1
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Ygberg S, Akkuratov EE, Howard RJ, Taylan F, Jans DC, Mahato DR, Katz A, Kinoshita PF, Portal B, Nennesmo I, Lindskog M, Karlish SJD, Andersson M, Lindstrand A, Brismar H, Aperia A. A missense mutation converts the Na +,K +-ATPase into an ion channel and causes therapy-resistant epilepsy. J Biol Chem 2021; 297:101355. [PMID: 34717959 PMCID: PMC8637647 DOI: 10.1016/j.jbc.2021.101355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 10/14/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022] Open
Abstract
The ion pump Na+,K+-ATPase is a critical determinant of neuronal excitability; however, its role in the etiology of diseases of the central nervous system (CNS) is largely unknown. We describe here the molecular phenotype of a Trp931Arg mutation of the Na+,K+-ATPase catalytic α1 subunit in an infant diagnosed with therapy-resistant lethal epilepsy. In addition to the pathological CNS phenotype, we also detected renal wasting of Mg2+. We found that membrane expression of the mutant α1 protein was low, and ion pumping activity was lost. Arginine insertion into membrane proteins can generate water-filled pores in the plasma membrane, and our molecular dynamic (MD) simulations of the principle states of Na+,K+-ATPase transport demonstrated massive water inflow into mutant α1 and destabilization of the ion-binding sites. MD simulations also indicated that a water pathway was created between the mutant arginine residue and the cytoplasm, and analysis of oocytes expressing mutant α1 detected a nonspecific cation current. Finally, neurons expressing mutant α1 were observed to be depolarized compared with neurons expressing wild-type protein, compatible with a lowered threshold for epileptic seizures. The results imply that Na+,K+-ATPase should be considered a neuronal locus minoris resistentia in diseases associated with epilepsy and with loss of plasma membrane integrity.
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Affiliation(s)
- Sofia Ygberg
- Neuropediatric Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden; Centre for Inherited Metabolic Diseases (CMMS), Karolinska University Hospital, Stockholm, Sweden
| | - Evgeny E Akkuratov
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
| | - Rebecca J Howard
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Daniel C Jans
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
| | | | - Adriana Katz
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovoth, Israel
| | - Paula F Kinoshita
- Department of Pharmacology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | - Benjamin Portal
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Inger Nennesmo
- Department of Pathology, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Lindskog
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Steven J D Karlish
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovoth, Israel
| | | | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Hjalmar Brismar
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden; Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
| | - Anita Aperia
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
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2
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A photoswitchable helical peptide with light-controllable interface/transmembrane topology in lipidic membranes. iScience 2021; 24:102771. [PMID: 34286233 PMCID: PMC8273423 DOI: 10.1016/j.isci.2021.102771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/02/2021] [Accepted: 06/19/2021] [Indexed: 11/21/2022] Open
Abstract
The spontaneous insertion of helical transmembrane (TM) polypeptides into lipid bilayers is driven by three sequential equilibria: solution-to-membrane interface (MI) partition, unstructured-to-helical folding, and MI-to-TM helix insertion. A bottleneck for understanding these three steps is the lack of experimental approaches to perturb membrane-bound hydrophobic polypeptides out of equilibrium rapidly and reversibly. Here, we report on a 24-residues-long hydrophobic α-helical polypeptide, covalently coupled to an azobenzene photoswitch (KCALP-azo), which displays a light-controllable TM/MI equilibrium in hydrated lipid bilayers. FTIR spectroscopy reveals that trans KCALP-azo folds as a TM α-helix (TM topology). After trans-to-cis photoisomerization of the azobenzene moiety with UV light (reversed with blue light), the helical structure of KCALP-azo is maintained, but its helix tilt increased from 32 ± 5° to 79 ± 8°, indication of a reversible TM-to-MI transition. Further analysis indicates that this transition is incomplete, with cis KCALP-azo existing in a ∼90% TM and ∼10% MI mixture. We present an α-helical transmembrane peptide modified with a molecular photoswitch The peptide exhibits reversible photocontrol of its membrane topology A fraction moves to the membrane interface with UV and inserts back with blue light This system will be useful to address the molecular mechanism for membrane insertion
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3
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Martinotti C, Ruiz-Perez L, Deplazes E, Mancera RL. Molecular Dynamics Simulation of Small Molecules Interacting with Biological Membranes. Chemphyschem 2020; 21:1486-1514. [PMID: 32452115 DOI: 10.1002/cphc.202000219] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/22/2020] [Indexed: 12/12/2022]
Abstract
Cell membranes protect and compartmentalise cells and their organelles. The semi-permeable nature of these membranes controls the exchange of solutes across their structure. Characterising the interaction of small molecules with biological membranes is critical to understanding of physiological processes, drug action and permeation, and many biotechnological applications. This review provides an overview of how molecular simulations are used to study the interaction of small molecules with biological membranes, with a particular focus on the interactions of water, organic compounds, drugs and short peptides with models of plasma cell membrane and stratum corneum lipid bilayers. This review will not delve on other types of membranes which might have different composition and arrangement, such as thylakoid or mitochondrial membranes. The application of unbiased molecular dynamics simulations and enhanced sampling methods such as umbrella sampling, metadynamics and replica exchange are described using key examples. This review demonstrates how state-of-the-art molecular simulations have been used successfully to describe the mechanism of binding and permeation of small molecules with biological membranes, as well as associated changes to the structure and dynamics of these membranes. The review concludes with an outlook on future directions in this field.
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Affiliation(s)
- Carlo Martinotti
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
| | - Lanie Ruiz-Perez
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
| | - Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
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4
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Anderson CM, Cardenas A, Elber R, Webb LJ. Preferential Equilibrium Partitioning of Positively Charged Tryptophan into Phosphatidylcholine Bilayer Membranes. J Phys Chem B 2019; 123:170-179. [PMID: 30481465 PMCID: PMC6331081 DOI: 10.1021/acs.jpcb.8b09872] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/19/2018] [Indexed: 11/29/2022]
Abstract
The interactions between small molecules and lipid bilayers play a critical role in the function of cellular membranes. Understanding how a small molecule interacts with the lipid bilayer differently based on its charge reveals primordial mechanisms of transport across membranes and assists in the design of drug molecules that can penetrate cells. We have previously reported that tryptophan permeated through a phosphatidylcholine lipid bilayer membrane at a faster rate when it was positively charged (Trp+) than when negatively charged (Trp-), which corresponded to a lower potential of mean force (PMF) barrier determined through simulations. In this report, we demonstrate that Trp+ partitions into the lipid bilayer membrane to a greater degree than Trp- by interacting with the ester linkage of a phosphatidylcholine lipid, where it is stabilized by the electron withdrawing glycerol functional group. These results are in agreement with tryptophan's known role as an anchor for transmembrane proteins, though the tendency for binding of a positively charged tryptophan is surprising. We discuss the implications of our results on the mechanisms of unassisted permeation and penetration of small molecules within and across lipid bilayer membranes based on molecular charge, shape, and molecular interactions within the bilayer structure.
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Affiliation(s)
- Cari M. Anderson
- Department
of Chemistry, Institute for Computational Engineering and Sciences, Institute for Cellular
and Molecular Biology, Texas Materials Institute, The University of Texas at Austin, 2506 Speedway STOP A5300, Austin, Texas 78712, United States
| | - Alfredo Cardenas
- Department
of Chemistry, Institute for Computational Engineering and Sciences, Institute for Cellular
and Molecular Biology, Texas Materials Institute, The University of Texas at Austin, 2506 Speedway STOP A5300, Austin, Texas 78712, United States
| | - Ron Elber
- Department
of Chemistry, Institute for Computational Engineering and Sciences, Institute for Cellular
and Molecular Biology, Texas Materials Institute, The University of Texas at Austin, 2506 Speedway STOP A5300, Austin, Texas 78712, United States
| | - Lauren J. Webb
- Department
of Chemistry, Institute for Computational Engineering and Sciences, Institute for Cellular
and Molecular Biology, Texas Materials Institute, The University of Texas at Austin, 2506 Speedway STOP A5300, Austin, Texas 78712, United States
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5
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Reißer S, Strandberg E, Steinbrecher T, Elstner M, Ulrich AS. Best of Two Worlds? How MD Simulations of Amphiphilic Helical Peptides in Membranes Can Complement Data from Oriented Solid-State NMR. J Chem Theory Comput 2018; 14:6002-6014. [PMID: 30289704 DOI: 10.1021/acs.jctc.8b00283] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The membrane alignment of helical amphiphilic peptides in oriented phospholipid bilayers can be obtained as ensemble and time averages from solid state 2H NMR by fitting the quadrupolar splittings to ideal α-helices. At the same time, molecular dynamics (MD) simulations can provide atomistic insight into peptide-membrane systems. Here, we evaluate the potential of MD simulations to complement the experimental NMR data that is available on three exemplary systems: the natural antimicrobial peptide PGLa and the two designer-made peptides MSI-103 and KIA14, whose sequences were derived from PGLa. Each peptide was simulated for 1 μs in a DMPC lipid bilayer. We calculated from the MD simulations the local angles which define the side chain geometry with respect to the peptide helix. The peptide orientation was then calculated (i) directly from the simulation, (ii) from back-calculated MD-derived NMR splittings, and (iii) from experimental 2H NMR splittings. Our findings are that (1) the membrane orientation and secondary structure of the peptides found in the NMR analysis are generally well reproduced by the simulations; (2) the geometry of the side chains with respect to the helix backbone can deviate significantly from the ideal structure depending on the specific residue, but on average all side chains have the same orientation; and (3) for all of our peptides, the azimuthal rotation angle found from the MD-derived splittings is about 15° smaller than the experimental value.
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Affiliation(s)
- Sabine Reißer
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Erik Strandberg
- Institute of Biological Interfaces (IBG-2), KIT , P.O. Box 3640, 76012 Karlsruhe , Germany
| | - Thomas Steinbrecher
- Institute of Physical Chemistry, KIT , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, KIT , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Anne S Ulrich
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany.,Institute of Biological Interfaces (IBG-2), KIT , P.O. Box 3640, 76012 Karlsruhe , Germany
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6
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Ulmschneider JP, Smith JC, White SH, Ulmschneider MB. The importance of the membrane interface as the reference state for membrane protein stability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2539-2548. [PMID: 30293965 DOI: 10.1016/j.bbamem.2018.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/14/2018] [Accepted: 09/16/2018] [Indexed: 11/26/2022]
Abstract
The insertion of nascent polypeptide chains into lipid bilayer membranes and the stability of membrane proteins crucially depend on the equilibrium partitioning of polypeptides. For this, the transfer of full sequences of amino-acid residues into the bilayer, rather than individual amino acids, must be understood. Earlier studies have revealed that the most likely reference state for partitioning very hydrophobic sequences is the membrane interface. We have used μs-scale simulations to calculate the interface-to-transmembrane partitioning free energies ΔGS→TM for two hydrophobic carrier sequences in order to estimate the insertion free energy for all 20 amino acid residues when bonded to the center of a partitioning hydrophobic peptide. Our results show that prior single-residue scales likely overestimate the partitioning free energies of polypeptides. The correlation of ΔGS→TM with experimental full-peptide translocon insertion data is high, suggesting an important role for the membrane interface in translocon-based insertion. The choice of carrier sequence greatly modulates the contribution of each single-residue mutation to the overall partitioning free energy. Our results demonstrate the importance of quantifying the observed full-peptide partitioning equilibrium, which is between membrane interface and transmembrane inserted, rather than combining individual water-to-membrane amino acid transfer free energies.
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Affiliation(s)
- Jakob P Ulmschneider
- School of Physics and Astronomy and the Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, China.
| | - Jeremy C Smith
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Biochemistry & Cellular Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Stephen H White
- Department of Physiology & Biophysics, University of California at Irvine, Irvine, CA, USA
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7
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Gumbart JC, Ulmschneider MB, Hazel A, White SH, Ulmschneider JP. Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method. J Membr Biol 2018; 251:345-356. [PMID: 29520628 PMCID: PMC6030508 DOI: 10.1007/s00232-018-0026-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/27/2018] [Indexed: 01/15/2023]
Abstract
We show that the free energy of inserting hydrophobic peptides into lipid bilayer membranes from surface-aligned to transmembrane inserted states can be reliably calculated using atomistic models. We use two entirely different computational methods: high temperature spontaneous peptide insertion calculations as well as umbrella sampling potential-of-mean-force (PMF) calculations, both yielding the same energetic profiles. The insertion free energies were calculated using two different protein and lipid force fields (OPLS protein/united-atom lipids and CHARMM36 protein/all-atom lipids) and found to be independent of the simulation parameters. In addition, the free energy of insertion is found to be independent of temperature for both force fields. However, we find major difference in the partitioning kinetics between OPLS and CHARMM36, likely due to the difference in roughness of the underlying free energy surfaces. Our results demonstrate not only a reliable method to calculate insertion free energies for peptides, but also represent a rare case where equilibrium simulations and PMF calculations can be directly compared.
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Affiliation(s)
| | | | | | - Stephen H White
- Department of Physiology & Biophysics, University of California at Irvine, Irvine, CA, USA
| | - Jakob P Ulmschneider
- Department of Physics and the Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China.
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8
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Ulmschneider JP, Ulmschneider MB. Molecular Dynamics Simulations Are Redefining Our View of Peptides Interacting with Biological Membranes. Acc Chem Res 2018; 51:1106-1116. [PMID: 29667836 DOI: 10.1021/acs.accounts.7b00613] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Ever since the first molecular mechanics computer simulations of biological molecules became possible, there has been the dream to study all complex biological phenomena in silico, simply bypassing the enormous experimental challenges and their associated costs. For this, two inherent requirements need to be met: First, the time scales achievable in simulations must reach up to the millisecond range and even longer. Second, the computational model must accurately reproduce what is measured experimentally. Despite some recent successes, the general consensus in the field to date has been that neither of these conditions have yet been met and that the dream will be realized, if at all, only in the distant future. In this Account, we show that this view is wrong; instead, we are actually in the middle of the in silico molecular dynamics (MD) revolution, which is reshaping how we think about protein function. The example explored in this Account is a recent advance in the field of membrane-active peptides (MAPs). MD simulations have succeeded in accurately capturing the process of peptide binding, folding, and partitioning into lipid bilayers as well as revealing how channels form spontaneously from polypeptide fragments and conduct ionic and other cargo across membranes, all at atomic resolution. These game-changing advances have been made possible by a combination of steadily advancing computational power, more efficient algorithms and techniques, clever accelerated sampling schemes, and thorough experimental verifications. The great advantage of MD is the spatial and temporal resolution, directly providing a molecular movie of a protein undergoing folding and cycling through a functional process. This is especially important for proteins with transitory functional states, such as pore-forming MAPs. Recent successes are demonstrated here for the large class of antimicrobial peptides (AMPs). These short peptides are an essential part of the nonadaptive immune system for many organisms, ubiquitous in nature, and of particular interest to the pharmaceutical industry in the age of rising bacterial resistance to conventional antibiotic treatments. Unlike integral membrane proteins, AMPs are sufficiently small to allow converged sampling with the unbiased high-temperature sampling methodology outlined here and are relatively easy to handle experimentally. At the same time, AMPs exhibit a wealth of complex and poorly understood interactions with lipid bilayers, which allow not only tuning and validation of the simulation methodology but also advancement of our knowledge of protein-lipid interactions at a fundamental level. Space constraints limit our discussion to AMPs, but the MD methodologies outlined here can be applied to all phenomena involving peptides in membranes, including cell-penetrating peptides, signaling peptides, viral channel forming peptides, and fusion peptides, as well as ab initio membrane protein folding and assembly. For these systems, the promise of MD simulations to predict the structure of channels and to provide complete-atomic-detail trajectories of the mechanistic processes underlying their biological functions appears to rapidly become a reality. The current challenge is to design joint experimental and computational benchmarks to verify and tune MD force fields. With this, MD will finally fulfill its promise to become an inexpensive, powerful, and easy-to-use tool providing atomic-detail insights to researchers as part of their investigations into membrane biophysics and beyond.
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Affiliation(s)
- Jakob P. Ulmschneider
- Institute of Natural Sciences and School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
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9
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Tian W, Lin M, Naveed H, Liang J. Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins. Bioinformatics 2018; 33:1664-1671. [PMID: 28158457 DOI: 10.1093/bioinformatics/btx053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/25/2017] [Indexed: 11/14/2022] Open
Abstract
Motivation Transmembrane beta-barrel proteins (TMBs) serve a multitude of essential cellular functions in Gram-negative bacteria, mitochondria and chloroplasts. Transfer free energies (TFEs) of residues in the transmembrane (TM) region provides fundamental quantifications of thermodynamic stabilities of TMBs, which are important for the folding and the membrane insertion processes, and may help in understanding the structure-function relationship. However, experimental measurement of TFEs of TMBs is challenging. Although a recent computational method can be used to calculate TFEs, the results of which are in excellent agreement with experimentally measured values, this method does not scale up, and is limited to small TMBs. Results We have developed an approximation method that calculates TFEs of TM residues in TMBs accurately, with which depth-dependent transfer free energy profiles can be derived. Our results are in excellent agreement with experimental measurements. This method is efficient and applicable to all bacterial TMBs regardless of the size of the protein. Availability and Implementation An online webserver is available at http://tanto.bioe.uic.edu/tmb-tfe . Contact : jliang@uic.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Wei Tian
- Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Meishan Lin
- Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Hammad Naveed
- Toyota Technological Institute at Chicago, Chicago, IL, USA
| | - Jie Liang
- Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
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10
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Wang Y, Chen CH, Hu D, Ulmschneider MB, Ulmschneider JP. Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide. Nat Commun 2016; 7:13535. [PMID: 27874004 PMCID: PMC5121426 DOI: 10.1038/ncomms13535] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 10/12/2016] [Indexed: 12/29/2022] Open
Abstract
Many antimicrobial peptides (AMPs) selectively target and form pores in microbial membranes. However, the mechanisms of membrane targeting, pore formation and function remain elusive. Here we report an experimentally guided unbiased simulation methodology that yields the mechanism of spontaneous pore assembly for the AMP maculatin at atomic resolution. Rather than a single pore, maculatin forms an ensemble of structurally diverse temporarily functional low-oligomeric pores, which mimic integral membrane protein channels in structure. These pores continuously form and dissociate in the membrane. Membrane permeabilization is dominated by hexa-, hepta- and octamers, which conduct water, ions and small dyes. Pores form by consecutive addition of individual helices to a transmembrane helix or helix bundle, in contrast to current poration models. The diversity of the pore architectures—formed by a single sequence—may be a key feature in preventing bacterial resistance and could explain why sequence–function relationships in AMPs remain elusive. Antimicrobial peptides (AMPs) selectively form pores in microbial membranes in process not fully understood. Here the authors use experimentally guided molecular dynamics to study maculatin pore formation, showing how this AMP assembles into transient and structurally diverse oligomeric pores in cell membranes.
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Affiliation(s)
- Yukun Wang
- Institute of Natural Sciences, Shanghai Jiao-Tong University, 800 Dongchuan Road, Shanghai 200240, China.,Department of Physics and Astronomy, Shanghai Jiao-Tong University, 800 Dongchuan Road, Shanghai 200240, China.,Institute of NanoBioTechnology, Johns Hopkins University, 204C Schaffer Hall, 3400 North Charles Street, Baltimore, Maryland 21218-2681, USA
| | - Charles H Chen
- Institute of NanoBioTechnology, Johns Hopkins University, 204C Schaffer Hall, 3400 North Charles Street, Baltimore, Maryland 21218-2681, USA.,Department of Materials Science and Engineering, Johns Hopkins University, 204C Schaffer Hall, 3400 North Charles Street, Baltimore, Maryland 21218-2681, USA
| | - Dan Hu
- Institute of Natural Sciences, Shanghai Jiao-Tong University, 800 Dongchuan Road, Shanghai 200240, China.,Department of Mathematics, Shanghai Jiao-Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Martin B Ulmschneider
- Institute of NanoBioTechnology, Johns Hopkins University, 204C Schaffer Hall, 3400 North Charles Street, Baltimore, Maryland 21218-2681, USA.,Department of Materials Science and Engineering, Johns Hopkins University, 204C Schaffer Hall, 3400 North Charles Street, Baltimore, Maryland 21218-2681, USA
| | - Jakob P Ulmschneider
- Institute of Natural Sciences, Shanghai Jiao-Tong University, 800 Dongchuan Road, Shanghai 200240, China.,Department of Physics and Astronomy, Shanghai Jiao-Tong University, 800 Dongchuan Road, Shanghai 200240, China
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11
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Qi Y, Cheng X, Lee J, Vermaas JV, Pogorelov TV, Tajkhorshid E, Park S, Klauda JB, Im W. CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model. Biophys J 2016; 109:2012-22. [PMID: 26588561 DOI: 10.1016/j.bpj.2015.10.008] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/06/2015] [Accepted: 10/09/2015] [Indexed: 12/12/2022] Open
Abstract
Slow diffusion of the lipids in conventional all-atom simulations of membrane systems makes it difficult to sample large rearrangements of lipids and protein-lipid interactions. Recently, Tajkhorshid and co-workers developed the highly mobile membrane-mimetic (HMMM) model with accelerated lipid motion by replacing the lipid tails with small organic molecules. The HMMM model provides accelerated lipid diffusion by one to two orders of magnitude, and is particularly useful in studying membrane-protein associations. However, building an HMMM simulation system is not easy, as it requires sophisticated treatment of the lipid tails. In this study, we have developed CHARMM-GUI HMMM Builder (http://www.charmm-gui.org/input/hmmm) to provide users with ready-to-go input files for simulating HMMM membrane systems with/without proteins. Various lipid-only and protein-lipid systems are simulated to validate the qualities of the systems generated by HMMM Builder with focus on the basic properties and advantages of the HMMM model. HMMM Builder supports all lipid types available in CHARMM-GUI and also provides a module to convert back and forth between an HMMM membrane and a full-length membrane. We expect HMMM Builder to be a useful tool in studying membrane systems with enhanced lipid diffusion.
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Affiliation(s)
- Yifei Qi
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Xi Cheng
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Jumin Lee
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Josh V Vermaas
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Taras V Pogorelov
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois; School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Soohyung Park
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering and the Biophysics Program, The University of Maryland, College Park, Maryland
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas.
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12
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La Rosa C, Scalisi S, Lolicato F, Pannuzzo M, Raudino A. Lipid-assisted protein transport: A diffusion-reaction model supported by kinetic experiments and molecular dynamics simulations. J Chem Phys 2016; 144:184901. [DOI: 10.1063/1.4948323] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Carmelo La Rosa
- Department of Chemical Science, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy
| | - Silvia Scalisi
- Department of Chemical Science, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy
| | - Fabio Lolicato
- Department of Chemical Science, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Martina Pannuzzo
- Department of Physics, Carnegie Mellon University, 5000 Forbes Ave., Pittsburgh, Pennsylvania 15213, USA
| | - Antonio Raudino
- Department of Chemical Science, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy
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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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14
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Ghahremanpour MM, Sardari S. The effect of structural parameters and positive charge distance on the interaction free energy of antimicrobial peptides with membrane surface. J Biomol Struct Dyn 2014; 33:502-12. [PMID: 24621111 DOI: 10.1080/07391102.2014.893204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Many attempts have been made to find hints explaining the relationship between physicochemical and structural properties of antimicrobial peptides (AMPs) which are relevant to their antimicrobial activities. We here found that there is a difference in the percentages of hydrophobic, hydrophilic, and charged residues between AMPs killing both bacteria and fungi (Group A) and AMPs that only kill bacteria (Group B). The percentage of charged residues in Group A AMPs is highly elevated, while in Group B the percentage of hydrophobic residues is increased. This result suggests a sequence-based mechanism of selectivity for AMPs. Moreover, we examined how the distance between basic residues affects the interaction free energy of AMPs with the membrane surface, since most of the known AMPs act by membrane perturbation. We measured the average distance between basic residues throughout the 3D structure of AMPs by defining Dpr parameter and calculated the interaction free energy for 10 AMPs that interacted with the DPPC membrane using molecular dynamics simulation. We found that the changes of the interaction free energy correlates with the change of Dpr by a linear regression coefficient of r(2 )= .47 and a cubic regression coefficient of r(2 )= .70.
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Affiliation(s)
- Mohammad Mehdi Ghahremanpour
- a Drug Design and Bioinformatics Unit, Department of Medical Biotechnology , Biotechnology Research Center, Pasteur Institute , No. 69, Pasteur Ave., Tehran , 13164, Iran
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15
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Vicatos S, Rychkova A, Mukherjee S, Warshel A. An effective Coarse-grained model for biological simulations: Recent refinements and validations. Proteins 2013; 82:1168-85. [DOI: 10.1002/prot.24482] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Spyridon Vicatos
- Department of Chemistry; University of Southern California; Los Angeles California 90089-1062
| | - Anna Rychkova
- Department of Chemistry; University of Southern California; Los Angeles California 90089-1062
| | - Shayantani Mukherjee
- 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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16
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Rychkova A, Warshel A. On the nature of the apparent free energy of inserting amino acids into membrane through the translocon. J Phys Chem B 2013; 117:13748-54. [PMID: 24087983 DOI: 10.1021/jp406925y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The nature of the biological free energy scale (ΔGapp), obtained from translocon mediated insertion studies, has been a major puzzle and the subject of major controversies. Part of the problem has been the complexity of the insertion process that discouraged workers from considering the feasible kinetics schemes and left the possible impression that ΔGapp presents some simple partition. Here we extend and clarify our recent analysis of the insertion problem using well-defined kinetics schemes and a free energy profile. We point out that although the rate constants of some steps are far from being obvious, it is essential to consider explicitly such schemes in order to advance in analyzing the meaning of ΔGapp. It is then shown that under some equilibrium conditions the kinetics scheme leads to a simple formula that allows one to relate ΔGapp to the actual free energy of partitioning between the water, the membrane, and the translocon. Other options are also considered (including limits with irreversible transitions that can be described by linear free energy relationships (LFERs)). It is concluded that it is unlikely that a kinetics plus thermodynamic based analysis can lead to a result that identifies ΔGapp with the partition between the membrane and the translocon. Thus, we argue that unless such analysis is presented, it is unjustified to assume that ΔGapp corresponds to the membrane translocon equilibrium or to some other arbitrary definition. Furthermore, we point out that the presumption that it is sufficient to just calculate the PMF for going from the translocon (TR) to the membrane and then to assume irreversible diffusive motion to water and for further entrance to the membrane is not a valid analysis. Overall, we point out that it is important to try to relate ΔGapp to a well-defined kinetics scheme (regardless of the complication of the system) in order to determine whether the energies of inserting positively charged residues to the membrane are related to the corresponding ΔGapp. It is also suggested that deviations from our simple formula for equilibrium conditions can help in identifying and analyzing kinetics barriers.
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Affiliation(s)
- Anna Rychkova
- Department of Genetics, Stanford University , 365 Lasuen Street, Littlefield Center, MC2069, Stanford, California 94305, United States
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Abstract
The physiological properties of biological soft matter are the product of collective interactions, which span many time and length scales. Recent computational modeling efforts have helped illuminate experiments that characterize the ways in which proteins modulate membrane physics. Linking these models across time and length scales in a multiscale model explains how atomistic information propagates to larger scales. This paper reviews continuum modeling and coarse-grained molecular dynamics methods, which connect atomistic simulations and single-molecule experiments with the observed microscopic or mesoscale properties of soft-matter systems essential to our understanding of cells, particularly those involved in sculpting and remodeling cell membranes.
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Affiliation(s)
- Ryan Bradley
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
- Author to whom correspondence should be addressed; ; Tel.: +1-215-898-0487; Fax: +1-215-573-2071
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18
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Taufer M, Ganesan N, Patel S. GPU-Enabled Macromolecular Simulation: Challenges and Opportunities. Comput Sci Eng 2013. [DOI: 10.1109/mcse.2012.42] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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Gofman Y, Haliloglu T, Ben-Tal N. The Transmembrane Helix Tilt May Be Determined by the Balance between Precession Entropy and Lipid Perturbation. J Chem Theory Comput 2012; 8:2896-2904. [PMID: 24932138 PMCID: PMC4053537 DOI: 10.1021/ct300128x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Indexed: 11/29/2022]
Abstract
Hydrophobic helical peptides interact with lipid bilayers
in various
modes, determined by the match between the length of the helix’s
hydrophobic core and the thickness of the hydrocarbon region of the
bilayer. For example, long helices may tilt with respect to the membrane
normal to bury their hydrophobic cores in the membrane, and the lipid
bilayer may stretch to match the helix length. Recent molecular dynamics
simulations and potential of mean force calculations have shown that
some TM helices whose lengths are equal to, or even shorter than,
the bilayer thickness may also tilt. The tilt is driven by a gain
in the helix precession entropy, which compensates for the free energy
penalty resulting from membrane deformation. Using this free energy
balance, we derived theoretically an equation of state, describing
the dependence of the tilt on the helix length and membrane thickness.
To this end, we conducted coarse-grained Monte Carlo simulations of
the interaction of helices of various lengths with lipid bilayers
of various thicknesses, reproducing and expanding the previous molecular
dynamics simulations. Insight from the simulations facilitated the
derivation of the theoretical model. The tilt angles calculated using
the theoretical model agree well with our simulations and with previous
calculations and measurements.
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Affiliation(s)
- Yana Gofman
- Helmholtz-Zentrum, 21502 Geesthacht, Germany ; The Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel
| | - Turkan Haliloglu
- Chemical Engineering Department, Polymer Research Center, Life Sciences and Technologies Research Center, Bogazici University, 34342 Bebek-Istanbul, Turkey
| | - Nir Ben-Tal
- The Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel
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20
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Jämbeck JPM, Lyubartsev AP. Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids. J Phys Chem B 2012; 116:3164-79. [PMID: 22352995 PMCID: PMC3320744 DOI: 10.1021/jp212503e] [Citation(s) in RCA: 418] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 02/18/2012] [Indexed: 11/29/2022]
Abstract
An all-atomistic force field (FF) has been developed for fully saturated phospholipids. The parametrization has been largely based on high-level ab initio calculations in order to keep the empirical input to a minimum. Parameters for the lipid chains have been developed based on knowledge about bulk alkane liquids, for which thermodynamic and dynamic data are excellently reproduced. The FFs ability to simulate lipid bilayers in the liquid crystalline phase in a tensionless ensemble was tested in simulations of three lipids: 1,2-diauroyl-sn-glycero-3-phospocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and 1,2-dipalmitoyl-sn-glycero-3-phospcholine (DPPC). Computed areas and volumes per lipid, and three different kinds of bilayer thicknesses, have been investigated. Most importantly NMR order parameters and scattering form factors agree in an excellent manner with experimental data under a range of temperatures. Further, the compatibility with the AMBER FF for biomolecules as well as the ability to simulate bilayers in gel phase was demonstrated. Overall, the FF presented here provides the important balance between the hydrophilic and hydrophobic forces present in lipid bilayers and therefore can be used for more complicated studies of realistic biological membranes with protein insertions.
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Affiliation(s)
- Joakim P. M. Jämbeck
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden
| | - Alexander P. Lyubartsev
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden
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Schiopu I, Mereuta L, Apetrei A, Park Y, Hahm KS, Luchian T. The role of tryptophan spatial arrangement for antimicrobial-derived, membrane-active peptides adsorption and activity. MOLECULAR BIOSYSTEMS 2012; 8:2860-3. [DOI: 10.1039/c2mb25221j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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