal N, Edsbäcker E, Cristobal S, Elofsson A, Kauko A. Folding of Aquaporin 1: multiple evidence that helix 3 can shift out of the membrane core. Protein Sci 2014; 23:981-92. [PMID: 24777974 PMCID: PMC4088982 DOI: 10.1002/pro.2483] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 04/23/2014] [Accepted: 04/24/2014] [Indexed: 12/29/2022]
Abstract
The folding of most integral membrane proteins follows a two-step process: initially, individual transmembrane helices are inserted into the membrane by the Sec translocon. Thereafter, these helices fold to shape the final conformation of the protein. However, for some proteins, including Aquaporin 1 (AQP1), the folding appears to follow a more complicated path. AQP1 has been reported to first insert as a four-helical intermediate, where helix 2 and 4 are not inserted into the membrane. In a second step, this intermediate is folded into a six-helical topology. During this process, the orientation of the third helix is inverted. Here, we propose a mechanism for how this reorientation could be initiated: first, helix 3 slides out from the membrane core resulting in that the preceding loop enters the membrane. The final conformation could then be formed as helix 2, 3, and 4 are inserted into the membrane and the reentrant regions come together. We find support for the first step in this process by showing that the loop preceding helix 3 can insert into the membrane. Further, hydrophobicity curves, experimentally measured insertion efficiencies and MD-simulations suggest that the barrier between these two hydrophobic regions is relatively low, supporting the idea that helix 3 can slide out of the membrane core, initiating the rearrangement process.
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Affiliation(s)
- Minttu T Virkki
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm UniversitySolna, SE-171 21, Sweden
| | - Nitin Agrawal
- Department of Biosciences, Biochemistry, Åbo AkademiTurku, FI-20520, Finland
| | - Elin Edsbäcker
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm UniversitySolna, SE-171 21, Sweden
| | - Susana Cristobal
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Health Science, Linköping UniversityLinköping, Sweden
- Department of Physiology, IKERBASQUE, Basque Foundation for Science, Faculty of Medicine and Dentistry, University of the Basque CountryLeioa, Spain
| | - Arne Elofsson
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm UniversitySolna, SE-171 21, Sweden
| | - Anni Kauko
- Department of Biosciences, Biochemistry, Åbo AkademiTurku, FI-20520, Finland
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94
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Van Lehn RC, Alexander-Katz A. Fusion of Ligand-Coated Nanoparticles with Lipid Bilayers: Effect of Ligand Flexibility. J Phys Chem A 2014; 118:5848-56. [DOI: 10.1021/jp411662c] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Reid C. Van Lehn
- Department of Materials Science
and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alfredo Alexander-Katz
- Department of Materials Science
and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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95
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Affiliation(s)
- Karen G. Fleming
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218;
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96
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Latorraca NR, Callenberg KM, Boyle JP, Grabe M. Continuum approaches to understanding ion and peptide interactions with the membrane. J Membr Biol 2014; 247:395-408. [PMID: 24652510 PMCID: PMC4096575 DOI: 10.1007/s00232-014-9646-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 02/22/2014] [Indexed: 12/22/2022]
Abstract
Experimental and computational studies have shown that cellular membranes deform to stabilize the inclusion of transmembrane (TM) proteins harboring charge. Recent analysis suggests that membrane bending helps to expose charged and polar residues to the aqueous environment and polar head groups. We previously used elasticity theory to identify membrane distortions that minimize the insertion of charged TM peptides into the membrane. Here, we extend our work by showing that it also provides a novel, computationally efficient method for exploring the energetics of ion and small peptide penetration into membranes. First, we show that the continuum method accurately reproduces energy profiles and membrane shapes generated from molecular simulations of bare ion permeation at a fraction of the computational cost. Next, we demonstrate that the dependence of the ion insertion energy on the membrane thickness arises primarily from the elastic properties of the membrane. Moreover, the continuum model readily provides a free energy decomposition into components not easily determined from molecular dynamics. Finally, we show that the energetics of membrane deformation strongly depend on membrane patch size both for ions and peptides. This dependence is particularly strong for peptides based on simulations of a known amphipathic, membrane binding peptide from the human pathogen Toxoplasma gondii. In total, we address shortcomings and advantages that arise from using a variety of computational methods in distinct biological contexts.
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Affiliation(s)
- Naomi R Latorraca
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
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97
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Wang Y, Hu D, Wei D. Transmembrane Permeation Mechanism of Charged Methyl Guanidine. J Chem Theory Comput 2014; 10:1717-26. [DOI: 10.1021/ct400738r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yukun Wang
- State Key Laboratory of Microbial Metabolism
and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Dan Hu
- Department
of Mathematics, Institute of Natural Sciences, and MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Dongqing Wei
- State Key Laboratory of Microbial Metabolism
and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
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98
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Hu Y, Liu X, Sinha SK, Patel S. Translocation thermodynamics of linear and cyclic nonaarginine into model DPPC bilayer via coarse-grained molecular dynamics simulation: implications of pore formation and nonadditivity. J Phys Chem B 2014; 118:2670-82. [PMID: 24506488 PMCID: PMC3983342 DOI: 10.1021/jp412600e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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Structural mechanisms
and underlying thermodynamic determinants
of efficient internalization of charged cationic peptides (cell-penetrating
peptides, CPPs) such as TAT, polyarginine, and their variants, into
cells, cellular constructs, and model membrane/lipid bilayers (large
and giant unilamellar or multilamelar vesicles) continue to garner
significant attention. Two widely held views on the translocation
mechanism center on endocytotic and nonendocytotic (diffusive) processes.
Espousing the view of a purely diffusive internalization process (supported
by recent experimental evidence, [Säälik, P.; et al. J. Controlled Release2011, 153, 117–125]), we consider the underlying free energetics of
the translocation of a nonaarginine peptide (Arg9) into
a model DPPC bilayer. In the case of the Arg9 cationic
peptide, recent experiments indicate a higher internalization efficiency
of the cyclic structure (cyclic Arg9) relative to the linear
conformer. Furthermore, recent all-atom resolution molecular dynamics
simulations of cyclic Arg9 [Huang, K.; et al. Biophys.
J., 2013, 104, 412–420]
suggested a critical stabilizing role of water- and lipid-constituted
pores that form within the bilayer as the charged Arg9 translocates
deep into the bilayer center. Herein, we use umbrella sampling molecular
dynamics simulations with coarse-grained Martini lipids, polarizable
coarse-grained water, and peptide to explore the dependence of translocation
free energetics on peptide structure and conformation via calculation
of potentials of mean force along preselected reaction paths allowing
and preventing membrane deformations that lead to pore formation.
Within the context of the coarse-grained force fields we employ, we
observe significant barriers for Arg9 translocation from
bulk aqueous solution to bilayer center. Moreover, we do not find
free-energy minima in the headgroup–water interfacial region,
as observed in simulations using all-atom force fields. The pore-forming
paths systematically predict lower free-energy barriers (ca. 90 kJ/mol
lower) than the non pore-forming paths, again consistent with all-atom
force field simulations. The current force field suggests no preference
for the more compact or covalently cyclic structures upon entering
the bilayer. Decomposition of the PMF into the system’s components
indicates that the dominant stabilizing contribution along the pore-forming
path originates from the membrane as both layers of it deformed due
to the formation of pore. Furthermore, our analysis revealed that
although there is significant entropic stabilization arising from
the enhanced configurational entropy exposing more states as the peptide
moves through the bilayer, the enthalpic loss (as predicted by the
interactions of this coarse-grained model) far outweighs any former
stabilization, thus leading to significant barrier to translocation.
Finally, we observe reduction in the translocation free-energy barrier
for a second Arg9 entering the bilayer in the presence
of an initial peptide restrained at the center, again, in qualitative
agreement with all-atom force fields.
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Affiliation(s)
- Yuan Hu
- Department of Chemistry and Biochemistry, University of Delaware , 238 Brown Laboratory, Newark, Delaware 19716, United States
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99
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Lazaridis T, Leveritt JM, PeBenito L. Implicit membrane treatment of buried charged groups: application to peptide translocation across lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2149-59. [PMID: 24525075 DOI: 10.1016/j.bbamem.2014.01.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 01/10/2014] [Indexed: 01/06/2023]
Abstract
The energetic cost of burying charged groups in the hydrophobic core of lipid bilayers has been controversial, with simulations giving higher estimates than certain experiments. Implicit membrane approaches are usually deemed too simplistic for this problem. Here we challenge this view. The free energy of transfer of amino acid side chains from water to the membrane center predicted by IMM1 is reasonably close to all-atom free energy calculations. The shape of the free energy profile, however, for the charged side chains needs to be modified to reflect the all-atom simulation findings (IMM1-LF). Membrane thinning is treated by combining simulations at different membrane widths with an estimate of membrane deformation free energy from elasticity theory. This approach is first tested on the voltage sensor and the isolated S4 helix of potassium channels. The voltage sensor is stably inserted in a transmembrane orientation for both the original and the modified model. The transmembrane orientation of the isolated S4 helix is unstable in the original model, but a stable local minimum in IMM1-LF, slightly higher in energy than the interfacial orientation. Peptide translocation is addressed by mapping the effective energy of the peptide as a function of vertical position and tilt angle, which allows identification of minimum energy pathways and transition states. The barriers computed for the S4 helix and other experimentally studied peptides are low enough for an observable rate. Thus, computational results and experimental studies on the membrane burial of peptide charged groups appear to be consistent. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.
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Affiliation(s)
- Themis Lazaridis
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, NY 10031, USA.
| | - John M Leveritt
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Leo PeBenito
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, NY 10031, USA
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100
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Vorobyov I, Olson TE, Kim JH, Koeppe RE, Andersen OS, Allen TW. Ion-induced defect permeation of lipid membranes. Biophys J 2014; 106:586-97. [PMID: 24507599 PMCID: PMC3945052 DOI: 10.1016/j.bpj.2013.12.027] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Revised: 11/07/2013] [Accepted: 12/09/2013] [Indexed: 01/07/2023] Open
Abstract
We have explored the mechanisms of uncatalyzed membrane ion permeation using atomistic simulations and electrophysiological recordings. The solubility-diffusion mechanism of membrane charge transport has prevailed since the 1960s, despite inconsistencies in experimental observations and its lack of consideration for the flexible response of lipid bilayers. We show that direct lipid bilayer translocation of alkali metal cations, Cl(-), and a charged arginine side chain analog occurs via an ion-induced defect mechanism. Contrary to some previous suggestions, the arginine analog experiences a large free-energy barrier, very similar to those for Na(+), K(+), and Cl(-). Our simulations reveal that membrane perturbations, due to the movement of an ion, are central for explaining the permeation process, leading to both free-energy and diffusion-coefficient profiles that show little dependence on ion chemistry and charge, despite wide-ranging hydration energies and the membrane's dipole potential. The results yield membrane permeabilities that are in semiquantitative agreement with experiments in terms of both magnitude and selectivity. We conclude that ion-induced defect-mediated permeation may compete with transient pores as the dominant mechanism of uncatalyzed ion permeation, providing new understanding for the actions of a range of membrane-active peptides and proteins.
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Affiliation(s)
- Igor Vorobyov
- Department of Chemistry, University of California, Davis, Davis, California
| | - Timothy E Olson
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Jung H Kim
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York.
| | - Toby W Allen
- School of Applied Sciences and Health Innovations Research Institute, RMIT University, Melbourne, Victoria, Australia; Department of Chemistry, University of California, Davis, Davis, California.
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